Modelreduction

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Revision as of 11:10, 15 December 2008 by Antonis (talk | contribs)

We provide here the code that was used to model order reduce the networks in the paper 'A systematic, algorithmic methodology for model reduction of large-scale biochemical networks' by Yo-Cheng Chang and Antonis Papachristodoulou.

The Yeast Glycolysis Pathway

One zip file containing:

  • The SIMULINK model: YGlyco_mdl.mdl
  • The S-function: YGlyco_sfun.mdl
  • The Parameters: YGlyco_para.m
  • The vector field: YGlyco_eqs.m
  • The ODE function: YGlycoode.m
  • The reduction algorithm: YGlyco_reduction.m
  • The system coordinate change function: findtransform.m
  • The norm coordinate change function: getQ.m

The EGFR-MAPK Pathway

One zip file containing:

  • The SIMULINK model: EGFRMAPK_mdl.mdl
  • The S-function: EGFRMAPK_sfun.mdl
  • The Parameters: EGFRMAPK_para.m
  • The total concentrations: EGFRMAPK_init.m
  • The ODE function: EGFRMAPKode.m
  • The reduction algorithm: EGFR_reduction.m
  • The system coordinate change function: findtransform.m
  • The norm coordinate change function: getQ.m