Merge branch 'anne-urai:main' into main

.spyproject/config/backups/workspace.ini.bak

@@ -4,7 +4,7 @@ save_data_on_exit = True
 save_history = True
 save_non_project_files = False
 project_type = 'empty-project-type'
-recent_files = ['..\\climate_dataviz\\carbon_budget.py', 'IBLdata_behav.md']
+recent_files = ['IBLdata_behav.md']
 
 [main]
 version = 0.2.0

IBLdata.md

@@ -12,6 +12,9 @@ Many projects make use of the large dataset collected by the [International Brai
 * [Video description of the data by Eric deWitt](https://www.youtube.com/watch?v=NofrFH8FRZU), for NeuroMatchAcademy.
 * Explore the data through the [old interactive portal](https://data-sciviz.internationalbrainlab.org/home) and the newer [interactive data explorer](https://viz.internationalbrainlab.org/).
 
+### ToDo: Colab for IBL data analysis without local Python install
+See [here](https://medium.com/@nogamudrik_96888/how-to-access-dandis-dandisets-for-your-neural-data-project-64a643760d2b)
+
 ### Behavioral data
 [Working with IBL behavioral data](https://anne-urai.github.io/lab_wiki/IBLdata_behav.html)
 
@@ -52,4 +55,4 @@ eids = pd.read_csv(os.path.join(save_dir,'eids_on_alice.csv'))
 eids = eids.eid.values
 print(len(eids)) # should be 51...
 
-```
+```

IBLdata_neural.md

@@ -7,6 +7,7 @@ title: IBL behavioral data
 * See [docs.internationalbrainlab.org/](https://int-brain-lab.github.io/iblenv/public_docs/public_introduction.html) for a landing page and overview.
 * You can find some example data and check out analyses [here](https://int-brain-lab.github.io/iblenv/notebooks_external/data_release_repro_ephys.html).
 * Browse the data in this [interactive visualization app](https://viz.internationalbrainlab.org/app).
+- See [here](https://docs.google.com/presentation/d/1hH-iv7721-5mnPSmqlSuZRyMTOVWQizjC0mymWX1z5U/edit#slide=id.g2b37c37de99_0_61) for a tutorial given at COSYNE 2024 (recording [here](https://drive.google.com/file/d/15uvU6A8eDyjVEhw_JOEzbqEbtt9U4-MX/view?usp=drive_link), accessible with an IBL account).
 
 ### Working with unpublished IBL data on ALICE
 

Practical.md

@@ -5,6 +5,7 @@ rank: 10
 ---
 
 ### Getting started in the lab
+- See [this page](https://www.medewerkers.universiteitleiden.nl/po/international-staff?cf=sociale-wetenschappen&cd=psychologie) for lots of resources for international staff at the university.
 - Get added to the _CoCoSys lab MS teams group_ (ask Anne)
 - Get added to the _Cognitive Psychology_, _Open Science Community Leiden_ and _Psychology Living Room_ MS teams groups. The _MS Teams_ group has a good wiki with a lot of department-related information. Make sure to check it out!
 - Get added to the Google lab calendar
@@ -37,27 +38,33 @@ Inspired by the [Voytek lab](https://github.com/voytekresearch), make a core Git
 - Olthoff room (CogPsy) for up to 8 ppl: there is a paper calendar at the secretariat.
 
 ### Conferences
-I normally go to the Dutch [NVP](https://www.societyforbrainandcognition.nl/) (more cognitive) or [DNM](https://dnm22.azuleon.org/) (more neuro) meetings in person, and to the virtual NeuroMatch conferences. Depending on your career stage and interests, you can consider attending FENS, SfN, ECVP, ASSC, CCN.
+Feel free to explore meetings and conferences, and discuss where you'd like to go!
 
