vivarium-chemotaxis

vivarium-chemotaxis is a library for chemotaxis-specific vivarium processes.

Visit the Vivarium Core documentation to learn how to use the core Vivarium engine to create computational biology models.

setup

Please refer to the Vivarium Core documentation for more complete instructions.

Make a python environment with Python 3 (pyenv is recommended) and install dependencies.

First install numpy:

$ pip install numpy

Then the remaining requirements:

$ pip install -r requirements.txt

run individual processes and composites

Each process file under chemotaxis/processes can run on its own. Some of these have their own command line options. For example, call the chemoreptor_cluster process with:

$ python chemotaxis/processes/chemoreptor_cluster.py

Composites with multiple integrated processes can also be executed on their own:

$ python chemotaxis/composites/chemotaxis_flagella.py

experiments

All experiments from the paper "A Multi-Scale Approach to Modeling E. coli Chemotaxis" are available in the file chemotaxis/experiments/paper_experiments.py. Run them from the command line by specifying the corresponding figure number.

$ python chemotaxis/experiments/paper_experiments.py 7b

tests

Tests are performed with pytest. Simply call the following to ensure everything is working properly:

$ pytest

To run only the fast tests:

$ pytest -m 'not slow'

logging

Logging is done with python logging. To print out logging information, run a simulation with:

$ LOGLEVEL=INFO python chemotaxis/..