From e3f1c9133c7f3e84407b9ed61f9d5256e9abdc90 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Fri, 7 Mar 2014 19:13:19 -0500 Subject: [PATCH 01/59] add subpage layout with header in page, change title of conference page --- _layouts/subpage.html | 8 ++++++++ conference/index.md | 6 ++---- 2 files changed, 10 insertions(+), 4 deletions(-) create mode 100644 _layouts/subpage.html diff --git a/_layouts/subpage.html b/_layouts/subpage.html new file mode 100644 index 0000000..1246af4 --- /dev/null +++ b/_layouts/subpage.html @@ -0,0 +1,8 @@ +--- +layout: default +--- +{{ page.title }} +================= + +{{ content }} + diff --git a/conference/index.md b/conference/index.md index 70639da..532bd2a 100644 --- a/conference/index.md +++ b/conference/index.md @@ -1,10 +1,8 @@ --- -layout: default -title: "Conference" +layout: subpage +title: "Rhythmic Dynamics and Cognition" --- -[Rhythmic Dynamics and Cognition]({{site.url}}/img/RhythmicDynamicsCognition_crc2013.pdf) -================================= ##June 4-5, 2013 [View Poster Here]({{site.url}}{{site.baseurl}}img/RhythmicDynamicsCognition_crc2013.pdf) From 301d0abd3d9aa53dcd019a776104abb54bf597c1 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Fri, 7 Mar 2014 19:17:58 -0500 Subject: [PATCH 02/59] blurb cleanup on markdown version of conference page --- conference/index.md | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/conference/index.md b/conference/index.md index 532bd2a..a9c383d 100644 --- a/conference/index.md +++ b/conference/index.md @@ -1,13 +1,14 @@ --- layout: subpage -title: "Rhythmic Dynamics and Cognition" +title: "Rhythmic Dynamics and Cognition Conference" --- ##June 4-5, 2013 -[View Poster Here]({{site.url}}{{site.baseurl}}img/RhythmicDynamicsCognition_crc2013.pdf) +[View event poster]({{site.url}}/img/RhythmicDynamicsCognition_crc2013.pdf) +[View event videos on The Science Network](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition) -The Rhythmic Dynamics and Cognition Conference was a two-day event sponsored by the [Cognitive Rhythms Collaborative (CRC)]({{site.url}}{{site.baseurl}}). The program was held at the Brain Building (Building 46) on the MIT campus and included lectures, a reception, and a poster session. +The Rhythmic Dynamics and Cognition Conference was a two-day event sponsored by the [Cognitive Rhythms Collaborative (CRC)]({{site.url}}{{site.baseurl}}), held at the Brain Building (Building 46) on the MIT campus in 2013. Proceedings included lectures, a reception, and a poster session. Videos of the lectures and an archive of the program are provided here. ##Invited speakers: From 7aea0e4fe3c4c7d2d833b0e6c0ac0f790c163fd6 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Wed, 23 Apr 2014 18:38:52 -0400 Subject: [PATCH 03/59] Delete new_index.md since index is now in markdown --- new_index.md | 15 --------------- 1 file changed, 15 deletions(-) delete mode 100644 new_index.md diff --git a/new_index.md b/new_index.md deleted file mode 100644 index 8f465a6..0000000 --- a/new_index.md +++ /dev/null @@ -1,15 +0,0 @@ ---- -layout: default -title: "Cognitive Rhythms Collaborative" ---- -

-The Cognitive Rhythms Collaborative (CRC) is a group of scientists in the Boston area who work together to advance our understanding of the brain dynamics underlying cognitive functions such as sensory processing, attention, -learning, memory and motor planning.

- -

The members of the CRC come from multiple institutions around the Boston area and beyond (see Faculty). We encourage those who are interested in working with us or participating in our events to contact Nancy Kopell (nk at bu.edu). -

The CRC is supported by the National Science Foundation and the McGovern Center.

- -

News and Events

-

Rhythmic Dynamics and Cognition Conference: Videos now available!

- - \ No newline at end of file From 372324bb3c4a9f647a696e7ec8a3dc72c7b35269 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Wed, 23 Apr 2014 18:53:55 -0400 Subject: [PATCH 04/59] make top.html contain only html head code --- _includes/{top.html => head.html} | 0 _layouts/default.html | 5 ++++- 2 files changed, 4 insertions(+), 1 deletion(-) rename _includes/{top.html => head.html} (100%) diff --git a/_includes/top.html b/_includes/head.html similarity index 100% rename from _includes/top.html rename to _includes/head.html diff --git a/_layouts/default.html b/_layouts/default.html index a7976b0..02e37cc 100644 --- a/_layouts/default.html +++ b/_layouts/default.html @@ -1,4 +1,7 @@ -{% include top.html %} + + + +{% include head.html %} From 464e7bfdc4e775b921484d3dbbc253e71057e6c8 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Wed, 23 Apr 2014 18:59:34 -0400 Subject: [PATCH 05/59] update index.md to use default template instead of blank template --- _layouts/blank.html | 3 -- index.md | 77 +-------------------------------------------- 2 files changed, 1 insertion(+), 79 deletions(-) delete mode 100644 _layouts/blank.html diff --git a/_layouts/blank.html b/_layouts/blank.html deleted file mode 100644 index 810b27d..0000000 --- a/_layouts/blank.html +++ /dev/null @@ -1,3 +0,0 @@ -{% include top.html %} - -{{ content }} \ No newline at end of file diff --git a/index.md b/index.md index 8180df5..2face92 100644 --- a/index.md +++ b/index.md @@ -1,44 +1,8 @@ --- -layout: blank +layout: default title: "Cognitive Rhythms Collaborative" --- - - - - - -
- - - -

The Cognitive Rhythms Collaborative (CRC) is a group of scientists in the Boston area who work together to advance our understanding of the brain dynamics underlying cognitive functions such as sensory processing, attention, learning, memory and motor planning.

@@ -81,44 +45,5 @@ Boston, MA 02215 --- - -
-
- - - - - - - - - From ae1ff85750d555169c12379bb65ca11e8aad6986 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Fri, 2 May 2014 19:13:42 -0400 Subject: [PATCH 06/59] moving conference flyer into conference directory --- calendar/index.md | 2 +- {img => conference}/CRC2012_Flyer.pdf | Bin 2 files changed, 1 insertion(+), 1 deletion(-) rename {img => conference}/CRC2012_Flyer.pdf (100%) diff --git a/calendar/index.md b/calendar/index.md index b924be3..224ce38 100644 --- a/calendar/index.md +++ b/calendar/index.md @@ -20,7 +20,7 @@ title: "Calendar"

[23 Feb 2012] CRC Dinner with speaker Matt Wilson

-

[1 Feb 2012] Mini-symposium Beta Rhythms and Cognition. Speakers: Earl Miller, Nancy Kopell, Stephanie Jones, Nicholas Schiff, Keith Purpura (Afternoon event with reception at the end)

+

[1 Feb 2012] Mini-symposium Beta Rhythms and Cognition. Speakers: Earl Miller, Nancy Kopell, Stephanie Jones, Nicholas Schiff, Keith Purpura (Afternoon event with reception at the end)

[26 Jan 2012] Special Talk: Natalie Adams, "Development of patterned activity in de novo neuronal networks," 4pm at BU

diff --git a/img/CRC2012_Flyer.pdf b/conference/CRC2012_Flyer.pdf similarity index 100% rename from img/CRC2012_Flyer.pdf rename to conference/CRC2012_Flyer.pdf From c88f77d1747e2c99cf2a40169d1b0c9871d81f53 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Fri, 2 May 2014 19:24:14 -0400 Subject: [PATCH 07/59] updating markdown pages to match html pages for commits e2c6a52 834eace aa660f4 --- groups/index.md | 10 ++++++++-- people/faculty/index.md | 7 ++++--- 2 files changed, 12 insertions(+), 5 deletions(-) diff --git a/groups/index.md b/groups/index.md index 2989412..f07e0f6 100644 --- a/groups/index.md +++ b/groups/index.md @@ -49,6 +49,12 @@ title: "Groups"
  • Dynamics in hippocampus
  • Synthesis and modeling of current results in hippocampus research
    • - -


    Registered members can login here

    +

    Sleep & Memory

    +
      +
    • Led by Charmaine Demanuelle and Bengi Baran
      • +
    • Brain oscillations during sleep that are critical for learning and memory and how they may go awry in neurological/psychiatric disorders
      • +
    • Human and animal work
      • +
    • Computational models
      • +
    • Aimed to provide a platform for local research groups to present their new hypotheses, experiments and data
      • +


    For more information, please contact cogweb at math.bu.edu

    diff --git a/people/faculty/index.md b/people/faculty/index.md index c97bec4..80ab109 100644 --- a/people/faculty/index.md +++ b/people/faculty/index.md @@ -186,11 +186,12 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Stan Goldin
    -
    +
    Harvard Medical School
    -

    Coming Soon -

    +

    Dr. Stan Goldin has been developing some new ideas on a carrier wave function for brain oscillations in discrete frequency bands. His early stage collaboration with BSF Fellow Prof. Ed Boyden of MIT is exploring new ways to design multichannel arrays for automated, rapid, delivery of pharmacological agents to key distributed locations in nerve networks, to help elucidate network function. His collaboration with Dr. Newton Howard of MIT on neural coding mechanisms has revealed novel photonic signaling pathways in the brain, powered by light-generating neuronal redox reactions and employing novel photon absorbing rhodopsin-like proteins discovered within the mammalian brain.

    +

    Dr. Goldin’s laboratory originated research techniques and devices that have been employed to elucidate molecular mechanisms underlying brain waves and brain oscillation circuitry--processes now known to play an important role in long term brain changes (neuroplasticity) and memory formation. He is now finishing a book, Ascent of the Human Brain—An Expanded view of Human Evolution, on modern neuroscience research’s impact on our understanding of human consciousness, selfhood & spirituality.

    +
    From 0a7bdde6ad2ae18014185e7cd0078ab5e240c106 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Fri, 2 May 2014 23:26:27 -0400 Subject: [PATCH 08/59] fix indentation and add p tags around Website links --- people/faculty/index.md | 397 ++++++++++++++++++++-------------------- 1 file changed, 196 insertions(+), 201 deletions(-) diff --git a/people/faculty/index.md b/people/faculty/index.md index 80ab109..fb55f5b 100644 --- a/people/faculty/index.md +++ b/people/faculty/index.md @@ -11,17 +11,17 @@ title: "People - Faculty"
    Nancy Kopell
    Boston University
    -
    Website and Publications +

    Website and Publications

    My major interest is dynamics of the nervous system, especially brain -rhythms associated with cognition. The central questions are: what are the -networks and physiology that produce these rhythms; how do the -physiological properties of those networks affect the use of the dynamics -in cognition; can changes in the rhythms in disease give insights into the -nature and treatments of diseases? I'm currently working on projects -relating to physiology and interaction of rhythms, attention, Parkinson's -disease, schizophrenia and anesthesia; with collaborators, the work -involves in vivo and in vitro experiments, dynamical systems modeling and -simulation, and geometric singular perturbations.

    + rhythms associated with cognition. The central questions are: what are the + networks and physiology that produce these rhythms; how do the + physiological properties of those networks affect the use of the dynamics + in cognition; can changes in the rhythms in disease give insights into the + nature and treatments of diseases? I'm currently working on projects + relating to physiology and interaction of rhythms, attention, Parkinson's + disease, schizophrenia and anesthesia; with collaborators, the work + involves in vivo and in vitro experiments, dynamical systems modeling and + simulation, and geometric singular perturbations.

    Executive Committee

    @@ -30,24 +30,24 @@ simulation, and geometric singular perturbations.

    Ed Boyden
    MIT
    -
    Website -

    We are inventing new tools for analyzing and engineering brain -circuits. For example, we have devised 'optogenetic' tools, which -enable the activation and silencing of neural circuit elements with -light, to understand their causal contribution to normal and -pathological neural computations, as well as to support the discovery -and repair of neural circuit targets in a therapeutic context. We are -using our inventions to enable systematic approaches to neuroscience, -revealing how neural circuits operate to generate behavior, and -empowering new therapeutic strategies for neurological and psychiatric -disorders.

    +

    Website

    +

    We are inventing new tools for analyzing and engineering brain + circuits. For example, we have devised 'optogenetic' tools, which + enable the activation and silencing of neural circuit elements with + light, to understand their causal contribution to normal and + pathological neural computations, as well as to support the discovery + and repair of neural circuit targets in a therapeutic context. We are + using our inventions to enable systematic approaches to neuroscience, + revealing how neural circuits operate to generate behavior, and + empowering new therapeutic strategies for neurological and psychiatric + disorders.

    Uri Eden
    Boston University
    -
    Website +

    Website

    My research focuses on developing mathematical and statistical methods to analyze neural spiking activity. I have worked to integrate methodologies related to model identification, statistical inference, signal processing, and stochastic estimation and control, and expand these methodologies to incorporate point process observation models, making them more appropriate for modeling the dynamics of neural systems observed through spike train data. This research can be divided into two categories; first, a methodological component, focused on developing a statistical framework for relating neural activity to biological and behavioral signals and developing estimation algorithms, goodness-of-fit analyses, and mathematical theory that can be applied to any neural spiking system; second, an application component, wherein these methods are applied to spiking observations in real neural systems to dynamically model the spiking properties of individual neurons, to characterize how ensembles maintain representations of associated biological and behavioral signals, and to reconstruct these signals in real time.

    @@ -56,26 +56,28 @@ disorders.

    MGH/Harvard Medical School/Martinos Imaging Center
    -Website -

    The Athinoula A. Martinos Center at the Massachusetts General Hospital has a twofold mission to advance the development of imaging technologies and -their integration with complementary technologies, and to apply these technologies to support basic -science and translational research that is driven by an overarching interest in the continuous long-term -improvement of clinical care. Martinos Center investigators are innovating in the areas of anatomical -and functional magnetic resonance imaging (MRI) and spectroscopy (MRS), magnetoencephalography -(MEG) and electroencephalography (EEG), near infrared spectroscopy (NIRS) and diffuse optical -tomography (DOT), and positron emission tomography (PET) as well as cutting-edge tools for -computational image analysis. The Center supports over 200 PHS-funded research projects at the -MGH and other Boston-areas institutions, as well as other institutions in the United States and abroad. -Research activities at the Martinos Center are supported institutionally as well as by Federal and -foundation grants. Martinos Center investigators and their broad network of colleagues are at the -forefront of developing advanced imaging technologies, integrating those technologies for multimodality -acquisition, and deriving novel acquisition and analysis methods for the rich body of imaging -data now acquired with these technologies. Funded by a P41 Regional Resource grant, from National -Center for Research Resources, the Martinos Center and its Center for Functional Neuroimaging -Technologies is a region-wide resource, broadly used by basic and clinical scientists who employ the -full range of imaging technologies available at the Center to address questions of fundamental -importance in fields ranging from neurovascular, neurological, and psychiatric disorders to cognitive -neuroscience to cancer and cardiovascular function.

    +

    Website

    +

    The Athinoula A. Martinos Center at the Massachusetts General Hospital has a twofold mission to + advance the development of imaging technologies and + their integration with complementary technologies, and to apply these technologies to support basic + science and translational research that is driven by an overarching interest in the continuous long-term + improvement of clinical care. Martinos Center investigators are innovating in the areas of anatomical + and functional magnetic resonance imaging (MRI) and spectroscopy (MRS), magnetoencephalography + (MEG) and electroencephalography (EEG), near infrared spectroscopy (NIRS) and diffuse optical + tomography (DOT), and positron emission tomography (PET) as well as cutting-edge tools for + computational image analysis. The Center supports over 200 PHS-funded research projects at the + MGH and other Boston-areas institutions, as well as other institutions in the United States and abroad. + Research activities at the Martinos Center are supported institutionally as well as by Federal and + foundation grants. Martinos Center investigators and their broad network of colleagues are at the + forefront of developing advanced imaging technologies, integrating those technologies for multimodality + acquisition, and deriving novel acquisition and analysis methods for the rich body of imaging + data now acquired with these technologies. Funded by a P41 Regional Resource grant, from National + Center for Research Resources, the Martinos Center and its Center for Functional Neuroimaging + Technologies is a region-wide resource, broadly used by basic and clinical scientists who employ the + full range of imaging technologies available at the Center to address questions of fundamental + importance in fields ranging from neurovascular, neurological, and psychiatric disorders to cognitive + neuroscience to cancer and cardiovascular function.

    +
    @@ -83,17 +85,13 @@ neuroscience to cancer and cardiovascular function.

    Brown University

    Dr. Jones uses her background in dynamical systems theory mathematics and computational neural modeling to study neural dynamics in health and disease. She is trained in MEG/EEG imaging and currently uses computational modeling techniques to bridge the critical gap between the non-invasive imaging observables and the underlying microscopic cellular and network level mechanisms. Her current projects and interest include:

    -
      -
    • Investigating the neural dynamics underlying normal development in children ages 0-6 as well as neural abnormalities in children with encephalopathy of -prematurity (EP). In collaboration with Drs. Ellen Grant and Yoshio Okada at CHB, we are studying development with a powerful combination of techniques including mathematical modeling, MR diffusion tensor imaging, and MEG imaging.
      • - -
    • Studying the mechanisms and functions of neural rhythms including their role in sensory perception, attentional processes, and healthy aging. We are also investigating the source of disruption in brain rhythms in diseases such as Parkinson's Disease, Obsessive Compulsive Disorder, and Attention Deficit Disorder.
      • - -
    • Investigating plasticity induced by training in perceptual attention. In collaboration with Dr. Cathy Kerr at HMS we are studying neurodynamics underlying Mindfulness Medidation Practice.
      • - -
    • Combing computational modeling and optogenetic techniques, in collaboration with Dr. Chris Moore at Brown University, to study neural dynamics. We are currently delineating the role of specific cell types in controlling neocortical rhythmicity and investigating the impact of these rhythms on sensory perception.
      • -
    -
    +
      +
    • Investigating the neural dynamics underlying normal development in children ages 0-6 as well as neural abnormalities in children with encephalopathy of prematurity (EP). In collaboration with Drs. Ellen Grant and Yoshio Okada at CHB, we are studying development with a powerful combination of techniques including mathematical modeling, MR diffusion tensor imaging, and MEG imaging.
      • +
    • Studying the mechanisms and functions of neural rhythms including their role in sensory perception, attentional processes, and healthy aging. We are also investigating the source of disruption in brain rhythms in diseases such as Parkinson's Disease, Obsessive Compulsive Disorder, and Attention Deficit Disorder.
      • +
    • Investigating plasticity induced by training in perceptual attention. In collaboration with Dr. Cathy Kerr at HMS we are studying neurodynamics underlying Mindfulness Medidation Practice.
      • +
    • Combing computational modeling and optogenetic techniques, in collaboration with Dr. Chris Moore at Brown University, to study neural dynamics. We are currently delineating the role of specific cell types in controlling neocortical rhythmicity and investigating the impact of these rhythms on sensory perception.
      • +
    +
    @@ -101,8 +99,8 @@ prematurity (EP). In collaboration with Drs. Ellen Grant and Yoshio Okada at CHB
    Earl Miller
    MIT
    -
    Website -

    The Miller Lab uses experimental and theoretical approaches to study the neural basis of the high-level cognitive functions that underlie complex goal-directed behavior. The focus is on the frontal lobe, the region of the brain most elaborated in humans and linked to neuropsychiatric disorders. They have provided insights into how categories, concepts, and rules are learned, how attention is focused, and how the brain coordinates thought and action. To this end, the Miller Lab has innovated techniques for studying the activity of many neurons in multiple brain areas simultaneously, which has provided insight into how interactions within local and global networks of neurons interact and collaborate. This work has established a foundation upon which to construct more detailed, mechanistic accounts of how executive control is implemented in the brain and its dysfunction in diseases such as autism, schizophrenia and attention deficit disorder.

    +

    Website

    +

    The Miller Lab uses experimental and theoretical approaches to study the neural basis of the high-level cognitive functions that underlie complex goal-directed behavior. The focus is on the frontal lobe, the region of the brain most elaborated in humans and linked to neuropsychiatric disorders. They have provided insights into how categories, concepts, and rules are learned, how attention is focused, and how the brain coordinates thought and action. To this end, the Miller Lab has innovated techniques for studying the activity of many neurons in multiple brain areas simultaneously, which has provided insight into how interactions within local and global networks of neurons interact and collaborate. This work has established a foundation upon which to construct more detailed, mechanistic accounts of how executive control is implemented in the brain and its dysfunction in diseases such as autism, schizophrenia and attention deficit disorder.

    Affiliated Faculty

    @@ -111,16 +109,16 @@ prematurity (EP). In collaboration with Drs. Ellen Grant and Yoshio Okada at CHB
    Seppo P. Ahlfors
    MGH/Harvard Medical School/Martinos Imaging Center
    -
    Website -

    My research concerns spatiotemporal imaging of human brain function. I have applied integrated magnetoencephalography (MEG), electroencephalography (EEG), and functional magnetic resonance imaging (fMRI) to studies of cortical processing of visual information. My research involves development of techniques for the analysis of multimodal biomedical imaging data, including the use of fMRI data to inform the source estimation (inverse problem) of MEG and EEG. Currently I am studying computationally the characteristics of the sensitivity of MEG and EEG sensor arrays as well as the relationship of MEG and EEG signals to the cortical anatomy and physiology. Collaborative work focuses on the application of MEG, EEG, and fMRI techniques to reveal neural activation patterns related to cognitive processing in normal and clinical populations.

    +

    Website

    +

    My research concerns spatiotemporal imaging of human brain function. I have applied integrated magnetoencephalography (MEG), electroencephalography (EEG), and functional magnetic resonance imaging (fMRI) to studies of cortical processing of visual information. My research involves development of techniques for the analysis of multimodal biomedical imaging data, including the use of fMRI data to inform the source estimation (inverse problem) of MEG and EEG. Currently I am studying computationally the characteristics of the sensitivity of MEG and EEG sensor arrays as well as the relationship of MEG and EEG signals to the cortical anatomy and physiology. Collaborative work focuses on the application of MEG, EEG, and fMRI techniques to reveal neural activation patterns related to cognitive processing in normal and clinical populations.

    Christoph Börgers
    Tufts University
    -
    Website -

    Most of my work is on designing and analyzing computational models in neuroscience. Current projects concern the role of different populations of inhibitory cells in gamma oscillations, modeling of the impact of astrocytes on neuronal activity, and synchronization via gap junctions. I also have one current research project unrelated to neuroscience, on numerical methods for linear Boltzmann equations.

    +

    Website

    +

    Most of my work is on designing and analyzing computational models in neuroscience. Current projects concern the role of different populations of inhibitory cells in gamma oscillations, modeling of the impact of astrocytes on neuronal activity, and synchronization via gap junctions. I also have one current research project unrelated to neuroscience, on numerical methods for linear Boltzmann equations.

    @@ -128,10 +126,9 @@ prematurity (EP). In collaboration with Drs. Ellen Grant and Yoshio Okada at CHB
    Syd Cash
    MGH
    -
    Website -

    Current research in the lab is, broadly speaking, dedicated to trying to understand normal and abnormal brain activity, particularly oscillations, using multi-modal and multi-scalar approaches. Specifically, we are combining novel microelectrode approaches with non-invasive techniques such as electroencephalography and magnetoencephalography to record directly from both human and animal cortex and subcortical structures. One part of the lab studies the neurophysiology of epilepsy; trying to understand how seizures start and stop and how they might be predicted and terminated. These questions overlap with investigations into the mechanisms of sleep, normal language, auditory, and other cognitive processing.

    -All of these projects are built on a foundation of combined microelectrode, macroelectrode and non-invasive recording techniques that span information from the level of single action potentials to aggregate activity of millions of neurons. Intensive signal processing and computational techniques are employed to analyze these data sets. Collaborative activities involving neural modeling are aimed at relating these multi-scalar data. Ultimately, all of these projects aim toward the creation of both invasive and non-invasive mechanisms for restoring damaged neuronal function. -

    +

    Website

    +

    Current research in the lab is, broadly speaking, dedicated to trying to understand normal and abnormal brain activity, particularly oscillations, using multi-modal and multi-scalar approaches. Specifically, we are combining novel microelectrode approaches with non-invasive techniques such as electroencephalography and magnetoencephalography to record directly from both human and animal cortex and subcortical structures. One part of the lab studies the neurophysiology of epilepsy; trying to understand how seizures start and stop and how they might be predicted and terminated. These questions overlap with investigations into the mechanisms of sleep, normal language, auditory, and other cognitive processing.

    +

    All of these projects are built on a foundation of combined microelectrode, macroelectrode and non-invasive recording techniques that span information from the level of single action potentials to aggregate activity of millions of neurons. Intensive signal processing and computational techniques are employed to analyze these data sets. Collaborative activities involving neural modeling are aimed at relating these multi-scalar data. Ultimately, all of these projects aim toward the creation of both invasive and non-invasive mechanisms for restoring damaged neuronal function.

    @@ -139,10 +136,9 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Ming Cheng
    Brown University
    -
    Website -

    Dr. Cheng is a neurosurgeon whose laboratory studies the neural basis of different cognitive processes that underlie diseases such as Parkinson's and other movement disorders, pain, epilepsy, depression, and other more rare neurological conditions. The goal of his laboratory is neurorestoration, the idea that therapies can be devised to restore the original function of the brain and spinal cord.

    -

    Our primary techniques include the use of psychopharmacology, electrical stimulation and reversible lesioning to enhance or alter brain, spine and peripheral nerve function. We measure the results in our subjects with behavioral tasks coupled with intraoperative and extraoperative electrophysiology in human subjects: EEG, electrocorticography (ECoG), extracellular field potential recordings, and single unit microelectrode recordings from multiple brain and spine structures (subthalamic nucleus, caudate, globus pallidus, thalamus, nucleus accumbens, substantia nigra, neocortical areas, dorsal columns, the dorsal horn, etc.). We also use these electrophysiological tools to complement molecular techniques in the study of animal models of hydrocephalus and neurodegenerative disease. We are ultimately interested in applying our findings to the creation of open and closed loop stimulatory devices that can help human patients with neurological and psychiatric diseases. Ultimately, the information we learn will help us create brain and spine machine interfaces to fight disease and change human interaction with the external world. -

    +

    Website

    +

    Dr. Cheng is a neurosurgeon whose laboratory studies the neural basis of different cognitive processes that underlie diseases such as Parkinson's and other movement disorders, pain, epilepsy, depression, and other more rare neurological conditions. The goal of his laboratory is neurorestoration, the idea that therapies can be devised to restore the original function of the brain and spinal cord.

    +

    Our primary techniques include the use of psychopharmacology, electrical stimulation and reversible lesioning to enhance or alter brain, spine and peripheral nerve function. We measure the results in our subjects with behavioral tasks coupled with intraoperative and extraoperative electrophysiology in human subjects: EEG, electrocorticography (ECoG), extracellular field potential recordings, and single unit microelectrode recordings from multiple brain and spine structures (subthalamic nucleus, caudate, globus pallidus, thalamus, nucleus accumbens, substantia nigra, neocortical areas, dorsal columns, the dorsal horn, etc.). We also use these electrophysiological tools to complement molecular techniques in the study of animal models of hydrocephalus and neurodegenerative disease. We are ultimately interested in applying our findings to the creation of open and closed loop stimulatory devices that can help human patients with neurological and psychiatric diseases. Ultimately, the information we learn will help us create brain and spine machine interfaces to fight disease and change human interaction with the external world.

    @@ -150,10 +146,9 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Robert Desimone
    MIT
    -
    Website -
    Neural basis for attention and executive control
    -

    A complex visual scene will typically contain many different objects, few of which are currently relevant to behavior. Thus, attentional mechanisms are needed to select the relevant objects from the scene and to reject the irrelevant ones. Neurophysiological studies in our own and other labs have identified some of the neural mechanisms of attentional selection within the ventral, "object recognition", stream of the cortex. At each stage along this stream, attended, or behaviorally relevant, stimuli are processed preferentially compared to irrelevant distracters. In recent years, we have found that the top-down attentional bias is expressed, at least in part, in visual cortex through an increase in high-frequency (gamma) synchronization of neurons carrying critical information about the location or features of the behaviorally relevant stimulus. Increases in gamma synchrony are found during both spatial attention and featural attention engaged during visual search, and the presence of synchrony predicts faster responses in visual tasks. Recent evidence shows that inputs from the frontal eye fields (FEF) in prefrontal cortex initiates coupled gamma-frequency oscillations between FEF and area V4 during attention, and these oscillations are shifted in time across the two areas to allow for maximally effective communication. Cross-area synchrony may be a general mechanism for regulating information flow through the brain and for regulating spike-timing dependent plasticity. -

    +

    Website

    +
    Neural basis for attention and executive control
    +

    A complex visual scene will typically contain many different objects, few of which are currently relevant to behavior. Thus, attentional mechanisms are needed to select the relevant objects from the scene and to reject the irrelevant ones. Neurophysiological studies in our own and other labs have identified some of the neural mechanisms of attentional selection within the ventral, "object recognition", stream of the cortex. At each stage along this stream, attended, or behaviorally relevant, stimuli are processed preferentially compared to irrelevant distracters. In recent years, we have found that the top-down attentional bias is expressed, at least in part, in visual cortex through an increase in high-frequency (gamma) synchronization of neurons carrying critical information about the location or features of the behaviorally relevant stimulus. Increases in gamma synchrony are found during both spatial attention and featural attention engaged during visual search, and the presence of synchrony predicts faster responses in visual tasks. Recent evidence shows that inputs from the frontal eye fields (FEF) in prefrontal cortex initiates coupled gamma-frequency oscillations between FEF and area V4 during attention, and these oscillations are shifted in time across the two areas to allow for maximally effective communication. Cross-area synchrony may be a general mechanism for regulating information flow through the brain and for regulating spike-timing dependent plasticity.

    @@ -161,9 +156,9 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Howard Eichenbaum
    Boston University
    -
    Website -

    The research program of this laboratory is focused on four closely related projects that seek to understand the brain circuity that supports memory. This research is guided by the hypothesis that our ability to remember specific experiences relies on an organization of memories about objects and the events in the context in which they occurred. We believe that associations between objects and context is accomplished through the circuitry of the medial temporal lobe, in which parallel pathways represent information about objects and about context, and these streams of information converge within the hippocampus. A project central to this goal seeks to characterize how neurons in key components of the medial temporal lobe encode these different types of information and how components of this brain system interact with one another. Another project explores how the hippocampus is initially critical to the associations between objects and context but eventually these associations consolidate in cortical areas with which the hippocampus is connected. Another project explores how the prefrontal cortex controls the retrieval of memories as they bear on ongoing cognitive processes. And yet another project explores how hippocampal networks represent objects in the spacial and temporal context in which they occur. Together these projects will provide new insights into how memories are organized within the medial temporal lobe memory system and how memories are retrieved when we recall our daily experiences. -

    +
    +

    Website

    +

    The research program of this laboratory is focused on four closely related projects that seek to understand the brain circuity that supports memory. This research is guided by the hypothesis that our ability to remember specific experiences relies on an organization of memories about objects and the events in the context in which they occurred. We believe that associations between objects and context is accomplished through the circuitry of the medial temporal lobe, in which parallel pathways represent information about objects and about context, and these streams of information converge within the hippocampus. A project central to this goal seeks to characterize how neurons in key components of the medial temporal lobe encode these different types of information and how components of this brain system interact with one another. Another project explores how the hippocampus is initially critical to the associations between objects and context but eventually these associations consolidate in cortical areas with which the hippocampus is connected. Another project explores how the prefrontal cortex controls the retrieval of memories as they bear on ongoing cognitive processes. And yet another project explores how hippocampal networks represent objects in the spacial and temporal context in which they occur. Together these projects will provide new insights into how memories are organized within the medial temporal lobe memory system and how memories are retrieved when we recall our daily experiences.

    @@ -171,15 +166,15 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Oded Ghitza
    Boston University
    -
    Website -
    Cortical and Computational Decoding of Speech
    -

    We conduct a tightly integrated computational and experimental research program across three sites (BU, NYU, Columbia) to study spoken language recognition from the psychophysical, neurophysiological, and engineering perspectives. The program proceeds in four fronts:

    -
      -
    • Psychophysics (Ghitza, BU). We measure and model the results of human performance in tasks designed to gain a better understanding on the interplay between neuronal oscillators in different frequency bands, and between the oscillations and the speech syllabic structure;
      • -
    • Human Neuroimaging. We formulate the intra-relationship among theta, beta and gamma oscillations, using MEG (David Poeppel, NYU) and ECoG (Charles Schroeder, Columbia) data recorded while subjects perform intelligibility tasks;
      • -
    • Monkey Electrophysiology (Charles Schroeder, Columbia). If the emerging cortical computation principles are fundamental, they must generalize across mammalian species. We are using high-resolution physiological methods to measure the intra-relationship among oscillations using multi-electrode recordings in monkeys listening to stimuli specifically designed to capture the rhythmic aspects of natural speech and music;
      • -
    • Automatic Speech Recognition (Ghitza, BU). We explore a new perspective to the development of ASR systems that incorporates the insights from the behavioral and brain sciences, specifically rhythmic brain activity. We ascertain whether the proposed cortical computation principle could be used as an adjunct to conventional features used in ASR systems, e.g. in lattice re-scoring of n-best lists – and ultimately result in a decrease in word error rate.
      • -
    +

    Website

    +
    Cortical and Computational Decoding of Speech
    +

    We conduct a tightly integrated computational and experimental research program across three sites (BU, NYU, Columbia) to study spoken language recognition from the psychophysical, neurophysiological, and engineering perspectives. The program proceeds in four fronts:

    +
      +
    • Psychophysics (Ghitza, BU). We measure and model the results of human performance in tasks designed to gain a better understanding on the interplay between neuronal oscillators in different frequency bands, and between the oscillations and the speech syllabic structure;
      • +
    • Human Neuroimaging. We formulate the intra-relationship among theta, beta and gamma oscillations, using MEG (David Poeppel, NYU) and ECoG (Charles Schroeder, Columbia) data recorded while subjects perform intelligibility tasks;
      • +
    • Monkey Electrophysiology (Charles Schroeder, Columbia). If the emerging cortical computation principles are fundamental, they must generalize across mammalian species. We are using high-resolution physiological methods to measure the intra-relationship among oscillations using multi-electrode recordings in monkeys listening to stimuli specifically designed to capture the rhythmic aspects of natural speech and music;
      • +
    • Automatic Speech Recognition (Ghitza, BU). We explore a new perspective to the development of ASR systems that incorporates the insights from the behavioral and brain sciences, specifically rhythmic brain activity. We ascertain whether the proposed cortical computation principle could be used as an adjunct to conventional features used in ASR systems, e.g. in lattice re-scoring of n-best lists – and ultimately result in a decrease in word error rate.
      • +
    @@ -191,7 +186,7 @@ All of these projects are built on a foundation of combined microelectrode, macr

    Dr. Stan Goldin has been developing some new ideas on a carrier wave function for brain oscillations in discrete frequency bands. His early stage collaboration with BSF Fellow Prof. Ed Boyden of MIT is exploring new ways to design multichannel arrays for automated, rapid, delivery of pharmacological agents to key distributed locations in nerve networks, to help elucidate network function. His collaboration with Dr. Newton Howard of MIT on neural coding mechanisms has revealed novel photonic signaling pathways in the brain, powered by light-generating neuronal redox reactions and employing novel photon absorbing rhodopsin-like proteins discovered within the mammalian brain.

    Dr. Goldin’s laboratory originated research techniques and devices that have been employed to elucidate molecular mechanisms underlying brain waves and brain oscillation circuitry--processes now known to play an important role in long term brain changes (neuroplasticity) and memory formation. He is now finishing a book, Ascent of the Human Brain—An Expanded view of Human Evolution, on modern neuroscience research’s impact on our understanding of human consciousness, selfhood & spirituality.

    -
    +
    @@ -199,9 +194,9 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Ann Graybiel
    MIT
    -
    Website -

    Ann Graybiel studies the basal ganglia, forebrain structures that are profoundly important for normal brain function but are also implicated in Parkinson's disease, Huntington's disease, obsessive-compulsive disorder, and addiction. Graybiel's work is uncovering neural deficits related to these disorders, as well as the role the basal ganglia play in guiding normal behavior. -

    +

    Website

    +

    Ann Graybiel studies the basal ganglia, forebrain structures that are profoundly important for normal brain function but are also implicated in Parkinson's disease, Huntington's disease, obsessive-compulsive disorder, and addiction. Graybiel's work is uncovering neural deficits related to these disorders, as well as the role the basal ganglia play in guiding normal behavior. +

    @@ -209,9 +204,9 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Xue Han
    Boston University
    -
    Website -

    Brain disorders represent the biggest unmet medical need, with many disorders being untreatable, and most treatments presenting serious side effects. Accordingly, we are discovering design principles for novel neuromodulation therapies. We invent and apply a variety of genetic, molecular, pharmacological, optical, and electrical tools to correct neural circuits that go awry within the brain. As an example, we have pioneered several technologies for silencing specific cells in the brain using pulses of light. We have also recently participated the first pre-clinical testing of a novel neurotechnology, optical neural modulation. Using these novel neurotechnologies and classical ones such as deep brain stimulation (DBS), we modulate the function of neural circuits to establish causal links between neural dynamics and behavioral phenomena (e.g., movement, attention, memory, and decision making). One of our current interests is the investigation of how neural synchrony arises within and across brain regions, and how synchronous activity contributes to normal cognition and pathology. -

    +

    Website

    +

    Brain disorders represent the biggest unmet medical need, with many disorders being untreatable, and most treatments presenting serious side effects. Accordingly, we are discovering design principles for novel neuromodulation therapies. We invent and apply a variety of genetic, molecular, pharmacological, optical, and electrical tools to correct neural circuits that go awry within the brain. As an example, we have pioneered several technologies for silencing specific cells in the brain using pulses of light. We have also recently participated the first pre-clinical testing of a novel neurotechnology, optical neural modulation. Using these novel neurotechnologies and classical ones such as deep brain stimulation (DBS), we modulate the function of neural circuits to establish causal links between neural dynamics and behavioral phenomena (e.g., movement, attention, memory, and decision making). One of our current interests is the investigation of how neural synchrony arises within and across brain regions, and how synchronous activity contributes to normal cognition and pathology. +

    @@ -219,9 +214,9 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Mike Hasselmo
    Boston University
    -
    Website -

    Coming Soon -

    +

    Website

    +

    Coming Soon +

    @@ -229,18 +224,18 @@ All of these projects are built on a foundation of combined microelectrode, macr
    Don Katz
    Brandeis
    -
    Website -

    -The Katz lab is actively engaged in the following research areas: -

      -
    • Dynamics of Taste Responses
      • -
    • Interactions Between Taste Neurons -
    • Rhythms and Taste Behavior -
    • Experience, Expectation and Coding -
    • Neural Plasticity and Taste Learning -
      • -
    -

    +

    Website

    +

    + The Katz lab is actively engaged in the following research areas: +

      +
    • Dynamics of Taste Responses
      • +
    • Interactions Between Taste Neurons +
    • Rhythms and Taste Behavior +
    • Experience, Expectation and Coding +
    • Neural Plasticity and Taste Learning +
      • +
    +

    @@ -248,12 +243,12 @@ The Katz lab is actively engaged in the following research areas:
    Bernat Kocsis
    Harvard Medical School
    -
    Website -
    Subcortical regulation of forebrain activity in the sleep-wake cycle.
    -

    The central focus of my research is the subcortical regulation of hippocampal function and is guided by the general hypothesis that the role of this regulation is to build dynamic associations between several limbic structures that are synchronized by oscillatory population activity. Phasic and rhythmic synchronization of neuronal activity is critical to control the concerted action of spatially separated structures in the brain. The general state and background activity of various brain structures determine how these structures will respond to different specific inputs and how they establish dynamical connections to perform complex functions. An important constituent of these states is the pattern of population activity including coherent oscillations in anatomically scattered structures which can establish functional networks during specific behaviors. Theta synchrony provides an excellent model to study these cooperations and the way in which they differ in specific behavioral states, such as waking exploration and REM sleep.

