Vivarium notebooks

This repository contains the simulations described in: Agmon, E., Spangler, R.K., Skalnik, C.J., Poole, W., Morrison, J.H., Peirce, S.M., and Covert, M.W. (2022). Vivarium: an interface and engine for integrative multi-scale modeling in computational biology. Bioinformatics.

Vivarium Core is required to start your own Vivarium project. See the documentation for more details, and the Vivarium Collective for available modules.

Notebooks

Notebooks can be found under notebooks/. These include:

• Lac Operon CRN
• Multi-Paradigm Composites
• Vivarium Interface Basics

Setup

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 https://github.com/vivarium-collective/vivarium-notebooks.git

   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 setup.py script of one of our dependencies requires it.

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 bioscrape_cobra_deterministic.py and bioscrape_cobra_stochastic.py. Simulation functions for running all of the examples in Multi-Paradigm-Composites.ipynb can be found in simulate.py. 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 documentation. It can then be triggered with the -d option:

python bioscrape_cobra/simulate --simulation_name -d

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'