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wc_lang

Data-driven, rule-based language for describing whole-cell models

Contents

• Overview
• Installation
• Documentation
• License
• Development team
• Questions and comments
• 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 for more information about WC modeling, including perspectives, reviews, and tutorials.

This package defines wc_lang, a data-driven, rule-based language for concisely describing WC models.

Installation

pip install git+https://github.com/KarrLab/wc_lang.git#egg=wc_lang

Documentation

Please see the API documentation.

License

The example model is released under the MIT license.

Development team

The model 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