    -
    Oscillatory processes in cardiovascular control.
    -

    Another model we use to study rhythmic synchronization among neural networks is the autonomic nervous system which is capable of generating different patterns of activity that control the response of the cardiovascular system to changes in the environment (e.g. chemoregulation, thermoregulation, etc.) and different behavioral states (e.g. defense reaction, eating, sleep, etc.). Our guiding hypothesis in this research is that sympathetic rhythm is generated by multiple oscillators and we study the changes in the relationship between these oscillators under different conditions of health and disease. -

    +

    Website

    +
    Subcortical regulation of forebrain activity in the sleep-wake cycle.
    +

    The central focus of my research is the subcortical regulation of hippocampal function and is guided by the general hypothesis that the role of this regulation is to build dynamic associations between several limbic structures that are synchronized by oscillatory population activity. Phasic and rhythmic synchronization of neuronal activity is critical to control the concerted action of spatially separated structures in the brain. The general state and background activity of various brain structures determine how these structures will respond to different specific inputs and how they establish dynamical connections to perform complex functions. An important constituent of these states is the pattern of population activity including coherent oscillations in anatomically scattered structures which can establish functional networks during specific behaviors. Theta synchrony provides an excellent model to study these cooperations and the way in which they differ in specific behavioral states, such as waking exploration and REM sleep.

    +
    Oscillatory processes in cardiovascular control.
    +

    Another model we use to study rhythmic synchronization among neural networks is the autonomic nervous system which is capable of generating different patterns of activity that control the response of the cardiovascular system to changes in the environment (e.g. chemoregulation, thermoregulation, etc.) and different behavioral states (e.g. defense reaction, eating, sleep, etc.). Our guiding hypothesis in this research is that sympathetic rhythm is generated by multiple oscillators and we study the changes in the relationship between these oscillators under different conditions of health and disease. +

    @@ -261,9 +256,9 @@ The Katz lab is actively engaged in the following research areas:
    Mark Kramer
    Boston University
    -
    Website -

    We study mathematical neuroscience, with particular emphasis on neural rhythms, brain diseases, dynamical systems, and data analysis. All of the research involves interdisciplinary collaborations with experimentalists and clinicians. We are currently focused on analysis and modeling of multiscale data recorded in vivo from human subjects, and the construction of computational models of multiscale neuronal activity. We are also interested in techniques to infer and analyze functional connectivity networks from multivariate time series data, and how neuroscience can motivate new research questions in mathematics. -

    +

    Website

    +

    We study mathematical neuroscience, with particular emphasis on neural rhythms, brain diseases, dynamical systems, and data analysis. All of the research involves interdisciplinary collaborations with experimentalists and clinicians. We are currently focused on analysis and modeling of multiscale data recorded in vivo from human subjects, and the construction of computational models of multiscale neuronal activity. We are also interested in techniques to infer and analyze functional connectivity networks from multivariate time series data, and how neuroscience can motivate new research questions in mathematics. +

    @@ -271,10 +266,10 @@ The Katz lab is actively engaged in the following research areas:
    Chris Moore
    Brown University
    -
    Website -

    Christopher Moore studies brain dynamics and how they change can change perception from moment to moment. -The brain's ability to shift the way it processes information—to shift its 'state'—is crucial to surviving in an ever-changing world. Dysregulation of these dynamics are a hallmark of neurologic and psychiatric disease. The laboratory is studying the mechanisms responsible for generating brain states, how they impact the representation of a sensory input, and how, ultimately, they change conscious perception. -

    +

    Website

    +

    Christopher Moore studies brain dynamics and how they change can change perception from moment to moment. + The brain's ability to shift the way it processes information—to shift its 'state'—is crucial to surviving in an ever-changing world. Dysregulation of these dynamics are a hallmark of neurologic and psychiatric disease. The laboratory is studying the mechanisms responsible for generating brain states, how they impact the representation of a sensory input, and how, ultimately, they change conscious perception. +

    @@ -282,26 +277,26 @@ The brain's ability to shift the way it processes information—to shift its 'st
    Daniel Polley
    Mass. Eye & Ear/Harvard Medical School
    -
    Website -

    Our work focuses on the role of sensory experience in the development and -maintenance of functional circuits in the auditory cortex. The auditory -cortex is powerfully influenced by experience during finite windows of -development known as critical periods, after which time significant changes -can only be brought about through learned associations between sounds and -behaviorally relevant consequences. We study the mechanisms and perceptual -correlates of cortical plasticity across the lifespan using a variety of -neurophysiological, genetic, behavioral and computational approaches. We -also record from subcortical auditory nuclei such as the inferior colliculus -and auditory thalamus to understand more about features that are relayed to -the cortex versus constructed there de novo. We believe this class of study -will contribute towards a richer understanding of normal function, but might -also hold the key for remediating abnormal auditory signal following a -history of degraded hearing or deafness in early life. A major goal for our -group is to apply what we've learned about the dynamic interplay between -plasticity and stability in animal models towards improving auditory -processing in humans that have been reconnected to the auditory world -following a period of prolonged hearing loss. -

    +

    Website

    +

    Our work focuses on the role of sensory experience in the development and + maintenance of functional circuits in the auditory cortex. The auditory + cortex is powerfully influenced by experience during finite windows of + development known as critical periods, after which time significant changes + can only be brought about through learned associations between sounds and + behaviorally relevant consequences. We study the mechanisms and perceptual + correlates of cortical plasticity across the lifespan using a variety of + neurophysiological, genetic, behavioral and computational approaches. We + also record from subcortical auditory nuclei such as the inferior colliculus + and auditory thalamus to understand more about features that are relayed to + the cortex versus constructed there de novo. We believe this class of study + will contribute towards a richer understanding of normal function, but might + also hold the key for remediating abnormal auditory signal following a + history of degraded hearing or deafness in early life. A major goal for our + group is to apply what we've learned about the dynamic interplay between + plasticity and stability in animal models towards improving auditory + processing in humans that have been reconnected to the auditory world + following a period of prolonged hearing loss. +

    @@ -310,8 +305,8 @@ following a period of prolonged hearing loss.
    Boston University
    -

    The Ritt lab concentrates on how organisms gather and use information from their environment, through processes of active sensing and sensory decision making. Current projects employ electrophysiological, behavioral, optogenetic and theoretical methods applied to the rodent whisker system, a highly refined tactile sensory system. Experiments combine multi-electrode recording of brain activity; high speed videography of behavior and development of automated image analysis algorithms; and optical stimulation of specific cell types (e.g., excitatory vs. inhibitory neurons) using genetically targeted expression of light sensitive ion channels. Parallel modeling uses tools from dynamical systems, control theory and decision theory. Augmenting experiments with model-driven, real-time feedback forms a basis for development of brain machine interfaces, with an emphasis on sensory neural prosthetics, in addition to providing state of the art tools to address basic questions of neural function. -

    +

    The Ritt lab concentrates on how organisms gather and use information from their environment, through processes of active sensing and sensory decision making. Current projects employ electrophysiological, behavioral, optogenetic and theoretical methods applied to the rodent whisker system, a highly refined tactile sensory system. Experiments combine multi-electrode recording of brain activity; high speed videography of behavior and development of automated image analysis algorithms; and optical stimulation of specific cell types (e.g., excitatory vs. inhibitory neurons) using genetically targeted expression of light sensitive ion channels. Parallel modeling uses tools from dynamical systems, control theory and decision theory. Augmenting experiments with model-driven, real-time feedback forms a basis for development of brain machine interfaces, with an emphasis on sensory neural prosthetics, in addition to providing state of the art tools to address basic questions of neural function. +

    @@ -319,9 +314,9 @@ following a period of prolonged hearing loss.
    Robert Sekuler
    Brandeis University
    -
    Website -

    Sekuler lab members are currently studying

    -
      +

      Website

      +

      Sekuler lab members are currently studying

      +
      • how we remember, forget, or mis-remember what we see
      • visual memory and perception in aging
      • perception of motion, particularly auditory and cognitive influences on visual motion
        • @@ -329,8 +324,8 @@ following a period of prolonged hearing loss.
      • EEG/ERP studies of the neural circuits in cognitive control of visual memory
      • how we are able to imitate actions and gestures that we see
      • how remember what we hear
        • -
      -
      +
    +
    @@ -338,10 +333,10 @@ following a period of prolonged hearing loss.
    Kamal Sen
    Boston University
    -
    Website -

    How do neurons in the brain encode complex natural sounds? What are the neural substrates of selectivity for and discrimination of different categories of natural sounds? Are these substrates innate or shaped by learning? -Our laboratory investigates these questions in the model system of the songbird. Electrophysiological techniques are used to record neural responses from hierarchical stages of auditory processing. Theoretical methods from areas such as statistical signal processing, systems theory, probability theory, information theory and pattern recognition are applied to characterize how neurons in the brain encode natural sounds. Computational models are constructed to understand the processing of natural sounds both at the single neuron and the network level, to model neural selectivity and discrimination, and to explore the role of learning in shaping the neural code. -

    +

    Website

    +

    How do neurons in the brain encode complex natural sounds? What are the neural substrates of selectivity for and discrimination of different categories of natural sounds? Are these substrates innate or shaped by learning? + Our laboratory investigates these questions in the model system of the songbird. Electrophysiological techniques are used to record neural responses from hierarchical stages of auditory processing. Theoretical methods from areas such as statistical signal processing, systems theory, probability theory, information theory and pattern recognition are applied to characterize how neurons in the brain encode natural sounds. Computational models are constructed to understand the processing of natural sounds both at the single neuron and the network level, to model neural selectivity and discrimination, and to explore the role of learning in shaping the neural code. +

    @@ -349,9 +344,9 @@ Our laboratory investigates these questions in the model system of the songbird.
    Barbara Shinn-Cunningham
    Boston University
    -
    Website -

    Research in the Auditory Neuroscience Laboratory addresses how listeners communicate and make sense of sounds in everyday settings. We study everything from basic perceptual sensitivity to the ways in which different brain regions coordinate their activity during complex tasks. We use a range of approaches to explore these issues, including human behavioral experiments, human neuroelectric imaging, computational modeling, and, in collaboration with other laboratories, fMRI, animal behavioral experiments, and animal neurophysiology. -

    +

    Website

    +

    Research in the Auditory Neuroscience Laboratory addresses how listeners communicate and make sense of sounds in everyday settings. We study everything from basic perceptual sensitivity to the ways in which different brain regions coordinate their activity during complex tasks. We use a range of approaches to explore these issues, including human behavioral experiments, human neuroelectric imaging, computational modeling, and, in collaboration with other laboratories, fMRI, animal behavioral experiments, and animal neurophysiology. +

    @@ -367,9 +362,9 @@ Our laboratory investigates these questions in the model system of the songbird.
    Steven Stufflebeam
    MGH/Harvard Medical School/Martinos Imaging Center
    -
    Website -

    Dr. Stufflebeam's goal is to develop and translate advanced technology at the Martinos Center into clinical practice. Currently, he is using MEG/EEG, fMRI, and optical imaging to understand how the brain processes neural information. He applies multiple imaging technologies to understand epilepsy, schizophrenia, and brain neoplasms. He is also setting up a clinical MEG service for New England. -

    +

    Website

    +

    Dr. Stufflebeam's goal is to develop and translate advanced technology at the Martinos Center into clinical practice. Currently, he is using MEG/EEG, fMRI, and optical imaging to understand how the brain processes neural information. He applies multiple imaging technologies to understand epilepsy, schizophrenia, and brain neoplasms. He is also setting up a clinical MEG service for New England. +

    @@ -377,9 +372,9 @@ Our laboratory investigates these questions in the model system of the songbird.
    Lucia Vaina
    Boston University
    -
    Website -

    Coming Soon. -

    +

    Website

    +

    Coming Soon. +

    @@ -388,9 +383,9 @@ Our laboratory investigates these questions in the model system of the songbird.
    Miles Whittington
    Newcastle Universtity, UK
    -
    Website -

    Dr. Whittington's group has a major interest in mechanisms that generate oscillatory activity with neural networks, how this activity is sustained and how is modulated in various normal and pathological conditions. -

    +

    Website

    +

    Dr. Whittington's group has a major interest in mechanisms that generate oscillatory activity with neural networks, how this activity is sustained and how is modulated in various normal and pathological conditions. +

    @@ -398,108 +393,108 @@ Our laboratory investigates these questions in the model system of the songbird.
    Matt Wilson
    MIT
    -
    Website -

    Research in the Wilson laboratory focuses on the study of information representation across large populations of neurons in the mammalian nervous system, as well as on the mechanisms that underlie formation and maintenance of distributed memories in freely behaving animals. To study the basis of these processes, the lab employs a combination of molecular genetic, electrophysiological, pharmacological, behavioral, and computational approaches. Using techniques that allow the simultaneous activity of ensembles of hundreds of single neurons to be examined in freely behaving animals, the lab examines how memories of places and events are encoded across networks of cells within the hippocampus ¬ a region of the brain long implicated in the processes underlying learning and memory. -

    -These studies of learning and memory in awake, behaving animals have led to the exploration of the nature of sleep and its role in memory. Previous theories have suggested that sleep states may be involved in the process of memory consolidation, in which memories are transferred from short to longer-term stores and possibly reorganized into more efficient forms. Recent evidence has shown that ensembles of neurons within the hippocampus, which had been activated during behavior are reactivated during periods of dreaming. By reconstructing the content of these states, specific memories can be tracked during the course of the consolidation process. -

    -Combining the measurement of ongoing neuronal activity with manipulation of molecular genetic targets has allowed the study of how specific cellular mechanisms regulate neural function to produce learning and memory at the behavioral level. Pharmacological blockage of these receptors has allowed the study of their involvement in the rapid changes that occur during both waking and sleeping states. Simultaneous monitoring of areas in the hippocampus and neocortex have allowed study of the downstream effects of activation. -

    -Taken together, these approaches contribute to the overall research objective: to understand the link from cellular/subcellular mechanisms of plasticity, to neural ensemble representations and interactions, to learning, memory, behavior, and cognition. -

    +

    Website

    +

    Research in the Wilson laboratory focuses on the study of information representation across large populations of neurons in the mammalian nervous system, as well as on the mechanisms that underlie formation and maintenance of distributed memories in freely behaving animals. To study the basis of these processes, the lab employs a combination of molecular genetic, electrophysiological, pharmacological, behavioral, and computational approaches. Using techniques that allow the simultaneous activity of ensembles of hundreds of single neurons to be examined in freely behaving animals, the lab examines how memories of places and events are encoded across networks of cells within the hippocampus ¬ a region of the brain long implicated in the processes underlying learning and memory. +

    + These studies of learning and memory in awake, behaving animals have led to the exploration of the nature of sleep and its role in memory. Previous theories have suggested that sleep states may be involved in the process of memory consolidation, in which memories are transferred from short to longer-term stores and possibly reorganized into more efficient forms. Recent evidence has shown that ensembles of neurons within the hippocampus, which had been activated during behavior are reactivated during periods of dreaming. By reconstructing the content of these states, specific memories can be tracked during the course of the consolidation process. +

    + Combining the measurement of ongoing neuronal activity with manipulation of molecular genetic targets has allowed the study of how specific cellular mechanisms regulate neural function to produce learning and memory at the behavioral level. Pharmacological blockage of these receptors has allowed the study of their involvement in the rapid changes that occur during both waking and sleeping states. Simultaneous monitoring of areas in the hippocampus and neocortex have allowed study of the downstream effects of activation. +

    + Taken together, these approaches contribute to the overall research objective: to understand the link from cellular/subcellular mechanisms of plasticity, to neural ensemble representations and interactions, to learning, memory, behavior, and cognition. +

    From 06ec417ec47d8b61ecaab8f5393a7edad10b9101 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Sat, 3 May 2014 15:46:37 -0400 Subject: [PATCH 09/59] fixing whitespace --- contact/index.md | 18 +- people/postdoc/index.md | 412 ++++++++++++++++++++-------------------- 2 files changed, 215 insertions(+), 215 deletions(-) diff --git a/contact/index.md b/contact/index.md index 0c6d92b..9bc1db8 100644 --- a/contact/index.md +++ b/contact/index.md @@ -4,12 +4,12 @@ title: "Contact" ---
    Contact
    -
    For more information or to be added to the CRC email distribution, please contact either of the following:
    -

    Xiaoshi Shi
    - Boston University
    - CompNET and CRC
    - Phone: 617.353.4587
    - Fax: 617.353.4889
    - Email: xiaoshi at bu.edu

    - -

    Webmaster: cogweb at math.bu.edu

    \ No newline at end of file +
    For more information or to be added to the CRC email distribution, please contact either of the following:
    +

    Xiaoshi Shi
    +Boston University
    +CompNET and CRC
    +Phone: 617.353.4587
    +Fax: 617.353.4889
    +Email: xiaoshi at bu.edu

    + +

    Webmaster: cogweb at math.bu.edu

    diff --git a/people/postdoc/index.md b/people/postdoc/index.md index bbf51e1..bd94949 100644 --- a/people/postdoc/index.md +++ b/people/postdoc/index.md @@ -3,264 +3,264 @@ layout: default title: "People - Postdoc" ---
    - People: Postdocs + People: Postdocs

    - Click on a name to view or hide details. + Click on a name to view or hide details.

    - Last update: 1 October 2012 + Last update: 1 October 2012

    -
    -
    - Natalie Adams -
    -
    -
    -
    -

    - My interests lie broadly in understanding how the brain represents perceptual information and why - this may differ in pathological states related to autism and schizophrenia. I am tackling this using - in vitro electrophysiological techniques in collaboration with mathematical modellers to look at - mechanisms of network rhythm generation, modulation and interaction in the anterior cingulate - region of prefrontal cortex. -

    -

    - Currently, my research is focussed on exploring aspects of frontal cortical function that facilitate - learning of sequences of sensory events (e.g. Siegel, M., et al 2009). I am interested in how precise - spike timing in individual neurons or small sub-populations relates to the local field oscillation as a - marker of the overall average of event timing relevant to a given stimulus. -

    -

    - So far my work has revealed that many neurons in the anterior cingulate cortex possess the ability - to intrinsically oscillate at sub-threshold levels. With varying degrees of tonic excitation these sub- - threshold oscillations (STOs) exist at a variety of frequencies up to c.30Hz. The anterior cingulate - cortex is known to have multiple mechanisms for the generation of gamma rhythms associated with - cognitive function and I will look at how these rhythms interact with cellular STOs to affect spike/ - phase relationships and perhaps code for sequences: The working hypothesis is that assemblies - of cells receiving higher levels of excitation increase the drive to the kinetics responsible for STOs, - ultimately leading to a spike phase-advance on each period of field gamma. -

    -

    - This work could uncover a substrate for the stable, computationally useful, temporal separation of - concurrently active sensory representations. -

    -
    +
    +
    + Natalie Adams +
    +
    +
    +
    +

    + My interests lie broadly in understanding how the brain represents perceptual information and why + this may differ in pathological states related to autism and schizophrenia. I am tackling this using + in vitro electrophysiological techniques in collaboration with mathematical modellers to look at + mechanisms of network rhythm generation, modulation and interaction in the anterior cingulate + region of prefrontal cortex. +

    +

    + Currently, my research is focussed on exploring aspects of frontal cortical function that facilitate + learning of sequences of sensory events (e.g. Siegel, M., et al 2009). I am interested in how precise + spike timing in individual neurons or small sub-populations relates to the local field oscillation as a + marker of the overall average of event timing relevant to a given stimulus. +

    +

    + So far my work has revealed that many neurons in the anterior cingulate cortex possess the ability + to intrinsically oscillate at sub-threshold levels. With varying degrees of tonic excitation these sub- + threshold oscillations (STOs) exist at a variety of frequencies up to c.30Hz. The anterior cingulate + cortex is known to have multiple mechanisms for the generation of gamma rhythms associated with + cognitive function and I will look at how these rhythms interact with cellular STOs to affect spike/ + phase relationships and perhaps code for sequences: The working hypothesis is that assemblies + of cells receiving higher levels of excitation increase the drive to the kinetics responsible for STOs, + ultimately leading to a spike phase-advance on each period of field gamma. +

    +

    + This work could uncover a substrate for the stable, computationally useful, temporal separation of + concurrently active sensory representations. +

    +
    -
    -
    - Mikio Aoi -
    -
    -
    -
    -

    - My work has been focused on two aspects of the analysis of neural rhythms. The first project, which I have been working on with Uri Eden, Mark Kramer, and Kyle Lepage, has focused on the spectral analysis of spike trains including coherence between signals when at least one of those signals is a spike train. I use point process theory to derive properties of point process spectra and the estimators, and try to understand how those properties may help or hinder our understanding of the underlying neural system. The second project is in collaboration with Timothy Gardner and Uri Eden in which we are investigating methods of multi-scale time-frequency analysis based on an object-based signal representation. This method will allow us to extract signal information using multiple times scales simultaneously. This method may help to construct sharper spectral representations than are currently possible and we believe this operation may help to understand the phenomenology of human auditory perception. -

    -
    +
    +
    + Mikio Aoi +
    +
    +
    +
    +

    + My work has been focused on two aspects of the analysis of neural rhythms. The first project, which I have been working on with Uri Eden, Mark Kramer, and Kyle Lepage, has focused on the spectral analysis of spike trains including coherence between signals when at least one of those signals is a spike train. I use point process theory to derive properties of point process spectra and the estimators, and try to understand how those properties may help or hinder our understanding of the underlying neural system. The second project is in collaboration with Timothy Gardner and Uri Eden in which we are investigating methods of multi-scale time-frequency analysis based on an object-based signal representation. This method will allow us to extract signal information using multiple times scales simultaneously. This method may help to construct sharper spectral representations than are currently possible and we believe this operation may help to understand the phenomenology of human auditory perception. +

    +
    -
    -
    - Justin Kinney -
    -
    -
    -
    -

    - Recording of neuronal spiking activity in distributed brain circuits - requires a scalable design for massively parallel recording of - extracellular field potentials. We are inventing such a system and - implementing a proof-of-concept instantiation. In this system, - multi-electrode arrays are used, which minimize tissue damage and help - with spike sorting, and time domain multiplexing of analog field - potential acquisition reduces interconnect. Channel data is then - relayed to a custom-designed terabyte capacity storage network via - custom digital circuitry. The storage network is designed to enable - neural data to be analyzed in flexible ways, including the evaluation - of spike sorting methods. -

    -

    - On the technical side, I am solely responsible for the design and implementation of the ethernet network and high-speed data storage software. In addition, I provide leadership to the project by staying well-versed in all aspects of the system design and maintaining open lines of communication between all technology developers, as well as organizing and documenting the design of the system. -

    -
    +
    +
    + Justin Kinney +
    +
    +
    +
    +

    + Recording of neuronal spiking activity in distributed brain circuits + requires a scalable design for massively parallel recording of + extracellular field potentials. We are inventing such a system and + implementing a proof-of-concept instantiation. In this system, + multi-electrode arrays are used, which minimize tissue damage and help + with spike sorting, and time domain multiplexing of analog field + potential acquisition reduces interconnect. Channel data is then + relayed to a custom-designed terabyte capacity storage network via + custom digital circuitry. The storage network is designed to enable + neural data to be analyzed in flexible ways, including the evaluation + of spike sorting methods. +

    +

    + On the technical side, I am solely responsible for the design and implementation of the ethernet network and high-speed data storage software. In addition, I provide leadership to the project by staying well-versed in all aspects of the system design and maintaining open lines of communication between all technology developers, as well as organizing and documenting the design of the system. +

    +
    -
    -
    - Jung Lee -
    -
    -
    -
    -

    - Jung has been working with Kopell and Whittington on several modeling projects. The main one concerns the effects of top-down beta rhythms on attention; Jung showed that such signals resonate with cells in the deep cortical layers, producing gain control and more gamma rhythms in the superficial layers; a paper is almost complete. This work is highly relevant to work done by Miller on top-down attention, and further collaborations are planned. The work also has relevance to aspects of schizophrenia, and conversations are beginning with the group of Kevin Spencer. A second project concerns multiple inhibitory cell types in the rat auditory cortex. See Schizophrenia. -

    -
    +
    +
    + Jung Lee +
    +
    +
    +
    +

    + Jung has been working with Kopell and Whittington on several modeling projects. The main one concerns the effects of top-down beta rhythms on attention; Jung showed that such signals resonate with cells in the deep cortical layers, producing gain control and more gamma rhythms in the superficial layers; a paper is almost complete. This work is highly relevant to work done by Miller on top-down attention, and further collaborations are planned. The work also has relevance to aspects of schizophrenia, and conversations are beginning with the group of Kevin Spencer. A second project concerns multiple inhibitory cell types in the rat auditory cortex. See Schizophrenia. +

    +
    -
    -
    - Kyle Lepage -
    -
    -
    -
    -

    - Kyle has been one of the most active members of the data analyis group. In the past year, he has been involved in CRC related activity involving three main subjects and two more tertiary ones. One primary project was a collaboration with the Kramer, Eden and Desimone groups on spike-field association (statistical procedures used to infer relations between a rhythm in a time series, such as a local field potential recording, and the firing activity of single neuron. Mikio Aoi is also involved. There is now a preprint. A second major project is a collaboration with the Eichenbaum and Eden groups on cells that measure time. More technically, the project deals with the development of statistical procedures to separate the relative influence of covariates of interest such as time and rodent position upon neural activity. There are two papers and several popular press articles about this work. The third major project is a collaboration with the Kramer lab, also involving postdoc ShiNung Ching; it is motivated by techniques used in MEG and EEG experiments to find functionally connected networks, as in the Human Connectome. This work deals with principled estimation of the statistical connectivity between nodes in an evoked network. In this paradigm a stimulus is repeatedly applied to network nodes, one at a time, and evoked activity at nodes is used to infer a statistical relation between node activity. There is a preprint. A smaller project with the group of Shinn-Cunningham concerns MEG eigensource. In this work local bias in MEG source estimates is traded for decreased non-spatially local bias due to unavoidable inverse-problem source localization limitation. A final project, with Kramer, deals with removing bias in EEG measurements due to activity present on either an EEG reference electrode or present in a "re-referencing method" -

    -
    +
    +
    + Kyle Lepage +
    +
    +
    +
    +

    + Kyle has been one of the most active members of the data analyis group. In the past year, he has been involved in CRC related activity involving three main subjects and two more tertiary ones. One primary project was a collaboration with the Kramer, Eden and Desimone groups on spike-field association (statistical procedures used to infer relations between a rhythm in a time series, such as a local field potential recording, and the firing activity of single neuron. Mikio Aoi is also involved. There is now a preprint. A second major project is a collaboration with the Eichenbaum and Eden groups on cells that measure time. More technically, the project deals with the development of statistical procedures to separate the relative influence of covariates of interest such as time and rodent position upon neural activity. There are two papers and several popular press articles about this work. The third major project is a collaboration with the Kramer lab, also involving postdoc ShiNung Ching; it is motivated by techniques used in MEG and EEG experiments to find functionally connected networks, as in the Human Connectome. This work deals with principled estimation of the statistical connectivity between nodes in an evoked network. In this paradigm a stimulus is repeatedly applied to network nodes, one at a time, and evoked activity at nodes is used to infer a statistical relation between node activity. There is a preprint. A smaller project with the group of Shinn-Cunningham concerns MEG eigensource. In this work local bias in MEG source estimates is traded for decreased non-spatially local bias due to unavoidable inverse-problem source localization limitation. A final project, with Kramer, deals with removing bias in EEG measurements due to activity present on either an EEG reference electrode or present in a "re-referencing method" +

    +
    -
    -
    - Martin Luessi -
    -
    -
    -
    -

    -
    +
    +
    + Martin Luessi +
    +
    +
    +
    +

    +
    -
    -
    - Morteza Moazami -
    -
    -
    -
    -

    - Morteza is a postdoc in the lab of Miller. He is interested in the functional circuitry for memory and context formation between and within the prefrontal cortex (PFC) and the medial temporal lobe (MTL). PFC neurons reflect the associative relations between stimuli, task instructions, behavioral responses, rewards, etc. Interestingly, MTL neurons show similar properties. Neurophysiological studies have been focused on either the MTL or PFC and the interaction between the MTL and PFC is still unclear. He will simultaneously record - with many electrodes- from the PFC and MTL areas while monkey perform a task that temporally separates neuronal information related to context, sample, and recall of the correct choice. He will investigate the modulation of oscillatory neuronal dynamics between and within the PFC and MTL, during different stage of the task. The second project of Morteza concerns the oscillatory neuronal dynamics of categorization in the PFC. Modulations of neuronal oscillations in the PFC with cognitive demands may regulate whether PFC neurons function as multitaskers. The data from these projects are essential to understanding central questions about the roles of rhythms in cognition, and will provide the basis for modeling efforts. In addition, Morteza helps to run the physiology working group. -

    -
    +
    +
    + Morteza Moazami +
    +
    +
    +
    +

    + Morteza is a postdoc in the lab of Miller. He is interested in the functional circuitry for memory and context formation between and within the prefrontal cortex (PFC) and the medial temporal lobe (MTL). PFC neurons reflect the associative relations between stimuli, task instructions, behavioral responses, rewards, etc. Interestingly, MTL neurons show similar properties. Neurophysiological studies have been focused on either the MTL or PFC and the interaction between the MTL and PFC is still unclear. He will simultaneously record - with many electrodes- from the PFC and MTL areas while monkey perform a task that temporally separates neuronal information related to context, sample, and recall of the correct choice. He will investigate the modulation of oscillatory neuronal dynamics between and within the PFC and MTL, during different stage of the task. The second project of Morteza concerns the oscillatory neuronal dynamics of categorization in the PFC. Modulations of neuronal oscillations in the PFC with cognitive demands may regulate whether PFC neurons function as multitaskers. The data from these projects are essential to understanding central questions about the roles of rhythms in cognition, and will provide the basis for modeling efforts. In addition, Morteza helps to run the physiology working group. +

    +
    -
    -
    - Lara Rangel -
    -
    -
    -
    -

    - Lara is a new postdoc in the lab of Eichebaum (BU). Her work was described above. She interacts frequently with members of the statistics and modeling groups (Eden, Kramer, Kopell). She also talks frequently with members of other CRC labs (Boyden lab, MIT : Annabelle Singer; Wilson lab, MIT : Greg Hale, Sage Chen, and Stuart Layton) to compare data, methodology, and analysis techniques. She is planning further interactions with Omar Ahmed of the Cash lab (MGH) on hippocampal oscillatory activity in humans, the Miller lab (MIT) on beta frequency oscillations, and the Jiamin Zhuo and Nick James of the Han lab (BU), on dentate gyrus function and beta rhythms, respectively. She has also interacted with Whittington at CRC events. She speaks frequently with postdocs Annabelle Singer, Justin Kinney, Omar Ahmed, and Kyle Lepage as well as graduate students Caroline Moore-Kochlacs, Greg Hale, and all the members of the Eichenbaum lab. Lara has already written a grant proposal based on this work: NIH F-32 Individual Postdoctoral Research Grant -

    -
    +
    +
    + Lara Rangel +
    +
    +
    +
    +

    + Lara is a new postdoc in the lab of Eichebaum (BU). Her work was described above. She interacts frequently with members of the statistics and modeling groups (Eden, Kramer, Kopell). She also talks frequently with members of other CRC labs (Boyden lab, MIT : Annabelle Singer; Wilson lab, MIT : Greg Hale, Sage Chen, and Stuart Layton) to compare data, methodology, and analysis techniques. She is planning further interactions with Omar Ahmed of the Cash lab (MGH) on hippocampal oscillatory activity in humans, the Miller lab (MIT) on beta frequency oscillations, and the Jiamin Zhuo and Nick James of the Han lab (BU), on dentate gyrus function and beta rhythms, respectively. She has also interacted with Whittington at CRC events. She speaks frequently with postdocs Annabelle Singer, Justin Kinney, Omar Ahmed, and Kyle Lepage as well as graduate students Caroline Moore-Kochlacs, Greg Hale, and all the members of the Eichenbaum lab. Lara has already written a grant proposal based on this work: NIH F-32 Individual Postdoctoral Research Grant +

    +
    -
    -
    - Wei Tang -
    -
    -
    -
    -

    - Wei studies large-scale networks in the resting human brain with data - from non-invasive imaging techniques. Under the hypothesis that - particular sets of brain regions interact with each other to maintain - an active yet stable intrinsic state, the goal of her work is to - uncover both the structure and dynamics of such intrinsic networks, in - the hope that knowledge of the resting state will lead to further - understanding of how neural electrophysiology gives rise to cognitive - phenomena. -

    -

    - Her current project involves collaborations between several - laboratories. With MEG data acquired by Stufflebeam’s group, Wei and - Steve are looking at seed-based Granger-causality maps, assessing - their spatiotemporal and spectral properties, to explore their - relationship with the proposed default-mode hypothesis. They will - later extend the analysis to task data from the same subjects and see - how the networks change undergoing different cognitive processes. - Meanwhile, supervised by Matti Hamalainen and Uri Eden, Wei interacts - with Patrick Purdon’s group at the Martinos Center, developing a - state-space model based approach to identify the full - source-connectivity matrix of the MEG signal and monitor its change - over time. Efforts are being made to advance the methodology dealing - with high-dimensionality of the data and make the full-network - tractable. The third collaboration is with Mark Kramer, aiming at - finding plausible biophysical models that can explain the observed - network properties. This is an open area of exploration and may serve - further modeling studies on brain disease such as epilepsy. Results - from these collaborations together may provide a comprehensive picture - of how the brain works at different levels. -

    -
    +
    +
    + Wei Tang +
    +
    +
    +
    +

    + Wei studies large-scale networks in the resting human brain with data + from non-invasive imaging techniques. Under the hypothesis that + particular sets of brain regions interact with each other to maintain + an active yet stable intrinsic state, the goal of her work is to + uncover both the structure and dynamics of such intrinsic networks, in + the hope that knowledge of the resting state will lead to further + understanding of how neural electrophysiology gives rise to cognitive + phenomena. +

    +

    + Her current project involves collaborations between several + laboratories. With MEG data acquired by Stufflebeam’s group, Wei and + Steve are looking at seed-based Granger-causality maps, assessing + their spatiotemporal and spectral properties, to explore their + relationship with the proposed default-mode hypothesis. They will + later extend the analysis to task data from the same subjects and see + how the networks change undergoing different cognitive processes. + Meanwhile, supervised by Matti Hamalainen and Uri Eden, Wei interacts + with Patrick Purdon’s group at the Martinos Center, developing a + state-space model based approach to identify the full + source-connectivity matrix of the MEG signal and monitor its change + over time. Efforts are being made to advance the methodology dealing + with high-dimensionality of the data and make the full-network + tractable. The third collaboration is with Mark Kramer, aiming at + finding plausible biophysical models that can explain the observed + network properties. This is an open area of exploration and may serve + further modeling studies on brain disease such as epilepsy. Results + from these collaborations together may provide a comprehensive picture + of how the brain works at different levels. +

    +
    -
    -
    - Sujith Vijayan -
    -
    -
    -
    -

    - Sujith was a former student of Wilson, now working mostly with Cash and Kopell on aspects of the alpha rhythm and sleep. Details are above. He is the organizer of the Alpha Working Group. -

    -
    +
    +
    + Sujith Vijayan +
    +
    +
    +
    +

    + Sujith was a former student of Wilson, now working mostly with Cash and Kopell on aspects of the alpha rhythm and sleep. Details are above. He is the organizer of the Alpha Working Group. +

    +
    From 01d16850bc68fa88c182d59133873e35ead22994 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 17:30:53 -0400 Subject: [PATCH 10/59] removing br tags and reordering empty header sections at top --- conference/index.md | 24 ++++++++++-------------- 1 file changed, 10 insertions(+), 14 deletions(-) diff --git a/conference/index.md b/conference/index.md index a9c383d..905507d 100644 --- a/conference/index.md +++ b/conference/index.md @@ -24,7 +24,6 @@ The Rhythmic Dynamics and Cognition Conference was a two-day event sponsored by * Markus Siegal (University of Tubingen) * Robert Knight (UC Berkely) -
    ##Organizing Committee: * E. Boyden @@ -35,29 +34,30 @@ The Rhythmic Dynamics and Cognition Conference was a two-day event sponsored by * M. Kramer * E. Miller -
    ###Talks: +##Markus Siegel: Spectral fingerprints of large-scale neuronal interactions. + +##Pascal Fries: Attentional selection and top-down signaling through inter-areal beta- and gamma-band synchronization. + +##Fiona leBeau: Region specific differences in the generation and modulation of fast network oscillations in the rodent prefrontal cortex in vitro and in vivo + +##Charles Wilson: Frequency Tuning of Striatal Interneurons + +##Bijan Peseran: Neuronal dynamics during coordination and decision + ##Beth Buffalo: [Neural Signals for Memory and Space in the Primate Medial Temporal Node](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/beth-buffalo) -##Pascal Fries: Attentional selection and top-down signaling through inter-areal beta- and gamma-band synchronization. - ##Earl Miller: [Cognition is Rhythmic](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/earl-miller) -##Markus Siegel: Spectral fingerprints of large-scale neuronal -interactions. - ##Bob Knight: [Oscillations and Human Prefrontal Cortex](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/robert-knight) - -##Fiona leBeau: Region specific differences in the generation and modulation of fast network oscillations in the rodent prefrontal cortex in vitro and in vivo - ##Peter Uhlhaas: [Neural Oscillations in Schizophrenia: Perspectives from MEG](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-uhlhaas) @@ -70,8 +70,6 @@ interactions. -##Charles Wilson: Frequency Tuning of Striatal Interneurons - ##Christa van Dort: [Optogenetic Activation of Cholinergic Neurons in the PPT Induces REM Sleep](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/christa-van-dort) @@ -79,8 +77,6 @@ interactions. ##Rosalyn Moran: [Dynamic Causal Modeling and Neurophysiology](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/rosalyn-moran) -##Bijan Peseran: Neuronal dynamics during coordination and decision - ##Liam Paninski: [Statistical Neuroscience](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/liam-paninski) From 43528e9b0f0ca9a8c7409774da6fa1b014bb8bf5 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 17:38:30 -0400 Subject: [PATCH 11/59] fix header syntax in subpage layout and conference page --- _layouts/subpage.html | 3 +-- conference/index.md | 33 ++++++++++++++++++--------------- 2 files changed, 19 insertions(+), 17 deletions(-) diff --git a/_layouts/subpage.html b/_layouts/subpage.html index 1246af4..602a551 100644 --- a/_layouts/subpage.html +++ b/_layouts/subpage.html @@ -1,8 +1,7 @@ --- layout: default --- -{{ page.title }} -================= +# {{ page.title }} {{ content }} diff --git a/conference/index.md b/conference/index.md index 905507d..d873415 100644 --- a/conference/index.md +++ b/conference/index.md @@ -36,49 +36,52 @@ The Rhythmic Dynamics and Cognition Conference was a two-day event sponsored by ###Talks: -##Markus Siegel: Spectral fingerprints of large-scale neuronal interactions. +####Markus Siegel: Spectral fingerprints of large-scale neuronal interactions. -##Pascal Fries: Attentional selection and top-down signaling through inter-areal beta- and gamma-band synchronization. +####Pascal Fries: Attentional selection and top-down signaling through inter-areal beta- and gamma-band synchronization. -##Fiona leBeau: Region specific differences in the generation and modulation of fast network oscillations in the rodent prefrontal cortex in vitro and in vivo +####Fiona leBeau: Region specific differences in the generation and modulation of fast network oscillations in the rodent prefrontal cortex in vitro and in vivo -##Charles Wilson: Frequency Tuning of Striatal Interneurons +####Charles Wilson: Frequency Tuning of Striatal Interneurons -##Bijan Peseran: Neuronal dynamics during coordination and decision +####Bijan Peseran: Neuronal dynamics during coordination and decision -##Beth Buffalo: [Neural Signals for Memory and Space in the Primate Medial Temporal Node](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/beth-buffalo) +####Beth Buffalo: [Neural Signals for Memory and Space in the Primate Medial Temporal Node](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/beth-buffalo) -##Earl Miller: [Cognition is Rhythmic](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/earl-miller) +####Earl Miller: [Cognition is Rhythmic](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/earl-miller) -##Bob Knight: [Oscillations and Human Prefrontal Cortex](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/robert-knight) +####Bob Knight: [Oscillations and Human Prefrontal Cortex](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/robert-knight) -##Peter Uhlhaas: [Neural Oscillations in Schizophrenia: Perspectives from MEG](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-uhlhaas) +####Peter Uhlhaas: [Neural Oscillations in Schizophrenia: Perspectives from MEG](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-uhlhaas) -##Charlie Schroeder: [Neural Substrates of Temporal Prediction in Active Sensing](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/charles-schroeder) +####Charlie Schroeder: [Neural Substrates of Temporal Prediction in Active Sensing](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/charles-schroeder) -##Peter Brown: [Beta Oscillations in the Human Basal Ganglia](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-brown) +####Peter Brown: [Beta Oscillations in the Human Basal Ganglia](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-brown) -##Christa van Dort: [Optogenetic Activation of Cholinergic Neurons in the PPT Induces REM Sleep](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/christa-van-dort) +####Christa van Dort: [Optogenetic Activation of Cholinergic Neurons in the PPT Induces REM Sleep](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/christa-van-dort) -##Rosalyn Moran: [Dynamic Causal Modeling and Neurophysiology](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/rosalyn-moran) +####Rosalyn Moran: [Dynamic Causal Modeling and Neurophysiology](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/rosalyn-moran) + -##Liam Paninski: [Statistical Neuroscience](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/liam-paninski) +####Liam Paninski: [Statistical Neuroscience](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/liam-paninski) + -##Astrid Prinz: [How do rhythmically active circuits "analyze" their own activity?](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/astrid-prinz) +####Astrid Prinz: [How do rhythmically active circuits "analyze" their own activity?](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/astrid-prinz) + From e9f0c71eef5e6c0f4c9a4308c0dd9b083d6f9925 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 17:45:31 -0400 Subject: [PATCH 12/59] fixing subpage layout. should be html. --- _layouts/subpage.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/subpage.html b/_layouts/subpage.html index 602a551..d36b22c 100644 --- a/_layouts/subpage.html +++ b/_layouts/subpage.html @@ -1,7 +1,7 @@ --- layout: default --- -# {{ page.title }} +

