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.