Generic Cell Cycle Model

How to run the models yourself

Here you can download the files necessary to run our generic cell cycle model.

Tutorial on WinPP can be found here.

Tutorial on Xpp-AUT can be found here. Also the book by Bard Ermentrout might help to make it work.

Files for simulations with WinPP:

budding yeast fission yeast mammalian cells*
buddingsim.ode / buddingsim.set pombesim.ode / pombesim.set mammaliansim.ode / mammaliansim.set

Files to create bifurcation diagrams with XPP-AUT:

budding yeast fission yeast mammalian cells*
buddingbif.ode / buddingbif.set pombebif.ode / pombebif.set mammalianbif.ode / mammalianbif.set

SBML files created by JigCell with estimated parameters (thanks to Kathy Chen and Jason Zwolak)

This model was used a use case for the JigCell software project. JigCell is designed to run multiple simulations to fit mutant behavior. On a separate webpage you can find the parameter sets and description how to use JigCell. We used a predecessor to Jason Zwolak's Parameter Estimation Toolkit (PET) to find better parameters to our mutants simulations. The parameters presented here give better fits for mutant behavior but qualitatively still produce the same results as it is published on this site.

With JigCell we created SBML files of the generic cell cycle model (generic = equations only):

generic budding yeast fission yeast mammalian cells*
generic.sbml bud.sbml pom.sbml mam.sbml

Bifurcation diagrams by Oscill8 (thanks to Kathy Chen and Emery Conrad)

Oscill8 is a newly developed tool for bifurcation analysis. It can read ODE, SBML and XML files.

The Oscill8 readable files for the generic cell cycle model (original, published parameters):

budding yeast fission yeast mammalian cells*
generic_bud_o8.ode generic_pom_o8.ode generic_mam_o8.ode

The Oscill8 readable files for the generic cell cycle model (JigCell fitted parameters):

budding yeast fission yeast mammalian cells*
generic_bud_jc_o8.ode generic_pom_jc_o8.ode generic_mam_jc_o8.ode

(* The mammalian parameters in these files were scaled in the the published parameter list, to have their dimension min-1. The parameters presented here are for a timescale 10 time units = 1 hour, following Novak & Tyson, 2004 )