National Resource for Network Biology (GenMAPP, Cytoscape and WikiPathways)
List of projects accepted into National Resource for Network Biology (GenMAPP, Cytoscape and WikiPathways)
The National Resource for Network Biology (NRNB) is organizing the joint efforts of GenMAPP, Cytoscape, and WikiPathways. This is a great opportunity to work at the intersection of biology and computing. 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. Tens of thousands of people from a hundred countries have registered to download the GenMAPP program. The GenMAPP group is coordinated by the Conklin Lab at the Gladstone Institutes (UCSF). Our development team is composed of biologists and programmers, providing a unique perspective on building and using open source tools. Cytoscape is a general network visualization tool that integrates network topology with data about the network into the visualization. Cytoscape is rapidly becoming a systems biology standard. Cytoscape consists of a plugin framework which extends functionality 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, Sloan-Kettering, Institut Pasteur and others. WikiPathways is a wiki for biological pathways. The wiki approach allows biologists and domain experts to easily create and 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. WikiPathways itself is completely open source and is built on top of MediaWiki, using PathVisio as the pathway editor and BridgeDb as the backend database. WikiPathways is developed and maintained by BiGCaT Bioinformatics (University of Maastricht) and the Conklin Lab at the Gladstone Institutes (UCSF).
Our code repository can be found here: http://code.google.com/p/google-summer-of-code-2011-nrnb/