COBRApy

COBRApy is a Python package that offers comprehensive support for the COBRA methodology. It follows an object-oriented design to accurately represent complex biological processes such as metabolism and gene expression. COBRApy is independent of MATLAB but includes an interface to the COBRA Toolbox for MATLAB to use existing codes. Additionally, it enables parallel processing for computationally demanding tasks, increasing efficiency.

Topic

Gene expression;Genomics;Molecular interactions, pathways and networks

Detail

  • Operation: Metabolic network modelling

  • Software interface: Command-line user interface

  • Language: Python

  • License: GNU General Public License v>=2, GNU Lesser General Public License v>=2

  • Cost: Free

  • Version name: 0.26.2

  • Credit: The US National Institute of Allergy and Infectious Diseases, the US Department of Health and Human Services, Seed Award from the San Diego Center for Systems Biology funded by NIH-NIGMS.

  • Input: -

  • Output: -

  • Contact: Ali Ebrahim aebrahim@ucsd.edu, Joshua A Lerman jalerman@ucsd.edu, Bernhard O Palsson palsson@ucsd.edu, Daniel R Hyduke hyduke@ucsd.edu

  • Collection: -

  • Maturity: -

Publications

  • COBRApy: COnstraints-Based Reconstruction and Analysis for Python.
  • Ebrahim A, et al. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. COBRApy: COnstraints-Based Reconstruction and Analysis for Python. 2013; 7:74. doi: 10.1186/1752-0509-7-74
  • https://doi.org/10.1186/1752-0509-7-74
  • PMID: 23927696
  • PMC: PMC3751080

Download and documentation

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