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<!DOCTYPE html>
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<title>Schedule - Omics integration and systems biology - 2024</title>
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<h1 class="title">Schedule - Omics integration and systems biology - 2024</h1>
</div>
<div class="quarto-title-meta">
</div>
</header>
<section id="before-the-course" class="level4">
<h4 class="anchored" data-anchor-id="before-the-course">Before the course</h4>
<p><strong>Prepare</strong> <a href="https://nbisweden.github.io/workshop_omics_integration/precourse.html">Pre-course materials</a>. In order to be able to access the lab notebooks for this course you need to have access to <a href="https://serve.scilifelab.se">SciLifeLab Serve</a>. For lunching practicals please follow the instructions <a href="./session_intro/Instructions%20for%20course%20OMICSINT_H24.pdf">here</a>.</p>
</section>
<section id="course-schedule" class="level4">
<h4 class="anchored"><img border="0" src="https://www.svgrepo.com/show/20800/event-date-and-time-symbol.svg" width="25" height="25"> Course schedule</h4>
<p><img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> - lecture</p>
<p><img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> - hands-on workshop</p>
<p><img border="0" src="https://www.svgrepo.com/show/307069/public-speaking-speak-tell-talk.svg" width="15" height="15"> - invited seminar</p>
<p><img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> - break</p>
<section id="day-1" class="level5">
<h5 class="anchored">Day 1</h5>
<strong>09.00 - 09.15</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Introduction and contextualization (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_intro/course_intro.pdf">Slides</a>
</li>
</ul>
</details>
<strong>09.15 - 09.55</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Machine Learning view of Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_ml/MachineLearningOmicsIntegration_Oskolkov.pdf">Slides</a>
</li>
</ul>
</details>
<p><strong>09.55 - 10.05</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>10.05 - 10.55</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Feature Selection and Supervised Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_ml/SupervisedOMICsIntegration/lab/SupervisedOmicsIntegration_Oskolkov.pdf">Slides</a>
</li>
</ul>
</details>
<p><strong>10.55 - 11.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>11.00 - 12.00</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Feature Selection and Supervised Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab feature selection</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Rstudio</code> app.
</li>
<li>
<a href="./session_ml/FeatureSelectionIntegrOMICs/lab/OmicsIntegration_FeatureSelection.html">Feature Selection lab Notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_feature_selection_amd_v.h24.9879876</code>
</li>
<br>
<li>
Launch <code>Lab supervised omics integration</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Rstudio</code> app.
</li>
<li>
<a href="./session_ml/SupervisedOMICsIntegration/lab/supervised_omics_integr_CLL.html">Supervised Integration lab Notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_supervised_omics_integration_amd_v.h24.38310b0</code>
</li>
</ul>
</details>
<p><strong>12.00 - 13.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Lunch</p>
<p><strong>13.00 - 13.10</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)</p>
<strong>13.10 - 14.00</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Unsupervised Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_ml/UnsupervisedOMICsIntegration/lab/Unsupervised_OmicsIntegration_Oskolkov.pdf">Slides</a>
</li>
</ul>
</details>
<p><strong>14.00 - 14.05</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>14.05 - 15.20</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Unsupervised Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab unsupervised omics integration</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Rstudio</code> app.
</li>
<li>
<a href="./session_ml/UnsupervisedOMICsIntegration/Multi-OMICs Factor Analysis (MOFA) and Unsupervised Data Learning.html">Unsupervised Integration lab Notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_unsupervised_omics_integration_amd_v.h24.6d635ce</code>
</li>
</ul>
</details>
<p><strong>15.20 - 15.30</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)</p>
<p><strong>15.30 - 17.00</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Assisted exercises</p>
<p><br></p>
<blockquote class="blockquote">
<h3 id="course-dinner-at-valvet-steakhouse" class="anchored" data-anchor-id="day-1"><strong>🌟 18:00</strong> <img border="0" src="https://www.svgrepo.com/show/11965/restaurant.svg" width="15" height="15"> <strong>Course Dinner</strong> at <a href="https://www.valvetsteakhouse.se">Valvet Steakhouse</a> 🌟</h3>
</blockquote>
<p><br></p>
</section>
<section id="day-2" class="level5">
<h5 class="anchored" data-anchor-id="day-2">Day 2</h5>
<p><strong>09.00 - 09.20</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Review (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)</p>
<strong>09.20 - 09.50</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Single Cell Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_ml/SingleCell/lab/Single_Cell_Integration_Oskolkov.pdf">Slides</a>
</li>
</ul>
</details>
<p><strong>09.50 - 10.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<p><strong>10.00 - 11.00</strong> <img border="0" src="https://www.svgrepo.com/show/307069/public-speaking-speak-tell-talk.svg" width="15" height="15"> <a href="https://www.linkedin.com/in/muthas/?originalSubdomain=se">Daniel Muthas</a> - “Deriving actionable insight from omics data – an industry perspective”</p>
<p><strong>11.00 - 11.15</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>11.15 - 12.00</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Single cell omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab single cell</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Rstudio</code> app.
