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integration.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>Reactome / WikiPathways Front-end</h1>
<h2>Motivation</h2>
<p>
<div style="background-color: red;">Hello everybody, after discussing this project with the members of WikiPathways and Reactome. We are currently restucturing it. The aim is still the integration of both databases but now with the focus on the creation of a JavaScript based library for SBGN files. This does not exculde the other goals mentioned below but we would really like to see an integration with the help of this library.</div>
<br />
<br />
Our primary goal when developing biographer in first place was to create a
software component which can visualize reaction networks without manual
intervention. The visualization follows the SBGN standard which defines the
symbolics that should be used for this type of networks. Clearly, the next step
would be to connect this component to the sources of such networks, large
biological reaction databases, among which <a href="http://www.reactome.org">Reactome</a> and <a href="http://wikipathways.org">WikiPathways</a> belong to
the most popular.
</p>
<p>
These databases contain information on reactions between thousands of compounds
(i.e. proteins, chemical species, complexes, nucleotide sequences). To make this
amount of information more accessible to the users, network diagrams are
provided which visualize the connections between the different entities. So far, these
visualizations are usually limited to manual laid out diagrams of single
biological pathways which are functionally strongly related parts of the whole network.
</p>
<p>
Here, we propose a more generic way of visualizing networks using the biographer
component. Arbitrary parts of the complete network, which could be the
aforementioned pathways or the neighborhoods of any compound, are visualized
automatically in a SBGN compliant manner.
</p>
<p>
The goal of this project will be to develop an alternative front-end for these databases
which uses the capabilities of biographer and which explores directions in which
web-interfaces for reaction database could develop in future. The project will be supported
on the technical side by Reactome and/or WikiPathways.
<!--Furthermore, the integrated editor functionality of biographer could be used to
propose/post corrections to the underlying network data or allow the user to
download modified versions of the pathways.-->
</p>
<p>
Student proposals would probably concentrate on one of the databases mentioned, or propose
an integrative way of displaying information of both DBs together. It should be noted, although more appealing, the latter
is a much more complex approach and we will more rigorously weigh the feasibility of such an proposal.
</p>
<h2>Specifications / Features</h2>
<ol>
<li>input based on REST API (at least for Reactome)
<li>development of navigation elements (e.g. pathway browser, etc.)
<li>display of node information
<li>automatic layout of neighborhoods, pathways
<li>alternatively: use of predefined layout information
<li>"click-through" network exploration (as in networkexplorer <a href="http://cheetah.biologie.hu-berlin.de/networkexplorer">demo</a>)
</ol>
<h2>General Specifications</h2>
<ol>
<li>JavaScript library</li>
<li>LGPL</li>
</ol>
<h2>Mentors</h2>
<ul>
<li>Falko
<li>Marvin Schulz
</ul>
</div>
</div>
</body>
</html>