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<title>C3 Boot Camp - Day 3: Proteins and Networks</title>

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<section>
<h2>Proteins and Networks</h2>
<h5><span style="font-size: 70%">Slides: <a href="https://cytoscape.org/cytoscape-tutorials/presentations/c3-proteins-networks-2024.html">c3-proteins-networks-2024.html</a></span></h5>
<br /><br />
<h5 style="font-size: 60%">Alex Pico and John "Scooter" Morris</h5>
<br />
<h5 style="font-size: 80%">C3 Boot Camp - Protein Day
<br/><span style="font-size: 80%">7 November 2024</span></h5>

<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<!-- General introduction to the goals of the workshop -->
<section>
<h1>Goals and Motivations</h1>
<highlight>What you should expect to get out of today:</highlight>
<br/>
<div>
<ul style="display:block;" data-fragment-index="1" class="fragment fade-in">
<li>Understand the major applications of network biology</li>
<li>Explore the taxonomy of networks</li>
<li>Learn about the data sources underlying protein interactions</li>
</ul><br/>
<ul style="display:block;" data-fragment-index="2" class="fragment fade-in">
<li>Measuring proteins with mass spectrometry</li>
<li>Proteomics technology and experimental design</li>
<li>Sources of proteomics data in cancer</li>
</ul><br/>
<ul style="display:block;" data-fragment-index="3" class="fragment fade-in">
<li>Introduction to Cytoscape</li>
<li>Find relevant networks and pathways </li>
<li>Know where to find relevant Cytoscape apps and tutorials</li>
</ul>
</div>
<aside class="notes" data-markdown>
We're going to start high-level looking at applications of network biology,
then get into the specifics: the different types of networks and how interaction data are generated.
Then we will dive even deeper into the details of mass spec proteomics, measuring proteins and peptides,
including differential protein abundance and PTMs, as well as where to find high-quality sources of proteomics data for cancer research.
We'll then introduce Cytoscape as a general-purpose tool for network visualization and analysis. We will take a little break and then in the last hour we'll give a practical demo of how
to perform network anlaysis of proteomics data using Cytoscape.
</aside>
</section>

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<section>
<a href="#" class="navigate-next"><ribbon>Intro to Network Biology</ribbon></a>
<a href="#/network-taxonomy" ><ribbon>Network Taxonomy</ribbon></a>
<a href="#/data-sources" ><ribbon>Protein Interaction Data</ribbon></a>
<a class="inactive"><ribbon>Proteomic Data Analysis</ribbon></a>
<a class="inactive"><ribbon>Tour of Cytoscape</ribbon></a>
<a class="inactive"><ribbon>Network Analysis</ribbon></a>
<a class="inactive"><ribbon>Additional Tutorials and Resources</ribbon></a>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

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<section id="intro-network-biology" data-external="modules/intro-network-biology2/module.html"></section>
<section id="network-taxonomy" data-external="modules/network-taxonomy/module.html"></section>
<section id="data-sources" data-external="modules/data-sources/module.html"></section>

<!-- Overview update slide -->
<section>
<a class="inactive"><ribbon>Intro to Network Biology</ribbon></a>
<a class="inactive"><ribbon>Network Taxonomy</ribbon></a>
<a class="inactive"><ribbon>Protein Interaction Data</ribbon></a>
<a href="#" class="navigate-next"><ribbon>Proteomic Data Analysis</ribbon></a>
<a class="inactive"><ribbon>Tour of Cytoscape</ribbon></a>
<a class="inactive"><ribbon>Network Analysis</ribbon></a>
<a class="inactive"><ribbon>Additional Tutorials and Resources</ribbon></a>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<!-- Insert New Slides Here -->
<section id="proteomic data analysis" data-external="modules/proteomics/module.html"></section>

