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Project description
Vivarium notebooks
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:
-
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.
-
(recommended but optional) Setup a Python virtual environment.
-
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.
Notebooks
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 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 docuentation.
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'
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