Numerical P system and Enzymatic Numerical P system simulator, written in Python 3 (with branch compatible for Python 2)
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README.md

PeP (Enzymatic) Numerical P System simulator written in Python 3 (with branch for Python 2).

Command line usage

python3 pep.py INPUT_FILE_NAME.pep [OPTIONS]

where OPTIONS can be:

  • --step: require the user to press enter after befor running the next simulation step;
  • -n NUMBER: stop the simulation after n simulation steps;
  • --csv: write a .csv document at the end of the simulation that contains the values of each variable at each simulation step;
  • --debug: increase verbosity by showing DEBUG messages
  • --error: reduce verbosity by showing only ERROR messages

If colorlog is installed, then messages will be coloured according to the level of importance.

Easy start - Docker

In order to simplify the installation procedure, users of Docker can use the start_pep_docker.sh script to run pep in a container.

On first run, the pre-built image of Python and PeP will download from the Docker repositories.

The start_pep_docker.sh script passes all command-line parameters directly to PeP.

Documentation

The documentation page, available at https://andrei91ro.github.io/pep contains:

  • getting started
  • input file syntax reference
  • several case studies
  • an API reference

Authors

Andrei George Florea, Cătălin Buiu

Department of Automatic Control And Systems Engineering,

Politehnica University of Bucharest

Bucharest, Romania.