Metadata-Version: 2.1
Name: biomass
Version: 0.13.0
Summary: A Python Framework for Modeling and Analysis of Signaling Systems
Author: Hiroaki Imoto
Maintainer-email: Hiroaki Imoto <hiroaki.imoto@ucd.ie>
License: Apache-2.0
Project-URL: repository, https://github.com/biomass-dev/biomass
Project-URL: documentation, https://biomass-core.readthedocs.io/en/latest/
Project-URL: bugtracker, https://github.com/biomass-dev/biomass/issues
Classifier: Development Status :: 4 - Beta
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Natural Language :: English
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.8
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Software Development
Classifier: Topic :: Software Development :: Libraries
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Requires-Python: >=3.8
Description-Content-Type: text/markdown
License-File: LICENSE
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Requires-Dist: numpy>=1.17
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<br>
<p align="center">
    <a href="https://biomass-core.readthedocs.io/en/latest">
        <img src="https://raw.githubusercontent.com/biomass-dev/biomass/master/docs/_static/img/biomass-logo.png" width="400">
    </a>
</p>

[![PyPI version](https://img.shields.io/pypi/v/biomass.svg?logo=PyPI&logoColor=white)](https://pypi.python.org/pypi/biomass)
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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*, 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)
