https://github.com/biosimulators/biosimulators_tutorials
Tutorials for BioSimulators
https://github.com/biosimulators/biosimulators_tutorials
biosimulations biosimulators combine computational-biology jupyter mathematical-modeling numerical-simulation omex sbml sed-ml systems-biology tutorial
Last synced: 2 days ago
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Tutorials for BioSimulators
- Host: GitHub
- URL: https://github.com/biosimulators/biosimulators_tutorials
- Owner: biosimulators
- License: mit
- Created: 2021-09-24T03:49:48.000Z (over 4 years ago)
- Default Branch: dev
- Last Pushed: 2023-05-01T14:39:46.000Z (almost 3 years ago)
- Last Synced: 2025-09-09T16:39:30.305Z (5 months ago)
- Topics: biosimulations, biosimulators, combine, computational-biology, jupyter, mathematical-modeling, numerical-simulation, omex, sbml, sed-ml, systems-biology, tutorial
- Language: Jupyter Notebook
- Homepage: https://tutorial.biosimulators.org
- Size: 1.71 MB
- Stars: 2
- Watchers: 7
- Forks: 0
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
- Code of conduct: CODE_OF_CONDUCT.md
- Governance: GOVERNANCE.md
Awesome Lists containing this project
README
[](https://tutorial.biosimulators.org/)
[](#contributors-)
# BioSimulators tutorials
This repository contains Jupyter notebooks with tutorials for the Python APIs for the simulation tools registered with BioSimulators and a Jupyter notebook server for running the notebooks.
The tutorials are located in the [`tutorials`](tutorials) subdirectory. The [README](tutorials/README.md) in this directory summarizes the content of the tutorials.
## Getting started
### Running the tutorials online with Binder
The easiest way to run the tutorials is with Binder. Simply open https://tutorial.biosimulators.org/ in your browser.
### Running the tutorials on your own machine
Run the following command to download the tutorials:
```
docker pull ghcr.io/biosimulators/tutorials
```
Run the following command to launch a Jupyter notebook server at http://localhost:8888 for the tutorials in this repository:
```
docker run -it --rm -p 8888:8888 ghcr.io/biosimulators/tutorials jupyter notebook --ip=0.0.0.0 --port=8888
```
Alternatively, run the following command to launch a Jupyter lab server at http://localhost:8888 for the tutorials in this repository:
```
docker run -it --rm -p 8888:8888 ghcr.io/biosimulators/tutorials jupyter lab --ip=0.0.0.0 --port=8888
```
## License
This package is released under the [MIT license](LICENSE).
## Development team
This package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York as part of the [Center for Reproducible Biomodeling Modeling](https://reproduciblebiomodels.org) with assistance from the contributors listed [here](CONTRIBUTORS.md).
- [Bilal Shaikh](https://www.bshaikh.com)
- [Jonathan Karr](https://www.karrlab.org)
## Funding
This package was developed with support from the National Institute for Bioimaging and Bioengineering (award P41EB023912).
## Questions and comments
Please contact us at [info@biosimulators.org](mailto:info@biosimulators.org) with any questions or comments.