is an academic organization that develops and supports GenMAPP (Gene Map Annotator and Pathway Profiler), a computer application designed to visualize gene expression data on maps representing biological pathways and groupings of genes.


We are developing a newly redesigned version of GenMAPP to meet current challenges for integrating, visualizing, and analyzing pathway data. This new version, called GenMAPP-CS, is being developed as an open-source, Java-based program in collaboration with the Cytoscape Consortium. GenMAPP-CS will incorporate core capabilities of Cytoscape, while adding GenMAPP-specific functionality. To learn more about specific aims for the GenMAPP-CS project, please visit our GenMAPP-CS wiki.

  PathVisio is a Java tool for displaying and editing pathways with a GenMAPP-like interface. PathVisio is developed as a collaboration with BiGCaT Bioinformatics. PathVisio supports import and export of pathways in GenMAPP format, as well as in the GPML (XML) format. Future versions of PathVisio will have the flexibility to display many different types of data, such as microarray and proteomics data, on familiar biological pathways.  
  In the tradition of Wikipedia and other wiki platforms, Wikipathways is an open, public space for content editing dedicated to biological pathways. WikiPathways is the first pathway database with wiki functionality and will now serve as the primary source of GenMAPP pathways. WikiPathways is being developed in collaboration with BiGCaT Bioinformatics.  
  Google Summer of Code  
  GenMAPP participates as an open source organization the Google Summer of Code.  To find out more about the GenMAPP Summer of Code projects, visit our GSoC wiki pages for 2007, 2008, 2009 and 2010. was founded in the Conklin Lab at the Gladstone Institutes at the University of California at San Francisco and is funded by the National Institute for General Medical Sciences, Agilent Foundation and NHLBI-BayGenomics.

Project Leader   Bruce Conklin 1,2
Software Design Group
Current Contributors
  Kristina Hanspers 1   Allan Kuchinsky 8
  Alex Pico 1,2   Karen Vranizan 1,3
  Nathan Salomonis 1,2   Jeff Lawlor 7
  Steven C. Lawlor 7  
  Scott Doniger 6   Lynn Ferrante 1,5
  Kam Dahlquist 4   Alex Zambon 9

1) J. David Gladstone Institutes, 2) University of California San Francisco, 3) University of California Berkeley, 4) Loyola Marymount University, 5) San Francisco State University, 6) Washington University, 7) The Curtis Company 8) Agilent Technologies 9) University of California San Diego
Website Development
  Nathan Salomonis   Alex Pico
Erik Ellestad Richard Trott
  Kristina Hanspers  
Organizations   NetPath
  BiGCaT University of Maastricht   UCSF Library CKM
  Agilent Technologies  



Creative Commons License