https://github.com/karrlab/wc_lang
Language for describing whole-cell models as reaction networks
https://github.com/karrlab/wc_lang
cell-biology computational-biology modeling simulation systems-biology whole-cell-modeling
Last synced: about 2 months ago
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Language for describing whole-cell models as reaction networks
- Host: GitHub
- URL: https://github.com/karrlab/wc_lang
- Owner: KarrLab
- License: mit
- Created: 2016-11-07T15:03:21.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2021-05-24T21:57:09.000Z (over 4 years ago)
- Last Synced: 2025-06-25T22:07:59.783Z (3 months ago)
- Topics: cell-biology, computational-biology, modeling, simulation, systems-biology, whole-cell-modeling
- Language: Python
- Homepage:
- Size: 13.1 MB
- Stars: 9
- Watchers: 5
- Forks: 3
- Open Issues: 30
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://pypi.python.org/pypi/wc_lang)
[](https://docs.karrlab.org/wc_lang)
[](https://circleci.com/gh/KarrLab/wc_lang)
[](https://coveralls.io/github/KarrLab/wc_lang)
[](https://codeclimate.com/github/KarrLab/wc_lang)
[](LICENSE)
# wc_lang
Language for describing whole-cell models as reaction networks
## Contents
* [Overview](#overview)
* [Installation](#installation)
* [Documentation](#documentation)
* [License](#license)
* [Development team](#development-team)
* [Questions and comments](#questions-and-comments)
* [References](#references)
## Overview
Whole-cell (WC) models are comprehensive computational models of all of the biochemical activity inside individaul cells [Karr et al., 2015; Macklin et al., 2014]. WC models have great potential to enable bioengineers to rationally design microorganisms for industrial and medical applications and to enable physicians to personalize medical therapy [Carrera and Covert, 2015]. Please see [WholeCell.org](https://www.wholecell.org) for more information about WC modeling.
This package defines `wc_lang`, a language for describing WC models as reaction networks.
## Installation
* Install latest release from PyPI
```
wc_lang
```
* Install latest revision from GitHub
```
pip install git+https://github.com/KarrLab/wc_utils.git#egg=wc_utils
pip install git+https://github.com/KarrLab/obj_tables.git#egg=obj_tables
pip install git+https://github.com/KarrLab/wc_lang.git#egg=wc_lang
```
## Documentation
Please see the [documentation](https://docs.karrlab.org/wc_lang).
## 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.
## Questions and comments
Please contact the [Karr Lab](https://www.karrlab.org) with any questions or comments.
## References
* Carrera J & Covert MW. (2015). Why Build Whole-Cell Models? *Trends in Cell Biology*, 25(12), 719-722. DOI: [10.1016/j.tcb.2015.09.004](https://doi.org/10.1016/j.tcb.2015.09.004)
* Karr JR, Takahashi K & Funahashi A. (2015). The principles of whole-cell modeling. *Current Opinion in Microbiology*, 27, 18-24. DOI: [10.1016/j.mib.2015.06.004](https://doi.org/10.1016/j.mib.2015.06.004)
* Macklin DN, Ruggero NA & Covert MW. (2014). The future of whole-cell modeling. *Current Opinion in Biotechnology*, 28, 111-115. DOI: [10.1016/j.copbio.2014.01.012](https://doi.org/10.1016/j.copbio.2014.01.012)