    {{ page.title }}

    {{ content }} From bf9a017c0338f089591e75466db534fc895998ae Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 17:47:42 -0400 Subject: [PATCH 13/59] fixing subpage layout again. Should be h1. --- _layouts/subpage.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_layouts/subpage.html b/_layouts/subpage.html index d36b22c..8678368 100644 --- a/_layouts/subpage.html +++ b/_layouts/subpage.html @@ -1,7 +1,7 @@ --- layout: default --- -

    {{ page.title }}

    +

    {{ page.title }}

    {{ content }} From f529a178cd959c9fd113f6acabacd807a95f8d5f Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 17:50:41 -0400 Subject: [PATCH 14/59] changing talk headers on conference page to h3 level --- conference/index.md | 32 ++++++++++++++++---------------- 1 file changed, 16 insertions(+), 16 deletions(-) diff --git a/conference/index.md b/conference/index.md index d873415..7fffff9 100644 --- a/conference/index.md +++ b/conference/index.md @@ -34,54 +34,54 @@ The Rhythmic Dynamics and Cognition Conference was a two-day event sponsored by * M. Kramer * E. Miller -###Talks: +##Talks: -####Markus Siegel: Spectral fingerprints of large-scale neuronal interactions. +###Markus Siegel: Spectral fingerprints of large-scale neuronal interactions. -####Pascal Fries: Attentional selection and top-down signaling through inter-areal beta- and gamma-band synchronization. +###Pascal Fries: Attentional selection and top-down signaling through inter-areal beta- and gamma-band synchronization. -####Fiona leBeau: Region specific differences in the generation and modulation of fast network oscillations in the rodent prefrontal cortex in vitro and in vivo +###Fiona leBeau: Region specific differences in the generation and modulation of fast network oscillations in the rodent prefrontal cortex in vitro and in vivo -####Charles Wilson: Frequency Tuning of Striatal Interneurons +###Charles Wilson: Frequency Tuning of Striatal Interneurons -####Bijan Peseran: Neuronal dynamics during coordination and decision +###Bijan Peseran: Neuronal dynamics during coordination and decision -####Beth Buffalo: [Neural Signals for Memory and Space in the Primate Medial Temporal Node](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/beth-buffalo) +###Beth Buffalo: [Neural Signals for Memory and Space in the Primate Medial Temporal Node](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/beth-buffalo) -####Earl Miller: [Cognition is Rhythmic](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/earl-miller) +###Earl Miller: [Cognition is Rhythmic](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/earl-miller) -####Bob Knight: [Oscillations and Human Prefrontal Cortex](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/robert-knight) +###Bob Knight: [Oscillations and Human Prefrontal Cortex](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/robert-knight) -####Peter Uhlhaas: [Neural Oscillations in Schizophrenia: Perspectives from MEG](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-uhlhaas) +###Peter Uhlhaas: [Neural Oscillations in Schizophrenia: Perspectives from MEG](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-uhlhaas) -####Charlie Schroeder: [Neural Substrates of Temporal Prediction in Active Sensing](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/charles-schroeder) +###Charlie Schroeder: [Neural Substrates of Temporal Prediction in Active Sensing](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/charles-schroeder) -####Peter Brown: [Beta Oscillations in the Human Basal Ganglia](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-brown) +###Peter Brown: [Beta Oscillations in the Human Basal Ganglia](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/peter-brown) -####Christa van Dort: [Optogenetic Activation of Cholinergic Neurons in the PPT Induces REM Sleep](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/christa-van-dort) +###Christa van Dort: [Optogenetic Activation of Cholinergic Neurons in the PPT Induces REM Sleep](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/christa-van-dort) -####Rosalyn Moran: [Dynamic Causal Modeling and Neurophysiology](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/rosalyn-moran) +###Rosalyn Moran: [Dynamic Causal Modeling and Neurophysiology](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/rosalyn-moran) -####Liam Paninski: [Statistical Neuroscience](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/liam-paninski) +###Liam Paninski: [Statistical Neuroscience](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/liam-paninski) -####Astrid Prinz: [How do rhythmically active circuits "analyze" their own activity?](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/astrid-prinz) +###Astrid Prinz: [How do rhythmically active circuits "analyze" their own activity?](http://thesciencenetwork.org/programs/rhythmic-dynamics-and-cognition/astrid-prinz) From 212a27124ea261ef21097a37e315a57ccd3d9583 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 17:57:47 -0400 Subject: [PATCH 15/59] updating people pages to use subpage layout and standard headers --- people/faculty/index.md | 12 +++++------- people/postdoc/index.md | 15 ++++----------- 2 files changed, 9 insertions(+), 18 deletions(-) diff --git a/people/faculty/index.md b/people/faculty/index.md index fb55f5b..1e6508f 100644 --- a/people/faculty/index.md +++ b/people/faculty/index.md @@ -1,11 +1,9 @@ --- -layout: default +layout: subpage title: "People - Faculty" --- -
    People: Faculty
    -

    Click on a name to view or hide details.

    -

    Last update: 10 December 2012

    -

    Director

    +####Click on a name to view or hide details. Last update: 10 December 2012 +##Director
    Nancy Kopell
    @@ -24,7 +22,7 @@ title: "People - Faculty" simulation, and geometric singular perturbations.

    -

    Executive Committee

    +##Executive Committee
    Ed Boyden
    @@ -103,7 +101,7 @@ title: "People - Faculty"

    The Miller Lab uses experimental and theoretical approaches to study the neural basis of the high-level cognitive functions that underlie complex goal-directed behavior. The focus is on the frontal lobe, the region of the brain most elaborated in humans and linked to neuropsychiatric disorders. They have provided insights into how categories, concepts, and rules are learned, how attention is focused, and how the brain coordinates thought and action. To this end, the Miller Lab has innovated techniques for studying the activity of many neurons in multiple brain areas simultaneously, which has provided insight into how interactions within local and global networks of neurons interact and collaborate. This work has established a foundation upon which to construct more detailed, mechanistic accounts of how executive control is implemented in the brain and its dysfunction in diseases such as autism, schizophrenia and attention deficit disorder.

    -

    Affiliated Faculty

    +##Affiliated Faculty
    Seppo P. Ahlfors
    diff --git a/people/postdoc/index.md b/people/postdoc/index.md index bd94949..ae795e5 100644 --- a/people/postdoc/index.md +++ b/people/postdoc/index.md @@ -1,16 +1,9 @@ --- -layout: default -title: "People - Postdoc" +layout: subpage +title: "People - Postdocs" --- -
    - People: Postdocs -
    -

    - Click on a name to view or hide details. -

    -

    - Last update: 1 October 2012 -

    +####Click on a name to view or hide details. Last update: 1 October 2012 +
    From 0b27fc35be738935541690173689819d811635e5 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 18:01:47 -0400 Subject: [PATCH 16/59] clean up index headers --- index.md | 21 ++++++++++----------- 1 file changed, 10 insertions(+), 11 deletions(-) diff --git a/index.md b/index.md index 2face92..a4f9c73 100644 --- a/index.md +++ b/index.md @@ -3,27 +3,26 @@ layout: default title: "Cognitive Rhythms Collaborative" --- -

    - The Cognitive Rhythms Collaborative (CRC) is a group of scientists in the Boston area who work together to advance our understanding of the brain dynamics underlying cognitive functions such as sensory processing, attention, -learning, memory and motor planning.

    +The Cognitive Rhythms Collaborative (CRC) is a group of scientists in the Boston area who work together to advance our understanding of the brain dynamics underlying cognitive functions such as sensory processing, attention, +learning, memory and motor planning. -

    The members of the CRC come from multiple institutions around the Boston area and beyond (see Faculty). We encourage those who are interested in working with us or participating in our events to contact Nancy Kopell (nk at bu.edu). -

    The CRC is supported by the National Science Foundation and the McGovern Center.

    +The members of the CRC come from multiple institutions around the Boston area and beyond (see Faculty). We encourage those who are interested in working with us or participating in our events to contact Nancy Kopell (nk at bu.edu). -

    News and Events

    - ---- +The CRC is supported by the National Science Foundation and the McGovern Center. +# News and Events # [Spring 2014 Mini-Symposium: Frontiers in Non-Invasive Brain Stimulation](img/CRC2014F-Mini-Symposium.pdf) ### Cognitive Rhythms Collaborative and Center for Computational Neuroscience and Neural Technology #### Registration free, but required. Email [xiaoshi@bu.edu](mailto:xiaoshi@bu.edu?Subject=Mini-Symposium%20registration"). -Wednesday, April 16, 2014 at 1 pm +### Wednesday, April 16, 2014 at 1 pm + +Boston University Photonics Center 206 + +8 Saint Mary Street -Boston University Photonics Center 206
    -8 Saint Mary Street
    Boston, MA 02215 * 1:00 - 1:15 Registration From 540958186020de6dfa92c596de1392190068145d Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 18:23:00 -0400 Subject: [PATCH 17/59] index: converting URLs to md, more html removal --- index.md | 15 ++++----------- 1 file changed, 4 insertions(+), 11 deletions(-) diff --git a/index.md b/index.md index a4f9c73..c6dc108 100644 --- a/index.md +++ b/index.md @@ -3,15 +3,14 @@ layout: default title: "Cognitive Rhythms Collaborative" --- -The Cognitive Rhythms Collaborative (CRC) is a group of scientists in the Boston area who work together to advance our understanding of the brain dynamics underlying cognitive functions such as sensory processing, attention, -learning, memory and motor planning. +The **Cognitive Rhythms Collaborative (CRC)** is a group of scientists in the Boston area who work together to advance our understanding of the brain dynamics underlying cognitive functions such as sensory processing, attention, learning, memory and motor planning. -The members of the CRC come from multiple institutions around the Boston area and beyond (see Faculty). We encourage those who are interested in working with us or participating in our events to contact Nancy Kopell (nk at bu.edu). +The members of the CRC come from multiple institutions around the Boston area and beyond [Faculty]({{ site.url }}{{ site.baseurl }}people/faculty/)). We encourage those who are interested in working with us or participating in our events to contact Nancy Kopell (nk at bu.edu). -The CRC is supported by the National Science Foundation and the McGovern Center. +The CRC is supported by the [National Science Foundation](http://www.nsf.org) and the [McGovern Center](http://mcgovern.mit.edu). # News and Events -# [Spring 2014 Mini-Symposium: Frontiers in Non-Invasive Brain Stimulation](img/CRC2014F-Mini-Symposium.pdf) +## [Spring 2014 Mini-Symposium: Frontiers in Non-Invasive Brain Stimulation](img/CRC2014F-Mini-Symposium.pdf) ### Cognitive Rhythms Collaborative and Center for Computational Neuroscience and Neural Technology @@ -20,9 +19,7 @@ The CRC is supported by the Nationa ### Wednesday, April 16, 2014 at 1 pm Boston University Photonics Center 206 - 8 Saint Mary Street - Boston, MA 02215 * 1:00 - 1:15 Registration @@ -37,10 +34,6 @@ Boston, MA 02215 * "Characterizing and guiding brain networks with noninvasive brain stimulation" * 4:30 Discussion / Reception ---- - -

    Rhythmic Dynamics and Cognition Conference: Videos now available!

    - --- From 36d2353901e9d1209f87454129e0cc9d0c7b9958 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 18:29:59 -0400 Subject: [PATCH 18/59] index: more cleanup, fixing link --- index.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/index.md b/index.md index c6dc108..9021459 100644 --- a/index.md +++ b/index.md @@ -5,19 +5,19 @@ title: "Cognitive Rhythms Collaborative" The **Cognitive Rhythms Collaborative (CRC)** is a group of scientists in the Boston area who work together to advance our understanding of the brain dynamics underlying cognitive functions such as sensory processing, attention, learning, memory and motor planning. -The members of the CRC come from multiple institutions around the Boston area and beyond [Faculty]({{ site.url }}{{ site.baseurl }}people/faculty/)). We encourage those who are interested in working with us or participating in our events to contact Nancy Kopell (nk at bu.edu). +The members of the CRC come from multiple institutions around the Boston area and beyond (see [Faculty]({{ site.url }}{{ site.baseurl }}people/faculty/)). We encourage those who are interested in working with us or participating in our events to contact Nancy Kopell (nk at bu.edu). The CRC is supported by the [National Science Foundation](http://www.nsf.org) and the [McGovern Center](http://mcgovern.mit.edu). # News and Events -## [Spring 2014 Mini-Symposium: Frontiers in Non-Invasive Brain Stimulation](img/CRC2014F-Mini-Symposium.pdf) +## Spring 2014 Mini-Symposium: Frontiers in Non-Invasive Brain Stimulation ### Cognitive Rhythms Collaborative and Center for Computational Neuroscience and Neural Technology #### Registration free, but required. Email [xiaoshi@bu.edu](mailto:xiaoshi@bu.edu?Subject=Mini-Symposium%20registration"). ### Wednesday, April 16, 2014 at 1 pm - +[Event flyer](img/CRC2014F-Mini-Symposium.pdf) Boston University Photonics Center 206 8 Saint Mary Street Boston, MA 02215 From 2cc663ead014cc13d72822c43edb0eb350a279ab Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 18:42:12 -0400 Subject: [PATCH 19/59] adjust h1 styling to have horizontal rule under it --- css/cbd.css | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/css/cbd.css b/css/cbd.css index 2637cae..4269253 100644 --- a/css/cbd.css +++ b/css/cbd.css @@ -110,10 +110,12 @@ img.map { } h1 { - margin: 10px 0px 6px 0px; + margin: 10px 0px 15px 0px; font-size: 20px; color: #ca0001; - } + border-bottom: 2px solid #BBB; +} + #title { margin: 0px 0px 15px 0px; font-size: 24px; From 6f4f522b8b5cb9d2eab8e927b3b229adb1b60474 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 18:43:40 -0400 Subject: [PATCH 20/59] adding padding to h1 styling --- css/cbd.css | 1 + 1 file changed, 1 insertion(+) diff --git a/css/cbd.css b/css/cbd.css index 4269253..2d687bd 100644 --- a/css/cbd.css +++ b/css/cbd.css @@ -111,6 +111,7 @@ img.map { h1 { margin: 10px 0px 15px 0px; + padding: 0px 0px 5px 0px; font-size: 20px; color: #ca0001; border-bottom: 2px solid #BBB; From 5d6f274cbd3e50056b3e61dbf6319b3bab0054e3 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 18:51:02 -0400 Subject: [PATCH 21/59] index: troubleshooting line breaks --- index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/index.md b/index.md index 9021459..546a25d 100644 --- a/index.md +++ b/index.md @@ -18,6 +18,7 @@ The CRC is supported by the [National Science Foundation](http://www.nsf.org) an ### Wednesday, April 16, 2014 at 1 pm [Event flyer](img/CRC2014F-Mini-Symposium.pdf) + Boston University Photonics Center 206 8 Saint Mary Street Boston, MA 02215 From 80500dd4c6e8ef25ccad92b246bcbfe3c099cc51 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 20:56:00 -0400 Subject: [PATCH 22/59] index: use way too many line breaks --- index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/index.md b/index.md index 546a25d..e117d3d 100644 --- a/index.md +++ b/index.md @@ -20,7 +20,9 @@ The CRC is supported by the [National Science Foundation](http://www.nsf.org) an [Event flyer](img/CRC2014F-Mini-Symposium.pdf) Boston University Photonics Center 206 + 8 Saint Mary Street + Boston, MA 02215 * 1:00 - 1:15 Registration From c40140ba464c8e86db529fb5708b3bf2f27ed0f1 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 21:05:43 -0400 Subject: [PATCH 23/59] index: you have to add two spaces before a line break --- index.md | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/index.md b/index.md index e117d3d..e1e27cd 100644 --- a/index.md +++ b/index.md @@ -19,10 +19,8 @@ The CRC is supported by the [National Science Foundation](http://www.nsf.org) an ### Wednesday, April 16, 2014 at 1 pm [Event flyer](img/CRC2014F-Mini-Symposium.pdf) -Boston University Photonics Center 206 - -8 Saint Mary Street - +Boston University Photonics Center 206 +8 Saint Mary Street Boston, MA 02215 * 1:00 - 1:15 Registration @@ -39,6 +37,6 @@ Boston, MA 02215 --- - + From a63983f49f0a6c8c3d83ab624e4677b50703650c Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 21:27:34 -0400 Subject: [PATCH 24/59] convert working groups page to markdown subpage --- groups/index.md | 106 ++++++++++++++++++++++-------------------------- 1 file changed, 48 insertions(+), 58 deletions(-) diff --git a/groups/index.md b/groups/index.md index f07e0f6..f467f80 100644 --- a/groups/index.md +++ b/groups/index.md @@ -1,60 +1,50 @@ --- -layout: default -title: "Groups" +layout: subpage +title: "Working Groups" --- -
    Working Groups
    -

    Group names, typical meeting times, and points of contact

    -

    Alpha rhythms

    -
      -
    • Led by Nancy Kopell and Sujith Vijayan
      • -
    • Mechanisms underlying alpha
      • -
    • Role of alpha in attention and cognitive tasks
      • -
    - -

    Auditory attention

    -
      -
    • Led by Dan Polley
      • -
    • Interaction of thalamus and cortex
      • -
    • Dynamics of layers in auditory cortex
      • -
    • Interaction with prefrontal cortex
      • -
    - -

    Beta rhythms

    -
      -
    • Led by Lara Rangel
      • -
    • Role of beta in learning, movement, and attention
      • -
    • Identification of other common beta themes
      • -
    - -

    Methods of data analysis (Fri 10:30-12:00)

    -
      -
    • Led by Mark Kramer and Uri Eden
      • -
    • Novel methodology
      • -
    • Network inference
      • -
    • Time-Frequency analysis: contours of constant phase
      • -
    • Estimating phases
      • -
    - -

    Physiology data analysis (Tues 4:00-5:00)

    -
      -
    • Led by Lara Rangel and Morteza Moazami
      • -
    • Current lab research
      • -
    • Data analysis
      • -
    - -

    Temporal Aspects of Neuronal Coding (TANK)

    -
      -
    • Led by Nancy Kopell and Jonathan Cannon
      • -
    • Connections between dynamic neural patterns and representation of information
      • -
    • Dynamics in hippocampus
      • -
    • Synthesis and modeling of current results in hippocampus research
      • -
    -

    Sleep & Memory

    -
      -
    • Led by Charmaine Demanuelle and Bengi Baran
      • -
    • Brain oscillations during sleep that are critical for learning and memory and how they may go awry in neurological/psychiatric disorders
      • -
    • Human and animal work
      • -
    • Computational models
      • -
    • Aimed to provide a platform for local research groups to present their new hypotheses, experiments and data
      • -
    -


    For more information, please contact cogweb at math.bu.edu

    + +## Working Groups +Group names, typical meeting times, and points of contact. + +## Alpha rhythms +* Led by Nancy Kopell and Sujith Vijayan +* Mechanisms underlying alpha +* Role of alpha in attention and cognitive tasks + +## Auditory attention +* Led by Dan Polley +* Interaction of thalamus and cortex +* Dynamics of layers in auditory cortex +* Interaction with prefrontal cortex + +## Beta rhythms +* Led by Lara Rangel +* Role of beta in learning, movement, and attention +* Identification of other common beta themes + +## Methods of data analysis (Fri 10:30-12:00) +* Led by Mark Kramer and Uri Eden +* Novel methodology +* Network inference +* Time-Frequency analysis: contours of constant phase +* Estimating phases + +## Physiology data analysis (Tues 4:00-5:00) +* Led by Lara Rangel and Morteza Moazami +* Current lab research +* Data analysis + +## Temporal Aspects of Neuronal Coding (TANK) +* Led by Nancy Kopell and Jonathan Cannon +* Connections between dynamic neural patterns and representation of information +* Dynamics in hippocampus +* Synthesis and modeling of current results in hippocampus research + +## Sleep & Memory +* Led by Charmaine Demanuelle and Bengi Baran +* Brain oscillations during sleep that are critical for learning and memory and how they may go awry in neurological/psychiatric disorders +* Human and animal work +* Computational models +* Aimed to provide a platform for local research groups to present their new hypotheses, experiments and data + +For more information, please contact *cogweb at math.bu.edu*. From e91e3dd30fad648bfa625bd2d1970365f499e5a5 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 21:30:39 -0400 Subject: [PATCH 25/59] missed a couple things on working group page cleanup --- groups/index.md | 55 ++++++++++++++++++++++++------------------------- 1 file changed, 27 insertions(+), 28 deletions(-) diff --git a/groups/index.md b/groups/index.md index f467f80..dc924d9 100644 --- a/groups/index.md +++ b/groups/index.md @@ -3,48 +3,47 @@ layout: subpage title: "Working Groups" --- -## Working Groups Group names, typical meeting times, and points of contact. ## Alpha rhythms -* Led by Nancy Kopell and Sujith Vijayan -* Mechanisms underlying alpha -* Role of alpha in attention and cognitive tasks +#### Led by Nancy Kopell and Sujith Vijayan +* Mechanisms underlying alpha +* Role of alpha in attention and cognitive tasks ## Auditory attention -* Led by Dan Polley -* Interaction of thalamus and cortex -* Dynamics of layers in auditory cortex -* Interaction with prefrontal cortex +#### Led by Dan Polley +* Interaction of thalamus and cortex +* Dynamics of layers in auditory cortex +* Interaction with prefrontal cortex ## Beta rhythms -* Led by Lara Rangel -* Role of beta in learning, movement, and attention -* Identification of other common beta themes +#### Led by Lara Rangel +* Role of beta in learning, movement, and attention +* Identification of other common beta themes ## Methods of data analysis (Fri 10:30-12:00) -* Led by Mark Kramer and Uri Eden -* Novel methodology -* Network inference -* Time-Frequency analysis: contours of constant phase -* Estimating phases +#### Led by Mark Kramer and Uri Eden +* Novel methodology +* Network inference +* Time-Frequency analysis: contours of constant phase +* Estimating phases ## Physiology data analysis (Tues 4:00-5:00) -* Led by Lara Rangel and Morteza Moazami -* Current lab research -* Data analysis +#### Led by Lara Rangel and Morteza Moazami +* Current lab research +* Data analysis ## Temporal Aspects of Neuronal Coding (TANK) -* Led by Nancy Kopell and Jonathan Cannon -* Connections between dynamic neural patterns and representation of information -* Dynamics in hippocampus -* Synthesis and modeling of current results in hippocampus research +#### Led by Nancy Kopell and Jonathan Cannon +* Connections between dynamic neural patterns and representation of information +* Dynamics in hippocampus +* Synthesis and modeling of current results in hippocampus research ## Sleep & Memory -* Led by Charmaine Demanuelle and Bengi Baran -* Brain oscillations during sleep that are critical for learning and memory and how they may go awry in neurological/psychiatric disorders -* Human and animal work -* Computational models -* Aimed to provide a platform for local research groups to present their new hypotheses, experiments and data +#### Led by Charmaine Demanuelle and Bengi Baran +* Brain oscillations during sleep that are critical for learning and memory and how they may go awry in neurological/psychiatric disorders +* Human and animal work +* Computational models +* Aimed to provide a platform for local research groups to present their new hypotheses, experiments and data For more information, please contact *cogweb at math.bu.edu*. From 0d613e0a2e15f12aa0e84c0f2680698ee08cb369 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 21:50:39 -0400 Subject: [PATCH 26/59] removing htm files --- calendar.htm | 154 ----------- conference.htm | 215 ---------------- contact.htm | 113 -------- courses.htm | 136 ---------- groups.htm | 163 ------------ people_faculty.htm | 609 -------------------------------------------- people_postdoc.htm | 395 ---------------------------- positions.htm | 135 ---------- research_papers.htm | 566 ---------------------------------------- research_topics.htm | 209 --------------- 10 files changed, 2695 deletions(-) delete mode 100644 calendar.htm delete mode 100644 conference.htm delete mode 100644 contact.htm delete mode 100644 courses.htm delete mode 100644 groups.htm delete mode 100644 people_faculty.htm delete mode 100644 people_postdoc.htm delete mode 100644 positions.htm delete mode 100644 research_papers.htm delete mode 100644 research_topics.htm diff --git a/calendar.htm b/calendar.htm deleted file mode 100644 index 2b8ae6b..0000000 --- a/calendar.htm +++ /dev/null @@ -1,154 +0,0 @@ - - - - - - Cognitive Rhythms Collaborative - - - - - - - - - - - - - - - - -
    - - - - -
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    [4-5 Jun 2013] CRC Conference: Rhythmic Dynamics and Cognition

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    [27 Sep 2012] CRC Dinner with speaker Kevin Spencer

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    [10 Sep 2012] CRC Lecture by Robert Kass

    - -

    [25 Jun 2012] CRC Dinner with -speaker Ed Boyden

    - -

    [4 Apr 2012] CRC Retreat

    - -

    [23 Feb 2012] CRC Dinner with speaker Matt Wilson

    - -

    [1 Feb 2012] Mini-symposium Beta Rhythms and Cognition. Speakers: Earl Miller, Nancy Kopell, Stephanie Jones, Nicholas Schiff, Keith Purpura (Afternoon event with reception at the end)

    - -

    [26 Jan 2012] Special Talk: Natalie Adams, "Development of patterned activity in de novo neuronal networks," 4pm at BU

    - -

    [16 Dec 2011] CRC Happy Hour 4-6

    - -

    [12 Dec 2011] CRC Dinner with speaker Emery Brown

    - -

    [7 Nov 2011] Grant Writing Seminar by Cyndi Bradham (Slides)

    - -

    [17 Oct 2011] CRC Dinner with speaker Earl Miller

    - -

    [12 July 2011] Talk by Yale Cohen on auditory processing

    - -

    [2 May 2011] CRC Dinner with speakers Barry Connors and Erika Fanslow

    - -

    [14 Apr 2011] CBD Spring -Mini-Symposium Brain -Rhythms and Audition hosted by the Center for Biodynamics and Bahaa -Hariri Institute for Computational Science and Engineering -

    - -

    [15 Feb 2011] CRC Dinner with speaker Ed Boyden

    - -

    [10 Dec 2010] CRC Dinner with speaker Mingzhou Ding

    - -

    [26 Oct 2010] CRC Dinner with speaker Syd Cash

    - -

    [11 Aug 2010] CRC Dinner with speaker Miles Whittington

    - -

    [28 Jun 2010] CRC Dinner with speakers Barb Shinn-Cunningham and Matti Hämäläinen

    - -

    [9 Mar 2010] CRC Dinner with speaker Mark Kramer

    -
    - -
    - -
    - - - - - - - - - - - diff --git a/conference.htm b/conference.htm deleted file mode 100644 index 023fd33..0000000 --- a/conference.htm +++ /dev/null @@ -1,215 +0,0 @@ - - - - - - Cognitive Rhythms Collaborative - - - - - - - - - - - - - - - - - - -
    - - - - -
    - - -

    The Rhythmic Dynamics and Cognition Conference was a two-day event sponsored by the Cognitive Rhythms Collaborative (CRC), held at the Brain Building (Building 46) on the MIT campus in 2013. Proceedings included lectures, a reception, and a poster session. Videos of the lectures and an archive of the program are provided here.

    - -

    June 4-5, 2013

    -

    Rhythmic Dynamics and Cognition Conference:

    -

    Videos of the event

    -

    View -event poster

    -

    Invited speakers include:

    -
      -
    • Pascal Fries, (Ernst Strungmann Institute (ESI), Frankfurt)
      • -
    • Elizabeth Buffalo (Emery University)
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    Organizing Committee:

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    • S. Jones
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    • N. Kopell
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    • M. Kramer
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    • E. Miller
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    Tentative Schedule:

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    June 4

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    Morning Session 1: 9:00 - 10:30

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    • Beth Buffalo: Rhythmic neural activity and memory formation
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    • Pascal Fries: Attentional selection and top-down signaling through -inter-areal beta- and gamma-band synchronization. 
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    Coffee Break: 10:30 - 11:00

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    Morning Session 2: 11:00 - 12:30

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    • Earl Miller: Brain Rhythms and Executive Control
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    • Markus Siegel: Spectral fingerprints of large-scale neuronal -interactions. 
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    Lunch: 12:30 - 2:15

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    Afternoon: 2:15 - 4:30

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    • Bob Knight:  Oscillations and Human Prefrontal Cortex. 
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    • Fiona leBeau: Region specific differences in the generation and -modulation of fast network oscillations in the rodent prefrontal cortex in -vitro and in vivo.
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    • Peter Uhlhaas: Neural Oscillations in Schizophrenia: Perspectives from -MEG.
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    Reception, poster session: 4:30 - 7

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    June 5

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    Morning 9:00 - 12:15

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    • Charlie Schroeder: Neuronal Dynamics Underlying Temporal -Prediction
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    • Peter Brown: Basal ganglia beta: idling, blocking or maintaining the -status quo?
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    • 15 min break
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    • Charles Wilson: Frequency Tuning of Striatal Interneurons.
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    • Christa van Dort: Optogenetic Activation of Cholinergic Neurons in the -PPT Induces REM Sleep.
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    Lunch: 12:15 - 2:00

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    Afternoon: 2:00 - 5:15 (emphasis on data analysis)

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    • Rosalyn Moran: Dynamic Causal Models to unpack the physiological -connectivity of oscillatory brain networks.
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    • Bijan Peseran: Neuronal dynamics during coordination and -decision.
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    • 15 min break
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    • Liam Paninski TBA
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    • Astrid Prinz: Recovery of rhythmic in a pattern-generating circuit -after injury
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    Poster Sessions

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    - - - - - - - - - - - diff --git a/contact.htm b/contact.htm deleted file mode 100644 index 57d4bb4..0000000 --- a/contact.htm +++ /dev/null @@ -1,113 +0,0 @@ - - - - - - Cognitive Rhythms Collaborative - - - - - - - - - - - - - - - - -
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    Contact
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    For more information or to be added to the CRC email distribution, please contact either of the following:
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    Xiaoshi Shi
    - Boston University
    - CompNET and CRC
    - Phone: 617.353.4587
    - Fax: 617.353.4889
    - Email: xiaoshi at bu.edu

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    Webmaster: cogweb at math.bu.edu

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    - - - - - - - - - - - diff --git a/courses.htm b/courses.htm deleted file mode 100644 index becbf74..0000000 --- a/courses.htm +++ /dev/null @@ -1,136 +0,0 @@ - - - - - - Cognitive Rhythms Collaborative - - - - - - - - - - - - - - - - - - - - -
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    Courses
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    Last update: 1 March 2011

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    -BU MA665: Introduction to Modeling and Data Analysis in Neuroscience. (Kramer). 2-credit course for intro neurosci students. Topics include: basic spike train analysis, basic computational models of spiking, the Hodgkin-Huxley model of spiking, an introduction to Fourier series, and an introduction to networks. Meets twice a week, with one lecture and one computer lab. -

    -BU MA666: Advanced Modeling and Data Analysis in Neuroscience. (Kramer). 2-credit course for more mathematically advanced neurosci students. Topics include introductions to: correlation and coherence analysis, cross frequency coupling, and bifurcations in model neurons. Meets twice a week, with one lecture and one computer lab. -

    -BU MA 568 Statistical Analysis of Point Process Data. (Eden). Introduces the theory of point processes and develops practical problem-solving skills to construct models, assess goodness-of-fit, and perform estimation from point process data. -

    -HST.576 Topics in Neural Signal Processing (Brown). Focuses on signal processing methods for the analysis of stochastic dynamical systems in neuroscience. Includes state-space methods and dynamic Baysian methods applied to continuous and point process observations. -

    -HST.460 Statistics for Neuroscience Research, (Brown) A survey of statistical methods for neuroscience research. Core topics include introductions to the theory of point processes, the generalized linear model, Monte Carlo methods, Bayesian methods, multivariate methods, time-series analysis, spectral analysis and state-space modeling. This course was developed jointly with Eden and a version is being planned for BU. (Eden) -

    -HST.563 Imaging Biophysics and Applications (S. Stufflebeam, D. Boas). Introduction to the connections and distinctions among various imaging modalities (ultrasound, MRI, EEG, optical), common goals of biomedical imaging, broadly defined target of biomedical imaging, and the current practical and economic landscape of biomedical imaging research. -

    -MIT- MAS.881/20.452/9.422, (Boyden), Principles of Neuroengineering. Tools and methods for analyzing brain dynamics, which was attended by undergraduate and graduate students throughout the CRC network. -

    -MIT- MAS.883/9.455/20.454/15.128/HST.588 (Boyden) Neurotechnology -Ventures. Special seminar on how to get neuroengineering innovations -out into the world. -

    -Tufts Math 150 (Borgers) Mathematical Neuroscience. Introduction to modeling neurons and -neuronal networks using differential equations. Hodgkin-Huxley equations; phase -plane analysis and bifurcation theory applied to neuronal models; reduced -models (integrate-and-fire neurons, theta neurons); modeling chemical and -electrical synapses; synchronization, rhythms, and waves in neuronal networks. -

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    -Last updated: 9 December 2011

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    Working Groups
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    Group names, typical meeting times, and points of contact

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    Alpha rhythms

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    • Led by Nancy Kopell and Sujith Vijayan
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    • Mechanisms underlying alpha
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    Auditory attention

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    • Led by Dan Polley
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    • Interaction of thalamus and cortex
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    • Interaction with prefrontal cortex
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    Beta rhythms

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    • Led by Lara Rangel
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    • Role of beta in learning, movement, and attention
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    • Identification of other common beta themes
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    Methods of data analysis (Fri 10:30-12:00)

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    • Led by Mark Kramer and Uri Eden
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    • Novel methodology
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    • Network inference
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    • Time-Frequency analysis: contours of constant phase
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    • Estimating phases
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    Physiology data analysis (Tues 4:00-5:00)

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    • Led by Lara Rangel and Morteza Moazami
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    • Current lab research
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    • Data analysis
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    Temporal Aspects of Neuronal Coding (TANK)

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    • Led by Nancy Kopell and Jonathan Cannon
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    • Connections between dynamic neural patterns and representation of information
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    • Dynamics in hippocampus
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    • Synthesis and modeling of current results in hippocampus research
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    Sleep & Memory

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    • Led by Charmaine Demanuelle and Bengi Baran
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    • Brain oscillations during sleep that are critical for learning and memory and how they may go awry in neurological/psychiatric disorders
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    • Human and animal work
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    • Computational models
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    • Aimed to provide a platform for local research groups to present their new hypotheses, experiments and data
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    For more information, please contact cogweb at math.bu.edu

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    People: Faculty
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    Click on a name to view or hide details.

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    Last update: 10 December 2012

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    Director

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    Nancy Kopell
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    Boston University
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    My major interest is dynamics of the nervous system, especially brain -rhythms associated with cognition. The central questions are: what are the -networks and physiology that produce these rhythms; how do the -physiological properties of those networks affect the use of the dynamics -in cognition; can changes in the rhythms in disease give insights into the -nature and treatments of diseases? I'm currently working on projects -relating to physiology and interaction of rhythms, attention, Parkinson's -disease, schizophrenia and anesthesia; with collaborators, the work -involves in vivo and in vitro experiments, dynamical systems modeling and -simulation, and geometric singular perturbations.

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    Executive Committee

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    Ed Boyden
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    MIT
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    We are inventing new tools for analyzing and engineering brain -circuits. For example, we have devised 'optogenetic' tools, which -enable the activation and silencing of neural circuit elements with -light, to understand their causal contribution to normal and -pathological neural computations, as well as to support the discovery -and repair of neural circuit targets in a therapeutic context. We are -using our inventions to enable systematic approaches to neuroscience, -revealing how neural circuits operate to generate behavior, and -empowering new therapeutic strategies for neurological and psychiatric -disorders.

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    Uri Eden
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    Boston University
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    My research focuses on developing mathematical and statistical methods to analyze neural spiking activity. I have worked to integrate methodologies related to model identification, statistical inference, signal processing, and stochastic estimation and control, and expand these methodologies to incorporate point process observation models, making them more appropriate for modeling the dynamics of neural systems observed through spike train data. This research can be divided into two categories; first, a methodological component, focused on developing a statistical framework for relating neural activity to biological and behavioral signals and developing estimation algorithms, goodness-of-fit analyses, and mathematical theory that can be applied to any neural spiking system; second, an application component, wherein these methods are applied to spiking observations in real neural systems to dynamically model the spiking properties of individual neurons, to characterize how ensembles maintain representations of associated biological and behavioral signals, and to reconstruct these signals in real time.

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    Matti Hämäläinen
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    MGH/Harvard Medical School/Martinos Imaging Center
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    The Athinoula A. Martinos Center at the Massachusetts General Hospital has a twofold mission to advance the development of imaging technologies and -their integration with complementary technologies, and to apply these technologies to support basic -science and translational research that is driven by an overarching interest in the continuous long-term -improvement of clinical care. Martinos Center investigators are innovating in the areas of anatomical -and functional magnetic resonance imaging (MRI) and spectroscopy (MRS), magnetoencephalography -(MEG) and electroencephalography (EEG), near infrared spectroscopy (NIRS) and diffuse optical -tomography (DOT), and positron emission tomography (PET) as well as cutting-edge tools for -computational image analysis. The Center supports over 200 PHS-funded research projects at the -MGH and other Boston-areas institutions, as well as other institutions in the United States and abroad. -Research activities at the Martinos Center are supported institutionally as well as by Federal and -foundation grants. Martinos Center investigators and their broad network of colleagues are at the -forefront of developing advanced imaging technologies, integrating those technologies for multimodality -acquisition, and deriving novel acquisition and analysis methods for the rich body of imaging -data now acquired with these technologies. Funded by a P41 Regional Resource grant, from National -Center for Research Resources, the Martinos Center and its Center for Functional Neuroimaging -Technologies is a region-wide resource, broadly used by basic and clinical scientists who employ the -full range of imaging technologies available at the Center to address questions of fundamental -importance in fields ranging from neurovascular, neurological, and psychiatric disorders to cognitive -neuroscience to cancer and cardiovascular function.

