• CoBAMP: a Python framework for...

Treffer: CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.

Title:
CoBAMP: a Python framework for metabolic pathway analysis in constraint-based models.
Authors:
Vieira V; Centre of Biological Engineering, University of Minho, Braga, Portugal., Rocha M; Centre of Biological Engineering, University of Minho, Braga, Portugal.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2019 Dec 15; Vol. 35 (24), pp. 5361-5362.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Metabolic Networks and Pathways* , Models, Biological*, Algorithms ; Programming, Linear ; Software
Entry Date(s):
Date Created: 20190731 Date Completed: 20200707 Latest Revision: 20200707
Update Code:
20250114
DOI:
10.1093/bioinformatics/btz598
PMID:
31359031
Database:
MEDLINE

Weitere Informationen

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.
(© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)