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GenMAPP GSoC 2009We are once again pooling the efforts of our colleagues and collaborators for this year's Google Summer of Code 2009. The GenMAPP organization will represent projects from Cytoscape, WikiPathways and PathVisio (see below). You'll notice that some of the projects are aimed at increasing cross-talk across these related projects. We like to get the most out of open source software development! This is a great opportunity to work at the intersection of biology and computing. 

Actual source code produced by the student participants in GSoC 2009 for our projects can be found here.

GenMAPP is a pathway visualization and analysis tool for biological data. GenMAPP illustrates the relationships between various genes and proteins to help researchers understand their data in terms of connected, biological pathways. Over 21,000 people from >70 countries have registered to download the GenMAPP program. The GenMAPP group is coordinated by the Conklin Lab at the Gladstone Institutes (University of California, San Francisco). There are 430 publications that reference GenMAPP or use GenMAPP to display data in the context of biological pathways. GenMAPP is 100% open source and all new development is in Java, MySQL, Derby, XML, and Web technologies such as wikis, in collaboration with the UCSF library, BiGCaT Bioinformatics, and the Cytoscape Consortium. Our development team is composed of individuals who are both biologists and programmers, providing a unique perspective on building and using open source tools. Links: Website Wiki

Cytoscape is a general network visualization tool that integrates network topology with data about the network into the visualization.  Cytoscape was developed in and finds most use in the Systems Biology community.  With over 2,500 downloads per month Cytoscape is rapidly becoming a standard within the community.  Cytoscape consists of a core application and a plugin framework which users exploit to extend the functionality of the application in new ways.  Our team consists of programmers and biologists from both academia and industry including: UC San Diego, UC San Francisco, U of Toronto, Agilent, Institute for Systems Biology, Unilever, Sloan-Kettering, Institut Pasteur, UT Health Science Center and others. Links: Website Wiki Javadoc WebStart

WikiPathways is a wiki for biological pathways, it does for pathway archives what WikiPedia does for the encyclopedia.  The wiki approach allows biologists with specific domain knowledge to easily create or update pathways. Pathways can be directly modified from a web browser using an embedded applet where you can draw genes, proteins and their interactions like in any popular drawing tool. The pathways can be used as images for publication and in data analysis tools such as GenMAPP, PathVisio and Cytoscape. There are currently about 600 pathways available, divided over 9 different species and  650 registered users. WikiPathways itself is completely open source and is built on top of MediaWiki, using PathVisio as the pathway editor. WikiPathways is developed and maintained by BiGCaT Bioinformatics (University of Maastricht) and the Conklin Lab at the Gladstone Institutes (University of California, San Francisco). Links: Website Source code

PathVisio is another pathway visualization tool. Like GenMAPP, it can display relations between genes, proteins and metabolites. PathVisio is focused more on the pathway creation rather than (microarray) data analysis. PathVisio started out as a test case for the development of GPML, an XML based format for storing pathways. Currently, PathVisio plays an important role as the editor applet of WikiPathways. Links: Website API docs Webstart

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