</li>
<li>
<a href="./session_ml/SingleCell/lab/OMICS Integration and Systems Biology Course_ Single Cell Omics Integration.html"> Single cell omics integration lab notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_single_cell_amd_v.h24.7054451</code>
</li>
<br>
<li>
Launch <code>Lab UMAP</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_ml/UMAP_DataIntegration/UMAP_DataIntegration.html"> UMAP lab notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_umap_data_integration_amd_v.h24.6d635ce</code>
</li>
</ul>
</details>
<p><strong>12.00 - 13.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Lunch</p>
<strong>13.00 - 13.45</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Single cell omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab single cell</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Rstudio</code> app.
</li>
<li>
<a href="./session_ml/SingleCell/lab/OMICS Integration and Systems Biology Course_ Single Cell Omics Integration.html"> Single cell omics integration lab notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_single_cell_amd_v.h24.7054451</code>
</li>
<br>
<li>
Launch <code>Lab UMAP</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_ml/UMAP_DataIntegration/UMAP_DataIntegration.html"> UMAP lab notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_umap_data_integration_amd_v.h24.6d635ce</code>
</li>
</ul>
</details>
<p><strong>13.45 - 13.55</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)</p>
<p><strong>13.55 - 14.05</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>14.05 - 14.45</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Deep Learning for Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_ml/DeepLearningDataIntegration/lab/DeepLearningOmicsIntegration_Oskolkov.pdf">Slides</a>
</li>
</ul>
</details>
<p><strong>14.45 - 15.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>15.00 - 16.15</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Deep Learning for Omics integration (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab deep learning integration</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_ml/DeepLearningDataIntegration/lab/DeepLearningDataIntegration.html">Deep Learning for data integration lab html</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_ml_deep_learning_integration_amd_v.h24.6d635ce</code>
</li>
</ul>
</details>
<p><strong>16.15 - 16.30</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay</a>)</p>
<p><strong>16.30 - 17.00</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Assisted exercises</p>
<p><br> <br></p>
</section>
<section id="day-3" class="level5">
<h5 class="anchored" data-anchor-id="day-3">Day 3</h5>
<strong>09.00 - 10.00</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Introduction to biological network analysis (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_topology/lab/lectures/1Introduction.pdf">Introduction</a>
</li>
<li>
<a href="./session_topology/lab/lectures/2Network_inference.pdf">Network inference</a>
</li>
<li>
<a href="./session_topology/lab/lectures/3Community_analysis.pdf">Community analysis</a>
</li>
</ul>
</details>
<p><strong>10.00 - 10.15</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>10.15 - 11.00</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Introduction to biological network analysis (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab topology</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_topology/lab/topology_lab_part1.html">Topology lab Notebook part 1</a>
</li>
<li>
<a href="./session_topology/lab/topology_lab_part2.html">Topology lab Notebook part 2</a>
</li>
<li>
<a href="./session_topology/lab/topology_lab_part3.html">Topology lab Notebook part 3</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_topology_amd_v.h24.a2b336c</code>
</li>
</ul>
</details>
<p><strong>11.00 - 11.30</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Review (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)</p>
<p><strong>12.00 - 13.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Lunch</p>
<strong>13.00 - 14.00</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Introduction to biological network analysis (continued) (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab topology</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_topology/lab/topology_lab_part1.html">Topology lab Notebook part 1</a>
</li>
<li>
<a href="./session_topology/lab/topology_lab_part2.html">Topology lab Notebook part 2</a>
</li>
<li>
<a href="./session_topology/lab/topology_lab_part3.html">Topology lab Notebook part 3</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_topology_amd_v.h24.a2b336c</code>
</li>
</ul>
</details>
<p><strong>14.00 - 14.15</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>14.15 - 16.15</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Machine learning on Graphs (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_graphnn/GNN_main.html">Graph neural networks (html)</a>
</li>
<li>
<a href="./session_graphnn/GNN_main.ipynb">Graph neural networks (notebook file)</a>
</li>
<li>
<a href="./session_graphnn/GNN_lab.html">Graph neural networks lab (html)</a>
</li>
<li>
<a href="./session_graphnn/GNN_lab.ipynb">Graph neural networks lab (notebook file)</a>
</li>
</ul>
</details>
<strong>16.15 - 16.30</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_graphnn/environment.html">Data engineering tutorial</a>
</li>
</ul>
</details>
<p><strong>16.30 - 17.00</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Assisted exercises</p>
<p><br> <br></p>
</section>
<section id="day-4" class="level5">
<h5 class="anchored" data-anchor-id="day-4">Day 4</h5>
