wc_lang documentation

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

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.

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

Contents

• 1. Installation
  • 1.1. Prerequisites
  • 1.2. Latest release from PyPI
  • 1.3. Latest revision from GitHub
• 2. Overview of wc_lang
  • 2.1. Units
• 3. Tutorial
• 4. API documentation
  • 4.1. wc_lang package
    • 4.1.1. Subpackages
    • 4.1.2. Submodules
    • 4.1.3. wc_lang.__main__ module
    • 4.1.4. wc_lang._version module
    • 4.1.5. wc_lang.core module
    • 4.1.6. wc_lang.io module
    • 4.1.7. wc_lang.util module
    • 4.1.8. Module contents
• 5. About
  • 5.1. License
  • 5.2. Development team
  • 5.3. Acknowledgements
  • 5.4. Questions and comments
• 6. References