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@paulflang paulflang released this 05 Mar 19:30
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v1.0.0
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cell_cycle_model

cell_cycle_model is a repository that stores several cell cycle model versions. It also provides utility functions to compare different cell cycle model versions.

Models

Models are of different degree of complexity. They typically include Copasi, BNGL or SBML model specifications.

  • v0.0.1: Submodels leading to the full model.
  • v1.0.0: Initial full cell cycle model.
  • v2.0.0: Rescaled cell cycle length to 20 h (H1 human embryonic stem cells). Hard coded/eliminated parameters f1-f4 that were once introduced to describe loss of enzymatic
    access if target is in complex. Renamed species to avoid ambiguity in case-insensitive software. Ran version 1.0.0 for 9950 time units and used this state as initial conditions in version 2.0.0. Deleted observables.
  • v2.1.0: Removed the simplifying assumption from the ODE model that (un)binding of transcription
    factor to promoter does not affect the concentration of free transcription factor.
  • v2.1.1: Created separate promoters for Ce, Ca, E2f, Emi and Fox from one E2f activated
    promoter (formerly called Px).
  • v2.1.2: Introduced observables for parameter optimisation purposes.
  • v2.1.3: ntroduced interfaces for small molecule mediated inhibition of Ce and transcriptional/translational inhibition for Cb.
  • v2.1.4: Introduced interface for small molecule mediated inhibition of Wee1 and removed it for Ce.
  • v3.0.0: same as v2.1.4 in BNGL and auto-generated SBML format.
  • v3.0.1: added refinements to reaction rules of v3.0.0.
  • v3.1.0: added DNA damage checkpoint (SKP2 and TP53 and CDKN1A).
  • v3.2.0: added CDKN1B.
  • v4.0.0: added compartments.
  • v4.0.1: scaled promoters to 2 per cell; added observables.

Development team

This package was developed by Paul F. Lang at the University of Oxford, UK.

Questions and comments

Please contact Paul F. Lang with any questions or comments.

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