CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 31359031.
- Also identified by DOI 10.1093/bioinformatics/btz598.
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Abstract
SUMMARY: CoBAMP is a modular framework for the enumeration of pathway analysis concepts, such as elementary flux modes (EFM) and minimal cut sets in genome-scale constraint-based models (CBMs) of metabolism. It currently includes the K-shortest EFM algorithm and facilitates integration with other frameworks involving reading, manipulation and analysis of CBMs. AVAILABILITY AND IMPLEMENTATION: The software is implemented in Python 3, supported on most operating systems and requires a mixed-integer linear programming optimizer supported by the optlang framework. Source-code is available at https://github.com/BioSystemsUM/cobamp.
Medical subject headings
- Metabolic Networks and Pathways
- Models, Biological