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To run the code used in this work, you will need to install the following modules:
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.pyscript of one of our dependencies requires it.
Notebooks can be found under
notebooks/. These include
All Python files can be found under
This includes Vivarium
Composers for deterministic and stochastic versions of the Bioscrape/COBRA composite models
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:
These can be called simply with:
python bioscrape_cobra/simulate --simulation_name
Parallelization can be triggered with the
python bioscrape_cobra/simulate --simulation_name -p
Saving the simulation output to a mongoDB database requires a running mongoDB instance, as described in the
It can then be triggered with the
python bioscrape_cobra/simulate --simulation_name -d
Tests are performed with pytest. Simply call the following to ensure everything is working properly:
To run only the fast tests:
$ pytest -m 'not slow'
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