matthiaskoenig/exsimo repository overview

⁠ EXSIMO: EXecutable SImulation MOdel

Matthias König

Data, model and code for executable simulation model of hepatic glucose metabolism.

• data - data sets
• docs - documentation, results, report, models
• docs/models - SBML model and model report
• pyexsimo - python package (model generation, simulation experiments, tests, ...)

Reports: https://matthiaskoenig.github.io/exsimo/⁠
Docker images: https://hub.docker.com/repository/docker/matthiaskoenig/exsimo⁠
Zenodo snapshots:
Github releases: https://github.com/matthiaskoenig/exsimo/releases⁠

⁠Setup local environment

To run the analysis locally create a python virtual environment and install pyexsimo.

Create virtual environment with python3.6, e.g., with virtualenv & virtualenvwrapper via

mkvirtualenv exsimo --python=python3.6

Install the dependencies in the virtualenv

git clone https://github.com/matthiaskoenig/exsimo.git
cd exsimo
(exsimo) pip install -r requirements.txt
(exsimo) pip install -e . --upgrade

To run the tests use pytest, to execute the analysis use execute.

⁠Setup docker container

For the master branch docker containers are built automatically. To start the respective execution environment use

docker run -it matthiaskoenig/exsimo:latest

To run a specific model version use the respective tag

docker run -it matthiaskoenig/exsimo:0.3.1

To run the tests use pytest, to execute the analysis use execute.

⁠Run tests

All tests can be run via

pytest

⁠Run analysis

The complete analysis can be run via

execute

which updates the results in the ./docs/ folder.

© 2019 Matthias König.