Computational protocol: Transcriptional Dynamics of the Embryonic Stem Cell Switch

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Protocol publication

[…] All simulations were carried out using the Systems Biology Workbench (SBW/BioSPICE) tools []: the network designer JDesigner, the simulation engine Jarnac []. Bifurcation diagrams were computed using SBW with an interface to MATLAB [], and a bifurcation discovery tool []. Bifurcation plots were also computed and cross-checked using Oscill8 (http://sourceforge.net/projects/oscill8), an interactive bifurcation software package which is linked to AUTO [] and SBW []. In all our simulations the species concentrations are regarded as dimensionless, whereas the kinetic constants have dimensions of inverse time, with dimensionless Michaelis–Menten constants. All models are available as standard SBML or Jarnac scripts. […]

Pipeline specifications

Software tools SBW, Jdesigner, Oscill8
Application Mathematical modeling
Organisms Homo sapiens, Mus musculus