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    Stephanie Jones
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    Brown University
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    Dr. Jones uses her background in dynamical systems theory mathematics and computational neural modeling to study neural dynamics in health and disease. She is trained in MEG/EEG imaging and currently uses computational modeling techniques to bridge the critical gap between the non-invasive imaging observables and the underlying microscopic cellular and network level mechanisms. Her current projects and interest include:

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    • Investigating the neural dynamics underlying normal development in children ages 0-6 as well as neural abnormalities in children with encephalopathy of -prematurity (EP). In collaboration with Drs. Ellen Grant and Yoshio Okada at CHB, we are studying development with a powerful combination of techniques including mathematical modeling, MR diffusion tensor imaging, and MEG imaging.
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    • Studying the mechanisms and functions of neural rhythms including their role in sensory perception, attentional processes, and healthy aging. We are also investigating the source of disruption in brain rhythms in diseases such as Parkinson's Disease, Obsessive Compulsive Disorder, and Attention Deficit Disorder.
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    • Investigating plasticity induced by training in perceptual attention. In collaboration with Dr. Cathy Kerr at HMS we are studying neurodynamics underlying Mindfulness Medidation Practice.
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    • Combing computational modeling and optogenetic techniques, in collaboration with Dr. Chris Moore at Brown University, to study neural dynamics. We are currently delineating the role of specific cell types in controlling neocortical rhythmicity and investigating the impact of these rhythms on sensory perception.
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    Earl Miller
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    MIT
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    The Miller Lab uses experimental and theoretical approaches to study the neural basis of the high-level cognitive functions that underlie complex goal-directed behavior. The focus is on the frontal lobe, the region of the brain most elaborated in humans and linked to neuropsychiatric disorders. They have provided insights into how categories, concepts, and rules are learned, how attention is focused, and how the brain coordinates thought and action. To this end, the Miller Lab has innovated techniques for studying the activity of many neurons in multiple brain areas simultaneously, which has provided insight into how interactions within local and global networks of neurons interact and collaborate. This work has established a foundation upon which to construct more detailed, mechanistic accounts of how executive control is implemented in the brain and its dysfunction in diseases such as autism, schizophrenia and attention deficit disorder.

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    Affiliated Faculty

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    Seppo P. Ahlfors
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    MGH/Harvard Medical School/Martinos Imaging Center
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    My research concerns spatiotemporal imaging of human brain function. I have applied integrated magnetoencephalography (MEG), electroencephalography (EEG), and functional magnetic resonance imaging (fMRI) to studies of cortical processing of visual information. My research involves development of techniques for the analysis of multimodal biomedical imaging data, including the use of fMRI data to inform the source estimation (inverse problem) of MEG and EEG. Currently I am studying computationally the characteristics of the sensitivity of MEG and EEG sensor arrays as well as the relationship of MEG and EEG signals to the cortical anatomy and physiology. Collaborative work focuses on the application of MEG, EEG, and fMRI techniques to reveal neural activation patterns related to cognitive processing in normal and clinical populations.

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    Christoph Börgers
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    Tufts University
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    Most of my work is on designing and analyzing computational models in neuroscience. Current projects concern the role of different populations of inhibitory cells in gamma oscillations, modeling of the impact of astrocytes on neuronal activity, and synchronization via gap junctions. I also have one current research project unrelated to neuroscience, on numerical methods for linear Boltzmann equations.

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    Syd Cash
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    MGH
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    Current research in the lab is, broadly speaking, dedicated to trying to understand normal and abnormal brain activity, particularly oscillations, using multi-modal and multi-scalar approaches. Specifically, we are combining novel microelectrode approaches with non-invasive techniques such as electroencephalography and magnetoencephalography to record directly from both human and animal cortex and subcortical structures. One part of the lab studies the neurophysiology of epilepsy; trying to understand how seizures start and stop and how they might be predicted and terminated. These questions overlap with investigations into the mechanisms of sleep, normal language, auditory, and other cognitive processing.

    -All of these projects are built on a foundation of combined microelectrode, macroelectrode and non-invasive recording techniques that span information from the level of single action potentials to aggregate activity of millions of neurons. Intensive signal processing and computational techniques are employed to analyze these data sets. Collaborative activities involving neural modeling are aimed at relating these multi-scalar data. Ultimately, all of these projects aim toward the creation of both invasive and non-invasive mechanisms for restoring damaged neuronal function. -

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    Ming Cheng
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    Brown University
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    Dr. Cheng is a neurosurgeon whose laboratory studies the neural basis of different cognitive processes that underlie diseases such as Parkinson's and other movement disorders, pain, epilepsy, depression, and other more rare neurological conditions. The goal of his laboratory is neurorestoration, the idea that therapies can be devised to restore the original function of the brain and spinal cord.

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    Our primary techniques include the use of psychopharmacology, electrical stimulation and reversible lesioning to enhance or alter brain, spine and peripheral nerve function. We measure the results in our subjects with behavioral tasks coupled with intraoperative and extraoperative electrophysiology in human subjects: EEG, electrocorticography (ECoG), extracellular field potential recordings, and single unit microelectrode recordings from multiple brain and spine structures (subthalamic nucleus, caudate, globus pallidus, thalamus, nucleus accumbens, substantia nigra, neocortical areas, dorsal columns, the dorsal horn, etc.). We also use these electrophysiological tools to complement molecular techniques in the study of animal models of hydrocephalus and neurodegenerative disease. We are ultimately interested in applying our findings to the creation of open and closed loop stimulatory devices that can help human patients with neurological and psychiatric diseases. Ultimately, the information we learn will help us create brain and spine machine interfaces to fight disease and change human interaction with the external world. -

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    Robert Desimone
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    MIT
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    Neural basis for attention and executive control
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    A complex visual scene will typically contain many different objects, few of which are currently relevant to behavior. Thus, attentional mechanisms are needed to select the relevant objects from the scene and to reject the irrelevant ones. Neurophysiological studies in our own and other labs have identified some of the neural mechanisms of attentional selection within the ventral, "object recognition", stream of the cortex. At each stage along this stream, attended, or behaviorally relevant, stimuli are processed preferentially compared to irrelevant distracters. In recent years, we have found that the top-down attentional bias is expressed, at least in part, in visual cortex through an increase in high-frequency (gamma) synchronization of neurons carrying critical information about the location or features of the behaviorally relevant stimulus. Increases in gamma synchrony are found during both spatial attention and featural attention engaged during visual search, and the presence of synchrony predicts faster responses in visual tasks. Recent evidence shows that inputs from the frontal eye fields (FEF) in prefrontal cortex initiates coupled gamma-frequency oscillations between FEF and area V4 during attention, and these oscillations are shifted in time across the two areas to allow for maximally effective communication. Cross-area synchrony may be a general mechanism for regulating information flow through the brain and for regulating spike-timing dependent plasticity. -

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    Howard Eichenbaum
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    Boston University
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    The research program of this laboratory is focused on four closely related projects that seek to understand the brain circuity that supports memory. This research is guided by the hypothesis that our ability to remember specific experiences relies on an organization of memories about objects and the events in the context in which they occurred. We believe that associations between objects and context is accomplished through the circuitry of the medial temporal lobe, in which parallel pathways represent information about objects and about context, and these streams of information converge within the hippocampus. A project central to this goal seeks to characterize how neurons in key components of the medial temporal lobe encode these different types of information and how components of this brain system interact with one another. Another project explores how the hippocampus is initially critical to the associations between objects and context but eventually these associations consolidate in cortical areas with which the hippocampus is connected. Another project explores how the prefrontal cortex controls the retrieval of memories as they bear on ongoing cognitive processes. And yet another project explores how hippocampal networks represent objects in the spacial and temporal context in which they occur. Together these projects will provide new insights into how memories are organized within the medial temporal lobe memory system and how memories are retrieved when we recall our daily experiences. -

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    Oded Ghitza
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    Boston University
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    Cortical and Computational Decoding of Speech
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    We conduct a tightly integrated computational and experimental research program across three sites (BU, NYU, Columbia) to study spoken language recognition from the psychophysical, neurophysiological, and engineering perspectives. The program proceeds in four fronts:

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    • Human Neuroimaging. We formulate the intra-relationship among theta, beta and gamma oscillations, using MEG (David Poeppel, NYU) and ECoG (Charles Schroeder, Columbia) data recorded while subjects perform intelligibility tasks;
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    • Monkey Electrophysiology (Charles Schroeder, Columbia). If the emerging cortical computation principles are fundamental, they must generalize across mammalian species. We are using high-resolution physiological methods to measure the intra-relationship among oscillations using multi-electrode recordings in monkeys listening to stimuli specifically designed to capture the rhythmic aspects of natural speech and music;
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    • Automatic Speech Recognition (Ghitza, BU). We explore a new perspective to the development of ASR systems that incorporates the insights from the behavioral and brain sciences, specifically rhythmic brain activity. We ascertain whether the proposed cortical computation principle could be used as an adjunct to conventional features used in ASR systems, e.g. in lattice re-scoring of n-best lists – and ultimately result in a decrease in word error rate.
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    Stan Goldin
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    Harvard Medical School
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    Dr. Stan Goldin has been developing some new ideas on a carrier wave function for brain oscillations in discrete frequency bands. His early stage collaboration with BSF Fellow Prof. Ed Boyden of MIT is exploring new ways to design multichannel arrays for automated, rapid, delivery of pharmacological agents to key distributed locations in nerve networks, to help elucidate network function. His collaboration with Dr. Newton Howard of MIT on neural coding mechanisms has revealed novel photonic signaling pathways in the brain, powered by light-generating neuronal redox reactions and employing novel photon absorbing rhodopsin-like proteins discovered within the mammalian brain.

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    Dr. Goldin’s laboratory originated research techniques and devices that have been employed to elucidate molecular mechanisms underlying brain waves and brain oscillation circuitry--processes now known to play an important role in long term brain changes (neuroplasticity) and memory formation. He is now finishing a book, Ascent of the Human Brain—An Expanded view of Human Evolution, on modern neuroscience research’s impact on our understanding of human consciousness, selfhood & spirituality.

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    Ann Graybiel
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    MIT
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    Ann Graybiel studies the basal ganglia, forebrain structures that are profoundly important for normal brain function but are also implicated in Parkinson's disease, Huntington's disease, obsessive-compulsive disorder, and addiction. Graybiel's work is uncovering neural deficits related to these disorders, as well as the role the basal ganglia play in guiding normal behavior. -

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    Xue Han
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    Boston University
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    Brain disorders represent the biggest unmet medical need, with many disorders being untreatable, and most treatments presenting serious side effects. Accordingly, we are discovering design principles for novel neuromodulation therapies. We invent and apply a variety of genetic, molecular, pharmacological, optical, and electrical tools to correct neural circuits that go awry within the brain. As an example, we have pioneered several technologies for silencing specific cells in the brain using pulses of light. We have also recently participated the first pre-clinical testing of a novel neurotechnology, optical neural modulation. Using these novel neurotechnologies and classical ones such as deep brain stimulation (DBS), we modulate the function of neural circuits to establish causal links between neural dynamics and behavioral phenomena (e.g., movement, attention, memory, and decision making). One of our current interests is the investigation of how neural synchrony arises within and across brain regions, and how synchronous activity contributes to normal cognition and pathology. -

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    Mike Hasselmo
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    Boston University
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    Coming Soon -

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    Don Katz
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    Brandeis
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    -The Katz lab is actively engaged in the following research areas: -

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    • Dynamics of Taste Responses
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    Bernat Kocsis
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    Harvard Medical School
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    Subcortical regulation of forebrain activity in the sleep-wake cycle.
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    The central focus of my research is the subcortical regulation of hippocampal function and is guided by the general hypothesis that the role of this regulation is to build dynamic associations between several limbic structures that are synchronized by oscillatory population activity. Phasic and rhythmic synchronization of neuronal activity is critical to control the concerted action of spatially separated structures in the brain. The general state and background activity of various brain structures determine how these structures will respond to different specific inputs and how they establish dynamical connections to perform complex functions. An important constituent of these states is the pattern of population activity including coherent oscillations in anatomically scattered structures which can establish functional networks during specific behaviors. Theta synchrony provides an excellent model to study these cooperations and the way in which they differ in specific behavioral states, such as waking exploration and REM sleep.

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    Oscillatory processes in cardiovascular control.
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    Another model we use to study rhythmic synchronization among neural networks is the autonomic nervous system which is capable of generating different patterns of activity that control the response of the cardiovascular system to changes in the environment (e.g. chemoregulation, thermoregulation, etc.) and different behavioral states (e.g. defense reaction, eating, sleep, etc.). Our guiding hypothesis in this research is that sympathetic rhythm is generated by multiple oscillators and we study the changes in the relationship between these oscillators under different conditions of health and disease. -

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    Mark Kramer
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    Boston University
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    We study mathematical neuroscience, with particular emphasis on neural rhythms, brain diseases, dynamical systems, and data analysis. All of the research involves interdisciplinary collaborations with experimentalists and clinicians. We are currently focused on analysis and modeling of multiscale data recorded in vivo from human subjects, and the construction of computational models of multiscale neuronal activity. We are also interested in techniques to infer and analyze functional connectivity networks from multivariate time series data, and how neuroscience can motivate new research questions in mathematics. -

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    Chris Moore
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    Brown University
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    Christopher Moore studies brain dynamics and how they change can change perception from moment to moment. -The brain's ability to shift the way it processes information—to shift its 'state'—is crucial to surviving in an ever-changing world. Dysregulation of these dynamics are a hallmark of neurologic and psychiatric disease. The laboratory is studying the mechanisms responsible for generating brain states, how they impact the representation of a sensory input, and how, ultimately, they change conscious perception. -

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    Daniel Polley
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    Mass. Eye & Ear/Harvard Medical School
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    Our work focuses on the role of sensory experience in the development and -maintenance of functional circuits in the auditory cortex. The auditory -cortex is powerfully influenced by experience during finite windows of -development known as critical periods, after which time significant changes -can only be brought about through learned associations between sounds and -behaviorally relevant consequences. We study the mechanisms and perceptual -correlates of cortical plasticity across the lifespan using a variety of -neurophysiological, genetic, behavioral and computational approaches. We -also record from subcortical auditory nuclei such as the inferior colliculus -and auditory thalamus to understand more about features that are relayed to -the cortex versus constructed there de novo. We believe this class of study -will contribute towards a richer understanding of normal function, but might -also hold the key for remediating abnormal auditory signal following a -history of degraded hearing or deafness in early life. A major goal for our -group is to apply what we've learned about the dynamic interplay between -plasticity and stability in animal models towards improving auditory -processing in humans that have been reconnected to the auditory world -following a period of prolonged hearing loss. -

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    Jason Ritt
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    The Ritt lab concentrates on how organisms gather and use information from their environment, through processes of active sensing and sensory decision making. Current projects employ electrophysiological, behavioral, optogenetic and theoretical methods applied to the rodent whisker system, a highly refined tactile sensory system. Experiments combine multi-electrode recording of brain activity; high speed videography of behavior and development of automated image analysis algorithms; and optical stimulation of specific cell types (e.g., excitatory vs. inhibitory neurons) using genetically targeted expression of light sensitive ion channels. Parallel modeling uses tools from dynamical systems, control theory and decision theory. Augmenting experiments with model-driven, real-time feedback forms a basis for development of brain machine interfaces, with an emphasis on sensory neural prosthetics, in addition to providing state of the art tools to address basic questions of neural function. -

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    Kamal Sen
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    How do neurons in the brain encode complex natural sounds? What are the neural substrates of selectivity for and discrimination of different categories of natural sounds? Are these substrates innate or shaped by learning? -Our laboratory investigates these questions in the model system of the songbird. Electrophysiological techniques are used to record neural responses from hierarchical stages of auditory processing. Theoretical methods from areas such as statistical signal processing, systems theory, probability theory, information theory and pattern recognition are applied to characterize how neurons in the brain encode natural sounds. Computational models are constructed to understand the processing of natural sounds both at the single neuron and the network level, to model neural selectivity and discrimination, and to explore the role of learning in shaping the neural code. -

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    Barbara Shinn-Cunningham
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    Research in the Auditory Neuroscience Laboratory addresses how listeners communicate and make sense of sounds in everyday settings. We study everything from basic perceptual sensitivity to the ways in which different brain regions coordinate their activity during complex tasks. We use a range of approaches to explore these issues, including human behavioral experiments, human neuroelectric imaging, computational modeling, and, in collaboration with other laboratories, fMRI, animal behavioral experiments, and animal neurophysiology. -

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    Kevin Spencer
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    Dr. Stufflebeam's goal is to develop and translate advanced technology at the Martinos Center into clinical practice. Currently, he is using MEG/EEG, fMRI, and optical imaging to understand how the brain processes neural information. He applies multiple imaging technologies to understand epilepsy, schizophrenia, and brain neoplasms. He is also setting up a clinical MEG service for New England. -

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    Lucia Vaina
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    Miles Whittington
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    Dr. Whittington's group has a major interest in mechanisms that generate oscillatory activity with neural networks, how this activity is sustained and how is modulated in various normal and pathological conditions. -

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    Research in the Wilson laboratory focuses on the study of information representation across large populations of neurons in the mammalian nervous system, as well as on the mechanisms that underlie formation and maintenance of distributed memories in freely behaving animals. To study the basis of these processes, the lab employs a combination of molecular genetic, electrophysiological, pharmacological, behavioral, and computational approaches. Using techniques that allow the simultaneous activity of ensembles of hundreds of single neurons to be examined in freely behaving animals, the lab examines how memories of places and events are encoded across networks of cells within the hippocampus ¬ a region of the brain long implicated in the processes underlying learning and memory. -

    -These studies of learning and memory in awake, behaving animals have led to the exploration of the nature of sleep and its role in memory. Previous theories have suggested that sleep states may be involved in the process of memory consolidation, in which memories are transferred from short to longer-term stores and possibly reorganized into more efficient forms. Recent evidence has shown that ensembles of neurons within the hippocampus, which had been activated during behavior are reactivated during periods of dreaming. By reconstructing the content of these states, specific memories can be tracked during the course of the consolidation process. -

    -Combining the measurement of ongoing neuronal activity with manipulation of molecular genetic targets has allowed the study of how specific cellular mechanisms regulate neural function to produce learning and memory at the behavioral level. Pharmacological blockage of these receptors has allowed the study of their involvement in the rapid changes that occur during both waking and sleeping states. Simultaneous monitoring of areas in the hippocampus and neocortex have allowed study of the downstream effects of activation. -

    -Taken together, these approaches contribute to the overall research objective: to understand the link from cellular/subcellular mechanisms of plasticity, to neural ensemble representations and interactions, to learning, memory, behavior, and cognition. -

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    - My interests lie broadly in understanding how the brain represents perceptual information and why - this may differ in pathological states related to autism and schizophrenia. I am tackling this using - in vitro electrophysiological techniques in collaboration with mathematical modellers to look at - mechanisms of network rhythm generation, modulation and interaction in the anterior cingulate - region of prefrontal cortex. -

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    - Currently, my research is focussed on exploring aspects of frontal cortical function that facilitate - learning of sequences of sensory events (e.g. Siegel, M., et al 2009). I am interested in how precise - spike timing in individual neurons or small sub-populations relates to the local field oscillation as a - marker of the overall average of event timing relevant to a given stimulus. -

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    - So far my work has revealed that many neurons in the anterior cingulate cortex possess the ability - to intrinsically oscillate at sub-threshold levels. With varying degrees of tonic excitation these sub- - threshold oscillations (STOs) exist at a variety of frequencies up to c.30Hz. The anterior cingulate - cortex is known to have multiple mechanisms for the generation of gamma rhythms associated with - cognitive function and I will look at how these rhythms interact with cellular STOs to affect spike/ - phase relationships and perhaps code for sequences: The working hypothesis is that assemblies - of cells receiving higher levels of excitation increase the drive to the kinetics responsible for STOs, - ultimately leading to a spike phase-advance on each period of field gamma. -

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    - This work could uncover a substrate for the stable, computationally useful, temporal separation of - concurrently active sensory representations. -

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    - My work has been focused on two aspects of the analysis of neural rhythms. The first project, which I have been working on with Uri Eden, Mark Kramer, and Kyle Lepage, has focused on the spectral analysis of spike trains including coherence between signals when at least one of those signals is a spike train. I use point process theory to derive properties of point process spectra and the estimators, and try to understand how those properties may help or hinder our understanding of the underlying neural system. The second project is in collaboration with Timothy Gardner and Uri Eden in which we are investigating methods of multi-scale time-frequency analysis based on an object-based signal representation. This method will allow us to extract signal information using multiple times scales simultaneously. This method may help to construct sharper spectral representations than are currently possible and we believe this operation may help to understand the phenomenology of human auditory perception. -

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    - Recording of neuronal spiking activity in distributed brain circuits - requires a scalable design for massively parallel recording of - extracellular field potentials. We are inventing such a system and - implementing a proof-of-concept instantiation. In this system, - multi-electrode arrays are used, which minimize tissue damage and help - with spike sorting, and time domain multiplexing of analog field - potential acquisition reduces interconnect. Channel data is then - relayed to a custom-designed terabyte capacity storage network via - custom digital circuitry. The storage network is designed to enable - neural data to be analyzed in flexible ways, including the evaluation - of spike sorting methods. -

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    - On the technical side, I am solely responsible for the design and implementation of the ethernet network and high-speed data storage software. In addition, I provide leadership to the project by staying well-versed in all aspects of the system design and maintaining open lines of communication between all technology developers, as well as organizing and documenting the design of the system. -

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    - Jung has been working with Kopell and Whittington on several modeling projects. The main one concerns the effects of top-down beta rhythms on attention; Jung showed that such signals resonate with cells in the deep cortical layers, producing gain control and more gamma rhythms in the superficial layers; a paper is almost complete. This work is highly relevant to work done by Miller on top-down attention, and further collaborations are planned. The work also has relevance to aspects of schizophrenia, and conversations are beginning with the group of Kevin Spencer. A second project concerns multiple inhibitory cell types in the rat auditory cortex. See Schizophrenia. -

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    - Kyle has been one of the most active members of the data analyis group. In the past year, he has been involved in CRC related activity involving three main subjects and two more tertiary ones. One primary project was a collaboration with the Kramer, Eden and Desimone groups on spike-field association (statistical procedures used to infer relations between a rhythm in a time series, such as a local field potential recording, and the firing activity of single neuron. Mikio Aoi is also involved. There is now a preprint. A second major project is a collaboration with the Eichenbaum and Eden groups on cells that measure time. More technically, the project deals with the development of statistical procedures to separate the relative influence of covariates of interest such as time and rodent position upon neural activity. There are two papers and several popular press articles about this work. The third major project is a collaboration with the Kramer lab, also involving postdoc ShiNung Ching; it is motivated by techniques used in MEG and EEG experiments to find functionally connected networks, as in the Human Connectome. This work deals with principled estimation of the statistical connectivity between nodes in an evoked network. In this paradigm a stimulus is repeatedly applied to network nodes, one at a time, and evoked activity at nodes is used to infer a statistical relation between node activity. There is a preprint. A smaller project with the group of Shinn-Cunningham concerns MEG eigensource. In this work local bias in MEG source estimates is traded for decreased non-spatially local bias due to unavoidable inverse-problem source localization limitation. A final project, with Kramer, deals with removing bias in EEG measurements due to activity present on either an EEG reference electrode or present in a "re-referencing method" -

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    - Morteza is a postdoc in the lab of Miller. He is interested in the functional circuitry for memory and context formation between and within the prefrontal cortex (PFC) and the medial temporal lobe (MTL). PFC neurons reflect the associative relations between stimuli, task instructions, behavioral responses, rewards, etc. Interestingly, MTL neurons show similar properties. Neurophysiological studies have been focused on either the MTL or PFC and the interaction between the MTL and PFC is still unclear. He will simultaneously record - with many electrodes- from the PFC and MTL areas while monkey perform a task that temporally separates neuronal information related to context, sample, and recall of the correct choice. He will investigate the modulation of oscillatory neuronal dynamics between and within the PFC and MTL, during different stage of the task. The second project of Morteza concerns the oscillatory neuronal dynamics of categorization in the PFC. Modulations of neuronal oscillations in the PFC with cognitive demands may regulate whether PFC neurons function as multitaskers. The data from these projects are essential to understanding central questions about the roles of rhythms in cognition, and will provide the basis for modeling efforts. In addition, Morteza helps to run the physiology working group. -

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    - Lara is a new postdoc in the lab of Eichebaum (BU). Her work was described above. She interacts frequently with members of the statistics and modeling groups (Eden, Kramer, Kopell). She also talks frequently with members of other CRC labs (Boyden lab, MIT : Annabelle Singer; Wilson lab, MIT : Greg Hale, Sage Chen, and Stuart Layton) to compare data, methodology, and analysis techniques. She is planning further interactions with Omar Ahmed of the Cash lab (MGH) on hippocampal oscillatory activity in humans, the Miller lab (MIT) on beta frequency oscillations, and the Jiamin Zhuo and Nick James of the Han lab (BU), on dentate gyrus function and beta rhythms, respectively. She has also interacted with Whittington at CRC events. She speaks frequently with postdocs Annabelle Singer, Justin Kinney, Omar Ahmed, and Kyle Lepage as well as graduate students Caroline Moore-Kochlacs, Greg Hale, and all the members of the Eichenbaum lab. Lara has already written a grant proposal based on this work: NIH F-32 Individual Postdoctoral Research Grant -

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    - Wei studies large-scale networks in the resting human brain with data - from non-invasive imaging techniques. Under the hypothesis that - particular sets of brain regions interact with each other to maintain - an active yet stable intrinsic state, the goal of her work is to - uncover both the structure and dynamics of such intrinsic networks, in - the hope that knowledge of the resting state will lead to further - understanding of how neural electrophysiology gives rise to cognitive - phenomena. -

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    - Her current project involves collaborations between several - laboratories. With MEG data acquired by Stufflebeam’s group, Wei and - Steve are looking at seed-based Granger-causality maps, assessing - their spatiotemporal and spectral properties, to explore their - relationship with the proposed default-mode hypothesis. They will - later extend the analysis to task data from the same subjects and see - how the networks change undergoing different cognitive processes. - Meanwhile, supervised by Matti Hamalainen and Uri Eden, Wei interacts - with Patrick Purdon’s group at the Martinos Center, developing a - state-space model based approach to identify the full - source-connectivity matrix of the MEG signal and monitor its change - over time. Efforts are being made to advance the methodology dealing - with high-dimensionality of the data and make the full-network - tractable. The third collaboration is with Mark Kramer, aiming at - finding plausible biophysical models that can explain the observed - network properties. This is an open area of exploration and may serve - further modeling studies on brain disease such as epilepsy. Results - from these collaborations together may provide a comprehensive picture - of how the brain works at different levels. -

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    - Sujith was a former student of Wilson, now working mostly with Cash and Kopell on aspects of the alpha rhythm and sleep. Details are above. He is the organizer of the Alpha Working Group. -

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    Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the Psychiatric Neuroimaging Division of the Psychiatry Department at Massachusetts General Hospital, Charlestown, MA

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    • Project: Development of accelerated diffusion and functional MRI scans with real-time motion tracking for children with autism
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    • PI: Dara S. Manoach, Ph.D.
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      Our team is developing several technical innovations that will significantly reduce the impact of head motion on fMRI and diffusion data. We are seeking a candidate to work with us to improve data analysis by making fMRI and diffusion analysis motion-aware using both the in-image data and the motion tracking data.

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      The Research Fellow will be expected to: -

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      1. 1) Assist with setting up the data acquisition to ensure that the protocols are well-designed for the analysis questions;
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      2. 2) Build motion-aware processing tools that work in concert with existing software packages to improve the analysis of fMRI and DWI data;
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      3. 3) Assist in the processing, interpretation and analysis of the results of both phantom and human studies; and
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      4. 4) Apply these methods to address clinical research questions in autism.
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      Our ideal candidate has a PhD in Computer Science, Electrical Engineering, or related fields, and has experience in signal processing and numerical methods. Candidates with experience in image processing and time series analysis, or specifically in fMRI and diffusion data analysis will be preferred. This position requires strong programming skills, and the candidate is expected to have experience working in C++, scripting languages (e.g., Python), and rapid-prototyping languages for numerical algorithms (e.g., Matlab, Mathematica). Strong communication skills are essential, as the position involves working with an interdisciplinary team of scientists in both MRI physics/engineering and psychology/neuroscience in addition to research coordinators and MRI technologists. Background in cognitive neuroscience and an interest in clinical applications are advantageous. Training in clinical research will be provided.

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      Position available immediately. Please send -

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    Last updated: 1 October 2012

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    2012

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    • -Börgers C, Talei Franzesi G, Lebeau FE, Boyden ES, Kopell NJ. Minimal size of cell assemblies coordinated by gamma oscillations. PLoS Comput Biol. 2012 Feb;8(2):e1002362. Epub 2012 Feb 9 -
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    • -Burke J, Desroches M, Barry AM, Kaper TJ, Kramer MA. A showcase of torus canards in neuronal bursters. J Math Neurosci. 2012 Feb 21;2(1):3 -
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    • -Carlén M, Meletis K, Siegle JH, Cardin JA, Futai K, Vierling-Claassen D, Rühlmann C, Jones SR, Deisseroth K, Sheng M, Moore CI, Tsai LH. A critical role for NMDA receptors in parvalbumin interneurons for gamma rhythm induction and behavior Mol Psychiatry. 2012 May;17(5):537-48. doi: 10.1038/mp.2011.31. Epub 2011 Apr 5 -
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    • -Chen Z, Purdon PL, Brown EN, Barbieri R. A unified point process probabilistic framework to assess heartbeat dynamics and autonomic cardiovascular control. Front Physiol. 2012;3:4. Epub 2012 Feb 1 -
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    • -Ching S, Purdon PL, Vijayan S, Kopell NJ, Brown EN. A neurophysiological-metabolic model for burst suppression. Proc Natl Acad Sci U S A. 2012 Feb 21;109(8):3095-100. Epub 2012 Feb 7 -
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    • -Chow BY, Han X, Boyden ES. Genetically encoded molecular tools for light-driven silencing of targeted neurons. Prog Brain Res. 2012;196:49-61 -
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    • -Chu CJ, Kramer MA, Pathmanathan J, Bianchi MT, Westover MB, Wizon L, Cash SS. Emergence of stable functional networks in long-term human electroencephalography. J Neurosci. 2012 Feb 22;32(8):2703-13 -
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    • -Desroches M, Burke J, Kaper TJ, Kramer MA. Canards of mixed type in a neural burster, Phys Rev E Stat Nonlin Soft Matter Phys. 2012 Feb;85(2 Pt 1):021920. Epub 2012 Feb 23 -
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    • -Gregoriou GG, Gotts SJ, Desimone R. Cell-type-specific synchronization of neural activity in FEF with V4 during attention. Neuron. 2012 Feb 9;73(3):581-94 -
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    • -Han X. Optogenetics in the nonhuman primate. Prog Brain Res. 2012;196:215-33 -
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    • -Kim KM, Baratta MV, Yang A, Lee D, Boyden ES, Fiorillo CD. Optogenetic mimicry of the transient activation of dopamine neurons by natural reward is sufficient for operant reinforcement. PLoS One. 2012;7(4):e33612. Epub 2012 Apr 10 -
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    • -Kittelberger K, Hur EE, Sazegar S, Keshavan V, Kocsis B. Comparison of the effects of acute and chronic administration of ketamine on hippocampal oscillations: relevance for the NMDA receptor hypofunction model of schizophrenia. Brain Struct Funct. 2012 Apr;217(2):395-409. Epub 2011 Oct 7 -
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    • -Kocsis B. Differential Role of NR2A and NR2B Subunits in N-Methyl-D-Aspartate Receptor Antagonist-Induced Aberrant Cortical Gamma Oscillations. Biol Psychiatry. 2012 Jun 1;71(11):987-95. Epub 2011 Nov 4 -
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    • -Kocsis B. State dependent increase of cortical gamma activity during REM sleep after selective blockade of NR2B subunit containing NMDA receptors. Sleep -
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    • -Kodandaramaiah SB, Franzesi GT, Chow BY, Boyden ES, Forest CR. Automated whole-cell patch clamp electrophysiology of neurons in vivo. Nat Methods. 2012 May 6. doi: 10.1038/nmeth.1993. [Epub ahead of print] -
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    • -Kramer MA, Cash SS. Epilepsy as a Disorder of Cortical Network Organization, Neuroscientist. 2012 Jan 10. [Epub ahead of print] -
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    • -Larson E, Maddox RK, Perrone BP, Sen K, Billimoria CP. Neuron-specific stimulus masking reveals interference in spike timing at the cortical level. J Assoc Res Otolaryngol. 2012 Feb;13(1):119-29. Epub 2011 Nov 29 -
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    • -Lepage KQ, Macdonald CJ, Eichenbaum H, Eden UT. The statistical analysis of partially confounded covariates important to neural spiking. J Neurosci Methods. 2012 Apr 15;205(2):295-304. Epub 2012 Jan 17 -
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    • -Maddox RK, Billimoria CP, Perrone BP, Shinn-Cunningham BG, Sen K. Competing sound sources reveal spatial effects in cortical processing. PLoS Biol. 2012 May;10(5):e1001319. Epub 2012 May 1 -
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    • -Madisen L, Mao T, Koch H, Zhuo JM, Berenyi A, Fujisawa S, Hsu YW, Garcia AJ 3rd, Gu X, Zanella S, Kidney J, Gu H, Mao Y, Hooks BM, Boyden ES, BuzsÃ?¡ki G, Ramirez JM, Jones AR, Svoboda K, Han X, Turner EE, Zeng H. A toolbox of Cre-dependent optogenetic transgenic mice for light-induced activation and silencing. Nat Neurosci. 2012 Mar 25;15(5):793-802. doi: 10.1038/nn.3078 -
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    • -Malerba P, Kopell N. Phase resetting reduces theta-gamma rhythmic interaction to a one-dimensional map. J Math Biol. 2012 Apr 21. [Epub ahead of print] -
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    • -McCarthy MM, Ching S, Whittington MA, Kopell N, Dynamical changes in neurological diseases and anesthesia, Curr Opin Neurobiol. 2012 Mar 23. [Epub ahead of print] -
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    • -Melzer S, Michael M, Caputi A, Eliava M, Fuchs EC, Whittington MA, Monyer H, Long-range-projecting GABAergic neurons modulate inhibition in hippocampus and entorhinal cortex, Science. 2012 Mar 23;335(6075):1506-10 -
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    • -Munro E, Kopell N, Subthreshold somatic voltage in neocortical pyramidal cells can control whether spikes propagate from the axonal plexus to axon terminals: a model study, J Neurophysiol. 2012 May;107(10):2833-52. Epub 2012 Feb 29 -
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    • -Peyrache A, Dehghani N, Eskandar EN, Madsen JR, Anderson WS, Donoghue JA, Hochberg LR, Halgren E, Cash SS, Destexhe A. Spatiotemporal dynamics of neocortical excitation and inhibition during human sleep. Proc Natl Acad Sci U S A. 2012 Jan 31;109(5):1731-6. Epub 2012 Jan 17 -
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    • -Puig MV, Miller EK. The role of prefrontal dopamine d1 receptors in the neural mechanisms of associative learning. Neuron. 2012 Jun 7;74(5):874-86 -
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    • -Siok CJ, Cogan SM, Shifflett LB, Doran AC, Kocsis B, Hajós M. Comparative analysis of the neurophysiological profile of group II metabotropic glutamate receptor activators and diazepam: effects on hippocampal and cortical EEG patterns in rats. Neuropharmacology. 2012 Jan;62(1):226-36. Epub 2011 Jul 26 -
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    • -Temereanca S, Hämäläinen MS, Kuperberg GR, Stufflebeam SM, Halgren E, Brown EN, Eye movements modulate the spatiotemporal dynamics of word processing J Neurosci. 2012 Mar 28;32(13):4482-94 -
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    • -Torii M, Hackett TA, Rakic P, Levitt P, Polley DB. EphA Signaling Impacts Development of Topographic Connectivity in Auditory Corticofugal Systems. Cereb Cortex. 2012 Apr 5. [Epub ahead of print] -
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    2011

