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README.md

PyPI package Documentation Test results Test coverage Code analysis License Analytics

wc_lang

Language for describing whole-cell models as reaction networks

Contents

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 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.

License

This package is released under the MIT license.

Development team

This package was developed by the Karr Lab at the Icahn School of Medicine at Mount Sinai in New York.

Questions and comments

Please contact the Karr Lab 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
  • 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
  • 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
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