biomass 0.14.0
A Python Framework for Modeling and Analysis of Signaling Systems
License: Apache-2.0
Requires Python: >=3.8

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_BioMASS_ is a computational framework for modeling and analysis of biological signaling systems in Python.

- **Documentation:** https://biomass-core.rtfd.io
- **Source code:** https://github.com/biomass-dev/biomass
- **Bug reports:** https://github.com/biomass-dev/biomass/issues
- **Citing in your work:** https://biomass-core.rtfd.io/en/latest/citing.html

It provides useful tools for numerical simulation, parameter estimation, network analysis, and result visualization.

## Installation

The BioMASS library is available at the [Python Package Index (PyPI)](https://pypi.org/project/biomass).

```shell
$ pip install biomass
```

BioMASS supports Python 3.8 or newer.

## References

- Imoto, H., Zhang, S. & Okada, M. A Computational Framework for Prediction and Analysis of Cancer Signaling Dynamics from RNA Sequencing Data—Application to the ErbB Receptor Signaling Pathway. _Cancers_ **12**, 2878 (2020). https://doi.org/10.3390/cancers12102878

- Imoto, H., Yamashiro, S. & Okada, M. A text-based computational framework for patient -specific modeling for classification of cancers. _iScience_ **25**, 103944 (2022). https://doi.org/10.1016/j.isci.2022.103944

- Arakane, K., Imoto, H., Ormersbach, F. & Okada, M. Extending BioMASS to construct mathematical models from external knowledge. _Bioinformatics Advances_ **4**, vbae042 (2024). https://doi.org/10.1093/bioadv/vbae042

## Author

[Hiroaki Imoto](https://github.com/himoto)

## License

[Apache License 2.0](https://github.com/biomass-dev/biomass/blob/master/LICENSE)