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    • -Ahveninen J, Hämäläinen M, Jääskeläinen IP, Ahlfors SP, Huang S, Lin FH, Raij T, Sams M, Vasios CE, Belliveau JW. Attention-driven auditory cortex short-term plasticity helps segregate relevant sounds from noise. Proc Natl Acad Sci U S A. 2011 Mar 8;108(10):4182-7. Epub 2011 Feb 22. -
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    • -Ainsworth M, Lee S, Cunningham MO, Roopun AK, Traub RD, Kopell NJ, Whittington MA, Dual γ rhythm generators control interlaminar synchrony in auditory cortex. J Neurosci. 2011 Nov 23;31(47):17040-51. Erratum in: J Neurosci. 2012 Feb 22;32(8):2911 -
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    • -Antzoulatos EG, Miller EK. Differences between neural activity in prefrontal cortex and striatum during learning of novel abstract categories. Neuron. 2011 Jul 28;71(2):243-9 -
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    • -Barkat TR, Polley DB, Hensch TK. A critical period for auditory thalamocortical connectivity, Nat Neurosci. 2011 Jul 31;14(9):1189-94. doi: 10.1038/nn.2882 -
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    • -Barnes TD, Mao JB, Hu D, Kubota Y, Dreyer AA, Stamoulis C, Brown EN, Graybiel AM, Advance cueing produces enhanced action-boundary patterns of spike activity in the sensorimotor striatum . J Neurophysiol. 2011 Apr;105(4):1861-78. Epub 2011 Feb 9 -
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    • -Brown EN, Purdon PL, and Van Dort CJ (2011) "General Anesthesia and Altered States of Arousal: A Systems Neuroscience Analysis", Annu Rev Neurosci. 2011 Apr 20. [Epub ahead of print] -
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    • -Buffalo EA, Fries P, Landman R, Buschman TJ, Desimone R. Laminar differences in gamma and alpha coherence in the ventral stream. Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11262-7. Epub 2011 Jun 20 -
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    • -Buschman TJ, Siegel M, Roy JE, Miller EK. Neural substrates of cognitive capacity limitations -Proc Natl Acad Sci U S A. 2011 Jul 5;108(27):11252-5. Epub 2011 Jun 20 -
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    • -Chu-Shore CJ., Kramer MA, Bianchi MT, Caviness VS, Cash SS (2011) "Network Analysis: Applications for the Developing Brain" J. Child Neurology, Apr; 26(2): 488-500 -
      • -
    • -Cimenser A, Purdon PL, Pierce ET, Walsh JL, Salazar-Gomez AF, Harrell PG, Tavares-Stoeckel C, Habeeb K, and Brown (2011) "Tracking brain states under general anesthesia by using global coherence analysis", EN. Proc Natl Acad Sci U S A. 2011 May 24;108(21):8832-7. Epub 2011 May 9. -
      • -
    • -Cromer JA, Roy JE, Buschman TJ, Miller EK. Comparison of primate prefrontal and premotor cortex neuronal activity during visual categorization. Cogn Neurosci. 2011 Nov;23(11):3355-65. Epub 2011 Mar 31 -
      • -
    • -Cromer JA, Roy JE, Buschman TJ, Miller EK. Rapid association learning in the primate prefrontal cortex in the absence of behavioral reversals. J Cogn Neurosci. 2011 Jul;23(7):1823-8. Epub 2010 Jul 28 -
      • -
    • -Dehghani N, Cash SS, Halgren E, (2011) "Emergence of synchronous EEG spindles from asynchronous MEG spindles" Hum Brain Mapp. Feb 17 (2011). -
      • -
    • -Eden UT, Amirnovin R, Eskandar EN. Using point process models to describe rhythmic spiking in the subthalamic nucleus of Parkinson's patients. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:757-60 -
      • -
    • -Ghitza, O. (2011). "Linking speech perception and neurophysiology: speech decoding -guided by cascaded oscillators locked to the input rhythm." Front. Psychology 2:130. doi: -10.3389/fpsyg.2011.00130. -
      • -
    • -Haas JS, Zavala B, Landisman CE. Activity-dependent long-term depression of electrical synapses. Science. 2011 Oct 21;334(6054):389-93 -
      • -
    • -Hackett TA, Barkat TR, O'Brien BM, Hensch TK, Polley DB. Linking topography to tonotopy in the mouse auditory thalamocortical circuit. J Neurosci. 2011 Feb 23;31(8):2983-95 -
      • -
    • -Han X, Chow BY, Zhou H, Klapoetke NC, Chuong A, Rajimehr R, Yang A, Baratta MV, Winkle J, Desimone R, Boyden ES. A high-light sensitivity optical neural silencer: development and application to optogenetic control of non-human primate cortex. Front Syst Neurosci. 2011;5:18. Epub 2011 Apr 13 -
      • -
    • -Halassa MM, Siegle JH, Ritt JT, Ting JT, Feng G, Moore CI. Selective optical drive of thalamic reticular nucleus generates thalamic bursts and cortical spindles. Nat Neurosci. 2011 Jul 24;14(9):1118-20. doi: 10.1038/nn.2880 -
      • -
    • -Howe MW, Atallah HE, McCool A, Gibson DJ, Graybiel AM. Habit learning is associated with major shifts in frequencies of oscillatory activity and synchronized spike firing in striatum. Proc Natl Acad Sci U S A. 2011 Oct 4;108(40):16801-6. Epub 2011 Sep 26 -Kahn I, Desai M, Knoblich U, Bernstein J, Henninger M, Graybiel AM, Boyden ES, Buckner RL, Moore CI. Characterization of the functional MRI response temporal linearity via optical control of neocortical pyramidal neurons. J Neurosci. 2011 Oct 19;31(42):15086-91 -
      • -
    • -Kajikawa Y, Schroeder CE. How local is the local field potential. Neuron. 2011 Dec 8;72(5):847-58 -
      • -
    • -Kerr CE, Jones SR, Wan Q, Pritchett DL, Wasserman RH, Wexler A., Villanueva JJ, et al. (2011) "Effects of mindfulness meditation training on anticipatory alpha modulation in -primary somatosensory cortex", Brain research bulletin, doi:10.1016/j.brainresbull, 03.026 -
      • -
    • -Kim T, McKenna JT, Brown RE, Winston S, Chen L, Bolortuya Y, Strecker RE, Kocsis B, Deisseroth K, McCarley RW, and Basheer R (2011) "Expression of channelrhodopsins in parvalbumin-positive basal forebrain neurons", Sleep 2011; 34:A14 -
      • -
    • -Kramer MA, Eden UT, Lepage KQ, Kolaczyk ED, Bianchi MT, Cash SS. Emergence of persistent networks in long-term intracranial EEG recordings. J Neurosci. 2011 Nov 2;31(44):15757-67 -
      • -
    • -Kveraga K., Ghuman AS, Kassam KS, Aminoff EA, Hämäläinen MS, Chaumon M, and Bar M (2011) "Early onset of neural synchronization in the contextual associations network", Proceedings of the National Academy of Sciences of the United States of America, 108(8), 3389-3394. doi:10.1073/pnas.1013760108 -
      • -
    • -Lamus C, Hämäläinen MS, Temereanca S, Brown EN, Purdon PL. A spatiotemporal dynamic distributed solution to the MEG inverse problem Neuroimage. 2011 Nov 30. [Epub ahead of print] -
      • -
    • -Lepage KQ, Kramer MA, Eden UT. The dependence of spike field coherence on expected intensity. Neural Comput. 2011 Sep;23(9):2209-41. Epub 2011 Jun 14 -
      • -
    • -Lindén H, Tetzlaff T, Potjans TC, Pettersen KH, Grün S, Diesmann M, Einevoll GT -Modeling the spatial reach of the LFP. Neuron. 2011 Dec 8;72(5):859-72 -
      • -
    • -Long CJ, Purdon PL, Temereanca S, Desai NU, Hämäläinen MS, Brown EN -State-space solutions to the dynamic magnetoencephalography inverse problem using high performance computing. Ann Appl Stat. 2011 Jun 1;5(2B):1207-1228 -
      • -
    • -MacDonald CJ, Lepage KQ, Eden UT, Eichenbaum H. Hippocampal "time cells" bridge the gap in memory for discontiguous events. Neuron. 2011 Aug 25;71(4):737-49 -
      • -
    • -McCarthy MM, Moore-Kochlacs C, Gu X, Boyden ES, Han X, Kopell N -Striatal origin of the pathologic beta oscillations in Parkinson's disease -Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11620-5. Epub 2011 Jun 22. -
      • -
    • -Palva S, Kulashekhar S, Hämäläinen M, and Palva JM (2011) "Localization of Cortical Phase and Amplitude Dynamics during Visual Working Memory Encoding and Retention", The Journal of neuroscience: the official journal of the Society for Neuroscience, 31(13), 5013-5025. doi:10.1523/JNEUROSCI.5592-10.2011 -
      • -
    • -Siegle JH, Carlen M, Meletis K, Tsai LH, Moore CI, Ritt J. Chronically implanted hyperdrive for cortical recording and optogenetic control in behaving mice. Conf Proc IEEE Eng Med Biol Soc. 2011;2011:7529-32 -
      • -
    • -Siegle JH, Moore CI. Cortical circuits: finding balance in the brain. Curr Biol. 2011 Dec 6;21(23):R956-7. Epub 2011 Dec 5 -
      • -
    • -Sorman E, Wang D, Hajos M, and Kocsis B (2011) "Control of hippocampal theta rhythm by serotonin: Role of 5-HT2c receptors", Neuropharmacology, 61:489-494, 2011. -
      • -
    • -Sternshein H, Agam Y, Sekuler R. EEG correlates of attentional load during multiple object tracking. PLoS One. 2011;6(7):e22660. Epub 2011 Jul 26 -
      • -
    • -Tort AB, Komorowski R, Kopell N, Eichenbaum H. A mechanism for the formation of hippocampal neuronal firing patterns that represent what happens where. Learn Mem. 2011 Oct 21;18(11):718-27. doi: 10.1101/lm.2307711. Print 2011 -
      • -
    • -Truccolo W, Donoghue J, Hochberg LR, Eskandar E, Madsen JR, Anderson WS, Brown EN, Halgren E, Cash SS (2011) "Dynamics of Single Neurons in Human Focal Epilepsy" Nature Neuroscience. May; 14(5):635-41 -
      • -
    • -Wan Q, Kerr C, Pritchett D, Hämäläinen M, Moore C, Jones S. Dynamics of dynamics within a single data acquisition session: variation in neocortical alpha oscillations in human MEG -PLoS One. 2011;6(9):e24941. Epub 2011 Sep 22. -
      • -
    • -Whittaker RG, Turnbull DM, Whittington MA, Cunningham MO. Impaired mitochondrial function abolishes gamma oscillations in the hippocampus through an effect on fast-spiking interneurons. Brain. 2011 Jul;134(Pt 7):e180; author reply e181. Epub 2011 Mar 4. -
      • -
    • -Whittington MA, Roopun AK, Traub RD, Davies CH. Circuits and brain rhythms in schizophrenia: a wealth of convergent targets. Curr Opin Pharmacol. 2011 Oct;11(5):508-14. Review -
      • -
    • -Yoshida T and Katz DB, (2011) "Control of Prestimulus Activity Related to Improved Sensory Coding within a Discrimination Task", J Neuroscience, 31:4101-4112 -
      • -
    - -

    2010

    -
      -
    • -Brown EN, Lydic R, and Schiff ND (2010) "General anesthesia, sleep, and coma", N Engl J Med. 2010 Dec 30;363(27):2638-50. -
      • -
    • -Cardin J, Carlen M, Meletis K, Knoblich U, Zhang F, Desseroth K, Tsai L-H, Moore CI (2010) "Targeted Optogenetic Stimulation and Recording of Neurons in vivo Using Cell Type-Specific Expression of Channelrhodopsin-2", Nature Protocols. 5:247-254. -
      • -
    • -Ching S, Cimenser A, Purdon PL, Brown EN, and Kopell NJ (2010) "Thalamocortical model for a propofol-induced alpha-rhythm associated with loss of consciousness", Proc Natl Acad Sci U S A. 2010 Dec 28;107(52):22665-70. Epub 2010 Dec 13. -
      • -
    • -Ciesielski KT, Ahlfors SP, Bedrick EJ, Kerwin AA, Hämäläinen MS (2010) "Top-down control of MEG alpha-band activity in children performing Categorical N-Back Task", 2010 Oct;48(12):3573-9. Epub 2010 Aug 14 -
      • -
    • -Csercsa R, Dombovári B, Fabó D, Wittner L, Eross L, Entz L, Sólyom A, Rásonyi G, Szucs A, Kelemen A, Jakus R, Juhos V, Grand L, Magony A, Halász P, Freund TF, Maglóczky Z, Cash SS, Papp L, Karmos G, Halgren E, Ulbert I., "Laminar analysis of slow wave activity in humans." Brain. 133(9):2814-2829 (2010). -
      • -
    • -Dehghani N, Cash SS, Rossetti A, Chen CC, Halgren E (2010) "Magnetoencephalography Demonstrates Multiple Asynchronous Generators of Human Sleep Spindles", J Neurophysiol., 104(1):179-88 -
      • -
    • -Dehghani N, Cash SS, Chen CC, Hagler DJ Jr, Huang M, Dale AM, Halgren E., "Divergent cortical generators of MEG and EEG during human sleep spindles suggested by distributed source modeling," PLoS One. 2010 Jul 7;5(7): -
      • -
    • -Dehghani N, Bédard C, Cash SS, Halgren E, Destexhe A., (2010) "Comparative power spectral analysis of simultaneous electroencephalographic and magnetoencephalographic recordings in humans suggests non-resistive extracellular media: EEG and MEG power spectra. J Comput Neurosci, epub Jun 17 (2010), ahead of print -
      • -
    • -Dehghani N, Cash SS, Halgren E, "Topographical frequency dynamics within EEG and MEG sleep spindles" Clinical Neurophys. 122:229-235 -
      • -
    • -Huang J and Sekuler R (2010) "Attention protects the fidelity of visual -memory: Behavioral and electrophysiological evidence",.Journal of -Neuroscience", 30 13461-13471 -
      • -
    • -Jones S, Kerr C, Wan Q, Pritchett D, Hamalainen M, Moore CI (2010) "Cued Spatial Attention Drives Functionally-Relevant Modulation of the Mu Rhythm in Primary Somatosensory Cortex", Journal of Neuroscience, Oct 13;30(41):13760-5 -
      • -
    • -Jones SR, Kerr CE, Wan Q Pritchett DL, Hämäläinen MS, and Moore CI (2010) "Cued Spatial Attention Drives Representation-Specific Modulation of The Alpha Rhythm in Primary Somatosensory Cortex", J. Neurosci. 2010 30(41):13760-5. -
      • -
    • -Keller K., Truccolo W., Gale J., Eskandar E., Thesen T., Carlson C., Devinsky O., Kuzniecky R., Doyle W., Madsen J., Schomer D., Mehta A., Brown E.N., Halgren E., Cash S.S., "Distinct Neuronal Firing Types During Interictal Epileptiform Discharges in the Human Cortex," Brain. Jun;133(Pt 6):1668-81. (2010). -
      • -
    • -Kocsis B, and Kittelberger K (2010) "The effect of NMDA antagonism on hippocampal oscillations in freely moving rats", Relevance to schizophrenia, FENS 2010-01-31 -
      • -
    • -Kopell N, Kramer MA, Malerba P, and Whittington MA (2010) "Are different rhythms good for different functions?", Front Hum Neurosci, 4:187 -
      • -
    • -Kramer MA, Eden UT, Kolaczyk ED, Zepeda R, Eskandar EN, and Cash SS, (2010) "Coalescence and Fragmentation of Cortical Networks During Focal Seizures," J. Neurosci. Jul 28; 30(30):10076-85 -
      • -
    • -Lanre-Amos T and Kocsis B (2010) "Hippocampal oscillations in the rodent model of schizophrenia induced by amygdala GABA receptor blockade", Frontiers in Psychiatry, 1:132, 2010 -
      • -
    • -Moore CI, Carlen M, Knoblich U, and Cardin J (2010) "Neocortical Interneurons: from Diversity, Strength", Cell, Jul 23;142(2):189 -93 -
      • -
    • -Raij T, Ahveninen J, Lin FH, Witzel T, Jääskeläinen IP, Letham B, Israeli E, Sahyoun C, Vasios C, Stufflebeam S, Hämäläinen M, Belliveau JW (2010) "", Eur J Neurosci, May;31(10):1772-82 -
      • -
    • -Tort ABL, Fontanini A, Kramer MA, Jones LM, Kopell N, Katz DB (2010) "Cortical networks produce three distinct 7-12 Hz rhythms during single sensory responses in the awake rat", The Journal of Neuroscience, 24 March 2010, 30:12 -
      • -
    • -Tort ABL, Komorowsi R. Eichenbaum H, and, Kopell N (2010) "Measuring phase-amplitude coupling between neural oscillations", Journal of Neurophysiology 104:1195-210. -
      • -
    • -Vaina LM, Calabro F, Lin,FH, Hamalainen M (2010) "Long-range coupling of prefrontal cortex and visual (MT) or polysensory (STP) cortical areas in motion perception", Biomag 2010, pp. 197-201, Springer Verlag -
      • -
    • -Vierling-Claassen D, Cardin JA, Moore CI, Jones SR (2010) "Computational modeling of distinct neocortical oscillations driven by cell-type selective optogenetic drive: Separable resonant circuits controlled by low-threshold spiking and fast-spiking interneurons", Frontiers in Human Neuroscience, 2010 Nov 22, 4:198. -
      • -
    • -Welbert P, Nguy L, Kocsis B (2010) "The effect of median raphe stimulation on the frequency and amplitude of hippocampal theta rhythm", FENS 2010-01-31 -
      • -
    • -Ziegler DA. Pritchett,DL, Hosseini-Varnamkhasti P, Corkin S, Hämäläinen M, Moore CI, and Jones SR (2010) "Transformations in oscillatory activity and evoked responses in primary somatosensory cortex in middle age: a combined computational neural modeling and MEG study", NeuroImage, 52(3), 897-912. doi:10.1016/j.neuroimage.2010.02.004 -
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    2009

    -
      -
    • -Feingold J, DePasquale BD, and Graybiel AM (2009) "Modulation of beta power in the prefrontal cortex and caudate nucleus of monkeys during self-timed sequential arm movements. Program No. 863.4. 2009, Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience, 2009. Online. -
      • -
    • -Ghitza, O. and Greenberg, S. (2009). "On the possible role of brain rhythms in speech -perception: Intelligibility of time compressed speech with periodic and aperiodic -insertions of silence." Phonetica 66:113–126. doi:10.1159/000208934 -
      • -
    • -Thorn CA and Graybiel AM (2009) "Projection neurons are entrained to different local field frequencies in dorsomedial and dorsolateral striatum", Program No. 567.9. 2009 Neuroscience Meeting Planner. Chicago, IL: Society for Neuroscience, 2009. Online. -
      • -
    - - -

    Book Chapters

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      -
    • -Jones SR. "Biophysically Principled Computational Neural Network Modeling of Magneto-/Electro- Encephalography Measured Human Brain Oscillations". In: Springer Neuromethods textbook series (#67) Neuronal Network Analysis; Editors: T. Fellin and M. Hallasa. 2011 -
      • - -
    • -Miller, E.K. and Buschman, T.J. (in press) Neural mechanisms for the executive control of attention. In: Oxford's Handbook of Attention, Kastner S. and Nobre, K. (eds). Oxford University Press. -
      • - -
    • -Miller, E.K. and Wallis, J.D. (in press) The prefrontal cortex and executive brain functions. In : Fundamental Neuroscience, 4th edition. -
      • - -
    • -Duncan, J. and Miller, E.K. (in press) Adaptive neural coding in frontal and parietal cortex. In: Stuss, D.T. and Knight, R.T. (Eds). -Principles of Frontal Lobe Function: Second Edition. -
      • - -
    • -Miller,E.K. and Buschman, T.J. (2012) Top-Down Control of Attention by Rhythmic Neural Computations. In: Posner, M.I. (ed) Cognitive Neuroscience of Attention New York: Guilford Press. -
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    - - - - - - - - - - - diff --git a/research_topics.htm b/research_topics.htm deleted file mode 100644 index 0125def..0000000 --- a/research_topics.htm +++ /dev/null @@ -1,209 +0,0 @@ - - - - - - Cognitive Rhythms Collaborative - - - - - - - - - - - - - - - - -
    - - - - -
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    Research: Topics
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    Researchers are listed below each major research area

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    Last update: 1 October 2012

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    "Wired" project

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    Boyden, Kopell, Wilson, Desimone, Eichenbaum, Graybiel, Miller, Eden, Kramer, Brown

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      -
    • Designing a system to collect and analyze electrical neural data from thousands of sites in the brain
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    • High-throughput digital data storage and analysis architectures
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    • Automated spike sorting methods
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    • Geometries of probes
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    Optogenetic perturbation of brain rhythms

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    Boyden, Han, Kopell, Desimone, Brown, Borgers, Kramer, Ritt, Eden

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    • Optogenetic perturbation of cognitive circuits
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    • Technologies for automating neural recording
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    • Protein delivery to neurons
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    • Somatosensory cortex oscillations
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    • Amygdala-hippocampal dynamics
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    • Cortical dynamics and attention using optogenetics
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    • Optogenetics and anesthesia effect analysis
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    • Gamma oscillations and cell assemblies
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    - -

    Neural Data Analysis

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    Desimone, Kramer, Eden, Eichenbaum, Whittington, Ritt, Cheng, Sarma, Kopell, Purdon, Cash, Stufflbeam, Hamalainen, Vaina

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    • Relationship between point processes and continuous signals
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    • Disambiguating statistical covariates
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    • Combining dynamical systems and statistical methods
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    • Dynamical properties of optogenetic stimulation
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    • Statistics of spiking in Parkinson's Disease
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    • Statistical changes in sleep and anesthesia
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    • Data analysis and epilepsy
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    • Analyzing connectivity from imaging data
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    - -

    Origins and propagation of rhythms

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    Moore, Jones, Kopell, Miller, Borgers, Boyden

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      -
    • Model and verification of MEG data
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    • Gamma rhythms in the frontal cortex
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    • Gamma rhythms and cell assemblies
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    • Origins of the local field potential
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    • Propagation of rhythms
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    - -

    Rhythms and cognition

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    Kopell, Jones, Moore, Whittington, Eichenbaum, Han, Miller, Wilson, Brown, Graybiel, Polley

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      -
    • Thalamic alpha Model
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    • Alpha rhythms and attention
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    • Beta rhythms and selective attention
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    • Beta rhythms and the hippocampus
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    • Causal evidence supporting a role for gamma and alpha oscillations in sensory information processing
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    • Cholinergic modulation of attention
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    • Multiple gamma rhythms in the auditory cortex and implications for bottom-up processing
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    • Encoding rules using rhythms
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    • Thalamic rhythms and cognition
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    • Non-Traditional Mechanisms for Regulating Neocortical Dynamics: The Hemo-Neural Hypothesis
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    Dynamics of anesthesia and sleep

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    Brown, Kopell, Purdon, Wilson, Cash

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    • Tracking coherence
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    • Anteriorizarion
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    • Burst suppression
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    • Identifying general anesthesia
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    • Mechanisms underlying ketamine anesthesia
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    • Anesthetics and aging
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    • Fibromyalgia and Sleep
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    • Sleep Oscillations During REM
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    • Ripple-Spindle Interactions during SWS
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    Parkinson's Disease

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    Han, Boyden, Kopell, Eden, Cheng, Jones, Ritt

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    • Dynamics in the basal ganglia loop
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    • Deep Brain Stimulation
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    Schizophrenia

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    Kopell, Le Beau, Whittington, Kocsis

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    • Aberrant interlaminar coupling
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    • A Link between NMDA synapses and pathology of schizophrenia
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    • Developmental models of schizophrenia
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    • Other animal models of schizophrenia
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    Epilepsy

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    Kramer, Cash, Moore, Eden, Jones, Stufflebeam, Hamalainen, Kopell, Borgers

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      -
    • Human brain voltage data during seizure
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    • Non-invasive control of neural circuits
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    • The "resting network"
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    • A rodent model of epilepsy
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    Pediatric abnormalities

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    Jones, Hamalainen, Eden, Kramer

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    - - - - - - - - - - - From 6971f955ebbd708641cad947b9bb0655db9f0e28 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 21:56:51 -0400 Subject: [PATCH 27/59] 0;256;0cremove all js from head, limit to one stylesheet --- _includes/head.html | 13 +- css/cbd.css | 223 ----------------- css/crc.css | 567 +++++++++++++++++--------------------------- 3 files changed, 223 insertions(+), 580 deletions(-) delete mode 100644 css/cbd.css diff --git a/_includes/head.html b/_includes/head.html index 92cd56f..8728088 100644 --- a/_includes/head.html +++ b/_includes/head.html @@ -1,18 +1,7 @@ - - {{ page.title }} - - - + - - - - - - - diff --git a/css/cbd.css b/css/cbd.css deleted file mode 100644 index 2d687bd..0000000 --- a/css/cbd.css +++ /dev/null @@ -1,223 +0,0 @@ -body { - font-family: arial, sans-serif; color: #494949; font-size: 13px; background-color: #fff; - } - -a:link, a:hover, a:active, a:visited { - color: #ca0001; - } - -#head, #foot { - position: relative; - top: 0; 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margin: 0px 0px 3px 0px; font-size: 14px; font-weight: bold; color: #494949; line-height: 1.6em - } - -.linkred { - display: block; margin: 0px 0px 3px 0px; font-size: 14px; font-weight: bold; text-decoration: underline; color: #cc0200; - } -.room { - font-size: 14px; font-weight: bold; line-height: 1.3em -} - -table.members { - width: 700px; height: auto; font-size: 13px; -} - -table.members th { - padding: 5px 0px 2px 0px; color: #b5b5b5; font-weight: bold; text-transform: uppercase; -} - -table.members tr.table-head { - border-bottom: 1px solid #b5b5b5; -} - -table.members td { - padding: 8px 10px 8px 0px; -} - -table.members td.name { - width: 110px; -} - -table.members td.department { - width: 250px; -} - -table.members td.phone { - width: 100px; -} - -table.members td.email { - width: 100px; -} - -ul.address { - margin: 0px 0px 14px 14px; - } - -ul.address li { - height: 14px; font-weight: bold; - } - -ul.bullets { - list-style-type: disc; - } - -ul.bullets li { - margin: 0px 0px 5px 14px; line-height: 18px; - } diff --git a/css/crc.css b/css/crc.css index d7c55a4..2d687bd 100644 --- a/css/crc.css +++ b/css/crc.css @@ -1,346 +1,223 @@ -/* - * Scaffolding - * - * Update the basics of our documents to prep for docs content. - */ - body { - position: relative; /* For scrollyspy */ - padding-top: 50px; /* Account for fixed navbar */ -} - -/* - * Main navigation - * - * Turn the `.navbar` at the top of the docs purple. - */ - -.crc-nav { - text-shadow: 0 -1px 0 rgba(0,0,0,.15); - background-color: #ca0000; - border-color: #A00000; - box-shadow: 0 1px 0 rgba(255,255,255,.1); -} -.crc-nav .navbar-collapse { - border-color: #A00000; -} -.crc-nav .navbar-brand { - color: #fff; -} -.crc-nav .navbar-nav > li > a { - color: #ffc8c8; -} -.crc-nav .navbar-nav > li > a:hover { - color: #fff; -} -.crc-nav .navbar-nav > .active > a, -.crc-nav .navbar-nav > .active > a:hover { - color: #fff; - background-color: #9E0000; -} -.crc-nav .navbar-toggle { - border-color: #A00000; -} -.crc-nav .navbar-toggle:hover { - background-color: #A00000; - border-color: #A00000; -} - - -/* - * Footer - * - * Separated section of content at the bottom of all pages, save the homepage. - */ - -.crc-footer { - padding-top: 40px; - padding-bottom: 30px; - margin-top: 100px; - color: #777; - text-align: center; - border-top: 1px solid #e5e5e5; -} -.footer-links { - margin: 10px 0; - padding-left: 0; -} -.footer-links li { - display: inline; - padding: 0 2px; -} -.footer-links li:first-child { - padding-left: 0; -} - -@media (min-width: 768px) { - .crc-footer { - text-align: left; - } - .crc-footer p { - margin-bottom: 0; - } -} - - -/* - * Homepage - * - * Tweaks to the custom homepage and the masthead (main jumbotron). - */ - -/* Masthead (headings and download button) */ -.crc-masthead { - position: relative; - padding: 30px 15px; - text-align: center; - text-shadow: 0 1px 0 rgba(0,0,0,.15); -} -.crc-masthead h1 { - font-size: 50px; - line-height: 1; - color: #fff; -} -.crc-masthead .btn-outline-inverse { - margin: 10px; -} - -/* Links to project-level content like the repo, Expo, etc */ -.crc-masthead-links { - margin-top: 20px; - margin-bottom: 40px; - padding: 0 15px; - list-style: none; - text-align: center; -} -.crc-masthead-links li { - display: inline; -} -.crc-masthead-links li + li { - margin-left: 20px; -} -.crc-masthead-links a { - color: #fff; -} - -@media (min-width: 768px) { - .crc-masthead { - text-align: left; - padding-top: 140px; - padding-bottom: 140px; - } - .crc-masthead h1 { - font-size: 100px; - } - .crc-masthead .lead { - margin-right: 25%; - font-size: 30px; - } - .crc-masthead .btn-outline-inverse { - width: auto; - margin: 20px 5px 20px 0; - padding: 18px 24px; - font-size: 21px; - } - .crc-masthead-links { - padding: 0; - text-align: left; - } -} - - -/* - * Page headers - * - * Jumbotron-esque headers at the top of every page that's not the homepage. - */ - - -/* Page headers */ - -.crc-header { - padding: 30px 15px 40px; /* side padding builds on .container 15px, so 30px */ - font-size: 16px; - text-align: center; - text-shadow: 0 1px 0 rgba(0,0,0,.15); - color: #A00000; -} -.crc-header h1 { - color: #ca0000; -} -.crc-header p { - font-weight: 300; - line-height: 1.5; -} -.crc-header .container { - position: relative; -} - -@media (min-width: 768px) { - .crc-header { - font-size: 21px; - text-align: left; - } - .crc-header h1 { - font-size: 60px; - line-height: 1; - } -} - -@media (min-width: 992px) { - .crc-header h1, - .crc-header p { - margin-right: 380px; - } -} - -/* - * Side navigation - * - * Scrollspy and affixed enhanced navigation to highlight sections and secondary - * sections of docs content. - */ - -/* By default it's not affixed in mobile views, so undo that */ -.crc-sidebar.affix { - position: static; -} - -/* First level of nav */ -.crc-sidenav { - margin-top: 30px; - margin-bottom: 30px; - padding-top: 10px; - padding-bottom: 10px; - text-shadow: 0 1px 0 #fff; - background-color: #f9f2f4; - border-radius: 5px; -} - -/* All levels of nav */ -.crc-sidebar .nav > li > a { - display: block; - color: #716b7a; - padding: 5px 20px; -} -.crc-sidebar .nav > li > a:hover, -.crc-sidebar .nav > li > a:focus { - text-decoration: none; - background-color: #e5e3e9; - border-right: 1px solid #dbd8e0; -} -.crc-sidebar .nav > .active > a, -.crc-sidebar .nav > .active:hover > a, -.crc-sidebar .nav > .active:focus > a { - font-weight: bold; - color: #600000; - background-color: transparent; - border-right: 1px solid #600000; -} - -/* Nav: second level (shown on .active) */ -.crc-sidebar .nav .nav { - display: none; /* Hide by default, but at >768px, show it */ - margin-bottom: 8px; -} -.crc-sidebar .nav .nav > li > a { - padding-top: 3px; - padding-bottom: 3px; - padding-left: 30px; - font-size: 90%; -} - -/* Show and affix the side nav when space allows it */ -@media (min-width: 992px) { - .crc-sidebar .nav > .active > ul { - display: block; - } - /* Widen the fixed sidebar */ - .crc-sidebar.affix, - .crc-sidebar.affix-bottom { - width: 213px; - } - .crc-sidebar.affix { - position: fixed; /* Undo the static from mobile first approach */ - top: 80px; - } - .crc-sidebar.affix-bottom { - position: absolute; /* Undo the static from mobile first approach */ - } - .crc-sidebar.affix-bottom .crc-sidenav, - .crc-sidebar.affix .crc-sidenav { - margin-top: 0; - margin-bottom: 0; - } -} -@media (min-width: 1200px) { - /* Widen the fixed sidebar again */ - .crc-sidebar.affix-bottom, - .crc-sidebar.affix { - width: 263px; - } -} - - -/* - * Docs sections - * - * Content blocks for each component or feature. - */ - -/* Space things out */ -.crc-section + .crc-section { - padding-top: 40px; -} - -/* Janky fix for preventing navbar from overlapping */ -h1[id] { - padding-top: 80px; - margin-top: -45px; -} - - -/* - * Callouts - * - * Not quite alerts, but custom and helpful notes for folks reading the docs. - * Requires a base and modifier class. - */ - -/* Common styles for all types */ -.crc-callout { - margin: 20px 0; - padding: 20px; - border-left: 3px solid #eee; -} -.crc-callout h4 { - margin-top: 0; - margin-bottom: 5px; -} -.crc-callout p:last-child { - margin-bottom: 0; -} - -/* Variations */ -.crc-callout-danger { - background-color: #fdf7f7; - border-color: #eed3d7; -} -.crc-callout-danger h4 { - color: #b94a48; -} -.crc-callout-warning { - background-color: #faf8f0; - border-color: #faebcc; -} -.crc-callout-warning h4 { - color: #c09853; -} -.crc-callout-info { - background-color: #f4f8fa; - border-color: #bce8f1; -} -.crc-callout-info h4 { - color: #3a87ad; -} - + font-family: arial, sans-serif; color: #494949; font-size: 13px; background-color: #fff; + } + +a:link, a:hover, a:active, a:visited { + color: #ca0001; + } + +#head, #foot { + position: relative; + top: 0; + left: 0; + width: 100%; + height: 164px; + text-align: center; + /* [disabled]background: #a72e11 url('../images/top-gradient.gif') top left repeat-x; */ + } + +#head img { + width: 943px; + height: 104px; + margin: 30px auto; + } + +#content { + position: relative; top: 0; left: 0; width: 943px; height: auto; margin: 0px auto; overflow: hidden; + } + +#foot { + height: 120px; + margin: 100px 0px 0px 0px; + background-color: #ddd; + background-image: url(../images/bottom-gradient.gif); + border-top: 1px solid #a3a3a3; + text-align: center; + width: 100%; + background-repeat: repeat-x; + background-position: left top; + position: relative; + } + +#footer-content { + position: relative; top: 0; left: 0; width: 943px; height: auto; margin: 0px auto; + } + +#footer-content img { + float: left; + margin: 16px 0px 0px 32px; + } + +#footer-content p { + float: left; + width: 300px; + height: auto; + margin: 16px 0px 0px 32px; + font-size: 11px; + line-height: 1.25em; + } + +#banner_img { + position: relative; top: 0; left: 0; width: 943px; height: 141px; margin: 25px auto; + } + +#left-col { + float: left; + top: 0; + left: 0; + width: 8em; + height: auto; + margin: 0px 0px 0px 0px; +} +#crc_menu { + margin: 0px 0px 0px 26px; +} + +#fat-col, #slim-col { + float: left; top: 0; left: 0; width: 500px; height: auto; margin: 0px 0px 0px 42px; + } + +#one-col { + float: left; top: 0; left: 0; width: 720px; height: auto; margin: 0px 0px 0px 42px; font-size: 14px; + } + +#right-col { + float: left; top: 0; left: 0; width: 200px; height: auto; min-height: 20px; margin: 0px 0px 0px 30px; +} + +#img.map { + float: left; top: 0; left: 0; width: 386px; height: auto; min-height: 20px; margin: 0px 0px 0px 25px; +} + +p.home { + font-size: 14px; line-height: 1.8em; + } + +#right-col img { + float: left; width: 200px; +} + +#slim-col { + width: 320px; +} + +#slim-col p, .lab { + margin: 0px 0px 15px 0px; font-size: 12px; line-height: 1.6em; +} + +img.map { + width: 386px; +} + +h1 { + margin: 10px 0px 15px 0px; + padding: 0px 0px 5px 0px; + font-size: 20px; + color: #ca0001; + border-bottom: 2px solid #BBB; +} + +#title { + margin: 0px 0px 15px 0px; + font-size: 24px; + color: #ca0001; + font-weight: bold; +} + +h2 { + margin: 0px 0px 4px 0px; font-size: 14px; font-weight: bold; + } + +h3 { + font-size: 15px; font-weight: bold; + } + +h4 { + font-size: 11px; font-weight: normal; font-style: italic; color: #ca0001; + } + +h5 { + font-size: 13px; font-weight: bold; margin: 25px 0px 15px 0px; + } + +.hr { + position: relative; top: 0; left: 0; width: 100%; height: 1px; margin: 0px 0px 15px 0px; background-color: #dadada; + } + +#one-col p, #fat-col p { + line-height: 18px; margin: 0px 0px 14px 0px; +} +.name { + margin: 0px 0px 4px 0px; + font-size: 15px; + font-weight: bold; +} +.inst { + font-size: 11px; + font-weight: normal; + font-style: italic; + color: #ca0001; +} + +.lab { + display: block; position: relative; top: 0; left: 0; font-size: 14px; margin: 0px 0px 25px 0px; + } + +.title { + display: block; margin: 0px 0px 3px 0px; font-size: 14px; font-weight: bold; color: #494949; line-height: 1.6em + } + +.linkred { + display: block; margin: 0px 0px 3px 0px; font-size: 14px; font-weight: bold; text-decoration: underline; color: #cc0200; + } +.room { + font-size: 14px; font-weight: bold; line-height: 1.3em +} + +table.members { + width: 700px; height: auto; font-size: 13px; +} + +table.members th { + padding: 5px 0px 2px 0px; color: #b5b5b5; font-weight: bold; text-transform: uppercase; +} + +table.members tr.table-head { + border-bottom: 1px solid #b5b5b5; +} + +table.members td { + padding: 8px 10px 8px 0px; +} + +table.members td.name { + width: 110px; +} + +table.members td.department { + width: 250px; +} + +table.members td.phone { + width: 100px; +} + +table.members td.email { + width: 100px; +} + +ul.address { + margin: 0px 0px 14px 14px; + } + +ul.address li { + height: 14px; font-weight: bold; + } + +ul.bullets { + list-style-type: disc; + } + +ul.bullets li { + margin: 0px 0px 5px 14px; line-height: 18px; + } From 775fcfcefc5dfcdc46ce367ca3eac0ff2bf3765c Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 22:34:19 -0400 Subject: [PATCH 28/59] remove js from subpages, convert lots of files to markdown subpages --- calendar/index.md | 5 +-- contact/index.md | 22 ++++----- courses/index.md | 61 +++++++++++++------------ people/faculty/index.md | 96 +--------------------------------------- people/postdoc/index.md | 52 +--------------------- positions/index.md | 59 +++++++++++------------- research/papers/index.md | 7 +-- research/topics/index.md | 4 +- 8 files changed, 79 insertions(+), 227 deletions(-) diff --git a/calendar/index.md b/calendar/index.md index 224ce38..596843a 100644 --- a/calendar/index.md +++ b/calendar/index.md @@ -1,11 +1,8 @@ --- -layout: default +layout: subpage title: "Calendar" --- -
    - Calendar -

    [4-5 Jun 2013] CRC Conference: Rhythmic Dynamics and Cognition

    diff --git a/contact/index.md b/contact/index.md index 9bc1db8..e8c9889 100644 --- a/contact/index.md +++ b/contact/index.md @@ -1,15 +1,17 @@ --- -layout: default +layout: subpage title: "Contact" --- -
    Contact
    -
    For more information or to be added to the CRC email distribution, please contact either of the following:
    -

    Xiaoshi Shi
    -Boston University
    -CompNET and CRC
    -Phone: 617.353.4587
    -Fax: 617.353.4889
    -Email: xiaoshi at bu.edu

    +For more information or to be added to the CRC email distribution, please contact either of the following: -

    Webmaster: cogweb at math.bu.edu

    +### Xiaoshi Shi +Xiaoshi Shi +Boston University +CompNET and CRC +Phone: 617.353.4587 +Fax: 617.353.4889 +Email: xiaoshi at bu.edu + +### Webmaster +cogweb at math.bu.edu diff --git a/courses/index.md b/courses/index.md index e99b59d..d5374c6 100644 --- a/courses/index.md +++ b/courses/index.md @@ -1,32 +1,37 @@ --- -layout: default +layout: subpage title: "Courses" --- -
    Courses
    -

    Last update: 9 December 2011

    -

    -BU MA665: Introduction to Modeling and Data Analysis in Neuroscience. (Kramer). 2-credit course for intro neurosci students. Topics include: basic spike train analysis, basic computational models of spiking, the Hodgkin-Huxley model of spiking, an introduction to Fourier series, and an introduction to networks. Meets twice a week, with one lecture and one computer lab. -

    -BU MA666: Advanced Modeling and Data Analysis in Neuroscience. (Kramer). 2-credit course for more mathematically advanced neurosci students. Topics include introductions to: correlation and coherence analysis, cross frequency coupling, and bifurcations in model neurons. Meets twice a week, with one lecture and one computer lab. -

    -BU MA 568 Statistical Analysis of Point Process Data. (Eden). Introduces the theory of point processes and develops practical problem-solving skills to construct models, assess goodness-of-fit, and perform estimation from point process data. -

    -HST.576 Topics in Neural Signal Processing (Brown). Focuses on signal processing methods for the analysis of stochastic dynamical systems in neuroscience. Includes state-space methods and dynamic Baysian methods applied to continuous and point process observations. -

    -HST.460 Statistics for Neuroscience Research, (Brown) A survey of statistical methods for neuroscience research. Core topics include introductions to the theory of point processes, the generalized linear model, Monte Carlo methods, Bayesian methods, multivariate methods, time-series analysis, spectral analysis and state-space modeling. This course was developed jointly with Eden and a version is being planned for BU. (Eden) -

    -HST.563 Imaging Biophysics and Applications (S. Stufflebeam, D. Boas). Introduction to the connections and distinctions among various imaging modalities (ultrasound, MRI, EEG, optical), common goals of biomedical imaging, broadly defined target of biomedical imaging, and the current practical and economic landscape of biomedical imaging research. -

    -MIT- MAS.881/20.452/9.422, (Boyden), Principles of Neuroengineering. Tools and methods for analyzing brain dynamics, which was attended by undergraduate and graduate students throughout the CRC network. -

    -MIT- MAS.883/9.455/20.454/15.128/HST.588 (Boyden) Neurotechnology -Ventures. Special seminar on how to get neuroengineering innovations -out into the world. -

    -Tufts Math 150 (Borgers) Mathematical Neuroscience. Introduction to modeling neurons and -neuronal networks using differential equations. Hodgkin-Huxley equations; phase -plane analysis and bifurcation theory applied to neuronal models; reduced -models (integrate-and-fire neurons, theta neurons); modeling chemical and -electrical synapses; synchronization, rhythms, and waves in neuronal networks. -

    +Last update: 9 December 2011 + +## Boston University +### MA665: Introduction to Modeling and Data Analysis in Neuroscience. (Kramer). +2-credit course for intro neurosci students. Topics include: basic spike train analysis, basic computational models of spiking, the Hodgkin-Huxley model of spiking, an introduction to Fourier series, and an introduction to networks. Meets twice a week, with one lecture and one computer lab. + +### MA666: Advanced Modeling and Data Analysis in Neuroscience. (Kramer). +2-credit course for more mathematically advanced neurosci students. Topics include introductions to: correlation and coherence analysis, cross frequency coupling, and bifurcations in model neurons. Meets twice a week, with one lecture and one computer lab. + +### MA 568 Statistical Analysis of Point Process Data. (Eden). +Introduces the theory of point processes and develops practical problem-solving skills to construct models, assess goodness-of-fit, and perform estimation from point process data. + +## Brown +### HST.576 Topics in Neural Signal Processing. +Focuses on signal processing methods for the analysis of stochastic dynamical systems in neuroscience. Includes state-space methods and dynamic Baysian methods applied to continuous and point process observations. + +### HST.460 Statistics for Neuroscience Research. +A survey of statistical methods for neuroscience research. Core topics include introductions to the theory of point processes, the generalized linear model, Monte Carlo methods, Bayesian methods, multivariate methods, time-series analysis, spectral analysis and state-space modeling. This course was developed jointly with Eden and a version is being planned for BU. (Eden) + +### HST.563 Imaging Biophysics and Applications (S. Stufflebeam, D. Boas). +Introduction to the connections and distinctions among various imaging modalities (ultrasound, MRI, EEG, optical), common goals of biomedical imaging, broadly defined target of biomedical imaging, and the current practical and economic landscape of biomedical imaging research. + +## MIT +### MAS.881/20.452/9.422, (Boyden), Principles of Neuroengineering. +Tools and methods for analyzing brain dynamics, which was attended by undergraduate and graduate students throughout the CRC network. + +### MAS.883/9.455/20.454/15.128/HST.588 (Boyden) Neurotechnology Ventures. +Special seminar on how to get neuroengineering innovations out into the world. + +## Tufts +### Math 150 (Borgers) Mathematical Neuroscience. +Introduction to modeling neurons and neuronal networks using differential equations. Hodgkin-Huxley equations; phase plane analysis and bifurcation theory applied to neuronal models; reduced models (integrate-and-fire neurons, theta neurons); modeling chemical and electrical synapses; synchronization, rhythms, and waves in neuronal networks. diff --git a/people/faculty/index.md b/people/faculty/index.md index 1e6508f..f34dbd2 100644 --- a/people/faculty/index.md +++ b/people/faculty/index.md @@ -2,6 +2,7 @@ layout: subpage title: "People - Faculty" --- + ####Click on a name to view or hide details. Last update: 10 December 2012 ##Director
    @@ -401,98 +402,3 @@ title: "People - Faculty" Taken together, these approaches contribute to the overall research objective: to understand the link from cellular/subcellular mechanisms of plasticity, to neural ensemble representations and interactions, to learning, memory, behavior, and cognition.

