GenMAPP, Cytoscape, WikiPathways & Reactome
List of projects accepted into GenMAPP, Cytoscape, WikiPathways & Reactome
Our GSoC code repository: http://code.google.com/p/google-summer-of-code-2010-genmapp/
We are a collection of academically-based, network biology-oriented, open source organizations:
- 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. Approximately 24,000 people from ~97 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 500 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 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.
- 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.
- 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 1,270 pathways available, divided over 15 different species and 1000 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).
- Reactome is a manually curated database of core pathways and reactions in human biology that functions as a data mining resource and electronic textbook. The Reactome data model describes diverse processes in the human system, including the pathways of intermediary metabolism, regulatory pathways, signal transduction, and high-level processes, such as the cell cycle. As of Release 31, Reactome contains 4490 human proteins, 3669 reactions and 1081 pathways. Reactome software uses only freely available (and often open source) components and has been created with cross-platform compatibility and wide usability in mind. Data is stored in a MySQL database, the web site is implemented in Perl and data entry tool in Java programming language. The Reactome team is composed of individuals who are both biologists and programmers at the Ontario Institute for Cancer Research, New York University Langone Medical Center, Cold Spring Harbor Laboratory, and The European Bioinformatics Institute.