CNORode-package: Logic based ODE extension for CellNOptR

Description Details Author(s) References See Also

Description

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

Details

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

Author(s)

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

References

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:

See Also

CellNOptR, parEstimationLBode, getLBodeModelSim, parEstimationLBode plotLBodeFitness.


CNORode documentation built on Nov. 8, 2020, 7:39 p.m.