https://github.com/matthiaskoenig/lisym-tutorial
LiSyM Modeling Tutorial Hünfeld
https://github.com/matthiaskoenig/lisym-tutorial
Last synced: 4 months ago
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LiSyM Modeling Tutorial Hünfeld
- Host: GitHub
- URL: https://github.com/matthiaskoenig/lisym-tutorial
- Owner: matthiaskoenig
- Created: 2017-11-20T20:26:42.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-11-22T15:40:42.000Z (over 7 years ago)
- Last Synced: 2025-01-04T20:24:43.517Z (5 months ago)
- Language: Jupyter Notebook
- Homepage: https://seek.lisym.org/events/18
- Size: 39.7 MB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
1st LiSyM Modeling Tutorial
[](https://badge.fury.io/gh/matthiaskoenig%2Flisym-tutorial)
[](https://www.zenodo.org/badge/latestdoi/111459301)
Matthias König
Modeling tutorial as part of the 1st LiSyM Retreat Meeting in Hünfeld (20-22 November 2017). The presentation slides are available [here](./presentation/lisym-tutorial.pdf).
This tutorial gives a quick introduction into standards used in computational modeling and visualizes, simulates and analysis showcase example models. A basic introduction to simple kinetic models is provided.
The entry point for the notebooks is the [index.ipynb](./index.ipynb).
## Resources
#### Standard formats
* [Systems Biology Markup Language (SBML)](http://sbml.org/Main_Page)
* [Simulation Experiment Description Markup Language (SED-ML)](https://sed-ml.github.io/)
#### Model repositories
* [BioModels](https://wwwdev.ebi.ac.uk/biomodels/)
#### Network visualization of SBML models
* [Cytoscape](http://www.cytoscape.org/) network visualization software
* SBML visualization with [`cy3sbml`](http://github.com/matthiaskoenig/cy3sbml) (http://apps.cytoscape.org/apps/cy3sbml)
#### Modeling software
* [tellurium](http://tellurium.analogmachine.org/): A Python Environment for Reproducible Dynamical Modeling of Biological Networks
* [tellurium readthedocs](https://tellurium.readthedocs.io/en/latest/) Tellurium documentation
* [libroadrunner](http://libroadrunner.org/) High performance SBML simulator used in Tellurium
#### Interactive notebooks
* [Jupyter notebooks](https://jupyter.org/)
## License and citation
If you refer to this material or reuse it cite
[](https://www.zenodo.org/badge/latestdoi/111459301)
* Source Code is licensed as [LGPLv3](http://opensource.org/licenses/LGPL-3.0)
* Documentation is licensed as [CC BY-SA 4.0](http://creativecommons.org/licenses/by-sa/4.0/)
## Funding
Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054).
## Instructions
To run the tutorial notebooks download the latest release from
https://github.com/matthiaskoenig/lisym-tutorial/releases
Extract the files, the notebooks are in the `./notebooks/` folder.
### Running examples with tellurium-notebook
For running the notebooks with tellurium-notebook [download the latest version](https://github.com/sys-bio/tellurium#installation-instructions). After installation open the notebooks via `File -> Open`.
### Running jupyter notebook in virtualenv
tellurium is also available as python package and can simply be installed in a virtual environment. Jupyter notebooks can than use the virtualenv as kernel.
```
git clone https://github.com/matthiaskoenig/lisym-tutorial.git
cd lisym-tutorial
mkvirtualenv lisym --python=python3
(lisym) pip install -r requirements.txt
# install kernel for ipython
(lisym) python -m ipykernel install --user --name=lisym
# start jupyter notbook
jupyter notebook index.ipynb
# select notebook for model and run notbook with the dfba kernel
Kernel -> Change kernel -> dfba
Kernel -> Restart & Run All
```