Add files via upload

_config.yml

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+# Welcome to Jekyll!
+#
+# This config file is meant for settings that affect your whole blog, values
+# which you are expected to set up once and rarely need to edit after that.
+# For technical reasons, this file is *NOT* reloaded automatically when you use
+# 'jekyll serve'. If you change this file, please restart the server process.
+
+# Site settings
+title: NILab
+email: [email protected]
+description: > # this means to ignore newlines until "baseurl:"
+  Home of the Neuroinformatics Lab at the Fondazione Bruno Kessler, Trento.
+baseurl: ""
+url: ""
+
+include:
+  - .htaccess
+  - _pages
+
+sass:
+  sass_dir: _sass
+
+# Conversion
+markdown: kramdown
+highlighter: rouge
+lsi: false
+excerpt_separator: "\n\n"
+incremental: false
+
+
+
+# Markdown Processing
+kramdown:
+  input: GFM
+  hard_wrap: false
+  auto_ids: true
+  footnote_nr: 1
+  entity_output: as_char
+  toc_levels: 1..6
+  smart_quotes: lsquo,rsquo,ldquo,rdquo
+  enable_coderay: false
+  parse_block_html: true # default for kramdown is false. This will enable using Markdown links
+

_data/alumni_bsc.yml

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+#- name: Vishnu Saj, Spring 2017
+
+#- name: Arjo Andringa, Spring 2016
+
+#- name: Joey Braspenning, Spring 2017
+
+#- name: Tjerk Benschop, Summer 2017
+
+#- name: Margot Leemker, Spring 2017
+
+#- name: Sietske Lensen, Spring 2017
+
+#- name: Daniëlle van Klink, Spring 2016
+
+#- name: Amber Vervloet, Spring 2019

_data/alumni_members.yml

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+- name: Laura Suarez
+  photo: laura.jpg
+  duration: Research Scientist at Mila Quebec
+  info: PhD student
+  email:
+  number_educ: 0
+  education1: 
+  education2:
+  education3:
+  education4:
+
+- name: Ross Markello
+  photo: ross.jpg
+  duration: Data Science Engineer at <a href='https://www.octavebio.com/'> Octave Biosciences</a>
+  info: PhD student
+  email:
+  number_educ: 0
+  education1:
+  education2:
+  education3:
+  education4:
+
+- name: Golia Shafiei
+  photo: golia.jpg
+  duration: Post-doc at U Penn
+  info: PhD student
+  email:
+  number_educ: 0
+  education1:
+  education2:
+  education3:
+  education4:
+
+- name: Ying-Qiu Zheng
+  photo: yingqiu.jpg
+  duration: PhD student at Oxford
+  info: MSc student
+  email:
+  number_educ: 0
+  education1:
+  education2:
+  education3:
+  education4:
+
+- name: Bertha Vazquez-Rodriguez
+  photo: bertha.jpg
+  duration: Data Science Engineer at <a href='https://clemex.com/'> Clemex</a>
+  info: Post-Doc
+  email: [email protected]
+  number_educ: 0
+  education1:
+  education2:
+  education3:
+  education4:
+
+- name: Nykan Mirchi
+  photo: nykan.jpg
+  duration: MD student at UofT
+  info: BSc student
+  email:
+  number_educ: 0
+  education1:
+  education2:
+  education3:
+  education4:

_data/alumni_msc.yml

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+#- name: Maarten Leeuwenhoek, Spring 2015
+
+#- name: Koen M Bastiaans, Spring 2015
+
+#- name: Farshaad Hoeseni, Fall 2015
+
+#- name: Oliver Ostojic, Spring 2016
+
+#- name: Tjerk Benschop, Spring 2016
+
+#- name: Bert Visscher, Fall 2017
+
+#- name: Ahmad Jamalzada, Fall 2017
+
+#- name: Corne Koks, Fall 2018
+
+#- name: Damian Bouwmeester, Summer 2019

_data/alumni_visitors.yml

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+#- name: Nikolaos Iliopoulos, Spring 2016
+
+#- name: Vitaly Fedoseev, all of 2016
+
+#- name: Alexander Vanstone, Spring 2016
+
+#- name: Ramakrishna Aluru, Summer 2018
+
+#- name: Changwei Zou, Spring 2018
+
+#- name: Kemal Demir, Summer 2019

_data/news.yml

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+- date: 22 July 2024
+  headline: "Gabriele Amorosino has been awarded cum laude a PhD in Cognitive and BrainSciences from the University of Trento. Doctoral thesis: “Deep Learning for Brain Structural Connectivity Analysis: from Tissue Segmentation to Tractogram Alignment”."
+
+- date: 16 May 2024
+  headline: "Paolo Avesani gives the talk “Artificial Intelligence and Neuroscience: a Strange Loop” at the event dedicated to AI and neuroscience organized by Accademia degli Agiati in Rovereto."