<!-- Overview update slide -->
<section>
<a class="inactive"><ribbon>Intro to Network Biology</ribbon></a>
<a class="inactive"><ribbon>Network Taxonomy</ribbon></a>
<a class="inactive"><ribbon>Protein Interaction Data</ribbon></a>
<a class="inactive"><ribbon>Proteomic Data Analysis</ribbon></a>
<a href="#/intro-cytoscape"><ribbon>Tour of Cytoscape</ribbon></a>
<a href="#/network-analysis"><ribbon>Network Analysis</ribbon></a>
<a href="#/additional"><ribbon>Additional Tutorials and Resources</ribbon></a>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section id="intro-cytoscape" data-external="modules/intro-cytoscape/module.html"></section>

<section>
<h1>Tour of Cytoscape</h1>
<p><highlight>A relaxing walkthrough:</highlight></p>
<ol>
<li>Loading networks</li>
<li>Loading tables</li>
<li>Selection and filtering</li>
<li>Changing visual attributes</li>
<li>Exporting images</li>
<li>Saving sessions</li>
</ol>
</section>

<section id="finding-network-data" data-external="modules/finding-network-data/module.html"></section>
<section id="network-analysis" data-external="modules/network-analysis/module.html"></section>
<section id="network-visualization" data-external="modules/network-visualization/module.html"></section>

<section id="network-analysis">
<section>
<h1>Network Analysis Protocols</h1>
<ul>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/stringApp/#/" target="_blank">STRING App</a></li>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/differentially-expressed-genes/#/" target="_blank">Omics Visualizer</a></li>
</ul>
</section>
</section>
<section id="additional">

<section>
<h1>Working with Your Data</h1>
<p>This afternoon you can take some time to use Cytoscape on your project data.
Start with one of the additional exercises below.</p>
<p><highlight>Exercises per Interest:</highlight></p>
<ol>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/rna-seq-data-analysis/" target="_blank">RNA-seq Data Analysis</a></li>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/differentially-expressed-genes/"target="_blank">Cancer Transcriptomics data</a></li>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/AP-MS-network-analysis/" target="_blank">Proteomics and AP-MS data</a></li>
<li><a href="https://cytoscape.org/cytoscape-tutorials/protocols/variant-data-analysis/" target="_blank">Cancer Genetics and Variant Data</a></li>
</ol>
<p>Other tutorials are available at: <a href="http://tutorials.cytoscape.org" target="_blank">tutorials.cytoscape.org</a></p>
</section>

<!-- Wrap up with helpful links -->
<section>
<h1>Where Can I Learn More?</h1>
<p><highlight>Other workshops</highlight>
<ul>
<li><a href="https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Introduction-to-Cytoscape-and-Network-Biology" target="blank">Introduction to Cytoscape and Network Biology</a> (Feb 2023)</li>
<li><a href="https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Intermediate-Cytoscape-Networks-and-Omics-Data-Visualization" target="blank">Intermediate Cytoscape: Network Visualization</a> (Feb 2023)</li>
<li><a href="https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Advanced-Cytoscape-Automation" target="_blank">Cytoscape Automation using R and Python</a> (15 Nov 2022)</li>
</ul></p>
</section>

<section>
<h1>Thank You!</h1>
<highlight>Here are additional resources you may find useful:</highlight>
<ul>
<li><a href="http://manual.cytoscape.org" target="_blank">manual.cytoscape.org</a></li>
<li><a href="http://tutorials.cytoscape.org" target="_blank">tutorials.cytoscape.org</a></li>
<li><a href="https://www.youtube.com/channel/UCv6auk9FK4NgXiXiqrDLccw" target="_blank">youtube demo videos</a></li>
<li><a href="http://apps.cytoscape.org" target="_blank">apps.cytoscape.org</a></li>
<li><a href="http://cytoscape-publications.tumblr.com" target="_blank">cytoscape-publications.tumblr.com</a></li>
<li><a href="https://cytoscape.org/documentation_users.html" target="_blank">cytoscape help page</a></li>
</ul>
<br/>
<p><highlight>Any questions?</highlight></p>

<aside class="notes" data-markdown>
4:50
Add speaker notes here...
</aside>
</section>
</section>
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