DreamModel: Model used for the DREAM3 challenge

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Model used for the DREAM3 challenge

Description

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"

Usage

data(DreamModel)

Format

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

Source

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

References

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 April 16, 2024, 5:21 a.m.