_data/projlist.yml

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+- title: "Neuroimaging Data Science"
+  image: res_neuromaps.png
+  description: Imaging technologies are increasingly used to generate high-resolution reference maps of brain structure and function. Modern scientific discovery relies on making comparisons between new maps (e.g. task activations, group structural differences) and these reference maps. We develop open tools for accessing, transforming, and analyzing structural and functional brain annotations.
+  highlight: 1
+
+- title: "Annotated Connectomics"
+  image: res_annot_vince.png
+  description: Brain regions differ in terms of their cytoarchitecture, neurotransmitter receptor profiles, gene expression, temporal dynamics, etc. We reconstruct “annotated” connectomes, enriched with features. The goal of this work is to understand how microscopic properties and macroscale network embedding interact to support the emergence of global dynamics and patterned neural activity.
+  highlight: 1
+
+- title: "Structure-Function Coupling"
+  image: res_scfc_2.png
+  description: Networks of white matter fibers projections form polyfunctional neural circuits that support cognition. We study how the structural organization of the brain supports emergent neural dynamics. We are primarily interested in how structure-function coupling varies across the cortical hierarchy, how it depends on local micro-architecture, and how it varies across time.
+  highlight: 1
+
+- title: "Neuromorphic Networks"
+  image: res_rc.png
+  description: How does connectome architecture shape computation? We are constructing bio-instantiated artificial neural networks by implementing real biological brain connectomes as artificial networks. Using realistic biophysical dynamics and connection patterns, we are developing neuromorphic reservoir computers - connectomes that can be trained to perform cognitive tasks, such as working memory, language comprehension, spatial navigation.
+  highlight: 1
+
+- title: "Disease Propagation"
+  image: res_agent.png
+  description: Axonal fibers provide a scaffold through which misfolded pathogenic proteins spread, shaping the course and expression of neurodegenerative diseases such as Parkinson’s (PD) and Alzheimer’s (AD) disease.  We develop generative models that integrate connectivity (diffusion MRI), co-activation (functional MRI) and genetics (mRNA transcription) to predict the evolution of neurodegenerative diseases. 
+  highlight: 1
+
+- title: "Statistical Connectomics"
+  image: res_stat.png
+  description: An emerging theme in network neuroscience emphasizes links between multiscale structural and functional features of the brain, and the rich cognitive-behavioural repertoire they support. We develop multivariate statistical learning techniques that map high-dimensional brain imaging modalities to phenotypic variation in healthy and clinical populations.
+  highlight: 1
+
+- title: "Null Models"
+  image: res_null.png
+  description: How do we demonstrate that a brain network feature is statistically unexpected? Null models are an inferential tool to assess the presence or magnitude of features, by selectively preserving specific architectural properties of brain networks while randomizing others. We develop and systematically benchmark null models to understand the architecture of brain networks.
+  highlight: 1
+
+- title: "Network Communication"
+  image: res_comm.png
+  description: A fundamental question in connectomics is how the organization of brain networks supports neural signaling. Using anatomically realistic brain networks derived from imaging and tracing, we develop computational models of inter-regional communication. We use these models to characterize how communication processes unfold on structural brain networks and how they support cognitive capacity.
+  highlight: 1

_data/publist.yml

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+- title: "Integrating direct electrical brain stimulation with the human connectome"
+  image: 
+  description: 
+  authors: Coletta, L, Avesani, P, Zigiotto, L, Venturini, M, Annicchiarico, L, Vavassori, L, Ng, S, Duffau, H, Sarubbo, S
+  link:
+    url: https://doi.org/10.1093/brain/awad402
+    display: Brain (2024)
+  highlight: 0
+
+- title: "brainlife.io: A decentralized and open source cloud platform to support neuroimaging research"
+  image: 
+  description: 
+  authors: Soichi Hayashi et al.
+  link:
+    url: https://doi.org/10.1038/s41592-024-02237-2 
+    display: Nature Methods (2024)
+  highlight: 0

_data/team_members.yml

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+- name: Paolo Avesani
+  photo: #bratislav.jpg
+  info: Principal Investigator
+  email: [email protected]
+  number_educ: 0
+  education1:
+  education2:
+  education3:
+  education4:
+  education5:
+
+- name: Ludovico Coletta
+  photo: #zhen-qi.jpg
+  info: Post-doc fellow
+  email: [email protected]
+  number_educ: 0
+  education1:
+  education2:
+  education3:
+  education4:

_includes/analytics.html

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+<script>
+  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){
+  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),
+  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)
+  })(window,document,'script','https://www.google-analytics.com/analytics.js','ga');
+
+  ga('create', 'UA-82164432-1', 'auto');
+  ga('send', 'pageview');
+
+</script>

_includes/footer.html

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+<div id="footer" class="panel">
+  <div class="panel-footer">
+	<div class="container-fluid">
+	  <div class="row">
+
+		  <p>&copy 2024 Avesani Paolo. Site made with <a href="https://jekyllrb.com">Jekyll</a> and <a href="https://getbootstrap.com/">Bootstrap</a>.</p>
+		  <p>  </p><p>
+
+	  </div>
+	</div>
+  </div>
+</div>
+
+<script src="https://ajax.googleapis.com/ajax/libs/jquery/1.11.3/jquery.min.js"></script>
+<script src="{{ site.url }}{{ site.baseurl }}/js/bootstrap.min.js"></script>

_includes/head.html

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+<head>
+  <meta charset="utf-8">
+  <meta http-equiv="X-UA-Compatible" content="IE=edge">
+  <meta name="viewport" content="width=device-width, initial-scale=1">
+  <title>{% if page.title %}{{ page.title | escape }}{% else %}{{ site.title | escape }}{% endif %}</title>
+  <meta name="description" content="{% if page.excerpt %}{{ page.excerpt | strip_html | strip_newlines | truncate: 160 }}{% else %}{{ site.description }}{% endif %}">
+  <link rel="stylesheet" href="{{ "/css/main.css" | prepend: site.baseurl | prepend: site.url}}">
+  <link rel="canonical" href="{{ page.url | replace:'index.html','' | prepend: site.baseurl | prepend: site.url }}">
+<link rel="shortcut icon" type ="image/x-icon" href="{{ site.url }}{{ site.baseurl }}/images/favicon.ico">
+
+{% if jekyll.environment == 'production' %}
+{% include analytics.html %}
+{% endif %}
+
+</head>

_includes/header.html

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+<div class="navbar navbar-default navbar-fixed-top" role="navigation">
+  <div class="container-fluid">
+	<div class="navbar-header">
+	  <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar-collapse-1" aria-expanded="false">
+		<span class="sr-only">Toggle navigation</span>
+		<span class="icon-bar"></span>
+		<span class="icon-bar"></span>
+		<span class="icon-bar"></span>
+	  </button>
+
+    <a class="navbar-brand" href="{{ site.url }}{{ site.baseurl }}/">Neuroinformatics Lab</a>
+	</div>
+	<div class="collapse navbar-collapse" id="navbar-collapse-1">
+	  <ul class="nav navbar-nav navbar-right">
+		<li><a href="{{ site.url }}{{ site.baseurl }}/">Home</a></li>
+		<li><a href="{{ site.url }}{{ site.baseurl }}/research">Research</a></li>		  
+		<li><a href="{{ site.url }}{{ site.baseurl }}/team">Team</a></li>
+		<li><a href="{{ site.url }}{{ site.baseurl }}/publications">Publications</a></li>
+	  </ul>
+	</div>
+  </div>
+</div>

_includes/news.html

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+
+<div class="well">
+<h4>News</h4>
+
+{% for article in site.data.news limit:9 %}
+{{ article.date }}
+<p>{{ article.headline }}</p>
+{% endfor %}
+
+<h4><a href="{{ site.url }}{{ site.baseurl }}/allnews.html">... see all News</a></h4>
+
+    </div>

_layouts/default.html

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+<!DOCTYPE html>
+<html>
+
+  {% include head.html %}
+
+  <body>
+
+    {% include header.html %}
+
+    <div class="container-fluid">
+      <div class="row">
+        {{ content }}
+      </div>
+    </div>
+
+    {% include footer.html %}
+
+  </body>
+
+</html>

_layouts/gridlay.html

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+---
+layout: default
+---
+<div id="gridid" class="col-sm-12">
+  {{ content }}
+</div>

_layouts/homelay.html

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+---
+layout: default
+---
+
+  <div id="homeid" class="col-sm-8">
+        <h1>Welcome to the Neuroinformatics Lab</h1>
+
+	{{ content }}
+  </div>
+  <div id="newsid" class="col-sm-4" >
+	{% include news.html %}
+  </div>

_layouts/page.html

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+---
+layout: default
+---
+<article class="post">
+
+  <header class="post-header">
+    <h1 class="post-title">{{ page.title }}</h1>
+  </header>
+
+  <div class="post-content">
+    {{ content }}
+  </div>
+
+</article>

_layouts/piclay.html

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+---
+layout: default
+---
+
+<div id="picid" class="col-sm-12">
+  {{ content }}
+</div>