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export.html
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<!DOCTYPE html>
<html>
<head>
<title>biographer: Google Summer of Code 2012</title>
<link rel="stylesheet" href="main.css" type="text/css" />
</head>
<body>
<div>
<div>
<h1>Export to CytoScape and CellDesigner</h1>
<h2>Motivation</h2>
<p>
<a href="http://www.celldesigner.org/">CellDesigner</a> and <a href="http://www.cytoscape.org/">Cytoscape</a> are widely used tools for visualizing and analyzing biological networks.
biographer on the other side is focussed on retrieving networks from databases and laying it out
in a visually appealing way. Consequently, a useful workflow for a researcher would be to create
an initial version of the network using biographer and then use other tools for either fine-tuning
the layout or for further analysis.
</p>
<p>
The two most import exchange formats for biological networks are <a href="http://sbml.org/">SBML</a>
and <a href="http://www.biopax.org/">BioPax</a> of which biographer
already supports SBML. The two mentioned tools also do support this format. However, SBML does not
support positional information (even though the latest format specification do define it, this is not
commonly used). This problem can be circumvented by a set of XML extensions which have
been introduced by Celldesigner. Within CytoScape, the plugin BiNoM support the visualization of
reaction networks and can import SBML files which can interprete the CellDesigner extensions.
</p>
<p>
An extension to project will be to develop a BioPax import/export module. As BioPax is one of the major formats
for exchanging reaction networks, this module will help to extend the reach of biographer. On the output
side, BioPax does also not support positional information directly, but there exist ideas that SBGM-ML
will be used for that. SBGN-ML support on the import side is already inlcuded in biographer.
</p>
<h2>Core specification</h2>
<ol>
<li>
Enable export of SBML from the internal biographer format (biographer so far only imports SBML)
</li>
<li>
Support of positional information (CellDesigner XML extensions)
</li>
<li>
Support for Protein Complexes and Modifications (CellDesigner XML extensions)
</li>
<li>
BioPAX support
</li>
</ol>
<h2>Coding Languages</h2>
<ol>
<li>
Integration into server component (python)
</li>
<li>
Some JavaScript/HTML would be good for interface connection
</li>
</ol>
<h2>Further resources</h2>
<ul>
<li><a href="http://sbml.org/images/2/26/Osana-celldesigner-layout.pdf">Converter From CellDesinger Layout extensions -> SBML layout extensions</a></li>
<li><a href="http://sbml.org/images/e/ec/Funahashi-celldesigner3.pdf">CellDesigner extensions - Presentation</a></li>
<li><a href="http://celldesigner.org/documents/CellDesigner4ExtensionTagSpecificationE.pdf">CellDesigner extensions - Specification</a></li>
</ul>
<h2>Mentors</h2>
<ul>
<li>Samuel Drulhe</li>
<li>Szymon Stoma</li>
</ul>
</div>
</div>
</body>
</html>