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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.