    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - diff --git a/people/postdoc/index.md b/people/postdoc/index.md index ae795e5..eaa95bc 100644 --- a/people/postdoc/index.md +++ b/people/postdoc/index.md @@ -2,6 +2,7 @@ layout: subpage title: "People - Postdocs" --- + ####Click on a name to view or hide details. Last update: 1 October 2012
    @@ -206,54 +207,3 @@ title: "People - Postdocs"

    - - - - - - - - - - - diff --git a/positions/index.md b/positions/index.md index 8b8bcb9..fdda8bd 100644 --- a/positions/index.md +++ b/positions/index.md @@ -1,36 +1,31 @@ --- -layout: default +layout: subpage title: "Positions" --- -
    - Positions -
    - -
    -

    Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the Psychiatric Neuroimaging Division of the Psychiatry Department at Massachusetts General Hospital, Charlestown, MA

    -
      -
    • Project: Development of accelerated diffusion and functional MRI scans with real-time motion tracking for children with autism
      • -
    • PI: Dara S. Manoach, Ph.D.
      • - -

      Our team is developing several technical innovations that will significantly reduce the impact of head motion on fMRI and diffusion data. We are seeking a candidate to work with us to improve data analysis by making fMRI and diffusion analysis motion-aware using both the in-image data and the motion tracking data.

      - -

      The Research Fellow will be expected to: -

        -
      1. 1) Assist with setting up the data acquisition to ensure that the protocols are well-designed for the analysis questions;
        2. -
      2. 2) Build motion-aware processing tools that work in concert with existing software packages to improve the analysis of fMRI and DWI data;
        3. -
      3. 3) Assist in the processing, interpretation and analysis of the results of both phantom and human studies; and
        4. -
      4. 4) Apply these methods to address clinical research questions in autism.
        5. -

      - -

      Our ideal candidate has a PhD in Computer Science, Electrical Engineering, or related fields, and has experience in signal processing and numerical methods. Candidates with experience in image processing and time series analysis, or specifically in fMRI and diffusion data analysis will be preferred. This position requires strong programming skills, and the candidate is expected to have experience working in C++, scripting languages (e.g., Python), and rapid-prototyping languages for numerical algorithms (e.g., Matlab, Mathematica). Strong communication skills are essential, as the position involves working with an interdisciplinary team of scientists in both MRI physics/engineering and psychology/neuroscience in addition to research coordinators and MRI technologists. Background in cognitive neuroscience and an interest in clinical applications are advantageous. Training in clinical research will be provided.

      - -

      Position available immediately. Please send -

    + +### Postdoctoral Fellowship at the Martinos Center for Biomedical Imaging and the Psychiatric Neuroimaging Division of the Psychiatry Department at Massachusetts General Hospital, Charlestown, MA + +Project: Development of accelerated diffusion and functional MRI scans with real-time motion tracking for children with autism +PI: Dara S. Manoach, Ph.D. +[Manoach Lab](http://nmr.mgh.harvard.edu/manoachlab) + +Our team is developing several technical innovations that will significantly reduce the impact of head motion on fMRI and diffusion data. We are seeking a candidate to work with us to improve data analysis by making fMRI and diffusion analysis motion-aware using both the in-image data and the motion tracking data. + +The Research Fellow will be expected to: + +1. Assist with setting up the data acquisition to ensure that the protocols are well-designed for the analysis questions; +2. Build motion-aware processing tools that work in concert with existing software packages to improve the analysis of fMRI and DWI data; +3. Assist in the processing, interpretation and analysis of the results of both phantom and human studies; and +4. Apply these methods to address clinical research questions in autism. + +Our ideal candidate has a PhD in Computer Science, Electrical Engineering, or related fields, and has experience in signal processing and numerical methods. Candidates with experience in image processing and time series analysis, or specifically in fMRI and diffusion data analysis will be preferred. This position requires strong programming skills, and the candidate is expected to have experience working in C++, scripting languages (e.g., Python), and rapid-prototyping languages for numerical algorithms (e.g., Matlab, Mathematica). Strong communication skills are essential, as the position involves working with an interdisciplinary team of scientists in both MRI physics/engineering and psychology/neuroscience in addition to research coordinators and MRI technologists. Background in cognitive neuroscience and an interest in clinical applications are advantageous. Training in clinical research will be provided. + +Position available immediately. Please send: + +* CV +* statement of post-doctoral and career goals +* writing sample (e.g., a published manuscript) +* letters and/or contact information for three references + +to Dara Manoach at *dara at nmr.mgh.harvard.edu*. diff --git a/research/papers/index.md b/research/papers/index.md index 3da0e0f..f7671d4 100644 --- a/research/papers/index.md +++ b/research/papers/index.md @@ -1,8 +1,8 @@ --- -layout: default +layout: subpage title: "Research - Papers" --- -
    Research: Papers
    +

    Last updated: 1 October 2012

    Published

    2012

    @@ -461,7 +461,4 @@ Talei Franzesi, G., Borgers, C., Qian, X., Li, M., Han, X., Kopell, N. J., Le Be Vaina LM, Rana K, and Hämäläinen M (2011) "Cortical dynamics of perception and decision in sensory tasks: an MEG study", HBM 2011 abstract, to be published in NeuroImage:" - ---> - diff --git a/research/topics/index.md b/research/topics/index.md index 0dc424f..79f8d5b 100644 --- a/research/topics/index.md +++ b/research/topics/index.md @@ -1,8 +1,8 @@ --- -layout: default +layout: subpage title: "Research - Topics" --- -
    Research: Topics
    +

    Researchers are listed below each major research area

    Last update: 1 October 2012

    From 1876fca212b88233ebff41885bc9fa67faff84fc Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 22:59:49 -0400 Subject: [PATCH 29/59] fix whitespace on footer --- _includes/footer.html | 33 +++++++++++++++------------------ 1 file changed, 15 insertions(+), 18 deletions(-) diff --git a/_includes/footer.html b/_includes/footer.html index acb4307..cfe6cea 100644 --- a/_includes/footer.html +++ b/_includes/footer.html @@ -1,22 +1,19 @@ - \ No newline at end of file From 9b9775a432ee96c0948346230470bdfc3fcec696 Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sat, 3 May 2014 23:00:52 -0400 Subject: [PATCH 30/59] ruthlessly cut CSS. Still need to sort out cohesive page structure styling.g --- css/crc.css | 282 ++++++++++++++++------------------------------------ 1 file changed, 84 insertions(+), 198 deletions(-) diff --git a/css/crc.css b/css/crc.css index 2d687bd..eb7e9d8 100644 --- a/css/crc.css +++ b/css/crc.css @@ -1,223 +1,109 @@ body { - font-family: arial, sans-serif; color: #494949; font-size: 13px; background-color: #fff; - } - -a:link, a:hover, a:active, a:visited { - color: #ca0001; - } + font-family: arial, sans-serif; + color: #494949; + font-size: 13px; + background-color: #fff; +} + +/* Page structure */ #head, #foot { - position: relative; - top: 0; - left: 0; - width: 100%; - height: 164px; - text-align: center; - /* [disabled]background: #a72e11 url('../images/top-gradient.gif') top left repeat-x; */ - } - -#head img { - width: 943px; - height: 104px; - margin: 30px auto; - } - -#content { - position: relative; top: 0; left: 0; width: 943px; height: auto; margin: 0px auto; overflow: hidden; - } + text-align: center; /*this appears to center the header image*/ + padding: 30px auto; +} + +#content {/*ugh. Where is a good cross-browser basic layout? I don't want to troubleshoot all these pieces.*/ + position: relative; + top: 0; + left: 0; + width: 943px; + height: auto; + margin: 0px auto; + overflow: hidden; +} #foot { - height: 120px; - margin: 100px 0px 0px 0px; - background-color: #ddd; - background-image: url(../images/bottom-gradient.gif); - border-top: 1px solid #a3a3a3; - text-align: center; - width: 100%; - background-repeat: repeat-x; - background-position: left top; - position: relative; - } + height: 120px; + margin: 100px 0px 0px 0px; + background-color: #ddd; + background-image: url(../images/bottom-gradient.gif); + border-top: 1px solid #a3a3a3; + text-align: center; + width: 100%; + background-repeat: repeat-x; + background-position: left top; + position: relative; +} #footer-content { - position: relative; top: 0; left: 0; width: 943px; height: auto; margin: 0px auto; - } + position: relative; + top: 0; + left: 0; + width: 943px; + height: auto; + margin: 0px auto; +} #footer-content img { - float: left; - margin: 16px 0px 0px 32px; - } + float: left; + margin: 16px 0px 0px 32px; +} #footer-content p { - float: left; - width: 300px; - height: auto; - margin: 16px 0px 0px 32px; - font-size: 11px; - line-height: 1.25em; - } - -#banner_img { - position: relative; top: 0; left: 0; width: 943px; height: 141px; margin: 25px auto; - } + float: left; + width: 300px; + height: auto; + margin: 16px 0px 0px 32px; + font-size: 11px; + line-height: 1.25em; +} #left-col { - float: left; - top: 0; - left: 0; - width: 8em; - height: auto; - margin: 0px 0px 0px 0px; -} -#crc_menu { - margin: 0px 0px 0px 26px; -} - -#fat-col, #slim-col { - float: left; top: 0; left: 0; width: 500px; height: auto; margin: 0px 0px 0px 42px; - } - -#one-col { - float: left; top: 0; left: 0; width: 720px; height: auto; margin: 0px 0px 0px 42px; font-size: 14px; - } - -#right-col { - float: left; top: 0; left: 0; width: 200px; height: auto; min-height: 20px; margin: 0px 0px 0px 30px; + float: left; + top: 0; + left: 0; + width: 8em; + height: auto; + margin: 0px 0px 0px 0px; } -#img.map { - float: left; top: 0; left: 0; width: 386px; height: auto; min-height: 20px; margin: 0px 0px 0px 25px; -} - -p.home { - font-size: 14px; line-height: 1.8em; - } - -#right-col img { - float: left; width: 200px; -} - -#slim-col { - width: 320px; -} - -#slim-col p, .lab { - margin: 0px 0px 15px 0px; font-size: 12px; line-height: 1.6em; +#one-col { + float: left; top: 0; left: 0; width: 720px; height: auto; margin: 0px 0px 0px 42px; font-size: 14px; } - -img.map { - width: 386px; + +/* Text Styling*/ + +a:link, a:hover, a:active, a:visited { + color: #ca0001; } - + h1 { - margin: 10px 0px 15px 0px; - padding: 0px 0px 5px 0px; - font-size: 20px; - color: #ca0001; - border-bottom: 2px solid #BBB; + margin: 10px 0px 15px 0px; + padding: 0px 0px 5px 0px; + font-size: 20px; + color: #ca0001; + border-bottom: 2px solid #BBB; } -#title { - margin: 0px 0px 15px 0px; - font-size: 24px; - color: #ca0001; - font-weight: bold; -} - h2 { - margin: 0px 0px 4px 0px; font-size: 14px; font-weight: bold; - } - + margin: 0px 0px 4px 0px; font-size: 14px; font-weight: bold; +} + h3 { - font-size: 15px; font-weight: bold; - } - + font-size: 15px; font-weight: bold; +} + h4 { - font-size: 11px; font-weight: normal; font-style: italic; color: #ca0001; - } - + font-size: 11px; font-weight: normal; font-style: italic; color: #ca0001; +} + h5 { - font-size: 13px; font-weight: bold; margin: 25px 0px 15px 0px; - } - + font-size: 13px; font-weight: bold; margin: 25px 0px 15px 0px; +} + .hr { - position: relative; top: 0; left: 0; width: 100%; height: 1px; margin: 0px 0px 15px 0px; background-color: #dadada; - } - -#one-col p, #fat-col p { - line-height: 18px; margin: 0px 0px 14px 0px; -} -.name { - margin: 0px 0px 4px 0px; - font-size: 15px; - font-weight: bold; -} -.inst { - font-size: 11px; - font-weight: normal; - font-style: italic; - color: #ca0001; -} - -.lab { - display: block; position: relative; top: 0; left: 0; font-size: 14px; margin: 0px 0px 25px 0px; - } - -.title { - display: block; margin: 0px 0px 3px 0px; font-size: 14px; font-weight: bold; color: #494949; line-height: 1.6em - } - -.linkred { - display: block; margin: 0px 0px 3px 0px; font-size: 14px; font-weight: bold; text-decoration: underline; color: #cc0200; - } -.room { - font-size: 14px; font-weight: bold; line-height: 1.3em -} - -table.members { - width: 700px; height: auto; font-size: 13px; -} - -table.members th { - padding: 5px 0px 2px 0px; color: #b5b5b5; font-weight: bold; text-transform: uppercase; -} - -table.members tr.table-head { - border-bottom: 1px solid #b5b5b5; -} - -table.members td { - padding: 8px 10px 8px 0px; -} - -table.members td.name { - width: 110px; -} - -table.members td.department { - width: 250px; -} - -table.members td.phone { - width: 100px; -} - -table.members td.email { - width: 100px; -} - -ul.address { - margin: 0px 0px 14px 14px; - } - -ul.address li { - height: 14px; font-weight: bold; - } - -ul.bullets { - list-style-type: disc; - } - -ul.bullets li { - margin: 0px 0px 5px 14px; line-height: 18px; - } + width: 100%; + height: 2px; + margin: 10px 0px 10px 0px; + background-color: #BBB; +} From d2caa6f56fad7ec5451a0a719d79413a6bd22dca Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sun, 4 May 2014 17:51:18 -0400 Subject: [PATCH 31/59] move all page structure html into default template (not includes), includes are 'content' html markup only. Restructure default page html. --- _includes/footer.html | 34 ++++++++++++++----------------- _includes/header.html | 5 ++--- _includes/side_nav.html | 44 ++++++++++++++++++++--------------------- _layouts/default.html | 37 +++++++++++++++++----------------- 4 files changed, 57 insertions(+), 63 deletions(-) diff --git a/_includes/footer.html b/_includes/footer.html index cfe6cea..e62268d 100644 --- a/_includes/footer.html +++ b/_includes/footer.html @@ -1,19 +1,15 @@ - +Boston University +MIT +Harvard University +Mass General Hospital +Martinos Imaging Center +National Science Foundation +McGovern Institute +

    + Cognitive Rhythms Collaborative
    + 111 Cummington Street
    + Boston, MA 02215
    +
    + Phone: 617-353-4587
    + Fax: 617-353-4889 +

    diff --git a/_includes/header.html b/_includes/header.html index c61bcc5..e416112 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -1,5 +1,4 @@ - + diff --git a/_includes/side_nav.html b/_includes/side_nav.html index ea196b9..906e524 100644 --- a/_includes/side_nav.html +++ b/_includes/side_nav.html @@ -1,23 +1,21 @@ - \ No newline at end of file + diff --git a/_layouts/default.html b/_layouts/default.html index 02e37cc..bb0a9fb 100644 --- a/_layouts/default.html +++ b/_layouts/default.html @@ -1,23 +1,24 @@ - -{% include head.html %} - - - -{% include header.html %} - -
    - -{% include side_nav.html %} - -
    - {{ content }} + {% include head.html %} + + +
    + +
    + +
    + {{ content }} +
    +
    + +
    -
    - -{% include footer.html %} - - + From 276b8c17df03c78db0c7f624ee0df4fb78666eab Mon Sep 17 00:00:00 2001 From: Kelly Buchanan Date: Sun, 4 May 2014 18:03:45 -0400 Subject: [PATCH 32/59] apply basic page structure CSS, including media queries. --- _layouts/default.html | 6 +- css/crc.css | 128 ++++++++++++++++++++++++------------------ 2 files changed, 75 insertions(+), 59 deletions(-) diff --git a/_layouts/default.html b/_layouts/default.html index bb0a9fb..f9855d4 100644 --- a/_layouts/default.html +++ b/_layouts/default.html @@ -4,10 +4,9 @@
    - - diff --git a/css/crc.css b/css/crc.css index eb7e9d8..7898184 100644 --- a/css/crc.css +++ b/css/crc.css @@ -1,76 +1,94 @@ -body { - font-family: arial, sans-serif; - color: #494949; - font-size: 13px; - background-color: #fff; +/* Page structure */ +#container { + padding: 5px; + width: 960px; + margin: 20px auto; +} +#header { + height: 180px; +} +#sidebar { + width: 300px; + float: left; +} +#content { + width: 600px; + float: right; +} +#footer { + clear: both; } -/* Page structure */ +/************************************* +Media queries for various screen sizes +**************************************/ +/* for 980px or less */ +@media screen and (max-width: 980px) { + + #container { + width: 94%; + } + #content { + width: 65%; + } + #sidebar { + width: 30%; + } + +} + +/* for 700px or less */ +@media screen and (max-width: 700px) { + + #content { + width: auto; + float: none; + } + #sidebar { + width: auto; + float: none; + } + +} + +/* for 480px or less */ +@media screen and (max-width: 480px) { + + #header { + height: auto; + } + h1 { + font-size: 24px; + } + #sidebar { + display: none; + } -#head, #foot { - text-align: center; /*this appears to center the header image*/ - padding: 30px auto; } -#content {/*ugh. Where is a good cross-browser basic layout? I don't want to troubleshoot all these pieces.*/ - position: relative; - top: 0; - left: 0; - width: 943px; - height: auto; - margin: 0px auto; - overflow: hidden; +/************************* +Styling main page elements +**************************/ +body { + font-family: arial, sans-serif; + color: #494949; + font-size: 13px; + background-color: #fff; } -#foot { - height: 120px; - margin: 100px 0px 0px 0px; +#footer { background-color: #ddd; background-image: url(../images/bottom-gradient.gif); border-top: 1px solid #a3a3a3; - text-align: center; - width: 100%; background-repeat: repeat-x; background-position: left top; - position: relative; } -#footer-content { - position: relative; - top: 0; - left: 0; - width: 943px; - height: auto; - margin: 0px auto; -} - -#footer-content img { +#footer img { float: left; margin: 16px 0px 0px 32px; } -#footer-content p { - float: left; - width: 300px; - height: auto; - margin: 16px 0px 0px 32px; - font-size: 11px; - line-height: 1.25em; -} - -#left-col { - float: left; - top: 0; - left: 0; - width: 8em; - height: auto; - margin: 0px 0px 0px 0px; -} - -#one-col { - float: left; top: 0; left: 0; width: 720px; height: auto; margin: 0px 0px 0px 42px; font-size: 14px; -} - /* Text Styling*/ a:link, a:hover, a:active, a:visited { From 0e4c594cfa010d0ac7be0ba01f140d7f0df54614 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Sun, 4 May 2014 22:06:07 -0400 Subject: [PATCH 33/59] removing unused CSS files --- css/cog.css | 128 ---------------------------- css/crc_accordion.css | 118 -------------------------- css/crc_menu.css | 149 --------------------------------- css/ie6.css | 7 -- css/layout.css | 188 ------------------------------------------ css/navigation.css | 23 ------ css/reset.css | 30 ------- 7 files changed, 643 deletions(-) delete mode 100644 css/cog.css delete mode 100644 css/crc_accordion.css delete mode 100644 css/crc_menu.css delete mode 100644 css/ie6.css delete mode 100644 css/layout.css delete mode 100644 css/navigation.css delete mode 100644 css/reset.css diff --git a/css/cog.css b/css/cog.css deleted file mode 100644 index dd429e0..0000000 --- a/css/cog.css +++ /dev/null @@ -1,128 +0,0 @@ -html, body { - position: relative; - margin-left: 10px; - padding: 0; - height: auto; -} - -img { - border-style: none; -} - -a:link, a:hover, a:active { - color: #ca0001; - text-decoration: none; -} - -a:visited { - color: #990000; - text-decoration: none; -} - -#header { - position: relative; - width: 650px; - height: 100px; - padding-bottom: 5px; - margin-top: 5px; - margin-bottom: 10px; - border-bottom: thin solid #8C8C8C; -} - -#footer { - width: 650px; - height: 120px; - margin-bottom: 10px; - padding-top: 5px; - border-top: thin solid #8C8C8C; -} - -h1 { - font-family: "Lucida Grande", Helvetica, Arial, sans-serif; - font-size: 24px; - color: #ca0001; - text-align: left; - line-height: 18px; - padding-top: 45px; - margin-bottom: 0px; -} - -h2 { - font-family: "Lucida Grande", Helvetica, Arial, sans-serif; - font-size: 18px; - color: #ca0001; - text-align: left; - font-variant: small-caps; - margin-top: 5px; -} - -#content-wrap { - width: 650px; -} - -.subtitle { - font-family: "Lucida Grande", Helvetica, Arial, sans-serif; - font-size: 16px; - text-align: left; - line-height: 18px; - font-weight: bold; - border-bottom: thin solid #8C8C8C; - margin-bottom: 5px; - padding-bottom: 2px; - color: #ca0001; -} - -.info { - font-family: "Lucida Grande", Helvetica, Arial, sans-serif; - font-size: 14px; - text-align: left; - line-height: 20px; - margin-bottom: 30px; -} - -table.members { - width: 650px; - height: auto; - font-size: 13px; -} - -table.members tr.even { - background-color: #ebebeb; -} - -table.members tr.odd { - background-color: #ffffff; -} - -table.members th { - padding: 10px 2px 5px 0px; - font-size: 13px; - color: #696565; - font-weight: bold; - text-align: left; -} - -table.members th.job-title { - font-family: "Lucida Grande", Helvetica, Arial, sans-serif; - font-size: 14px; - font-variant: small-caps; - text-align: left; - color: #000000; -} - -table.members td { - padding: 5px 2px 5px 0px; -} - -table.members td.name { - width: 300px; - padding: 0px 0px 0px 5px; -} - -table.members td.phone { - width: 150px; -} - -table.members td.email { - width: 200px; -} diff --git a/css/crc_accordion.css b/css/crc_accordion.css deleted file mode 100644 index f9f9d94..0000000 --- a/css/crc_accordion.css +++ /dev/null @@ -1,118 +0,0 @@ -@charset "UTF-8"; - -/* SpryAccordion.css - version 0.5 - Spry Pre-Release 1.6.1 */ - -/* Copyright (c) 2006. Adobe Systems Incorporated. All rights reserved. */ - -/* This is the selector for the main Accordion container. For our default style, - * we draw borders on the left, right, and bottom. The top border of the Accordion - * will be rendered by the first AccordionPanelTab which never moves. - * - * If you want to constrain the width of the Accordion widget, set a width on - * the Accordion container. By default, our accordion expands horizontally to fill - * up available space. - * - * The name of the class ("Accordion") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style the - * Accordion container. - */ -.Accordion { - border-bottom: solid 1px black; - overflow: hidden; - margin-bottom: 20px; -} -.AccordionHeader { - margin: 0px; - padding: 0px; -} -.AccordionHeaderTab { - margin: 0px 0px 10px 0px; - font-size: 18px; - color: #ca0001; -} - -/* This is the selector for the AccordionPanel container which houses the - * panel tab and a panel content area. It doesn't render visually, but we - * make sure that it has zero margin and padding. - * - * The name of the class ("AccordionPanel") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style an - * accordion panel container. -*/ -.AccordionPanel { - border-left: solid 1px gray; - border-right: solid 1px black; - margin: 0px; - padding: 0px; -} - -/* This is the selector for the AccordionPanelTab. This container houses - * the title for the panel. This is also the container that the user clicks - * on to open a specific panel. - * - * The name of the class ("AccordionPanelTab") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style an - * accordion panel tab container. - * - * NOTE: - * This rule uses -moz-user-select and -khtml-user-select properties to prevent the - * user from selecting the text in the AccordionPanelTab. These are proprietary browser - * properties that only work in Mozilla based browsers (like FireFox) and KHTML based - * browsers (like Safari), so they will not pass W3C validation. If you want your documents to - * validate, and don't care if the user can select the text within an AccordionPanelTab, - * you can safely remove those properties without affecting the functionality of the widget. - */ -.AccordionPanelTab { - background-color: #CCCCCC; - border-top: solid 1px black; - border-bottom: solid 1px gray; - margin: 0px; - padding: 2px; - cursor: pointer; - -moz-user-select: none; - -khtml-user-select: none; -} - -/* This is the selector for a Panel's Content area. It's important to note that - * you should never put any padding on the panel's content area if you plan to - * use the Accordions panel animations. Placing a non-zero padding on the content - * area can cause the accordion to abruptly grow in height while the panels animate. - * - * Anyone who styles an Accordion *MUST* specify a height on the Accordion Panel - * Content container. - * - * The name of the class ("AccordionPanelContent") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style an - * accordion panel content container. - */ -.AccordionPanelContent { - overflow: auto; - margin: 0px; - padding: 0px; - /* [disabled]height: 200px; */ -} - -/* This is an example of how to change the appearance of the panel tab that is - * currently open. The class "AccordionPanelOpen" is programatically added and removed - * from panels as the user clicks on the tabs within the Accordion. - */ -.AccordionPanelOpen .AccordionPanelTab { - background-color: #EEEEEE; -} -.AccordionPanelOpen .AccordionPanelTabHover { - color: #555555; -} -/* Rules for Printing */ - -@media print { - - .Accordion { - overflow: visible !important; - } - - .AccordionPanelContent { - display: block !important; - overflow: visible !important; - height: auto !important; - } -} diff --git a/css/crc_menu.css b/css/crc_menu.css deleted file mode 100644 index 039098d..0000000 --- a/css/crc_menu.css +++ /dev/null @@ -1,149 +0,0 @@ -@charset "UTF-8"; - -/* SpryMenuBarVertical.css - version 0.6 - Spry Pre-Release 1.6.1 */ - -/* Copyright (c) 2006. Adobe Systems Incorporated. All rights reserved. */ - -/******************************************************************************* - - LAYOUT INFORMATION: describes box model, positioning, z-order - - *******************************************************************************/ - -/* The outermost container of the Menu Bar, a fixed width box with no margin or padding */ -ul.MenuBarVertical -{ - margin: 0px 0px 0px 26px; - padding: 0; - list-style-type: none; - font-size: 100%; - cursor: default; - width: 8em; - font-weight: bold; -} -/* Set the active Menu Bar with this class, currently setting z-index to accomodate IE rendering bug: http://therealcrisp.xs4all.nl/meuk/IE-zindexbug.html */ -ul.MenuBarActive -{ - z-index: 1000; -} -/* Menu item containers, position children relative to this container and are same fixed width as parent */ -ul.MenuBarVertical li -{ - margin: 0; - padding: 0; - list-style-type: none; - font-size: 100%; - position: relative; - text-align: left; - cursor: pointer; - width: 8em; -} -/* Submenus should appear slightly overlapping to the right (95%) and up (-5%) with a higher z-index, but they are initially off the left side of the screen (-1000em) */ -ul.MenuBarVertical ul -{ - margin: -5% 0 0 95%; - padding: 0; - list-style-type: none; - font-size: 100%; - position: absolute; - z-index: 1020; - cursor: default; - width: 8.2em; - left: -1000em; - top: 0; -} -/* Submenu that is showing with class designation MenuBarSubmenuVisible, we set left to 0 so it comes onto the screen */ -ul.MenuBarVertical ul.MenuBarSubmenuVisible -{ - left: 0; -} -/* Menu item containers are same fixed width as parent */ -ul.MenuBarVertical ul li -{ - width: 8.2em; -} - -/******************************************************************************* - - DESIGN INFORMATION: describes color scheme, borders, fonts - - *******************************************************************************/ - -/* Outermost menu container has borders on all sides */ -ul.MenuBarVertical -{ - border: 1px solid #CCC; -} -/* Submenu containers have borders on all sides */ -ul.MenuBarVertical ul -{ - border: 1px solid #CCC; -} -/* Menu items are a light gray block with padding and no text decoration */ -ul.MenuBarVertical a -{ - display: block; - cursor: pointer; - background-color: #EEE; - padding: 0.5em 0.75em; - color: #333; - text-decoration: none; -} -/* Menu items that have mouse over or focus have a blue background and white text */ -ul.MenuBarVertical a:hover, ul.MenuBarVertical a:focus -{ - background-color: #CCC; - /* [disabled]color: #FFF; */ -} -/* Menu items that are open with submenus are set to MenuBarItemHover with a blue background and white text */ -ul.MenuBarVertical a.MenuBarItemHover, ul.MenuBarVertical a.MenuBarItemSubmenuHover, ul.MenuBarVertical a.MenuBarSubmenuVisible -{ - background-color: #CCC; - /* [disabled]color: #FFF; */ -} - -/******************************************************************************* - - SUBMENU INDICATION: styles if there is a submenu under a given menu item - - *******************************************************************************/ - -/* Menu items that have a submenu have the class designation MenuBarItemSubmenu and are set to use a background image positioned on the far left (95%) and centered vertically (50%) */ -ul.MenuBarVertical a.MenuBarItemSubmenu -{ - background-image: url(../SpryAssets/SpryMenuBarRight.gif); - background-repeat: no-repeat; - background-position: 95% 50%; -} - -/* Menu items that are open with submenus have the class designation MenuBarItemSubmenuHover and are set to use a "hover" background image positioned on the far left (95%) and centered vertically (50%) */ -ul.MenuBarVertical a.MenuBarItemSubmenuHover -{ - background-image: url(../SpryAssets/SpryMenuBarRightHover.gif); - background-repeat: no-repeat; - background-position: 95% 50%; -} - -/******************************************************************************* - - BROWSER HACKS: the hacks below should not be changed unless you are an expert - - *******************************************************************************/ - -/* HACK FOR IE: to make sure the sub menus show above form controls, we underlay each submenu with an iframe */ -ul.MenuBarVertical iframe -{ - position: absolute; - z-index: 1010; - filter:alpha(opacity:0.1); -} -/* HACK FOR IE: to stabilize appearance of menu items; the slash in float is to keep IE 5.0 from parsing */ -@media screen, projection -{ - ul.MenuBarVertical li.MenuBarItemIE - { - display: inline; - f\loat: left; - background: #FFF; - } -} diff --git a/css/ie6.css b/css/ie6.css deleted file mode 100644 index b981e20..0000000 --- a/css/ie6.css +++ /dev/null @@ -1,7 +0,0 @@ -#fat-col, #slim-col, #one-col { - margin: 0px 0px 0px 35px; - } - -#right-col, img.map { - margin: 0px 0px 0px 15px; - } diff --git a/css/layout.css b/css/layout.css deleted file mode 100644 index daf4820..0000000 --- a/css/layout.css +++ /dev/null @@ -1,188 +0,0 @@ -#header { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 22px; - text-align: center; - font-weight: bold; - line-height: 33px; - width: 800px; - margin: 0 0; -} - -.headline { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 28px; - text-align: left; - font-weight: bold; - line-height: 33px; - width: 800px; - margin: 0 0; -} - -#announce { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 20px; - text-align: left; - line-height: 25px; - width: 800px; - margin: 0 0; -} - -#links_main { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 18px; - text-align: center; - font-weight: bold; - width: 800px; - margin: 0 0; - height: 150px; -} - -#links { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 18px; - text-align: center; - font-weight: bold; - width: 800px; - margin: 0 0; -} - -#subtitle { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 18px; - text-align: center; - font-weight: bold; - width: 800px; - margin: 0 0; -} - -#sponsors { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 18px; - text-align: center; - font-weight: bold; - width: 800px; - margin: 0 0; -} - -a img{ - border: 0px; -} - -#content { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 14px; - text-align: left; - width: 800px; - line-height: 18px; - margin: 0 0 0 5px; - height: auto !important; -} - -#sessions { - position: absolute; - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 14px; - text-align: left; - width: 700px; - line-height: 18px; - margin: 0 0 0 5px; - left: 0; - float: left; -} - -#session-time { - font-family: "Lucida Grande", Verdana,Arial,Helvetica,sans-serif; - font-size: 14px; - text-align: left; - width: 100px; - line-height: 18px; - height: 125px; - margin-left: 605px; - margin-top: 0px; - position: relative; -} - -#cheat { - height: 100 px; -} - -.solid-bottom-border-box { - border-style: none none solid none; - border-width: 0px 0px 1px 0px; - border-bottom: 1px solid #aaaaaa; - font-family: verdana,arial,helvetica; - font-size: 10px; - font-weight: bold; - color: #333333; - text-decoration: none; -} - -.general-medium { - font-family: "Lucida Grande",verdana,arial,helvetica; - font-size: 12px; - color: #333333; - text-decoration: none; - font-weight: none; - line-height: 17px; -} - -.general-medium a { - font-family: "Lucida Grande",verdana,arial,helvetica; - font-size: 12px; - color: #222222; - line-height: 17px; -} - -.general-medium a:hover { - color: #555555; - font-size: 12px; -} - -.solid-border-box { - border-top: 1px solid #aaaaaa; - border-bottom: 1px solid #aaaaaa; - border-left: 1px solid #aaaaaa; - border-right: 1px solid #aaaaaa; - padding: 5px 5px 5px 5px; -} - -.general-small { - font-family: "Lucida Grande",verdana,arial,helvetica; - font-size: 9px; - color: #333333; - text-decoration: none; -} - -.general-small a { - font-family: "Lucida Grande",verdana,arial,helvetica; - font-size: 9px; - color: #222222; -} - -.general-small a:hover { - color: #000000; - font-weight: bold; - font-size: 9px; -} - -.general-large-bold { - font-family: "Lucida Grande",verdana,arial,helvetica; - font-size: 18px; - color: #333333; - text-decoration: none; - font-weight: bold; -} - -.general-large-bold a { - font-family: "Lucida Grande",verdana,arial,helvetica; - font-size: 18px; - color: #222222; - font-weight: bold; -} - -.general-large-bold a:hover { - color: #555555; - font-size: 18px; - font-weight: bold; -} - diff --git a/css/navigation.css b/css/navigation.css deleted file mode 100644 index ba4afd8..0000000 --- a/css/navigation.css +++ /dev/null @@ -1,23 +0,0 @@ -#left-col { - float: left; top: 0; left: 0; width: auto; height: auto; - } - -ul#nav { - display: block; width: 140px; margin: 0px 0px 0px 26px; padding: 0px; list-style-type: none; font-size: 11px; - } - -ul#nav li { - margin: 0px; - } - -ul#nav a:link, ul#nav a:hover, ul#nav a:active, ul#nav a:visited { - display: block; width: 100%; height: 24px; padding-left: 13px; text-decoration: none; color: #494949; font-weight: bold; background-color: #dadada; border-top: 1px solid #fff; line-height: 24px; - } - -ul#nav a:hover, ul#nav li a.active { - background-color: #c2ddf2; color: #11538d; - } - -ul#nav li a.research { - background-color: #c2ddf2; border-color: #c2ddf2; height: 20px; line-height: 20px; - } \ No newline at end of file diff --git a/css/reset.css b/css/reset.css deleted file mode 100644 index 31c09db..0000000 --- a/css/reset.css +++ /dev/null @@ -1,30 +0,0 @@ -html,body,div,span, -applet,object,iframe, -h1,h2,h3,h4,h5,h6,p,blockquote,pre, -a,abbr,acronym,address,big,cite,code, -del,dfn,em,font,img,ins,kbd,q,s,samp, -small,strike,strong,sub,sup,tt,var, -dd,dl,dt,li,ol,ul, -fieldset,form,label,legend, -table,caption,tbody,tfoot,thead,tr,th,td { - margin: 0; - padding: 0; - border: 0; - font-weight: normal; - font-style: normal; - font-size: 100%; - line-height: 1; - font-family: inherit; - text-align: left; -} -table { - border-collapse: collapse; - border-spacing: 0; -} -ol,ul { - list-style: none; -} -q:before,q:after, -blockquote:before,blockquote:after { - content: ""; -} From e6395fab71faeca8c6e3dec7cc883da21ce7be42 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Sun, 4 May 2014 22:07:06 -0400 Subject: [PATCH 34/59] fix dimensions of main page elements --- css/crc.css | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/css/crc.css b/css/crc.css index 7898184..5f27027 100644 --- a/css/crc.css +++ b/css/crc.css @@ -5,14 +5,14 @@ margin: 20px auto; } #header { - height: 180px; + height: 130px; } #sidebar { - width: 300px; + width: 150px; float: left; } #content { - width: 600px; + width: 780px; float: right; } #footer { From 2a2eb26fdbf91a7d10aa1a6229f7b38efc282946 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Sun, 4 May 2014 22:22:27 -0400 Subject: [PATCH 35/59] styling footer --- _includes/footer.html | 18 ++++++++++-------- css/crc.css | 3 ++- 2 files changed, 12 insertions(+), 9 deletions(-) diff --git a/_includes/footer.html b/_includes/footer.html index e62268d..494658f 100644 --- a/_includes/footer.html +++ b/_includes/footer.html @@ -5,11 +5,13 @@ Martinos Imaging Center National Science Foundation McGovern Institute -

    - Cognitive Rhythms Collaborative
    - 111 Cummington Street
    - Boston, MA 02215
    -
    - Phone: 617-353-4587
    - Fax: 617-353-4889 -

    +
    +

    + Cognitive Rhythms Collaborative
    + 111 Cummington Street
    + Boston, MA 02215
    +
    + Phone: 617-353-4587
    + Fax: 617-353-4889 +

