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Executable simulation model of the liver
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.gitignore h5 and svg updates Jan 2, 2020
Dockerfile updated release information Jan 2, 2020

EXSIMO: EXecutable SImulation MOdel

DOI Build Status GitHub version codecov Docker Cloud Build Status Docker Pulls

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, ...)

Docker images:
Zenodo snapshots: DOI
Github 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
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


Run analysis

The complete analysis can be run via


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

© 2019 Matthias König.

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