<strong>09.00 - 10.00</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Genome-scale metabolic models for integration (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_gems/GEMs_concept.pdf">Introduction – Constraint-based modeling concepts</a>
</li>
</ul>
</details>
<p><strong>10.00 - 10.15</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>10.15 - 11.30</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Genome-scale metabolic models for integration (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab GEMs</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_gems_amd_v.h24.a2b336c</code>
</li>
</ul>
</details>
<p><strong>11.30 - 11.45</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)</p>
<p><strong>12.00 - 13.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Lunch</p>
<p><strong>13.00 - 14.00</strong> <img border="0" src="https://www.svgrepo.com/show/307069/public-speaking-speak-tell-talk.svg" width="15" height="15"> <a href="https://getzlab.org/team/postdoctoral%20researcher/gustafsson-johan">Johan Gustafsson</a> - “Generation of context-specific genome-scale metabolic models using single-cell RNA-Seq data”</p>
<p><strong>14.00 - 14.15</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>14.15 - 14.45</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Non-negative matrix factorization (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_nmf/NMF_main.html">Non-negative Matrix Factorization</a>
</li>
</ul>
</details>
<strong>14.45 - 15.15</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Non-negative matrix factorization (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab NMF & SNF</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_nmf/NMF_lab.html">NMF lab Notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_nmf_amd_v.h24.1b36f11</code>
</li>
</ul>
</details>
<p><strong>15.15 - 15.30</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<strong>15.30 - 16.00</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Similarity network fusion (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_nmf/SNF_main.html">Similarity network fusion</a>
</li>
</ul>
</details>
<strong>16.00 - 16.30</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Similarity network fusion (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab NMF & SNF</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_nmf/SNF_lab.html">SNF lab Notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_nmf_amd_v.h24.1b36f11</code>
</li>
</ul>
</details>
<p><strong>16.30 - 16.45</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://www.chalmers.se/en/persons/netotea/">Sergiu</a>)</p>
<p><br> <br></p>
</section>
<section id="day-5" class="level5">
<h5 class="anchored" data-anchor-id="day-5">Day 5</h5>
<strong>09.00 - 09.45</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Gene set analysis and reporter features (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_gsa/GEM_GSA.pdf"> Gene set analysis via GEMs</a>
</li>
</ul>
</details>
<p><strong>09.55 - 10.00</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Break</p>
<p><strong>10.00 - 11.00</strong> <img border="0" src="https://www.svgrepo.com/show/307069/public-speaking-speak-tell-talk.svg" width="15" height="15"> <a href="https://www.su.se/english/profiles/matsn-1.191373">Mats Nilsson</a> - “Targeted in situ sequencing for characterization of the genetic, molecular and cellular diversity of healthy and disease tissues”</p>
<strong>11.00 - 11.45</strong> <img border="0" src="https://www.svgrepo.com/show/7421/computer.svg" width="15" height="15"> Gene set analysis and reporter features (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
Launch <code>Lab GEM GSA</code> on <a href="https://serve.scilifelab.se/projects/">Scilifelab Serve</a>, use <code>Jupyter</code> app.
</li>
<li>
<a href="./session_gsa/GEM_GSA.html">Gene set analysis lab Notebook</a>
</li>
<li>
Docker image: <code>docker pull rasoolsnbis/omicsint_h24:session_gsa_amd_v.h24.a1ae0fc</code>
</li>
</ul>
</details>
<p><strong>11.45 - 12.00</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Lab recap (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)</p>
<p><strong>12.00 - 13.10</strong> <img border="0" src="https://www.svgrepo.com/show/21938/time.svg" width="15" height="15"> Lunch</p>
<strong>13.00 - 14.00</strong> <img border="0" src="https://www.svgrepo.com/show/7321/teacher.svg" width="15" height="15"> Discussions and course end (<a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool</a>)
<details>
<summary>
Resources
</summary>
<ul>
<li>
<a href="./session_intro/closing remark.pdf">Closing remarks!</a>
</li>
<li>
<a href="https://docs.google.com/forms/d/e/1FAIpQLSekELo0i71zPUpH-QYvi2TSFREIDH1g_y6qWZTlI_owLiHdcA/viewform">Course Evaluation</a>
</li>
</ul>
</details>
<p><br> <br></p>
<p><strong>Teachers:</strong> - <a href="https://portal.research.lu.se/en/persons/nikolay-oskolkov">Nikolay Oskolkov</a> - <a href="https://www.chalmers.se/en/persons/rasools/?tab=0">Rasool Saghaleyni</a> - <a href="https://www.chalmers.se/en/persons/netotea/">Sergiu Netotea</a></p>
<p><strong>Teaching assistants:</strong> - <a href="https://portal.research.lu.se/en/persons/yuan-li">Yuan Li</a> - <a href="https://www.uu.se/en/contact-and-organisation/staff?query=N23-2571">Jennifer Fransson</a> - <a href="https://www.linkedin.com/posts/ebmeyerst_antibiotic-bioinformatics-wastewater-activity-7049055463090343936-pM0I/">Stefan Ebmeyer</a></p>
<p><a href="https://nbisweden.github.io/workshop_omics_integration/">Back to Homepage</a></p>
</section>
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