This repo contains various scripts to make modelling with Copasi easier. All Python scripts (except for copasi.py) can be called with -h or --help to get instructions.

• copasi.py (python3; not for direct call)

  Contains the Copasi class that is used by many other scripts. This script is thought to be imported by other python scripts.

• updateMCAOptimizationTarget.py (python3, depends on copasi.py)

  Creates new Copasi files with changed targets for FCC optimization.

• extractFluxConcFromResults.py (python3)

  Extracts species concentrations and reaction fluxes from steady state results.

• extractMCAOptimizationResults.py (python3)

  Extracts results from MCA optimizations.

• parallelCopasi.py (python3, depends on copasi.py and GNU parallel)

  Copies a given Copasi file n times while changing the optimization output file name. Then sends every copy to GNU parallel for parallel execution.