-I strongly encourage students and postdocs to attend at least one summer school. Neuromatch Academy is fantastic, as is the in-person [Rauischolzhausen vision science](http://www.allpsych.uni-giessen.de/rauisch/) one.
+I normally go to the Dutch [NVP](https://www.societyforbrainandcognition.nl/) (more cognitive) or [DNM](https://dnm22.azuleon.org/) (more neuro) meetings in person, and to the virtual NeuroMatch conferences. Depending on your career stage and interests, you can consider attending [FENS](https://fensforum.org/), [SfN](https://www.sfn.org/), [ECVP](https://ecvp.eu/), [ASSC](https://theassc.org/), CCN, [Cosyne](https://www.cosyne.org/), [CogSci](https://cognitivesciencesociety.org/).
 
-Feel free to explore meetings and conferences, and discuss where you'd like to go!
+#### Smaller meetings
+- [Society for the Biology of Decision Making](https://sbdm2023.sciencesconf.org/)
+- [Bernstein Conference](https://bernstein-network.de/en/bernstein-conference/bernstein-conference-2024/)
 
 ### Summer schools
+I strongly encourage students and postdocs to attend at least one summer school.  
+- [overview of summer schools by Natalie Schaworonkow](https://docs.google.com/spreadsheets/d/1nezjxkU8kGsA9MUI3Eph60s303VwfQLqMSNrSnnRSzk/edit#gid=1015366364)
 - Rauischolzhausen, vision science
 - CSHL, vision science
 - Neuromatch Academy
 - Barcelona behavioral modelling
 - Nencki School of Ideas, Poland
 - Mathematical Methods in Computational Neurosciences, Norway
+- [Cajal course in computational neuroscience](https://cajal-training.org/on-site/computational-neuroscience-2024/)
 
 ### Laptop
 Once you get a university laptop (talk to Anne before ordering it, to make sure we get you something useful) request it to switch to ['semi-managed'](https://helpdesk.universiteitleiden.nl/tas/public/ssp/content/serviceflow?unid=2c19d2f22cde4c509ff4958b173a2fba). Without doing this, you won't be able to install much software. Ask Anne how to best do this.
 
 ### Funding - PhD
-These are some funding opportunities to check out:
+These are some funding opportunities to check out for coming to Leiden:
 - [CAPES](https://www.iie.org/Programs/CAPES), PhD funding for students from Brazil
 - [ANID](https://anid.cl/), PhD funding for students from Chile
+- [LPDP](https://www.universiteitleiden.nl/leiden-indonesia/education/scholarships) for students from Indonesia
 - [CSC](https://www.universiteitleiden.nl/en/scholarships/sea/csc-leiden-university-scholarship), PhD funding for students from China
 - [Tata trusts](https://www.tatatrusts.org/our-work/individual-grants-programme/education-grants), funding for students from India
 - [FCT](https://www.fct.pt/apoios/bolsas/concursos/individuais2021.phtml.en), PhD funding for students from Portugal with a stay abroad
@@ -71,13 +78,16 @@ See [this older list](https://anneurai.net/2016/10/16/postdoctoral-fellowship-pr
 - [AXA](https://www.axa-research.org/en/page/AXA-Fellowships?xtatc=INT-1-%5BAXA_FELLOWSHIPS%5D)
 - [Branco Weiss](https://brancoweissfellowship.org/) 
 - KNAW grants
-- Women in Science Fellowship (L’Oréal-UNESCO)  
+- [Women in Science Fellowship (L’Oréal-UNESCO)](https://www.forwomeninscience.com/authority/international-awards)
+- [Graduate Women in Science Fellowship](https://www.gwis.org/page/fellowship_program)
 - Narsad Young investigator
 - [EMBO](https://www.embo.org/funding/fellowships-grants-and-career-support/postdoctoral-fellowships/) biology
 - [Human Frontier Science Program](https://www.hfsp.org/funding/hfsp-funding/postdoctoral-fellowships)
 - [LUF Praesidium Libertatis](https://www.luf.nl/en/apply-for-grants/researchers/praesidium-libertatis) for a postdoc already working in Leiden
 - [NWO Veni](https://www.nwo.nl/en/researchprogrammes/nwo-talent-programme/projects-veni/veni-2022) or [NWO ENW-M](https://www.nwo.nl/en/researchprogrammes/open-competition-enw)
 - other [LUF grants](https://www.luf.nl/en/apply-for-grants/researchers/academic-project)
+- after doing a PhD in NL, for going abroad: NWO Rubicon 
+- postdoc abroad (after PhD in NL) or postdoc in NL (after PhD abroad): [Ammodo Science Award](https://ammodo-science-award.org/en/fellowship/regulations/)
 