    +
    diff --git a/css/crc.css b/css/crc.css index 5f27027..12252d9 100644 --- a/css/crc.css +++ b/css/crc.css @@ -82,9 +82,10 @@ body { border-top: 1px solid #a3a3a3; background-repeat: repeat-x; background-position: left top; + padding: 10px 0px 10px 0px; } -#footer img { +#footer img, #footer div { float: left; margin: 16px 0px 0px 32px; } From 1aa5703a8e3615296205bbabc4a9c084d2aeed14 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Sun, 4 May 2014 22:29:58 -0400 Subject: [PATCH 36/59] fix footer height issue --- css/crc.css | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/css/crc.css b/css/crc.css index 12252d9..35db00b 100644 --- a/css/crc.css +++ b/css/crc.css @@ -16,6 +16,7 @@ float: right; } #footer { + height: 150px; /*uncertain of implications this has on media queries, need it because the footer no longer has any content that gives it height*/ clear: both; } @@ -77,7 +78,7 @@ body { } #footer { - background-color: #ddd; + background-color: #fff; background-image: url(../images/bottom-gradient.gif); border-top: 1px solid #a3a3a3; background-repeat: repeat-x; From b77f68bc8782585f8177ee1fcd89fb7ce74586bc Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Mon, 5 May 2014 13:08:36 -0400 Subject: [PATCH 37/59] remove margin and padding from html and body tags --- css/crc.css | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/css/crc.css b/css/crc.css index 35db00b..f9b9513 100644 --- a/css/crc.css +++ b/css/crc.css @@ -1,4 +1,8 @@ /* Page structure */ +html, body { + padding: 0px: + margin: 0px; +} #container { padding: 5px; width: 960px; From 55a63632f0d66b39f22590383c036d79232b2b4a Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Mon, 5 May 2014 13:20:49 -0400 Subject: [PATCH 38/59] let footer images be inline, center all inline elements, fix padding --- _layouts/default.html | 12 ++++++------ css/crc.css | 9 +++++---- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/_layouts/default.html b/_layouts/default.html index f9855d4..b866b5b 100644 --- a/_layouts/default.html +++ b/_layouts/default.html @@ -7,16 +7,16 @@ - -
    - {{ content }} -
    + +
    + {{ content }}
    +
    diff --git a/css/crc.css b/css/crc.css index f9b9513..cbf10df 100644 --- a/css/crc.css +++ b/css/crc.css @@ -87,12 +87,13 @@ body { border-top: 1px solid #a3a3a3; background-repeat: repeat-x; background-position: left top; - padding: 10px 0px 10px 0px; + padding: 20px 0px 20px 0px; + } -#footer img, #footer div { - float: left; - margin: 16px 0px 0px 32px; +#footer img { + margin-left: 16px; + margin-right: 16px; } /* Text Styling*/ From 371aa289294dd1152fca4c130e7a24e23a2af6e8 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Mon, 5 May 2014 13:22:26 -0400 Subject: [PATCH 39/59] fix syntax error --- css/crc.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/css/crc.css b/css/crc.css index cbf10df..d2223d8 100644 --- a/css/crc.css +++ b/css/crc.css @@ -1,6 +1,6 @@ /* Page structure */ html, body { - padding: 0px: + padding: 0px; margin: 0px; } #container { From e7d717c6231fe7678afd8f4fc2bab5f60a0e9b6b Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Mon, 5 May 2014 13:24:55 -0400 Subject: [PATCH 40/59] center inline elements in footer for serious --- css/crc.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/css/crc.css b/css/crc.css index d2223d8..180e449 100644 --- a/css/crc.css +++ b/css/crc.css @@ -88,7 +88,7 @@ body { background-repeat: repeat-x; background-position: left top; padding: 20px 0px 20px 0px; - + text-align: center; } #footer img { From efd2b5464ad85fc3452f2a5327cc28c1a64d2cf4 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Mon, 5 May 2014 13:27:19 -0400 Subject: [PATCH 41/59] pad bottom of content well --- css/crc.css | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/css/crc.css b/css/crc.css index 180e449..0bb5178 100644 --- a/css/crc.css +++ b/css/crc.css @@ -81,6 +81,10 @@ body { background-color: #fff; } +#content, #sidebar { + padding-bottom: 20px; +} + #footer { background-color: #fff; background-image: url(../images/bottom-gradient.gif); From 3125a8aa3b5132f4d5902424132df23c0bc2e0a8 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Fri, 9 May 2014 18:24:01 -0400 Subject: [PATCH 42/59] move footer out of container so it spans full page width --- _layouts/default.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_layouts/default.html b/_layouts/default.html index b866b5b..6b96239 100644 --- a/_layouts/default.html +++ b/_layouts/default.html @@ -13,9 +13,9 @@
    {{ content }}
    - +
    + From d2d6c07f06cc2fc6a2c183e2b3f2d821c07feef5 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Fri, 9 May 2014 18:27:38 -0400 Subject: [PATCH 43/59] increase padding above footer --- css/crc.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/css/crc.css b/css/crc.css index 0bb5178..b70730f 100644 --- a/css/crc.css +++ b/css/crc.css @@ -82,7 +82,7 @@ body { } #content, #sidebar { - padding-bottom: 20px; + padding-bottom: 50px; } #footer { From 81f92c22c66fd4b0e6f2857efc6a02e0b4c437eb Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Fri, 3 Oct 2014 00:47:10 -0400 Subject: [PATCH 44/59] styling sidebar. Noticed it disappears in small window size. --- css/crc.css | 14 ++++++++++++++ 1 file changed, 14 insertions(+) diff --git a/css/crc.css b/css/crc.css index b70730f..35cf23a 100644 --- a/css/crc.css +++ b/css/crc.css @@ -85,6 +85,20 @@ body { padding-bottom: 50px; } +#sidebar { + background-color: #efefef; + border: 1px solid #ccc; +} + +#sidebar ul { + list-style-type: none; +} + +#sidebar ul li ul { + list-style-type: disc; + padding-left: 15px; +} + #footer { background-color: #fff; background-image: url(../images/bottom-gradient.gif); From 53804804f90f4e01bc151c7a03a91e799ba104c3 Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Fri, 5 Dec 2014 23:11:56 -0500 Subject: [PATCH 45/59] delete all Spry and js --- SpryAssets/SpryAccordion.css | 131 ----- SpryAssets/SpryAccordion.js | 561 -------------------- SpryAssets/SpryCollapsiblePanel.css | 108 ---- SpryAssets/SpryCollapsiblePanel.js | 535 ------------------- SpryAssets/SpryMenuBar.js | 763 --------------------------- SpryAssets/SpryMenuBarRight.gif | Bin 55 -> 0 bytes SpryAssets/SpryMenuBarRightHover.gif | Bin 55 -> 0 bytes SpryAssets/SpryMenuBarVertical.css | 148 ------ js/controllers.js | 3 - js/crc.js | 45 -- js/pictures.js | 7 - js/poster_session.js | 282 ---------- 12 files changed, 2583 deletions(-) delete mode 100644 SpryAssets/SpryAccordion.css delete mode 100644 SpryAssets/SpryAccordion.js delete mode 100644 SpryAssets/SpryCollapsiblePanel.css delete mode 100644 SpryAssets/SpryCollapsiblePanel.js delete mode 100644 SpryAssets/SpryMenuBar.js delete mode 100644 SpryAssets/SpryMenuBarRight.gif delete mode 100644 SpryAssets/SpryMenuBarRightHover.gif delete mode 100644 SpryAssets/SpryMenuBarVertical.css delete mode 100644 js/controllers.js delete mode 100644 js/crc.js delete mode 100644 js/pictures.js delete mode 100644 js/poster_session.js diff --git a/SpryAssets/SpryAccordion.css b/SpryAssets/SpryAccordion.css deleted file mode 100644 index 604a3c6..0000000 --- a/SpryAssets/SpryAccordion.css +++ /dev/null @@ -1,131 +0,0 @@ -@charset "UTF-8"; - -/* SpryAccordion.css - version 0.5 - Spry Pre-Release 1.6.1 */ - -/* Copyright (c) 2006. Adobe Systems Incorporated. All rights reserved. */ - -/* This is the selector for the main Accordion container. For our default style, - * we draw borders on the left, right, and bottom. The top border of the Accordion - * will be rendered by the first AccordionPanelTab which never moves. - * - * If you want to constrain the width of the Accordion widget, set a width on - * the Accordion container. By default, our accordion expands horizontally to fill - * up available space. - * - * The name of the class ("Accordion") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style the - * Accordion container. - */ -.Accordion { - border-left: solid 1px gray; - border-right: solid 1px black; - border-bottom: solid 1px gray; - overflow: hidden; -} - -/* This is the selector for the AccordionPanel container which houses the - * panel tab and a panel content area. It doesn't render visually, but we - * make sure that it has zero margin and padding. - * - * The name of the class ("AccordionPanel") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style an - * accordion panel container. -*/ -.AccordionPanel { - margin: 0px; - padding: 0px; -} - -/* This is the selector for the AccordionPanelTab. This container houses - * the title for the panel. This is also the container that the user clicks - * on to open a specific panel. - * - * The name of the class ("AccordionPanelTab") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style an - * accordion panel tab container. - * - * NOTE: - * This rule uses -moz-user-select and -khtml-user-select properties to prevent the - * user from selecting the text in the AccordionPanelTab. These are proprietary browser - * properties that only work in Mozilla based browsers (like FireFox) and KHTML based - * browsers (like Safari), so they will not pass W3C validation. If you want your documents to - * validate, and don't care if the user can select the text within an AccordionPanelTab, - * you can safely remove those properties without affecting the functionality of the widget. - */ -.AccordionPanelTab { - background-color: #CCCCCC; - border-top: solid 1px black; - border-bottom: solid 1px gray; - margin: 0px; - padding: 2px; - cursor: pointer; - -moz-user-select: none; - -khtml-user-select: none; -} - -/* This is the selector for a Panel's Content area. It's important to note that - * you should never put any padding on the panel's content area if you plan to - * use the Accordions panel animations. Placing a non-zero padding on the content - * area can cause the accordion to abruptly grow in height while the panels animate. - * - * Anyone who styles an Accordion *MUST* specify a height on the Accordion Panel - * Content container. - * - * The name of the class ("AccordionPanelContent") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style an - * accordion panel content container. - */ -.AccordionPanelContent { - overflow: auto; - margin: 0px; - padding: 0px; - height: 200px; -} - -/* This is an example of how to change the appearance of the panel tab that is - * currently open. The class "AccordionPanelOpen" is programatically added and removed - * from panels as the user clicks on the tabs within the Accordion. - */ -.AccordionPanelOpen .AccordionPanelTab { - background-color: #EEEEEE; -} - -/* This is an example of how to change the appearance of the panel tab as the - * mouse hovers over it. The class "AccordionPanelTabHover" is programatically added - * and removed from panel tab containers as the mouse enters and exits the tab container. - */ -.AccordionPanelTabHover { - color: #555555; -} -.AccordionPanelOpen .AccordionPanelTabHover { - color: #555555; -} - -/* This is an example of how to change the appearance of all the panel tabs when the - * Accordion has focus. The "AccordionFocused" class is programatically added and removed - * whenever the Accordion gains or loses keyboard focus. - */ -.AccordionFocused .AccordionPanelTab { - background-color: #3399FF; -} - -/* This is an example of how to change the appearance of the panel tab that is - * currently open when the Accordion has focus. - */ -.AccordionFocused .AccordionPanelOpen .AccordionPanelTab { - background-color: #33CCFF; -} -/* Rules for Printing */ - -@media print { - - .Accordion { - overflow: visible !important; - } - - .AccordionPanelContent { - display: block !important; - overflow: visible !important; - height: auto !important; - } -} \ No newline at end of file diff --git a/SpryAssets/SpryAccordion.js b/SpryAssets/SpryAccordion.js deleted file mode 100644 index 3fafa99..0000000 --- a/SpryAssets/SpryAccordion.js +++ /dev/null @@ -1,561 +0,0 @@ -// SpryAccordion.js - version 0.17 - Spry Pre-Release 1.6.1 -// -// Copyright (c) 2006. Adobe Systems Incorporated. -// All rights reserved. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are met: -// -// * Redistributions of source code must retain the above copyright notice, -// this list of conditions and the following disclaimer. -// * Redistributions in binary form must reproduce the above copyright notice, -// this list of conditions and the following disclaimer in the documentation -// and/or other materials provided with the distribution. -// * Neither the name of Adobe Systems Incorporated nor the names of its -// contributors may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE -// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR -// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF -// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS -// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN -// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE -// POSSIBILITY OF SUCH DAMAGE. - -(function() { // BeginSpryComponent - -if (typeof Spry == "undefined") window.Spry = {}; if (!Spry.Widget) Spry.Widget = {}; - -Spry.Widget.Accordion = function(element, opts) -{ - this.element = this.getElement(element); - this.defaultPanel = 0; - this.hoverClass = "AccordionPanelTabHover"; - this.openClass = "AccordionPanelOpen"; - this.closedClass = "AccordionPanelClosed"; - this.focusedClass = "AccordionFocused"; - this.enableAnimation = true; - this.enableKeyboardNavigation = true; - this.currentPanel = null; - this.animator = null; - this.hasFocus = null; - - this.previousPanelKeyCode = Spry.Widget.Accordion.KEY_UP; - this.nextPanelKeyCode = Spry.Widget.Accordion.KEY_DOWN; - - this.useFixedPanelHeights = true; - this.fixedPanelHeight = 0; - - Spry.Widget.Accordion.setOptions(this, opts, true); - - if (this.element) - this.attachBehaviors(); -}; - -Spry.Widget.Accordion.prototype.getElement = function(ele) -{ - if (ele && typeof ele == "string") - return document.getElementById(ele); - return ele; -}; - -Spry.Widget.Accordion.prototype.addClassName = function(ele, className) -{ - if (!ele || !className || (ele.className && ele.className.search(new RegExp("\\b" + className + "\\b")) != -1)) - return; - ele.className += (ele.className ? " " : "") + className; -}; - -Spry.Widget.Accordion.prototype.removeClassName = function(ele, className) -{ - if (!ele || !className || (ele.className && ele.className.search(new RegExp("\\b" + className + "\\b")) == -1)) - return; - ele.className = ele.className.replace(new RegExp("\\s*\\b" + className + "\\b", "g"), ""); -}; - -Spry.Widget.Accordion.setOptions = function(obj, optionsObj, ignoreUndefinedProps) -{ - if (!optionsObj) - return; - for (var optionName in optionsObj) - { - if (ignoreUndefinedProps && optionsObj[optionName] == undefined) - continue; - obj[optionName] = optionsObj[optionName]; - } -}; - -Spry.Widget.Accordion.prototype.onPanelTabMouseOver = function(e, panel) -{ - if (panel) - this.addClassName(this.getPanelTab(panel), this.hoverClass); - return false; -}; - -Spry.Widget.Accordion.prototype.onPanelTabMouseOut = function(e, panel) -{ - if (panel) - this.removeClassName(this.getPanelTab(panel), this.hoverClass); - return false; -}; - -Spry.Widget.Accordion.prototype.openPanel = function(elementOrIndex) -{ - var panelA = this.currentPanel; - var panelB; - - if (typeof elementOrIndex == "number") - panelB = this.getPanels()[elementOrIndex]; - else - panelB = this.getElement(elementOrIndex); - - if (!panelB || panelA == panelB) - return null; - - var contentA = panelA ? this.getPanelContent(panelA) : null; - var contentB = this.getPanelContent(panelB); - - if (!contentB) - return null; - - if (this.useFixedPanelHeights && !this.fixedPanelHeight) - this.fixedPanelHeight = (contentA.offsetHeight) ? contentA.offsetHeight : contentA.scrollHeight; - - if (this.enableAnimation) - { - if (this.animator) - this.animator.stop(); - this.animator = new Spry.Widget.Accordion.PanelAnimator(this, panelB, { duration: this.duration, fps: this.fps, transition: this.transition }); - this.animator.start(); - } - else - { - if(contentA) - { - contentA.style.display = "none"; - contentA.style.height = "0px"; - } - contentB.style.display = "block"; - contentB.style.height = this.useFixedPanelHeights ? this.fixedPanelHeight + "px" : "auto"; - } - - if(panelA) - { - this.removeClassName(panelA, this.openClass); - this.addClassName(panelA, this.closedClass); - } - - this.removeClassName(panelB, this.closedClass); - this.addClassName(panelB, this.openClass); - - this.currentPanel = panelB; - - return panelB; -}; - -Spry.Widget.Accordion.prototype.closePanel = function() -{ - // The accordion can only ever have one panel open at any - // give time, so this method only closes the current panel. - // If the accordion is in fixed panel heights mode, this - // method does nothing. - - if (!this.useFixedPanelHeights && this.currentPanel) - { - var panel = this.currentPanel; - var content = this.getPanelContent(panel); - if (content) - { - if (this.enableAnimation) - { - if (this.animator) - this.animator.stop(); - this.animator = new Spry.Widget.Accordion.PanelAnimator(this, null, { duration: this.duration, fps: this.fps, transition: this.transition }); - this.animator.start(); - } - else - { - content.style.display = "none"; - content.style.height = "0px"; - } - } - this.removeClassName(panel, this.openClass); - this.addClassName(panel, this.closedClass); - this.currentPanel = null; - } -}; - -Spry.Widget.Accordion.prototype.openNextPanel = function() -{ - return this.openPanel(this.getCurrentPanelIndex() + 1); -}; - -Spry.Widget.Accordion.prototype.openPreviousPanel = function() -{ - return this.openPanel(this.getCurrentPanelIndex() - 1); -}; - -Spry.Widget.Accordion.prototype.openFirstPanel = function() -{ - return this.openPanel(0); -}; - -Spry.Widget.Accordion.prototype.openLastPanel = function() -{ - var panels = this.getPanels(); - return this.openPanel(panels[panels.length - 1]); -}; - -Spry.Widget.Accordion.prototype.onPanelTabClick = function(e, panel) -{ - if (panel != this.currentPanel) - this.openPanel(panel); - else - this.closePanel(); - - if (this.enableKeyboardNavigation) - this.focus(); - - if (e.preventDefault) e.preventDefault(); - else e.returnValue = false; - if (e.stopPropagation) e.stopPropagation(); - else e.cancelBubble = true; - - return false; -}; - -Spry.Widget.Accordion.prototype.onFocus = function(e) -{ - this.hasFocus = true; - this.addClassName(this.element, this.focusedClass); - return false; -}; - -Spry.Widget.Accordion.prototype.onBlur = function(e) -{ - this.hasFocus = false; - this.removeClassName(this.element, this.focusedClass); - return false; -}; - -Spry.Widget.Accordion.KEY_UP = 38; -Spry.Widget.Accordion.KEY_DOWN = 40; - -Spry.Widget.Accordion.prototype.onKeyDown = function(e) -{ - var key = e.keyCode; - if (!this.hasFocus || (key != this.previousPanelKeyCode && key != this.nextPanelKeyCode)) - return true; - - var panels = this.getPanels(); - if (!panels || panels.length < 1) - return false; - var currentPanel = this.currentPanel ? this.currentPanel : panels[0]; - var nextPanel = (key == this.nextPanelKeyCode) ? currentPanel.nextSibling : currentPanel.previousSibling; - - while (nextPanel) - { - if (nextPanel.nodeType == 1 /* Node.ELEMENT_NODE */) - break; - nextPanel = (key == this.nextPanelKeyCode) ? nextPanel.nextSibling : nextPanel.previousSibling; - } - - if (nextPanel && currentPanel != nextPanel) - this.openPanel(nextPanel); - - if (e.preventDefault) e.preventDefault(); - else e.returnValue = false; - if (e.stopPropagation) e.stopPropagation(); - else e.cancelBubble = true; - - return false; -}; - -Spry.Widget.Accordion.prototype.attachPanelHandlers = function(panel) -{ - if (!panel) - return; - - var tab = this.getPanelTab(panel); - - if (tab) - { - var self = this; - Spry.Widget.Accordion.addEventListener(tab, "click", function(e) { return self.onPanelTabClick(e, panel); }, false); - Spry.Widget.Accordion.addEventListener(tab, "mouseover", function(e) { return self.onPanelTabMouseOver(e, panel); }, false); - Spry.Widget.Accordion.addEventListener(tab, "mouseout", function(e) { return self.onPanelTabMouseOut(e, panel); }, false); - } -}; - -Spry.Widget.Accordion.addEventListener = function(element, eventType, handler, capture) -{ - try - { - if (element.addEventListener) - element.addEventListener(eventType, handler, capture); - else if (element.attachEvent) - element.attachEvent("on" + eventType, handler); - } - catch (e) {} -}; - -Spry.Widget.Accordion.prototype.initPanel = function(panel, isDefault) -{ - var content = this.getPanelContent(panel); - if (isDefault) - { - this.currentPanel = panel; - this.removeClassName(panel, this.closedClass); - this.addClassName(panel, this.openClass); - - // Attempt to set up the height of the default panel. We don't want to - // do any dynamic panel height calculations here because our accordion - // or one of its parent containers may be display:none. - - if (content) - { - if (this.useFixedPanelHeights) - { - // We are in fixed panel height mode and the user passed in - // a panel height for us to use. - - if (this.fixedPanelHeight) - content.style.height = this.fixedPanelHeight + "px"; - } - else - { - // We are in variable panel height mode, but since we can't - // calculate the panel height here, we just set the height to - // auto so that it expands to show all of its content. - - content.style.height = "auto"; - } - } - } - else - { - this.removeClassName(panel, this.openClass); - this.addClassName(panel, this.closedClass); - - if (content) - { - content.style.height = "0px"; - content.style.display = "none"; - } - } - - this.attachPanelHandlers(panel); -}; - -Spry.Widget.Accordion.prototype.attachBehaviors = function() -{ - var panels = this.getPanels(); - for (var i = 0; i < panels.length; i++) - this.initPanel(panels[i], i == this.defaultPanel); - - // Advanced keyboard navigation requires the tabindex attribute - // on the top-level element. - - this.enableKeyboardNavigation = (this.enableKeyboardNavigation && this.element.attributes.getNamedItem("tabindex")); - if (this.enableKeyboardNavigation) - { - var self = this; - Spry.Widget.Accordion.addEventListener(this.element, "focus", function(e) { return self.onFocus(e); }, false); - Spry.Widget.Accordion.addEventListener(this.element, "blur", function(e) { return self.onBlur(e); }, false); - Spry.Widget.Accordion.addEventListener(this.element, "keydown", function(e) { return self.onKeyDown(e); }, false); - } -}; - -Spry.Widget.Accordion.prototype.getPanels = function() -{ - return this.getElementChildren(this.element); -}; - -Spry.Widget.Accordion.prototype.getCurrentPanel = function() -{ - return this.currentPanel; -}; - -Spry.Widget.Accordion.prototype.getPanelIndex = function(panel) -{ - var panels = this.getPanels(); - for( var i = 0 ; i < panels.length; i++ ) - { - if( panel == panels[i] ) - return i; - } - return -1; -}; - -Spry.Widget.Accordion.prototype.getCurrentPanelIndex = function() -{ - return this.getPanelIndex(this.currentPanel); -}; - -Spry.Widget.Accordion.prototype.getPanelTab = function(panel) -{ - if (!panel) - return null; - return this.getElementChildren(panel)[0]; -}; - -Spry.Widget.Accordion.prototype.getPanelContent = function(panel) -{ - if (!panel) - return null; - return this.getElementChildren(panel)[1]; -}; - -Spry.Widget.Accordion.prototype.getElementChildren = function(element) -{ - var children = []; - var child = element.firstChild; - while (child) - { - if (child.nodeType == 1 /* Node.ELEMENT_NODE */) - children.push(child); - child = child.nextSibling; - } - return children; -}; - -Spry.Widget.Accordion.prototype.focus = function() -{ - if (this.element && this.element.focus) - this.element.focus(); -}; - -Spry.Widget.Accordion.prototype.blur = function() -{ - if (this.element && this.element.blur) - this.element.blur(); -}; - -///////////////////////////////////////////////////// - -Spry.Widget.Accordion.PanelAnimator = function(accordion, panel, opts) -{ - this.timer = null; - this.interval = 0; - - this.fps = 60; - this.duration = 500; - this.startTime = 0; - - this.transition = Spry.Widget.Accordion.PanelAnimator.defaultTransition; - - this.onComplete = null; - - this.panel = panel; - this.panelToOpen = accordion.getElement(panel); - this.panelData = []; - this.useFixedPanelHeights = accordion.useFixedPanelHeights; - - Spry.Widget.Accordion.setOptions(this, opts, true); - - this.interval = Math.floor(1000 / this.fps); - - // Set up the array of panels we want to animate. - - var panels = accordion.getPanels(); - for (var i = 0; i < panels.length; i++) - { - var p = panels[i]; - var c = accordion.getPanelContent(p); - if (c) - { - var h = c.offsetHeight; - if (h == undefined) - h = 0; - - if (p == panel && h == 0) - c.style.display = "block"; - - if (p == panel || h > 0) - { - var obj = new Object; - obj.panel = p; - obj.content = c; - obj.fromHeight = h; - obj.toHeight = (p == panel) ? (accordion.useFixedPanelHeights ? accordion.fixedPanelHeight : c.scrollHeight) : 0; - obj.distance = obj.toHeight - obj.fromHeight; - obj.overflow = c.style.overflow; - this.panelData.push(obj); - - c.style.overflow = "hidden"; - c.style.height = h + "px"; - } - } - } -}; - -Spry.Widget.Accordion.PanelAnimator.defaultTransition = function(time, begin, finish, duration) { time /= duration; return begin + ((2 - time) * time * finish); }; - -Spry.Widget.Accordion.PanelAnimator.prototype.start = function() -{ - var self = this; - this.startTime = (new Date).getTime(); - this.timer = setTimeout(function() { self.stepAnimation(); }, this.interval); -}; - -Spry.Widget.Accordion.PanelAnimator.prototype.stop = function() -{ - if (this.timer) - { - clearTimeout(this.timer); - - // If we're killing the timer, restore the overflow - // properties on the panels we were animating! - - for (i = 0; i < this.panelData.length; i++) - { - obj = this.panelData[i]; - obj.content.style.overflow = obj.overflow; - } - } - - this.timer = null; -}; - -Spry.Widget.Accordion.PanelAnimator.prototype.stepAnimation = function() -{ - var curTime = (new Date).getTime(); - var elapsedTime = curTime - this.startTime; - - var i, obj; - - if (elapsedTime >= this.duration) - { - for (i = 0; i < this.panelData.length; i++) - { - obj = this.panelData[i]; - if (obj.panel != this.panel) - { - obj.content.style.display = "none"; - obj.content.style.height = "0px"; - } - obj.content.style.overflow = obj.overflow; - obj.content.style.height = (this.useFixedPanelHeights || obj.toHeight == 0) ? obj.toHeight + "px" : "auto"; - } - if (this.onComplete) - this.onComplete(); - return; - } - - for (i = 0; i < this.panelData.length; i++) - { - obj = this.panelData[i]; - var ht = this.transition(elapsedTime, obj.fromHeight, obj.distance, this.duration); - obj.content.style.height = ((ht < 0) ? 0 : ht) + "px"; - } - - var self = this; - this.timer = setTimeout(function() { self.stepAnimation(); }, this.interval); -}; - -})(); // EndSpryComponent diff --git a/SpryAssets/SpryCollapsiblePanel.css b/SpryAssets/SpryCollapsiblePanel.css deleted file mode 100644 index a4bef40..0000000 --- a/SpryAssets/SpryCollapsiblePanel.css +++ /dev/null @@ -1,108 +0,0 @@ -@charset "UTF-8"; - -/* SpryCollapsiblePanel.css - version 0.5 - Spry Pre-Release 1.6.1 */ - -/* Copyright (c) 2006. Adobe Systems Incorporated. All rights reserved. */ - -/* This is the selector for the main CollapsiblePanel container. For our - * default style, the CollapsiblePanel is responsible for drawing the borders - * around the widget. - * - * If you want to constrain the width of the CollapsiblePanel widget, set a width on - * the CollapsiblePanel container. By default, our CollapsiblePanel expands horizontally to fill - * up available space. - * - * The name of the class ("CollapsiblePanel") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style the - * CollapsiblePanel container. - */ -.CollapsiblePanel { - margin: 0px; - padding: 0px; - border-left: solid 1px #CCC; - border-right: solid 1px #999; - border-top: solid 1px #999; - border-bottom: solid 1px #CCC; -} - -/* This is the selector for the CollapsiblePanelTab. This container houses - * the title for the panel. This is also the container that the user clicks - * on to open or close the panel. - * - * The name of the class ("CollapsiblePanelTab") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style an - * CollapsiblePanel panel tab container. - */ -.CollapsiblePanelTab { - font: bold 0.7em sans-serif; - background-color: #EEE; - border-bottom: solid 1px #CCC; - margin: 0px; - padding: 2px; - cursor: pointer; - -moz-user-select: none; - -khtml-user-select: none; -} - -/* This is the selector for a CollapsiblePanel's Content area. It's important to note that - * you should never put any padding on the content area element if you plan to - * use the CollapsiblePanel's open/close animations. Placing a non-zero padding on the content - * element can cause the CollapsiblePanel to abruptly grow in height while the panels animate. - * - * The name of the class ("CollapsiblePanelContent") used in this selector is not necessary - * to make the widget function. You can use any class name you want to style a - * CollapsiblePanel content container. - */ -.CollapsiblePanelContent { - margin: 5px 0px 0px 0px; - padding: 0px; -} - -/* An anchor tag can be used inside of a CollapsiblePanelTab so that the - * keyboard focus ring appears *inside* the tab instead of around the tab. - * This is an example of how to make the text within the anchor tag look - * like non-anchor (normal) text. - */ -.CollapsiblePanelTab a { - color: black; - text-decoration: none; -} - -/* This is an example of how to change the appearance of the panel tab that is - * currently open. The class "CollapsiblePanelOpen" is programatically added and removed - * from panels as the user clicks on the tabs within the CollapsiblePanel. - */ -.CollapsiblePanelOpen .CollapsiblePanelTab { - background-color: #EEE; -} - -/* This is an example of how to change the appearance of the panel tab when the - * CollapsiblePanel is closed. The "CollapsiblePanelClosed" class is programatically added and removed - * whenever the CollapsiblePanel is closed. - */ - -.CollapsiblePanelClosed .CollapsiblePanelTab { - /* background-color: #EFEFEF */ -} - -/* This is an example of how to change the appearance of the panel tab as the - * mouse hovers over it. The class "CollapsiblePanelTabHover" is programatically added - * and removed from panel tab containers as the mouse enters and exits the tab container. - */ -.CollapsiblePanelTabHover, .CollapsiblePanelOpen .CollapsiblePanelTabHover { - background-color: #CCC; -} - -/* This is an example of how to change the appearance of all the panel tabs when the - * CollapsiblePanel has focus. The "CollapsiblePanelFocused" class is programatically added and removed - * whenever the CollapsiblePanel gains or loses keyboard focus. - */ -.CollapsiblePanelFocused .CollapsiblePanelTab { - background-color: #CCC; -} -.CollapsiblePanelContent h5 { - margin-top: 10px; - margin-right: 0px; - margin-bottom: 15px; - margin-left: 0px; -} diff --git a/SpryAssets/SpryCollapsiblePanel.js b/SpryAssets/SpryCollapsiblePanel.js deleted file mode 100644 index ff4d49e..0000000 --- a/SpryAssets/SpryCollapsiblePanel.js +++ /dev/null @@ -1,535 +0,0 @@ -// SpryCollapsiblePanel.js - version 0.8 - Spry Pre-Release 1.6.1 -// -// Copyright (c) 2006. Adobe Systems Incorporated. -// All rights reserved. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are met: -// -// * Redistributions of source code must retain the above copyright notice, -// this list of conditions and the following disclaimer. -// * Redistributions in binary form must reproduce the above copyright notice, -// this list of conditions and the following disclaimer in the documentation -// and/or other materials provided with the distribution. -// * Neither the name of Adobe Systems Incorporated nor the names of its -// contributors may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE -// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR -// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF -// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS -// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN -// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE -// POSSIBILITY OF SUCH DAMAGE. - -(function() { // BeginSpryComponent - -if (typeof Spry == "undefined") window.Spry = {}; if (!Spry.Widget) Spry.Widget = {}; - -Spry.Widget.CollapsiblePanel = function(element, opts) -{ - this.element = this.getElement(element); - this.focusElement = null; - this.hoverClass = "CollapsiblePanelTabHover"; - this.openClass = "CollapsiblePanelOpen"; - this.closedClass = "CollapsiblePanelClosed"; - this.focusedClass = "CollapsiblePanelFocused"; - this.enableAnimation = true; - this.enableKeyboardNavigation = true; - this.animator = null; - this.hasFocus = false; - this.contentIsOpen = true; - - this.openPanelKeyCode = Spry.Widget.CollapsiblePanel.KEY_DOWN; - this.closePanelKeyCode = Spry.Widget.CollapsiblePanel.KEY_UP; - - Spry.Widget.CollapsiblePanel.setOptions(this, opts); - - this.attachBehaviors(); -}; - -Spry.Widget.CollapsiblePanel.prototype.getElement = function(ele) -{ - if (ele && typeof ele == "string") - return document.getElementById(ele); - return ele; -}; - -Spry.Widget.CollapsiblePanel.prototype.addClassName = function(ele, className) -{ - if (!ele || !className || (ele.className && ele.className.search(new RegExp("\\b" + className + "\\b")) != -1)) - return; - ele.className += (ele.className ? " " : "") + className; -}; - -Spry.Widget.CollapsiblePanel.prototype.removeClassName = function(ele, className) -{ - if (!ele || !className || (ele.className && ele.className.search(new RegExp("\\b" + className + "\\b")) == -1)) - return; - ele.className = ele.className.replace(new RegExp("\\s*\\b" + className + "\\b", "g"), ""); -}; - -Spry.Widget.CollapsiblePanel.prototype.hasClassName = function(ele, className) -{ - if (!ele || !className || !ele.className || ele.className.search(new RegExp("\\b" + className + "\\b")) == -1) - return false; - return true; -}; - -Spry.Widget.CollapsiblePanel.prototype.setDisplay = function(ele, display) -{ - if( ele ) - ele.style.display = display; -}; - -Spry.Widget.CollapsiblePanel.setOptions = function(obj, optionsObj, ignoreUndefinedProps) -{ - if (!optionsObj) - return; - for (var optionName in optionsObj) - { - if (ignoreUndefinedProps && optionsObj[optionName] == undefined) - continue; - obj[optionName] = optionsObj[optionName]; - } -}; - -Spry.Widget.CollapsiblePanel.prototype.onTabMouseOver = function(e) -{ - this.addClassName(this.getTab(), this.hoverClass); - return false; -}; - -Spry.Widget.CollapsiblePanel.prototype.onTabMouseOut = function(e) -{ - this.removeClassName(this.getTab(), this.hoverClass); - return false; -}; - -Spry.Widget.CollapsiblePanel.prototype.open = function() -{ - this.contentIsOpen = true; - if (this.enableAnimation) - { - if (this.animator) - this.animator.stop(); - this.animator = new Spry.Widget.CollapsiblePanel.PanelAnimator(this, true, { duration: this.duration, fps: this.fps, transition: this.transition }); - this.animator.start(); - } - else - this.setDisplay(this.getContent(), "block"); - - this.removeClassName(this.element, this.closedClass); - this.addClassName(this.element, this.openClass); -}; - -Spry.Widget.CollapsiblePanel.prototype.close = function() -{ - this.contentIsOpen = false; - if (this.enableAnimation) - { - if (this.animator) - this.animator.stop(); - this.animator = new Spry.Widget.CollapsiblePanel.PanelAnimator(this, false, { duration: this.duration, fps: this.fps, transition: this.transition }); - this.animator.start(); - } - else - this.setDisplay(this.getContent(), "none"); - - this.removeClassName(this.element, this.openClass); - this.addClassName(this.element, this.closedClass); -}; - -Spry.Widget.CollapsiblePanel.prototype.onTabClick = function(e) -{ - if (this.isOpen()) - this.close(); - else - this.open(); - - this.focus(); - - return this.stopPropagation(e); -}; - -Spry.Widget.CollapsiblePanel.prototype.onFocus = function(e) -{ - this.hasFocus = true; - this.addClassName(this.element, this.focusedClass); - return false; -}; - -Spry.Widget.CollapsiblePanel.prototype.onBlur = function(e) -{ - this.hasFocus = false; - this.removeClassName(this.element, this.focusedClass); - return false; -}; - -Spry.Widget.CollapsiblePanel.KEY_UP = 38; -Spry.Widget.CollapsiblePanel.KEY_DOWN = 40; - -Spry.Widget.CollapsiblePanel.prototype.onKeyDown = function(e) -{ - var key = e.keyCode; - if (!this.hasFocus || (key != this.openPanelKeyCode && key != this.closePanelKeyCode)) - return true; - - if (this.isOpen() && key == this.closePanelKeyCode) - this.close(); - else if ( key == this.openPanelKeyCode) - this.open(); - - return this.stopPropagation(e); -}; - -Spry.Widget.CollapsiblePanel.prototype.stopPropagation = function(e) -{ - if (e.preventDefault) e.preventDefault(); - else e.returnValue = false; - if (e.stopPropagation) e.stopPropagation(); - else e.cancelBubble = true; - return false; -}; - -Spry.Widget.CollapsiblePanel.prototype.attachPanelHandlers = function() -{ - var tab = this.getTab(); - if (!tab) - return; - - var self = this; - Spry.Widget.CollapsiblePanel.addEventListener(tab, "click", function(e) { return self.onTabClick(e); }, false); - Spry.Widget.CollapsiblePanel.addEventListener(tab, "mouseover", function(e) { return self.onTabMouseOver(e); }, false); - Spry.Widget.CollapsiblePanel.addEventListener(tab, "mouseout", function(e) { return self.onTabMouseOut(e); }, false); - - if (this.enableKeyboardNavigation) - { - // XXX: IE doesn't allow the setting of tabindex dynamically. This means we can't - // rely on adding the tabindex attribute if it is missing to enable keyboard navigation - // by default. - - // Find the first element within the tab container that has a tabindex or the first - // anchor tag. - - var tabIndexEle = null; - var tabAnchorEle = null; - - this.preorderTraversal(tab, function(node) { - if (node.nodeType == 1 /* NODE.ELEMENT_NODE */) - { - var tabIndexAttr = tab.attributes.getNamedItem("tabindex"); - if (tabIndexAttr) - { - tabIndexEle = node; - return true; - } - if (!tabAnchorEle && node.nodeName.toLowerCase() == "a") - tabAnchorEle = node; - } - return false; - }); - - if (tabIndexEle) - this.focusElement = tabIndexEle; - else if (tabAnchorEle) - this.focusElement = tabAnchorEle; - - if (this.focusElement) - { - Spry.Widget.CollapsiblePanel.addEventListener(this.focusElement, "focus", function(e) { return self.onFocus(e); }, false); - Spry.Widget.CollapsiblePanel.addEventListener(this.focusElement, "blur", function(e) { return self.onBlur(e); }, false); - Spry.Widget.CollapsiblePanel.addEventListener(this.focusElement, "keydown", function(e) { return self.onKeyDown(e); }, false); - } - } -}; - -Spry.Widget.CollapsiblePanel.addEventListener = function(element, eventType, handler, capture) -{ - try - { - if (element.addEventListener) - element.addEventListener(eventType, handler, capture); - else if (element.attachEvent) - element.attachEvent("on" + eventType, handler); - } - catch (e) {} -}; - -Spry.Widget.CollapsiblePanel.prototype.preorderTraversal = function(root, func) -{ - var stopTraversal = false; - if (root) - { - stopTraversal = func(root); - if (root.hasChildNodes()) - { - var child = root.firstChild; - while (!stopTraversal && child) - { - stopTraversal = this.preorderTraversal(child, func); - try { child = child.nextSibling; } catch (e) { child = null; } - } - } - } - return stopTraversal; -}; - -Spry.Widget.CollapsiblePanel.prototype.attachBehaviors = function() -{ - var panel = this.element; - var tab = this.getTab(); - var content = this.getContent(); - - if (this.contentIsOpen || this.hasClassName(panel, this.openClass)) - { - this.addClassName(panel, this.openClass); - this.removeClassName(panel, this.closedClass); - this.setDisplay(content, "block"); - this.contentIsOpen = true; - } - else - { - this.removeClassName(panel, this.openClass); - this.addClassName(panel, this.closedClass); - this.setDisplay(content, "none"); - this.contentIsOpen = false; - } - - this.attachPanelHandlers(); -}; - -Spry.Widget.CollapsiblePanel.prototype.getTab = function() -{ - return this.getElementChildren(this.element)[0]; -}; - -Spry.Widget.CollapsiblePanel.prototype.getContent = function() -{ - return this.getElementChildren(this.element)[1]; -}; - -Spry.Widget.CollapsiblePanel.prototype.isOpen = function() -{ - return this.contentIsOpen; -}; - -Spry.Widget.CollapsiblePanel.prototype.getElementChildren = function(element) -{ - var children = []; - var child = element.firstChild; - while (child) - { - if (child.nodeType == 1 /* Node.ELEMENT_NODE */) - children.push(child); - child = child.nextSibling; - } - return children; -}; - -Spry.Widget.CollapsiblePanel.prototype.focus = function() -{ - if (this.focusElement && this.focusElement.focus) - this.focusElement.focus(); -}; - -///////////////////////////////////////////////////// - -Spry.Widget.CollapsiblePanel.PanelAnimator = function(panel, doOpen, opts) -{ - this.timer = null; - this.interval = 0; - - this.fps = 60; - this.duration = 500; - this.startTime = 0; - - this.transition = Spry.Widget.CollapsiblePanel.PanelAnimator.defaultTransition; - - this.onComplete = null; - - this.panel = panel; - this.content = panel.getContent(); - this.doOpen = doOpen; - - Spry.Widget.CollapsiblePanel.setOptions(this, opts, true); - - this.interval = Math.floor(1000 / this.fps); - - var c = this.content; - - var curHeight = c.offsetHeight ? c.offsetHeight : 0; - this.fromHeight = (doOpen && c.style.display == "none") ? 