DreamModel: Model used for the DREAM3 challenge

Description Usage Format Source References


This data object contains the model used in the package vignette, already loaded and formatted as a Model object. This is to be used with the data in "CNOListDREAM"




DreamModel is a list with fields "reacID" (character vector), "namesSpecies" (character vector), "interMat" (numerical matrix), "notMat"(numerical matrix).


This data and model is extracted from the Matlab version of CellNOpt1.0 (http://www.ebi.ac.uk/saezrodriguez/software.html#CellNetOptimizer).


  1. J. Saez-Rodriguez, L. G. Alexopoulos, J. Epperlein, R. Samaga, D. A. Lauffenburger, S. Klamt and P. K. Sorger. Discrete logic modeling as a means to link protein signaling networks with functional analysis of mammalian signal transduction, Molecular Systems Biology, 5:331, 2009.

  2. Prill RJ, Marbach D, Saez-Rodriguez J, Sorger PK, Alexopoulos LG, Xue X, Clarke ND, Altan-Bonnet G, and Stolovitzky G. Towards a rigorous assessment of systems biology models: the DREAM3 challenges. PLoS One, 5(2):e9202, 2010.

saezlab/CellNOptR documentation built on Nov. 15, 2018, 10:53 p.m.