 ### Funding - travel grants
 - [IBRO exchange grants](https://www.fens.org/careers/grants-and-stipends/grant/fens-ibro-perc-exchange-fellowships) for research visits to another lab (1-3 months).
@@ -90,3 +100,4 @@ See [this older list](https://anneurai.net/2016/10/16/postdoctoral-fellowship-pr
 - [FENS/IBRO exchange visits](https://www.fens.org/careers/grants-and-stipends/grant/fens-ibro-perc-exchange-fellowships)
 - [Travelling fellowships](https://www.biologists.com/travelling-fellowships/), Company of Biologists
 - [LNVH Distinguished Women Scientist Fund](https://www.lnvh.nl/dws-fund) travel funding for women postdocs in NL less than 3 years from PhD
+- [EMBO Scientific Exchange grant](https://www.embo.org/funding/fellowships-grants-and-career-support/scientific-exchange-grants/) for research visits 1 week - 3 months in another European country

ProjectIdeas.md

@@ -24,15 +24,22 @@ _See [here](https://anne-urai.github.io/lab_wiki/IBLdata.html) for some examples
 - Fit data from [Gupta et al](https://doi.org/10.1101/2023.01.18.524599) with a history-dependent DDM, does the pattern found in [humans and mice](https://2023.ccneuro.org/view_paper.php?PaperNum=1119) also hold in rats? 
 - Can we detect cognitive strategies using constrained RNNs? Fit new models (e.g. [here](https://www.biorxiv.org/content/10.1101/2023.04.12.536629v2), [here](https://www.biorxiv.org/content/10.1101/2023.05.17.541226v1), [here](https://www.biorxiv.org/content/10.1101/2023.06.23.546250v1), [tutorial](https://github.com/kstach01/CogModelingRNNsTutorial)) to perceptual decision-making data.
 - Do mice show the same history-dependent choice history bias as humans? Implement [this work](https://2023.ccneuro.org/proceedings/0000544.pdf) in the new [HSSM package](https://github.com/lnccbrown/HSSM) and be a beta-tester. Together with Alex Fengler, Brown University.
-
-
+- How are fatigue reports related to reaction times in a task with physically effortful responses? Using data from [Mathews et al., 2023](https://www.sciencedirect.com/science/article/pii/S0010027723002378).
+- Do implicit and explicit priors differentially change biases in evidence accumulation? Fit a DDM to [these data](https://www.biorxiv.org/content/10.1101/2023.08.18.553834v1).
+- Do Hidden Markov Models of disengagement during decision-making (e.g. [here](https://www.nature.com/articles/s41593-021-01007-z)) capture the same disengaged states that participants report using _mind-wandering probes_? Collaboration with [Marieke van Vugt](https://mkvanvugt.wordpress.com/). 
+- With Steven Miletic: why do some find that history biases the starting point of evidence accumulation, and others the drift? Potential Averserial Collaboration.
+- With data from [Eisenberg et al](https://www.nature.com/articles/s41467-019-10301-1), quantify test-retest reliability of choice history bias within and across tasks.
 
