<commit_before><section>
<h1>Introduction to Cytoscape</h1>
<ul>
	<li>Overview</li>
	<li>Core Concepts
		<ul>
			<li>Networks and Tables</li>
			<li>Visual Properties</li>
			<li>Cytoscape Apps</li>
		</ul>
	</li>
	<li>Working with Data
		<ul>
			<li>Loading network from files and online databases</li>
			<li>Loading data tables from CSV or Excel files</li>
			<li>The Table Panel</li>
		</ul>
	</li>
</ul>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Cytoscape</h1>
<div style="float: left; width: 60%">
				<img src="modules/intro-cytoscape/gal-screenshot.png"/>
</div>
<ul>
	<li>Open source</li>
	<li>Cross platform</li>
	<li>Consortium
	</li>
	<img src="modules/intro-cytoscape/CytoscapeConsortium.png" width="80%"/>
</ul>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<!-- All sorts of weirdness to get this to look right -->
<section data-transition="none">
<h1>Core Concepts</h1>
<h4>Networks and Tables</h4>
<div style="float: left; width: 50%">
	<img src="modules/intro-cytoscape/SimpleNetwork.png" width="55%" align="center"/>
	<p style="text-align: center"><b>Networks</b><br/>
	<span class="fragment fade-out" data-fragment-index=1">e.g., PPIs or pathways</span></p>
	<!-- Wierd order is so we can get the fragment right -->
	<img class="fragment" data-fragment-index="2" src="modules/intro-cytoscape/StyledNetwork.png" style="position:relative; top:-470px;left:0;" width="65%" align="center"/>
</div>
<div style="float:right; width: 50%">
	<img src="modules/intro-cytoscape/SpreadSheet.png" width="100%" align="center"/>
	<p style="text-align: center"><b>Tables</b><br/>
	<span class="fragment fade-out" data-fragment-index=1">e.g., data or annotations</span></p>
</div>
<div class="fragment" data-fragment-index="1" style="width:100%; position:relative; left:-320px; top:-100px">
<img class="plain" src="modules/intro-cytoscape/Arrow.png" align="center"/>
<p style="text-align: center"><b>Visual Styles</b></p>
</div>

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

<section>
<h1>Core Concepts</h1>
<h3>Cytoscape Apps!</h3>
<h4 style="margin-top: 10%"><a href="http://apps.cytoscape.org">apps.cytoscape.org</a></h4>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-1.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-2.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-3.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-4.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<p style="font-size: 72pt; margin-top: 300px; margin-left: 400px; text-align: center; background-color: #ffffff88;">295 Apps!</p>
</div>
	
