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<title>Cytoscape Workshop: Advanced Automation</title>

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<!-- Customizable title slide -->
<section>
<img class="plain" src="../assets/images/Cytoscape.png" style="height:100%;margin-bottom:30px;">
<h2>Advanced Topic: <highlight>Automation</highlight></h2>
<h5><span style="font-size: 70%"><a href="https://cytoscape.github.io/cytoscape-tutorials/presen
tations/advanced-automation-2023-ucsf.html">cytoscape.github.io/cytoscape-tutorials/presentations/advanced-automation-2023-ucsf.html</a></span></h5>
<br /><br />
<h5 style="font-size: 80%">Virtual
<br/><span style="font-size: 80%">May 2024</span></h5>
<div class="footer" style="position: absolute; left: 0em; bottom: 0em; ">
<img class="plain" src="../assets/images/Cytoscape.png" style="height:70px;opacity:0.5">
</div>
<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>By the end of this workshop you should be able to:</highlight>
<ul>
<li>Command programmatic control over Cytoscape </li>
<li>Integrate Cytoscape into your bioinformatics pipelines </li>
<li>Publish and share Cytoscape-powered notebooks </li>
</ul>

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


<!-- Define upto 5 Ribbons per slide to compose links to a set of modules -->
<section>
<a href="#" class="navigate-next"><ribbon>Introductions</ribbon></a>
<a href="#/automation"><ribbon>Cytoscape Automation</ribbon></a>
<a href="#/walkthrough"><ribbon>Guided Walkthrough</ribbon></a>
<a href="#/usecases"><ribbon>Automation Use Cases</ribbon></a>
<a href="#/exam"><ribbon>Wrap-up</ribbon></a>

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


<!-- Add introduction slides for all presenters -->
<section>
<section>
<h1>Introductions</h1>
<highlight>Alex Pico, Gladstone Institutes</highlight><br />
<ul>
<li>Director, Bioinformatics Core</li>
<li>Executive director, National Resource for Network Biology</li>
<li>Cytoscape team since 2006</li>
<li>Co-author of over a dozen Cytoscape apps</li>
<li>Co-author of RCy3 Bioconductor package</li>
</ul>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>
<section>
<h1>Introductions</h1>
<highlight>Yihang Xin, Gladstone Institutes</highlight><br />
<ul>
<li>Software Engineer, National Resource for Network Biology</li>
<li>Cytoscape team since 2020</li>
<li>Co-author of Cytoscape apps</li>
<li>Co-author of RCy3 and py4cytoscape packages</li>
</ul>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>
<section>
<h1>Introductions</h1>
<div style="margin-left:200px;">
<img class="plain fragment fade-right" style="float:left; height:350px; margin:80px 0 0 0;" src="assets/introduction-distro.png">
<p style="text-align:left"><highlight>What about you?</highlight></p>
<ul style="display:block;margin-left:260px">
<li>Clinicians</li>
<li>Bench Biologists</li>
<li>Bioinformaticians</li>
<li>Computer Scientists</li>
<li>Chemists</li>
<li>Mathematicians</li>
<li>Other</li>
</ul>
</div>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>
</section>

<section>
<a href="#" class="inactive"><ribbon>Introductions</ribbon></a>
<a href="#/automation" class="navigate-next"><ribbon>Cytoscape Automation</ribbon></a>
<a href="#/walkthrough"><ribbon>Guided Walkthrough</ribbon></a>
<a href="#/usecases"><ribbon>Automation Use Cases</ribbon></a>
<a href="#/exam"><ribbon>Wrap-up</ribbon></a>
</section>

<section id="automation" data-external="modules/intro-automation/module.html"></section>
<section data-external="modules/RCy3_primer/module.html" style="font-size: 80%"></section>

<section>
<a href="#" class="inactive"><ribbon>Introductions</ribbon></a>
<a href="#/automation" class="inactive"><ribbon>Cytoscape Automation</ribbon></a>
<a href="#/walkthrough" class="navigate-next"><ribbon>Guided Walkthrough</ribbon></a>
<a href="#/usecases"><ribbon>Automation Use Cases</ribbon></a>
<a href="#/exam"><ribbon>Wrap-up</ribbon></a>
</section>

<section id="walkthrough" data-external="modules/basic-data-vis-walkthrough/module.html" style="font-size: 80%"></section>