 ### Neuroscience
 - Test prediction: does inactivation of PPC (LIP inactivation in monkeys or TMS to IPS0/1 or IPS 2/3 in humans) during the ITI reduce choice history bias? Find data or run a TMS experiment.
 - Do mice show 'handedness', i.e. a preference to respond with 'rightward' choices? Based on observation by Sebastian Bruijns, early on in the IBL task. Combine with literature review on handedness across decision-making tasks (especially in mice) with different response modalities.
 - Using data from [Ni et al](https://www.pnas.org/doi/10.1073/pnas.2120529119), link changes in motivation under methylphenidate (Ritalin) to the Expected Value of Control theory. With Bryant Jongkees. Apply a DDM to go beyond simple P(correct).
 - [Murray et al. 2014](https://www.nature.com/articles/nn.3862) found that cortical neurons display intrinsic timescales which become longer along the cortical hierarchy, and probably play an important role in longer-timescale functions like information maintenance. Has this finding been replicated in mice (beyond visual areas, see [Siegle et al.](https://www.nature.com/articles/s41586-020-03171-x)), and extended to subcortical areas (using the IBL dataset)? Does longer-timescale prior encoding (tracking of the block) mostly depend on neurons with long timescales in the IBL dataset? See also [Imani et al. 2023](https://www.biorxiv.org/content/10.1101/2023.01.01.522410v1).
     - Related: Cortical neurons display different degrees of intrinsic timescales, with longer timescales towards anterior cortical regions in primates (https://www.nature.com/articles/nn.3862). How do these timescales arise, and what are their roles in computation? One hypothesis is that these gradients arise from the genetic profile of different areas. As we're collecting the first brain-wide map of mouse neural activity during rest, this idea proposes to decompose the intrinsic timescale structure throughout the brain to different profiles of gene expression (from the Allen Atlas). See also [here](https://www.jneurosci.org/content/38/34/7476.long), [here](https://elifesciences.org/articles/61277).
+- Use platform like The Virtual Brain or the Human Neocortical Solver to make EEG predictions when we change low-level Fano Factors/noise correlations.
+- Can we use DeepLabCut to extract measures of heart rate and breathing from IBL video data?
+- Do neural waveform features change with age? Compare IBL ephys atlas with aging neural recordings.
+- Test ideas about [control-limited decision-making](https://doi.org/10.1101/2022.06.24.497481) in our DM data (perhaps applied to ageing and/or arousal). Potential collab with Alfonso Renart and/or Tobias Donner.
 
 ### Decision-making: data collection
 - How do decision-making strategies differ across mammalian species? Build and run a human version of the [IBL decision task](https://elifesciences.org/articles/63711), online and/or in the lab with EEG. 

PythonSetup.md

@@ -30,7 +30,7 @@ rank: 6
   * Further practice: pull this wiki repo, add something in the [Markdown language](https://guides.github.com/features/mastering-markdown/), and submit a pull request (see Home for instructions on how to contribute to the wiki).
 * Learn the basics of Python
   * [DataCamp](https://www.datacamp.com/groups/shared_links/bdca0f873fb4e2a3d00f489268470b8eef78a1eafcde11c025950376eed73c9c) has very good adaptive programming courses. Sign up with your _@umail.leidenuniv.nl_ address using the link for free access.
-  * [Intro to Python](http://gureckislab.org/courses/fall20/labincp/chapters/03/00-python.html) & [lab in cognition & perception](http://gureckislab.org/courses/fall19/labincp/intro.html), both by Todd Gureckis.
+  * [Lab in cognition & perception](https://teaching.gureckislab.org/fall22/labincp/course-content/syllabus.html), both by Todd Gureckis.
   * Students at Leiden University can follow the [Introduction to Python course, offered by LIACS](https://stepik.org/course/73333/promo).
    *  You can also access [DataCamp learning resources](https://www.datacamp.com/groups/shared_links/a6bb93f6866b8ced468d96d1406e020a421592ea) with your Leiden Uni account.
 * Think about the **structure of data**

Reading.md

@@ -5,6 +5,7 @@ rank: 5
 ---
 
 Read widely, deeply and regularly. Read weird things. Keep track of what you read, and make notes; I strongly recommend Zotero with the Zotfile plugin for managing both pdfs and references.
+[Here](https://www.cameronbrick.com/literature-search) is a useful overview by Cameron Brick on how to stay on top of the literature.
 
