ODE model for P. tricornutum associated microbial community

Pre-print doi: http://dx.doi.org/10.1101/077768

Content

This model defines a Ordinary Differential Equations system to describe the dynamic evolution of an ecosystem of five organisms (one diatom and four bacteria). //: # (Also provided is a genetic algorithm code used to define the model parameters.)

The code is made available under the GNU General Public License (see LICENSE) at no warranty.

Macros to run are available in:

macros/examples/
macros/diatom-comm/

Installation

This code requires some external open-source packages.

We use virtual environment, if you don't have it please install like one of:

apt-get install python-virtualenv
dnf install python-virtualenv
pip install virtualenv

Generate a virtual environment for python2 or python3 like:

virtualenv -p /yourlocalpathto/pythonX yourprojectfolder/venv

e.g.

virtualenv -p /usr/bin/python2.7 $HOME/diatom-comm/venv

Then activate virtualenv and install the requirements:

cd yourprojectfolder
source venv/bin/activate
pip install -r code/python/requirements.txt

You are ready to run! When done, leave the virtualenv like:

deactivate