<section>
<a href="#" class="inactive"><ribbon>Introductions</ribbon></a>
<a href="#/automation" class="inactive"><ribbon>Cytoscape Automation</ribbon></a>
<a href="#/walkthrough" class="inactive"><ribbon>Guided Walkthrough</ribbon></a>
<a href="#/usecases" class="navigate-next"><ribbon>Automation Use Cases</ribbon></a>
<a href="#/exam"><ribbon>Wrap-up</ribbon></a>
</section>

<section id="usecases" style="font-size:80%">
<h1>Automation Use Cases</h1>
<p>Here are some common automation workflows. Pick one that is similar to the type of data you work with. Follow the steps to learn about package functions.</p>
<p> Ask questions if anything is unclear!</p>
<ol>
<li><b>Transcriptomic data</b>:
<a href="https://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Differentially-expressed-genes.nb.html">Rmd</a>,
<a href="https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/Python/differentially-expressed-genes-network-analysis.ipynb">ipynb</a></li>
<li><b>Tumor expression and mutation data</b>:
<a href="http://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/Cancer-networks-and-data.nb.html">Rmd</a>,
<a href="https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/Python/advanced-cancer-networks-and-data.ipynb">ipynb</a></li>
<li><b>Proteomics data</b>:
<a href="http://cytoscape.org/cytoscape-automation/for-scripters/R/notebooks/AP-MS-network-analysis.nb.html">Rmd</a>,
<a href="https://github.com/cytoscape/cytoscape-automation/blob/master/for-scripters/Python/affinity-purification-mass-spectrometry.ipynb">ipynb</a></li>

</ol>

</section>


<section>
<a href="#" class="inactive"><ribbon>Introductions</ribbon></a>
<a href="#/automation" class="inactive"><ribbon>Cytoscape Automation</ribbon></a>
<a href="#/walkthrough" class="inactive"><ribbon>Guided Walkthrough</ribbon></a>
<a href="#/usecases" class="inactive"><ribbon>Automation Use Cases</ribbon></a>
<a href="#/wrap" class="navigate-next"><ribbon>Wrap-up</ribbon></a>
</section>

<section id="wrap">
<section>
<h1>Wrap-up</h1>
<p><b>What have we learned?</b></p>
<ul style="font-size: 0.8em;">
<li>Helper packages for Cytoscape from Python and R (JS eary development).</li>
<li>Load networks from STRING (also works for NDEx, WikiPathways, etc.)</li>
<li>Load my data as data frames from local files (also cloud: github, drive, etc.)</li>
<li>Perform data visualization, mapping my data to network visual properties.</li>
<li>Perform layouts, subnetworks, filters, and analyses (including many apps).</li>
<li>Export networks and publication-quality image formats.</li>
</ul>
</section>
<section>
<h1>Wrap-up</h1>
<p><b>Don't forget about Notebooks!</b></p>
<ul>
<li>Notebooks: ipynb and Rmd files</li>
<li>GitHub: ipynb and Rmd(nb.html) files</li>
<li>Google Colab:
<a href="https://colab.research.google.com/github/cytoscape/cytoscape-automation/blob/master/for-scripters/Python/basic-data-visualization.ipynb" target="_blank">Python</a>
and <a href="https://colab.research.google.com/drive/1iiYtjVrc0qFjzDAAdccgwByZWH1DPp2U?usp=sharing" target="_blank">R</a>
</li>
</ul>
</section>
<section>
<h1>Wrap-up</h1>
<p><b>Questions and Discussion</b></p>
<ul>
<li>Anything unclear?</li>
<li>Anything missing?</li>
</ul>

</section>
</section>

<!-- Wrap up with helpful links -->
<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="http://automation.cytoscape.org" target="_blank">automation.cytoscape.org</a></li>
<li><a href="http://apps.cytoscape.org" target="_blank">apps.cytoscape.org</a></li>
<li><a href="https://www.ncbi.nlm.nih.gov/pmc/?term=(cytoscape+AND+network)+AND+(%222022/01/01%22[PUBDATE]+%3A+%223000/01/01%22[PUBDATE])&report=imagesdocsum&dispmax=100" target="_blank">cytoscape publications</a>
</li>
<li><a href="https://cytoscape.org/documentation_users.html" target="_blank">cytoscape help page</a></li>
<li><a href="https://cytoscape.org/documentation_developers.html" target="_blank">cytoscape developer
page</a></li>
<li><a href="http://nrnb.org/training.html" target="_blank">nrnb.org/training.html</a></li>
</ul>

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