CNORode-package: Logic based ODE extension for CellNOptR
In CNORode: ODE add-on to CellNOptR

Description Details Author(s) References See Also

This package is used for the simulation and fitting of logic based ODE models based on the Odefy approach.

Package:	CNORode
Type:	Package
Version:	1.2.0
Date:	2012-03-14
License:	GPL-3
LazyLoad:	yes

David Henriques, Thomas Cokelaer Maintainer: David Henriques <dhenriques@ebi.ac.uk>

Dominik Wittmann, Jan Krumsiek, Julio S. Rodriguez, Douglas Lauffenburger, Steffen Klamt, and Fabian Theis. Transforming boolean models to continuous models: methodology and application to t-cell receptor signaling. BMC Systems Biology, 3(1):98+, September 2009.

Egea, J.A., Maria, R., Banga, J.R. (2010) An evolutionary method for complex-process optimization. Computers & Operations Research 37(2): 315-324.

Egea, J.A., Balsa-Canto, E., Garcia, M.S.G., Banga, J.R. (2009) Dynamic optimization of nonlinear processes with an enhanced scatter search method. Industrial & Engineering Chemistry Research 49(9): 4388-4401.

Jan Krumsiek, Sebastian Polsterl, Dominik Wittmann, and Fabian Theis. Odefy - from discrete to continuous models. BMC Bioinformatics, 11(1):233+, 2010.

R. Serban and A. C. Hindmarsh, "CVODES: the Sensitivity-Enabled ODE Solver in SUNDIALS," Proceedings of IDETC/CIE 2005, Sept. 2005, Long Beach, CA. Also available as LLNL technical report UCRL-JP-200039.

C. Terfve, T. Cokelaer, A. MacNamara, D. Henriques, E. Goncalves, MK. Morris, M. van Iersel, DA Lauffenburger, J. Saez-Rodriguez. CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms. BMC Systems Biology, 2012, 6:133:

CellNOptR, parEstimationLBode, getLBodeModelSim, parEstimationLBode plotLBodeFitness.