Presenter: Piet Molenaar, AMC Human Genetics, Amsterdam, The Netherlands

Title: R2 and Cytoscape: Graph based integration and analysis of molecular biological data


  Like each wet-lab working on large scale pathway identification, we also face the problem to store, integrate, retrieve and select high-throughput data in a way that identifies novel pathways and make complex interactions comprehensible.
  To solve this problem we are developing a plugin for Cytoscape  that maintains the current state of knowledge in our group and enables analysis in a graph based way. The actual evidence from wet-lab experiments can be retrieved and analyzed in combination with array data via our in-house developed web based tool R2 . Cytoscape facilitates integration of these data with data from external databases and enables analysis through our own algorithms and a wealth of plugins published by other groups. In the near future we will make these tools available through our website (
  In my demo I'll focus on the analysis of data from timeseries experiments in a transcription factor context.

CytoscapeRetreat2008/Piet (last edited 2009-02-12 01:03:11 by localhost)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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