GP-DREAM network inference platform (DECOMISSIONED)

GP-DREAM was a web platform providing a handful of network inference tools from the DREAM Network Inference Challenge (in addition, Sushmita Roy contributed the MERLIN tool). These tools could be launched via a webplatform on the Broad computing cluster.

GP-DREAM has been decomissioned in 2016. We are sorry that we are no longer able to provide this service to the community due to a lack of funding. If you are interested in GP-DREAM and the DREAM Network Inference Challenges, please subscribe to our mailing list (see below). We will notify you when a new community resource for network inference becomes available.

The code of the GP-DREAM modules is provided in this archive (this is intended for method developers who want to explore or extend the code, it is not user friendly).

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Related work

• regulatorycircuits.org: A collection of 394 tissue-specific regulatory circuits (Marbach et al., Nature Methods, 2016 [PDF, PubMed])

• Disease Module Identification DREAM Challenge: Community assessment of module identification in genomic networks (manuscript in preparation).

Papers

• Wisdom of crowds for robust gene network inference.
  Marbach D*, Costello JC*, Küffner R*, Vega NM, Prill RJ, Camacho DM, Allison KR, The DREAM5 Consortium, Kellis M, Collins JJ, Stolovitzky G. Nature Methods, 9(8):796-804, 2012.
  [From the cover] [PubMed] [pdf] [Supplement] [MIT news feature]

• GenePattern 2.0. Reich M, Liefeld T, Gould J, Lerner J, Tamayo P, Mesirov JP. Nature Genetics, 38:500–501, 2006. [PubMed]