  Some of my favorite papers and books:
 
@@ -19,6 +20,7 @@ Read widely, deeply and regularly. Read weird things. Keep track of what you rea
 - Siegel M, Donner TH, Engel AK (2012) Spectral fingerprints of large-scale neuronal interactions. Nature Reviews Neuroscience 13:121–134.
 - Summerfield C, de Lange FP (2014) Expectation in perceptual decision making: neural and computational mechanisms. Nat Rev Neurosci 15:745–756.
 - O’Connell RG, Kelly SP (2021) Neurophysiology of Human Perceptual Decision-Making. Annual Review of Neuroscience 44:null.
+- Carandini M (2024) Sensory choices as logisitic classification. [bioRXiv](https://www.biorxiv.org/content/10.1101/2024.01.17.576029v1)
 
 #### Statistics
 - Aarts E, Verhage M, Veenvliet JV, Dolan CV, van der Sluis S (2014) A solution to dependency: using multilevel analysis to accommodate nested data. Nature Neuroscience 17:491–496.
@@ -45,4 +47,4 @@ As a scientists you'll develop many other skills. Via [Mark Humphries](https://w
 - [Data visualization](https://drive.google.com/file/d/1LouVvISCRlWkItZgzoHcgoU5Q1VyHT4U/view)
 - [Giving a talk](https://drive.google.com/file/d/13efH6iA6toPtJ91KBt_QCeAyQBcSN7SA/view)
 - [Clean code](https://drive.google.com/file/d/1TraVwRkbkCbHq-s_-NS69ZEbRNwH8XNh/view)
-- [Peer review](https://drive.google.com/file/d/1g7VSbUkF9wBszcjHCeZlGHoHqUqYfDC0/view)
+- [Peer review](https://drive.google.com/file/d/1g7VSbUkF9wBszcjHCeZlGHoHqUqYfDC0/view)

Vision.md

@@ -10,6 +10,14 @@ Figuring out how the world works, [for the sake of knowledge itself](https://www
 ### [Ethics](https://www.cmu.edu/dietrich/psychology/cognitiveaxon/documents/Verstynen_PES.pdf) and open science
 With this [privilege of doing science](https://www.codykommers.com/post/57-nancy-kanwisher) comes the responsibility of doing it well (or at least, in the best way we can). We're responsible to taxpayers for getting the most out of their hard-earned euros; to our academic communities for not mislead each other purposefully or waste time on dead-ends; and to ourselves for spending our time well.
 
+See also the [European Code of Conduct for Research Integrity](https://allea.org/code-of-conduct/#toggle-id-2), which lists the following principles as guidelines: 
+
+> - Reliability in ensuring the quality of research, reflected in the design, methodology, analysis, and use of resources.
+> - Honesty in developing, undertaking, reviewing, reporting, and communicating research in a transparent, fair, full, and unbiased way.
+> - Respect for colleagues, research, participants, research subjects, society, ecosystems, cultural heritage, and the environment.
+> - Accountability for the research from idea to publication, for its management and organisation, for training, supervision, and mentoring, and for its wider societal impacts.
+> From: [ALLEA](https://allea.org/code-of-conduct/)
+
 To maximize the usefulness of our science, we must do our work ethically and openly. This means being honest (with ourselves and others), transparent, and always open to learning and improving how we work. Collaborate, don't compete. 
 
 **Make your work accessible**. Publish your paper as a preprint (on bioRxiv, arXiv, psyArXiv or OSF); choose open-access journals; [avoid Elsevier](https://www.talyarkoni.org/blog/2016/12/12/why-i-still-wont-review-for-or-publish-with-elsevier-and-think-you-shouldnt-either/) when possible; get on Twitter/Mastodon and write accessible summaries of your findings: [it'll even help your career.](http://dx.doi.org/10.7554/eLife.16800.001)