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Core Concepts</h1>
<h3>Cytoscape Apps!</h3>
<h4 style="margin-top: 10%"><a href="http://apps.cytoscape.org">apps.cytoscape.org</a></h4>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img src="modules/intro-cytoscape/Apps-5.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img src="modules/intro-cytoscape/Apps-6.png"/>
</div>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Loading Data</h1>
<ul style="margin-bottom: 0px">
	<li>Cytoscape can import network data from:
		<ul style="margin-top: 0px; margin-bottom: 0px">
			<li>Files (or URLs)
				<ul style="margin-top: 0px; margin-bottom: 0px">
					<li><b>Excel, TSV, CSV</b></li>
					<li><b>eXtensible Graph Markup and Modelling Language: XGMML</b></li>
					<li><b>Systems Biology Markup Language (SBML)</b></li>
					<li><b>BioPAX</b></li>
					<li><b>PCI-MI</b></li>
					<li>Simple Interaction Format: SIF</li>
					<li>Graph Markup Language: GML </li>
					<li>... and others depending on loaded Apps</li>
				</ul>
			</li>
		</ul>
	</li>
</ul>
<p style="font-size: 60%">* <b>Bold:</b> loads table data also</p>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Loading Data</h1>
<ul style="margin-bottom: 0px">
	<li>Cytoscape can import network data from:
		<ul style="margin-top: 0px; margin-bottom: 0px">
			<li>Public repositories:<commit_msg>fixed PSI-MI typo<commit_after><section>
<h1>Introduction to Cytoscape</h1>
<ul>
	<li>Overview</li>
	<li>Core Concepts
		<ul>
			<li>Networks and Tables</li>
			<li>Visual Properties</li>
			<li>Cytoscape Apps</li>
		</ul>
	</li>
	<li>Working with Data
		<ul>
			<li>Loading network from files and online databases</li>
			<li>Loading data tables from CSV or Excel files</li>
			<li>The Table Panel</li>
		</ul>
	</li>
</ul>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Cytoscape</h1>
<div style="float: left; width: 60%">
				<img src="modules/intro-cytoscape/gal-screenshot.png"/>
</div>
<ul>
	<li>Open source</li>
	<li>Cross platform</li>
	<li>Consortium
	</li>
	<img src="modules/intro-cytoscape/CytoscapeConsortium.png" width="80%"/>
</ul>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<!-- All sorts of weirdness to get this to look right -->
<section data-transition="none">
<h1>Core Concepts</h1>
<h4>Networks and Tables</h4>
<div style="float: left; width: 50%">
	<img src="modules/intro-cytoscape/SimpleNetwork.png" width="55%" align="center"/>
	<p style="text-align: center"><b>Networks</b><br/>
	<span class="fragment fade-out" data-fragment-index=1">e.g., PPIs or pathways</span></p>
	<!-- Wierd order is so we can get the fragment right -->
	<img class="fragment" data-fragment-index="2" src="modules/intro-cytoscape/StyledNetwork.png" style="position:relative; top:-470px;left:0;" width="65%" align="center"/>
</div>
<div style="float:right; width: 50%">
	<img src="modules/intro-cytoscape/SpreadSheet.png" width="100%" align="center"/>
	<p style="text-align: center"><b>Tables</b><br/>
	<span class="fragment fade-out" data-fragment-index=1">e.g., data or annotations</span></p>
</div>
<div class="fragment" data-fragment-index="1" style="width:100%; position:relative; left:-320px; top:-100px">
<img class="plain" src="modules/intro-cytoscape/Arrow.png" align="center"/>
<p style="text-align: center"><b>Visual Styles</b></p>
</div>

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

<section>
<h1>Core Concepts</h1>
<h3>Cytoscape Apps!</h3>
<h4 style="margin-top: 10%"><a href="http://apps.cytoscape.org">apps.cytoscape.org</a></h4>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-1.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-2.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-3.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img class="plain" src="modules/intro-cytoscape/Apps-4.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<p style="font-size: 72pt; margin-top: 300px; margin-left: 400px; text-align: center; background-color: #ffffff88;">295 Apps!</p>
</div>
	
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Core Concepts</h1>
<h3>Cytoscape Apps!</h3>
<h4 style="margin-top: 10%"><a href="http://apps.cytoscape.org">apps.cytoscape.org</a></h4>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img src="modules/intro-cytoscape/Apps-5.png"/>
</div>
<div class="fragment" style="position:absolute; top: 40px; left: 40px">
	<img src="modules/intro-cytoscape/Apps-6.png"/>
</div>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Loading Data</h1>
<ul style="margin-bottom: 0px">
	<li>Cytoscape can import network data from:
		<ul style="margin-top: 0px; margin-bottom: 0px">
			<li>Files (or URLs)
				<ul style="margin-top: 0px; margin-bottom: 0px">
					<li><b>Excel, TSV, CSV</b></li>
					<li><b>eXtensible Graph Markup and Modelling Language: XGMML</b></li>
					<li><b>Systems Biology Markup Language (SBML)</b></li>
					<li><b>BioPAX</b></li>
					<li><b>PSI-MI</b></li>
					<li>Simple Interaction Format: SIF</li>
					<li>Graph Markup Language: GML </li>
					<li>... and others depending on loaded Apps</li>
				</ul>
			</li>
		</ul>
	</li>
</ul>
<p style="font-size: 60%">* <b>Bold:</b> loads table data also</p>
<aside class="notes" data-markdown>
Add speaker notes here...
</aside>
</section>

<section>
<h1>Loading Data</h1>
<ul style="margin-bottom: 0px">
	<li>Cytoscape can import network data from:
		<ul style="margin-top: 0px; margin-bottom: 0px">
			<li>Public repositories:
{'fraction_non_alphanumeric': 0.20532030401737242, 'fraction_numerical': 0.025407166123778503, 'mean_word_length': 4.973411154345007, 'pattern_counts': {'":': 0, '<': 373, '<?xml version=': 0, '>': 373, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6121', 'n_tokens_mistral': 3886, 'n_tokens_neox': 3445, 'n_words': 801}