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Vivarium notebooks


To run the code used in this work, you will need to install the following modules: vivarium-core, vivarium-cobra, vivarium-bioscrape, and vivarium-multibody. These modules can be installed locally by executing the following command in the root directory:

  1. Clone the repository.

    $ git clone

    Alternatively, you can simply extract an archive of the source code if you got the code in that format.

  2. (recommended but optional) Setup a Python virtual environment.

  3. Install Python dependencies

    $ pip install -r requirements.txt

    Note that you have to install numpy first because the script of one of our dependencies requires it.


Notebooks can be found under notebooks/. These include Vivarium_interface_basics.ipynb and Multi-Paradigm-Composites.ipynb.

Python files

All Python files can be found under bioscrape_cobra/. This includes Vivarium Composers for deterministic and stochastic versions of the Bioscrape/COBRA composite models called and Simulation functions for running all of the examples in Multi-Paradigm-Composites.ipynb can be found in This file also includes command-line run options for six different simulations with these names: [deterministic, stochastic, deterministic_divide, stochastic_divide, deterministic_spatial, stochastic_spatial]. These can be called simply with:

python bioscrape_cobra/simulate --simulation_name

Parallelization can be triggered with the -p option:

python bioscrape_cobra/simulate --simulation_name -p

Saving the simulation output to a mongoDB database requires a running mongoDB instance, as described in the Vivarium docuentation. It can then be triggered with the -d option:

python bioscrape_cobra/simulate --simulation_name -d


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'

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