0 : curHeight; - - if (!doOpen) - this.toHeight = 0; - else - { - if (c.style.display == "none") - { - // The content area is not displayed so in order to calculate the extent - // of the content inside it, we have to set its display to block. - - c.style.visibility = "hidden"; - c.style.display = "block"; - } - - // Clear the height property so we can calculate - // the full height of the content we are going to show. - - c.style.height = ""; - this.toHeight = c.offsetHeight; - } - - this.distance = this.toHeight - this.fromHeight; - this.overflow = c.style.overflow; - - c.style.height = this.fromHeight + "px"; - c.style.visibility = "visible"; - c.style.overflow = "hidden"; - c.style.display = "block"; -}; - -Spry.Widget.CollapsiblePanel.PanelAnimator.defaultTransition = function(time, begin, finish, duration) { time /= duration; return begin + ((2 - time) * time * finish); }; - -Spry.Widget.CollapsiblePanel.PanelAnimator.prototype.start = function() -{ - var self = this; - this.startTime = (new Date).getTime(); - this.timer = setTimeout(function() { self.stepAnimation(); }, this.interval); -}; - -Spry.Widget.CollapsiblePanel.PanelAnimator.prototype.stop = function() -{ - if (this.timer) - { - clearTimeout(this.timer); - - // If we're killing the timer, restore the overflow property. - - this.content.style.overflow = this.overflow; - } - - this.timer = null; -}; - -Spry.Widget.CollapsiblePanel.PanelAnimator.prototype.stepAnimation = function() -{ - var curTime = (new Date).getTime(); - var elapsedTime = curTime - this.startTime; - - if (elapsedTime >= this.duration) - { - if (!this.doOpen) - this.content.style.display = "none"; - this.content.style.overflow = this.overflow; - this.content.style.height = this.toHeight + "px"; - if (this.onComplete) - this.onComplete(); - return; - } - - var ht = this.transition(elapsedTime, this.fromHeight, this.distance, this.duration); - - this.content.style.height = ((ht < 0) ? 0 : ht) + "px"; - - var self = this; - this.timer = setTimeout(function() { self.stepAnimation(); }, this.interval); -}; - -Spry.Widget.CollapsiblePanelGroup = function(element, opts) -{ - this.element = this.getElement(element); - this.opts = opts; - - this.attachBehaviors(); -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.setOptions = Spry.Widget.CollapsiblePanel.prototype.setOptions; -Spry.Widget.CollapsiblePanelGroup.prototype.getElement = Spry.Widget.CollapsiblePanel.prototype.getElement; -Spry.Widget.CollapsiblePanelGroup.prototype.getElementChildren = Spry.Widget.CollapsiblePanel.prototype.getElementChildren; - -Spry.Widget.CollapsiblePanelGroup.prototype.setElementWidget = function(element, widget) -{ - if (!element || !widget) - return; - if (!element.spry) - element.spry = new Object; - element.spry.collapsiblePanel = widget; -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.getElementWidget = function(element) -{ - return (element && element.spry && element.spry.collapsiblePanel) ? element.spry.collapsiblePanel : null; -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.getPanels = function() -{ - if (!this.element) - return []; - return this.getElementChildren(this.element); -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.getPanel = function(panelIndex) -{ - return this.getPanels()[panelIndex]; -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.attachBehaviors = function() -{ - if (!this.element) - return; - - var cpanels = this.getPanels(); - var numCPanels = cpanels.length; - for (var i = 0; i < numCPanels; i++) - { - var cpanel = cpanels[i]; - this.setElementWidget(cpanel, new Spry.Widget.CollapsiblePanel(cpanel, this.opts)); - } -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.openPanel = function(panelIndex) -{ - var w = this.getElementWidget(this.getPanel(panelIndex)); - if (w && !w.isOpen()) - w.open(); -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.closePanel = function(panelIndex) -{ - var w = this.getElementWidget(this.getPanel(panelIndex)); - if (w && w.isOpen()) - w.close(); -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.openAllPanels = function() -{ - var cpanels = this.getPanels(); - var numCPanels = cpanels.length; - for (var i = 0; i < numCPanels; i++) - { - var w = this.getElementWidget(cpanels[i]); - if (w && !w.isOpen()) - w.open(); - } -}; - -Spry.Widget.CollapsiblePanelGroup.prototype.closeAllPanels = function() -{ - var cpanels = this.getPanels(); - var numCPanels = cpanels.length; - for (var i = 0; i < numCPanels; i++) - { - var w = this.getElementWidget(cpanels[i]); - if (w && w.isOpen()) - w.close(); - } -}; - -})(); // EndSpryComponent diff --git a/SpryAssets/SpryMenuBar.js b/SpryAssets/SpryMenuBar.js deleted file mode 100644 index c6af890..0000000 --- a/SpryAssets/SpryMenuBar.js +++ /dev/null @@ -1,763 +0,0 @@ -// SpryMenuBar.js - version 0.13 - Spry Pre-Release 1.6.1 -// -// Copyright (c) 2006. Adobe Systems Incorporated. -// All rights reserved. -// -// Redistribution and use in source and binary forms, with or without -// modification, are permitted provided that the following conditions are met: -// -// * Redistributions of source code must retain the above copyright notice, -// this list of conditions and the following disclaimer. -// * Redistributions in binary form must reproduce the above copyright notice, -// this list of conditions and the following disclaimer in the documentation -// and/or other materials provided with the distribution. -// * Neither the name of Adobe Systems Incorporated nor the names of its -// contributors may be used to endorse or promote products derived from this -// software without specific prior written permission. -// -// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" -// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE -// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE -// ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE -// LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR -// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF -// SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS -// INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN -// CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) -// ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE -// POSSIBILITY OF SUCH DAMAGE. - -/******************************************************************************* - - SpryMenuBar.js - This file handles the JavaScript for Spry Menu Bar. You should have no need - to edit this file. Some highlights of the MenuBar object is that timers are - used to keep submenus from showing up until the user has hovered over the parent - menu item for some time, as well as a timer for when they leave a submenu to keep - showing that submenu until the timer fires. - - *******************************************************************************/ - -(function() { // BeginSpryComponent - -if (typeof Spry == "undefined") window.Spry = {}; if (!Spry.Widget) Spry.Widget = {}; - -Spry.BrowserSniff = function() -{ - var b = navigator.appName.toString(); - var up = navigator.platform.toString(); - var ua = navigator.userAgent.toString(); - - this.mozilla = this.ie = this.opera = this.safari = false; - var re_opera = /Opera.([0-9\.]*)/i; - var re_msie = /MSIE.([0-9\.]*)/i; - var re_gecko = /gecko/i; - var re_safari = /(applewebkit|safari)\/([\d\.]*)/i; - var r = false; - - if ( (r = ua.match(re_opera))) { - this.opera = true; - this.version = parseFloat(r[1]); - } else if ( (r = ua.match(re_msie))) { - this.ie = true; - this.version = parseFloat(r[1]); - } else if ( (r = ua.match(re_safari))) { - this.safari = true; - this.version = parseFloat(r[2]); - } else if (ua.match(re_gecko)) { - var re_gecko_version = /rv:\s*([0-9\.]+)/i; - r = ua.match(re_gecko_version); - this.mozilla = true; - this.version = parseFloat(r[1]); - } - this.windows = this.mac = this.linux = false; - - this.Platform = ua.match(/windows/i) ? "windows" : - (ua.match(/linux/i) ? "linux" : - (ua.match(/mac/i) ? "mac" : - ua.match(/unix/i)? "unix" : "unknown")); - this[this.Platform] = true; - this.v = this.version; - - if (this.safari && this.mac && this.mozilla) { - this.mozilla = false; - } -}; - -Spry.is = new Spry.BrowserSniff(); - -// Constructor for Menu Bar -// element should be an ID of an unordered list (
      tag) -// preloadImage1 and preloadImage2 are images for the rollover state of a menu -Spry.Widget.MenuBar = function(element, opts) -{ - this.init(element, opts); -}; - -Spry.Widget.MenuBar.prototype.init = function(element, opts) -{ - this.element = this.getElement(element); - - // represents the current (sub)menu we are operating on - this.currMenu = null; - this.showDelay = 250; - this.hideDelay = 600; - if(typeof document.getElementById == 'undefined' || (navigator.vendor == 'Apple Computer, Inc.' && typeof window.XMLHttpRequest == 'undefined') || (Spry.is.ie && typeof document.uniqueID == 'undefined')) - { - // bail on older unsupported browsers - return; - } - - // Fix IE6 CSS images flicker - if (Spry.is.ie && Spry.is.version < 7){ - try { - document.execCommand("BackgroundImageCache", false, true); - } catch(err) {} - } - - this.upKeyCode = Spry.Widget.MenuBar.KEY_UP; - this.downKeyCode = Spry.Widget.MenuBar.KEY_DOWN; - this.leftKeyCode = Spry.Widget.MenuBar.KEY_LEFT; - this.rightKeyCode = Spry.Widget.MenuBar.KEY_RIGHT; - this.escKeyCode = Spry.Widget.MenuBar.KEY_ESC; - - this.hoverClass = 'MenuBarItemHover'; - this.subHoverClass = 'MenuBarItemSubmenuHover'; - this.subVisibleClass ='MenuBarSubmenuVisible'; - this.hasSubClass = 'MenuBarItemSubmenu'; - this.activeClass = 'MenuBarActive'; - this.isieClass = 'MenuBarItemIE'; - this.verticalClass = 'MenuBarVertical'; - this.horizontalClass = 'MenuBarHorizontal'; - this.enableKeyboardNavigation = true; - - this.hasFocus = false; - // load hover images now - if(opts) - { - for(var k in opts) - { - if (typeof this[k] == 'undefined') - { - var rollover = new Image; - rollover.src = opts[k]; - } - } - Spry.Widget.MenuBar.setOptions(this, opts); - } - - // safari doesn't support tabindex - if (Spry.is.safari) - this.enableKeyboardNavigation = false; - - if(this.element) - { - this.currMenu = this.element; - var items = this.element.getElementsByTagName('li'); - for(var i=0; i 0 && this.enableKeyboardNavigation) - items[i].getElementsByTagName('a')[0].tabIndex='-1'; - - this.initialize(items[i], element); - if(Spry.is.ie) - { - this.addClassName(items[i], this.isieClass); - items[i].style.position = "static"; - } - } - if (this.enableKeyboardNavigation) - { - var self = this; - this.addEventListener(document, 'keydown', function(e){self.keyDown(e); }, false); - } - - if(Spry.is.ie) - { - if(this.hasClassName(this.element, this.verticalClass)) - { - this.element.style.position = "relative"; - } - var linkitems = this.element.getElementsByTagName('a'); - for(var i=0; i 0) - { - layers[0].parentNode.removeChild(layers[0]); - } -}; - -// clearMenus for Menu Bar -// root is the top level unordered list (
        tag) -Spry.Widget.MenuBar.prototype.clearMenus = function(root) -{ - var menus = root.getElementsByTagName('ul'); - for(var i=0; i 0 ? submenus[0] : null); - - if(menu) - this.addClassName(link, this.hasSubClass); - - if(!Spry.is.ie) - { - // define a simple function that comes standard in IE to determine - // if a node is within another node - listitem.contains = function(testNode) - { - // this refers to the list item - if(testNode == null) - return false; - - if(testNode == this) - return true; - else - return this.contains(testNode.parentNode); - }; - } - - // need to save this for scope further down - var self = this; - this.addEventListener(listitem, 'mouseover', function(e){self.mouseOver(listitem, e);}, false); - this.addEventListener(listitem, 'mouseout', function(e){if (self.enableKeyboardNavigation) self.clearSelection(); self.mouseOut(listitem, e);}, false); - - if (this.enableKeyboardNavigation) - { - this.addEventListener(link, 'blur', function(e){self.onBlur(listitem);}, false); - this.addEventListener(link, 'focus', function(e){self.keyFocus(listitem, e);}, false); - } -}; -Spry.Widget.MenuBar.prototype.keyFocus = function (listitem, e) -{ - this.lastOpen = listitem.getElementsByTagName('a')[0]; - this.addClassName(this.lastOpen, listitem.getElementsByTagName('ul').length > 0 ? this.subHoverClass : this.hoverClass); - this.hasFocus = true; -}; -Spry.Widget.MenuBar.prototype.onBlur = function (listitem) -{ - this.clearSelection(listitem); -}; -Spry.Widget.MenuBar.prototype.clearSelection = function(el){ - //search any intersection with the current open element - if (!this.lastOpen) - return; - - if (el) - { - el = el.getElementsByTagName('a')[0]; - - // check children - var item = this.lastOpen; - while (item != this.element) - { - var tmp = el; - while (tmp != this.element) - { - if (tmp == item) - return; - try{ - tmp = tmp.parentNode; - }catch(err){break;} - } - item = item.parentNode; - } - } - var item = this.lastOpen; - while (item != this.element) - { - this.hideSubmenu(item.parentNode); - var link = item.getElementsByTagName('a')[0]; - this.removeClassName(link, this.hoverClass); - this.removeClassName(link, this.subHoverClass); - item = item.parentNode; - } - this.lastOpen = false; -}; -Spry.Widget.MenuBar.prototype.keyDown = function (e) -{ - if (!this.hasFocus) - return; - - if (!this.lastOpen) - { - this.hasFocus = false; - return; - } - - var e = e|| event; - var listitem = this.lastOpen.parentNode; - var link = this.lastOpen; - var submenus = listitem.getElementsByTagName('ul'); - var menu = (submenus.length > 0 ? submenus[0] : null); - var hasSubMenu = (menu) ? true : false; - - var opts = [listitem, menu, null, this.getSibling(listitem, 'previousSibling'), this.getSibling(listitem, 'nextSibling')]; - - if (!opts[3]) - opts[2] = (listitem.parentNode.parentNode.nodeName.toLowerCase() == 'li')?listitem.parentNode.parentNode:null; - - var found = 0; - switch (e.keyCode){ - case this.upKeyCode: - found = this.getElementForKey(opts, 'y', 1); - break; - case this.downKeyCode: - found = this.getElementForKey(opts, 'y', -1); - break; - case this.leftKeyCode: - found = this.getElementForKey(opts, 'x', 1); - break; - case this.rightKeyCode: - found = this.getElementForKey(opts, 'x', -1); - break; - case this.escKeyCode: - case 9: - this.clearSelection(); - this.hasFocus = false; - default: return; - } - switch (found) - { - case 0: return; - case 1: - //subopts - this.mouseOver(listitem, e); - break; - case 2: - //parent - this.mouseOut(opts[2], e); - break; - case 3: - case 4: - // left - right - this.removeClassName(link, hasSubMenu ? this.subHoverClass : this.hoverClass); - break; - } - var link = opts[found].getElementsByTagName('a')[0]; - if (opts[found].nodeName.toLowerCase() == 'ul') - opts[found] = opts[found].getElementsByTagName('li')[0]; - - this.addClassName(link, opts[found].getElementsByTagName('ul').length > 0 ? this.subHoverClass : this.hoverClass); - this.lastOpen = link; - opts[found].getElementsByTagName('a')[0].focus(); - - //stop further event handling by the browser - return Spry.Widget.MenuBar.stopPropagation(e); -}; -Spry.Widget.MenuBar.prototype.mouseOver = function (listitem, e) -{ - var link = listitem.getElementsByTagName('a')[0]; - var submenus = listitem.getElementsByTagName('ul'); - var menu = (submenus.length > 0 ? submenus[0] : null); - var hasSubMenu = (menu) ? true : false; - if (this.enableKeyboardNavigation) - this.clearSelection(listitem); - - if(this.bubbledTextEvent()) - { - // ignore bubbled text events - return; - } - - if (listitem.closetime) - clearTimeout(listitem.closetime); - - if(this.currMenu == listitem) - { - this.currMenu = null; - } - - // move the focus too - if (this.hasFocus) - link.focus(); - - // show menu highlighting - this.addClassName(link, hasSubMenu ? this.subHoverClass : this.hoverClass); - this.lastOpen = link; - if(menu && !this.hasClassName(menu, this.subHoverClass)) - { - var self = this; - listitem.opentime = window.setTimeout(function(){self.showSubmenu(menu);}, this.showDelay); - } -}; -Spry.Widget.MenuBar.prototype.mouseOut = function (listitem, e) -{ - var link = listitem.getElementsByTagName('a')[0]; - var submenus = listitem.getElementsByTagName('ul'); - var menu = (submenus.length > 0 ? submenus[0] : null); - var hasSubMenu = (menu) ? true : false; - if(this.bubbledTextEvent()) - { - // ignore bubbled text events - return; - } - - var related = (typeof e.relatedTarget != 'undefined' ? e.relatedTarget : e.toElement); - if(!listitem.contains(related)) - { - if (listitem.opentime) - clearTimeout(listitem.opentime); - this.currMenu = listitem; - - // remove menu highlighting - this.removeClassName(link, hasSubMenu ? this.subHoverClass : this.hoverClass); - if(menu) - { - var self = this; - listitem.closetime = window.setTimeout(function(){self.hideSubmenu(menu);}, this.hideDelay); - } - if (this.hasFocus) - link.blur(); - } -}; -Spry.Widget.MenuBar.prototype.getSibling = function(element, sibling) -{ - var child = element[sibling]; - while (child && child.nodeName.toLowerCase() !='li') - child = child[sibling]; - - return child; -}; -Spry.Widget.MenuBar.prototype.getElementForKey = function(els, prop, dir) -{ - var found = 0; - var rect = Spry.Widget.MenuBar.getPosition; - var ref = rect(els[found]); - - var hideSubmenu = false; - //make the subelement visible to compute the position - if (els[1] && !this.hasClassName(els[1], this.MenuBarSubmenuVisible)) - { - els[1].style.visibility = 'hidden'; - this.showSubmenu(els[1]); - hideSubmenu = true; - } - - var isVert = this.hasClassName(this.element, this.verticalClass); - var hasParent = els[0].parentNode.parentNode.nodeName.toLowerCase() == 'li' ? true : false; - - for (var i = 1; i < els.length; i++){ - //when navigating on the y axis in vertical menus, ignore children and parents - if(prop=='y' && isVert && (i==1 || i==2)) - { - continue; - } - //when navigationg on the x axis in the FIRST LEVEL of horizontal menus, ignore children and parents - if(prop=='x' && !isVert && !hasParent && (i==1 || i==2)) - { - continue; - } - - if (els[i]) - { - var tmp = rect(els[i]); - if ( (dir * tmp[prop]) < (dir * ref[prop])) - { - ref = tmp; - found = i; - } - } - } - - // hide back the submenu - if (els[1] && hideSubmenu){ - this.hideSubmenu(els[1]); - els[1].style.visibility = ''; - } - - return found; -}; -Spry.Widget.MenuBar.camelize = function(str) -{ - if (str.indexOf('-') == -1){ - return str; - } - var oStringList = str.split('-'); - var isFirstEntry = true; - var camelizedString = ''; - - for(var i=0; i < oStringList.length; i++) - { - if(oStringList[i].length>0) - { - if(isFirstEntry) - { - camelizedString = oStringList[i]; - isFirstEntry = false; - } - else - { - var s = oStringList[i]; - camelizedString += s.charAt(0).toUpperCase() + s.substring(1); - } - } - } - - return camelizedString; -}; - -Spry.Widget.MenuBar.getStyleProp = function(element, prop) -{ - var value; - try - { - if (element.style) - value = element.style[Spry.Widget.MenuBar.camelize(prop)]; - - if (!value) - if (document.defaultView && document.defaultView.getComputedStyle) - { - var css = document.defaultView.getComputedStyle(element, null); - value = css ? css.getPropertyValue(prop) : null; - } - else if (element.currentStyle) - { - value = element.currentStyle[Spry.Widget.MenuBar.camelize(prop)]; - } - } - catch (e) {} - - return value == 'auto' ? null : value; -}; -Spry.Widget.MenuBar.getIntProp = function(element, prop) -{ - var a = parseInt(Spry.Widget.MenuBar.getStyleProp(element, prop),10); - if (isNaN(a)) - return 0; - return a; -}; - -Spry.Widget.MenuBar.getPosition = function(el, doc) -{ - doc = doc || document; - if (typeof(el) == 'string') { - el = doc.getElementById(el); - } - - if (!el) { - return false; - } - - if (el.parentNode === null || Spry.Widget.MenuBar.getStyleProp(el, 'display') == 'none') { - //element must be visible to have a box - return false; - } - - var ret = {x:0, y:0}; - var parent = null; - var box; - - if (el.getBoundingClientRect) { // IE - box = el.getBoundingClientRect(); - var scrollTop = doc.documentElement.scrollTop || doc.body.scrollTop; - var scrollLeft = doc.documentElement.scrollLeft || doc.body.scrollLeft; - ret.x = box.left + scrollLeft; - ret.y = box.top + scrollTop; - } else if (doc.getBoxObjectFor) { // gecko - box = doc.getBoxObjectFor(el); - ret.x = box.x; - ret.y = box.y; - } else { // safari/opera - ret.x = el.offsetLeft; - ret.y = el.offsetTop; - parent = el.offsetParent; - if (parent != el) { - while (parent) { - ret.x += parent.offsetLeft; - ret.y += parent.offsetTop; - parent = parent.offsetParent; - } - } - // opera & (safari absolute) incorrectly account for body offsetTop - if (Spry.is.opera || Spry.is.safari && Spry.Widget.MenuBar.getStyleProp(el, 'position') == 'absolute') - ret.y -= doc.body.offsetTop; - } - if (el.parentNode) - parent = el.parentNode; - else - parent = null; - if (parent.nodeName){ - var cas = parent.nodeName.toUpperCase(); - while (parent && cas != 'BODY' && cas != 'HTML') { - cas = parent.nodeName.toUpperCase(); - ret.x -= parent.scrollLeft; - ret.y -= parent.scrollTop; - if (parent.parentNode) - parent = parent.parentNode; - else - parent = null; - } - } - return ret; -}; - -Spry.Widget.MenuBar.stopPropagation = function(ev) -{ - if (ev.stopPropagation) - ev.stopPropagation(); - else - ev.cancelBubble = true; - if (ev.preventDefault) - ev.preventDefault(); - else - ev.returnValue = false; -}; - -Spry.Widget.MenuBar.setOptions = function(obj, optionsObj, ignoreUndefinedProps) -{ - if (!optionsObj) - return; - for (var optionName in optionsObj) - { - if (ignoreUndefinedProps && optionsObj[optionName] == undefined) - continue; - obj[optionName] = optionsObj[optionName]; - } -}; - -})(); // EndSpryComponent diff --git a/SpryAssets/SpryMenuBarRight.gif b/SpryAssets/SpryMenuBarRight.gif deleted file mode 100644 index e9a42848b8e0378a5a674b2a17430198e4e32dda..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 55 zcmZ?wbhEHbWMN=un8?6jY;61=3>X*~6o0ZXvNJF-=m6OaAbAERjut+(%r~p2XfRj< E0HH_?@Bjb+ diff --git a/SpryAssets/SpryMenuBarRightHover.gif b/SpryAssets/SpryMenuBarRightHover.gif deleted file mode 100644 index 18167be67dff3a18268b806542dcd707ed1f70a5..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 55 zcmZ?wbhEHbWMN=un8?8J9|jm07!-f9FtRf+G3Wr<3?O+1CXN<9wahoGr)V%(0{{bC B5L5sF diff --git a/SpryAssets/SpryMenuBarVertical.css b/SpryAssets/SpryMenuBarVertical.css deleted file mode 100644 index 0d216c9..0000000 --- a/SpryAssets/SpryMenuBarVertical.css +++ /dev/null @@ -1,148 +0,0 @@ -@charset "UTF-8"; - -/* SpryMenuBarVertical.css - version 0.6 - Spry Pre-Release 1.6.1 */ - -/* Copyright (c) 2006. Adobe Systems Incorporated. All rights reserved. */ - -/******************************************************************************* - - LAYOUT INFORMATION: describes box model, positioning, z-order - - *******************************************************************************/ - -/* The outermost container of the Menu Bar, a fixed width box with no margin or padding */ -ul.MenuBarVertical -{ - margin: 0px 0px 0px 26px; - padding: 0; - list-style-type: none; - font-size: 100%; - cursor: default; - width: 8em; -} -/* Set the active Menu Bar with this class, currently setting z-index to accomodate IE rendering bug: http://therealcrisp.xs4all.nl/meuk/IE-zindexbug.html */ -ul.MenuBarActive -{ - z-index: 1000; -} -/* Menu item containers, position children relative to this container and are same fixed width as parent */ -ul.MenuBarVertical li -{ - margin: 0; - padding: 0; - list-style-type: none; - font-size: 100%; - position: relative; - text-align: left; - cursor: pointer; - width: 8em; -} -/* Submenus should appear slightly overlapping to the right (95%) and up (-5%) with a higher z-index, but they are initially off the left side of the screen (-1000em) */ -ul.MenuBarVertical ul -{ - margin: -5% 0 0 95%; - padding: 0; - list-style-type: none; - font-size: 100%; - position: absolute; - z-index: 1020; - cursor: default; - width: 8.2em; - left: -1000em; - top: 0; -} -/* Submenu that is showing with class designation MenuBarSubmenuVisible, we set left to 0 so it comes onto the screen */ -ul.MenuBarVertical ul.MenuBarSubmenuVisible -{ - left: 0; -} -/* Menu item containers are same fixed width as parent */ -ul.MenuBarVertical ul li -{ - width: 8.2em; -} - -/******************************************************************************* - - DESIGN INFORMATION: describes color scheme, borders, fonts - - *******************************************************************************/ - -/* Outermost menu container has borders on all sides */ -ul.MenuBarVertical -{ - border: 1px solid #CCC; -} -/* Submenu containers have borders on all sides */ -ul.MenuBarVertical ul -{ - border: 1px solid #CCC; -} -/* Menu items are a light gray block with padding and no text decoration */ -ul.MenuBarVertical a -{ - display: block; - cursor: pointer; - background-color: #EEE; - padding: 0.5em 0.75em; - color: #333; - text-decoration: none; -} -/* Menu items that have mouse over or focus have a blue background and white text */ -ul.MenuBarVertical a:hover, ul.MenuBarVertical a:focus -{ - background-color: #33C; - color: #FFF; -} -/* Menu items that are open with submenus are set to MenuBarItemHover with a blue background and white text */ -ul.MenuBarVertical a.MenuBarItemHover, ul.MenuBarVertical a.MenuBarItemSubmenuHover, ul.MenuBarVertical a.MenuBarSubmenuVisible -{ - background-color: #33C; - color: #FFF; -} - -/******************************************************************************* - - SUBMENU INDICATION: styles if there is a submenu under a given menu item - - *******************************************************************************/ - -/* Menu items that have a submenu have the class designation MenuBarItemSubmenu and are set to use a background image positioned on the far left (95%) and centered vertically (50%) */ -ul.MenuBarVertical a.MenuBarItemSubmenu -{ - background-image: url(SpryMenuBarRight.gif); - background-repeat: no-repeat; - background-position: 95% 50%; -} - -/* Menu items that are open with submenus have the class designation MenuBarItemSubmenuHover and are set to use a "hover" background image positioned on the far left (95%) and centered vertically (50%) */ -ul.MenuBarVertical a.MenuBarItemSubmenuHover -{ - background-image: url(SpryMenuBarRightHover.gif); - background-repeat: no-repeat; - background-position: 95% 50%; -} - -/******************************************************************************* - - BROWSER HACKS: the hacks below should not be changed unless you are an expert - - *******************************************************************************/ - -/* HACK FOR IE: to make sure the sub menus show above form controls, we underlay each submenu with an iframe */ -ul.MenuBarVertical iframe -{ - position: absolute; - z-index: 1010; - filter:alpha(opacity:0.1); -} -/* HACK FOR IE: to stabilize appearance of menu items; the slash in float is to keep IE 5.0 from parsing */ -@media screen, projection -{ - ul.MenuBarVertical li.MenuBarItemIE - { - display: inline; - f\loat: left; - background: #FFF; - } -} diff --git a/js/controllers.js b/js/controllers.js deleted file mode 100644 index 4cd8d61..0000000 --- a/js/controllers.js +++ /dev/null @@ -1,3 +0,0 @@ -/** - * Created by nbenes on 11/16/13. - */ diff --git a/js/crc.js b/js/crc.js deleted file mode 100644 index a8007a4..0000000 --- a/js/crc.js +++ /dev/null @@ -1,45 +0,0 @@ -/** - * Created by nbenes on 11/16/13. - */ - -var $window = $(window) -var $body = $(document.body) - -var navHeight = $('.navbar').outerHeight(true) + 10 - -$body.scrollspy({ - target: '.crc-sidebar', - offset: navHeight -}) - -$window.on('load', function () { - $body.scrollspy('refresh') -}) - -$('.crc-container [href=#]').click(function (e) { - e.preventDefault() -}) - -// back to top -setTimeout(function () { - var $sideBar = $('.crc-sidebar') - - $sideBar.affix({ - offset: { - top: function () { - var offsetTop = $sideBar.offset().top - var sideBarMargin = parseInt($sideBar.children(0).css('margin-top'), 10) - var navOuterHeight = $('.crc-nav').height() - - return (this.top = offsetTop - navOuterHeight - sideBarMargin) - } - , bottom: function () { - return (this.bottom = $('.crc-footer').outerHeight(true)) - } - } - }) -}, 100) - -setTimeout(function () { - $('.crc-top').affix() -}, 100) \ No newline at end of file diff --git a/js/pictures.js b/js/pictures.js deleted file mode 100644 index 9c5a21e..0000000 --- a/js/pictures.js +++ /dev/null @@ -1,7 +0,0 @@ -var imagenumber = 2 ; -var randomnumber = Math.random() ; -var rand1 = Math.round( (imagenumber-1) * randomnumber) + 1 ; -images = new Array -images[1] = "images/cajal.jpg" -images[2] = "images/fhn.png" -var image = images[rand1] diff --git a/js/poster_session.js b/js/poster_session.js deleted file mode 100644 index a7b03da..0000000 --- a/js/poster_session.js +++ /dev/null @@ -1,282 +0,0 @@ - function SessionCtrl($scope) { - $scope.sessions = [ - { - "Session": "Poster Session 1 (Tuesday Morning through Lunch)", - "Themes": [ - { - "Name": "Rhythms in decision making, performance social interactions & emotion", - "Posters": [ - { - "Author": "Cavanagh, James F", - "Title": "A Cortico – Subthalamic Network Contributes to Post Error Slowing" - }, - { - "Author": "Denovellis, Eric", - "Title": "Contributions of Prefrontal Cortical Areas during Task Switching" - }, - { - "Author": "Amadei, Elizabeth", - "Title": "Neural coherence between social reward sites in monogamous prairie voles during social behaviors" - }, - { - "Author": "Wang, Shuo", - "Title": "Neurons in the Human Amygdala Selective for Perceived Emotion" - }, - { - "Author": "Lemaire, Nune", - "Title": "Effects of local dopamine depletion on LFP oscillations in dorsolateral striatum are task and learning-dependent and are partially reversed by levodopa administration" - } - ] - }, - { - "Name": "Auditory entrainment dynamics", - "Posters": [ - { - "Author": "Henry, Molly", - "Title": "Neural entrainment to simultaneous frequency and amplitude modulation influences human gap-detection performance" - }, - { - "Author": "Herrmann, Björn", - "Title": "Oscillatory Phase Precision in Neural Entrainment Underpins Illusory Time Percepts" - }, - { - "Author": "Morillon, Benjamin", - "Title": "Influence of motor activity on the rhythmic selection of auditory information" - } - ] - }, - { - "Name": "Neuropathology", - "Posters": [ - { - "Author": "Weber, Kirsten", - "Title": "Oscillations during basic sentence comprehension in patients with schizophrenia" - }, - { - "Author": "Hall, Mei-Hua", - "Title": "Abnormalities of Neuronal Oscillations in Schizophrenia and Bipolar Disorder" - }, - { - "Author": "Manoach, Dara", - "Title": "The effects of eszopiclone on sleep spindles and memory consolidation in schizophrenia" - }, - { - "Author": "Lii, Theresa/Saab, Carl", - "Title": "Altered thalamocortical connectivity in chronic pain" - }, - { - "Author": "Hashmi, Javeria Ali", - "Title": "Expectancy based pain modulation in chronic knee pain patients is predicted by small world brain metrics." - }, - { - "Author": "Khan, Sheraz", - "Title": "Neurophysiological Correlates of Tactile Sensitivities in ASD" - }, - { - "Author": "Kramer, Mark", - "Title": "Human seizures self-terminate across spatial scales via a critical transition" - }, - { - "Author": "Sherman, Maxwell", - "Title": "Beta rhythm disruption in mental health" - } - ] - } - ] - }, - { - "Session": "Poster Session 2 (Tuesday Afternoon through the Reception)", - "Themes": [ - { - "Name": "Gamma", - "Posters": [ - { - "Author": "Keeley, Stephen", - "Title": "Modeling Fast and Slow Gamma Bands in the Rat Hippocampus" - }, - { - "Author": "McNally, James", - "Title": "Characterization of the Effects of Acute Ketamine on Cortical Gamma Band Oscillations in Both In Vitro & In Vivo Model Systems" - }, - { - "Author": "Cannon, Jonathan", - "Title": "Gamma Rhythms Under Periodic Forcing" - }, - { - "Author": "Brown, Ritchie E.", - "Title": "Subcortical control of gamma oscillations: role of basal forebrain parvalbumin neurons" - } - ] - }, - { - "Name": "Theta & Theta-gamma coupling", - "Posters": [ - { - "Author": "Polletta, Ben", - "Title": "State-Dependent Changes in Theta-Gamma Phase-Amplitude Coupling following Subtype-Specific Blockade of NMDA Receptors" - }, - { - "Author": "Stark, Eran/Rotstein, Horacio", - "Title": "Mechanism of generation of theta spiking resonance in a hippocampal network" - }, - { - "Author": "Nyhus, Erika", - "Title": "Brain Networks Related to Theta Oscillatory Activity During Episodic Memory Retrieval " - }, - { - "Author": "Neymotin, Sam", - "Title": "Ih-dependent tuning of theta and gamma oscillations in a multiscale computer model of CA3" - } - ] - }, - { - "Name": "Alpha", - "Posters": [ - { - "Author": "Haegens, Saskia", - "Title": "Laminar profile of the sensorimotor (rolandic) alpha rhythm: generation and modulation" - }, - { - "Author": "Piantoni, Gio", - "Title": "EEG Alpha Power Correlates with the Duration of Bistable Perception" - } - ] - }, - { - "Name": "Beta / delta", - "Posters": [ - { - "Author": "Arnal, Huc H.", - "Title": "Sensorimotor (delta-beta) coupled oscillations underlie temporal prediction accuracy" - }, - { - "Author": "Reimers, Mark", - "Title": "A model for delta rhythm fit to high-resolution cortical activity data" - } - ] - }, - { - "Name": "Attention", - "Posters": [ - { - "Author": "Baldauf, Daniel", - "Title": "Neural mechanisms of object-based attention" - }, - { - "Author": "Daitch, Amy L.", - "Title": "Low frequency phase modulations with spatial attention relate to visually induced response and reaction time" - }, - { - "Author": "Howe, W.M./Kozak, Rouba", - "Title": "Distinct behavioral and neurophysiological correlates of prefrontal acetylcholine and glutamate transients during attentional task performance" - }, - { - "Author": "Gola, Mateusz", - "Title": "EEG beta band activity is related to attention and attentional deficits in the visual performance of elderly subjects." - }, - { - "Author": "Lee, Jung Hoon", - "Title": "Potential mechanisms underlying intercortical signal regulation via cholinergic neuromodulators" - }, - { - "Author": "Bastos, Andre", - "Title": "Inter-areal directed interactions define a functional and dynamic heirachy of the primate visual system" - } - ] - } - ] - }, - { - "Session": "Poster Session 3 (Wednesday Morning through Lunch)", - "Themes": [ - { - "Name": "Data Analysis", - "Posters": [ - { - "Author": "Krishnaswamy, Pavitra", - "Title": "New Methods to Remove Cardiac Pulsation Artifacts and Analyze EEG Rhythms Recorded in the MR Scanner" - }, - { - "Author": "Moore-Kochlacs, Caroline", - "Title": "Spike sorting for spatially dense, high channel count extracellular recordings" - }, - { - "Author": "Tang, Wei", - "Title": "Granger causality analysis with resting-state MEG revealed default-mode network connectivity" - }, - { - "Author": "Rastelli, Federica", - "Title": "Towards new oscillation-based neurostimulation strategies to rehabilitate visuo-spatial neglect: Evidence from left prefrontal beta activity and visual awareness in stroke patients" - }, - { - "Author": "Martinet, Louis-Emmanuel", - "Title": "Characterization of local spatial propagation of ictal activity" - }, - { - "Author": "Perge, Janos", - "Title": "Decoding arm movements from action potentials and local field potentials in human motor cortex" - }, - { - "Author": "Deng, Xinyi", - "Title": "A point process approach to identifying and tracking transitions in neural spiking dynamics in the subthalamic nucleus of Parkinson's patients" - }, - { - "Author": "Stephen, Emily", - "Title": "Assessing dynamics, spatial scale, and uncertainty in task-related brain network analyses" - }, - { - "Author": "Franzesi, Giovanni Talei", - "Title": "Awake Autopatching: Automatic whole cell patch clamp of hippocampal neurons in awake behaving animals" - }, - { - "Author": "King, Allen", - "Title": "YAAGIL Cognitive Architecture" - } - ] - }, - { - "Name": "Resting State", - "Posters": [ - { - "Author": "Groppe, David", - "Title": "Dominant frequencies of resting human brain activity as measured by the electrocorticogram" - }, - { - "Author": "Nagao, Kikuko", - "Title": "Prediction of cognitive ability and resting state MEG based on conscious self-regulating behavior for 3-4-year-old children" - } - ] - }, - { - "Name": "TMS tADCs", - "Posters": [ - { - "Author": "Kar, Kohitij", - "Title": "Transcranial alternating current stimulation affects motion adaptation in V1 and MT neurons in awake, behaving macaques" - }, - { - "Author": "Chanes, Lorena", - "Title": "Hemisphere-specific causal contributions of left and right frontal oscillatory activity to human visual perception: A Transcranial Magnetic Stimulation (TMS) study" - }, - { - "Author": "Rastelli, Federica", - "Title": "Towards new oscillation-based neurostimulation strategies to rehabilitate visuo-spatial neglect: Evidence from left prefrontal beta activity and visual awareness in stroke patients" - } - ] - }, - { - "Name": "Human intracortical recordings: connections between population rhythms and spiking", - "Posters": [ - { - "Author": "Dehghani, Nima", - "Title": "The geometry of excitation-inhibition balance in human neocortex" - }, - { - "Author": "Honey, Christopher", - "Title": "Topography of Suppressing Rhythms in Human Cerebral Cortex" - } - ] - } - ] - }]; -} \ No newline at end of file From 09a874c52b446277a407ab3a4513ef936e5b9bed Mon Sep 17 00:00:00 2001 From: hurtstotouchfire Date: Fri, 5 Dec 2014 23:14:32 -0500 Subject: [PATCH 46/59] strip empty links from sidenav --- _includes/side_nav.html | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_includes/side_nav.html b/_includes/side_nav.html index 906e524..03de12d 100644 --- a/_includes/side_nav.html +++ b/_includes/side_nav.html @@ -1,12 +1,12 @@ -