CmePy Documentation

Contents:

• Getting started
  • Dependencies
  • Obtaining CmePy
  • Testing and installation
  • Uninstalling CmePy
• Example: a single reaction
  • Defining the model
  • Solving the model
  • Recording and plotting results
  • Bringing everything together
• Example: enzyme kinetics
  • Defining the model
  • Solving the model and plotting results
• Important cmepy modules
  • cmepy.model
  • cmepy.recorder
  • cmepy.solver
• Advanced features
  • Finite state projection (FSP)
  • Sparse state spaces
  • Time-dependent propensity functions
• Models included in cmepy.models
  • burr08 : two competing clonotypes
  • catalytic_reaction
  • dsmts : a birth-death model
  • dual_enzymatic : coupled enzymatic reactions
  • gou07 : unidirection dimerisation and quadratic autocatalator
  • michaelis_menten : an enzymatic reaction
  • mono_molecular : mono molecular systems
  • munk08 : gene toggle
  • pap_pili : pap-pili epigenetic switch
  • transcription_regulation : time dependent transcription regulation
• api documentation
  • cme_matrix
  • domain
  • fsp
  • lazy_dict
  • lexarrayset
  • measurement
  • model
  • models
  • ode_solver
  • recorder
  • restorable_solver
  • solver
  • state_enum
  • statistics
  • tests
  • util