Mackinac: A bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models

Michael Mundy, Helena Mendes-Soares, Nicholas D Chia

Research output: Contribution to journalArticle

3 Citations (Scopus)

Abstract

Summary: Reconstructing and analyzing a large number of genome-scale metabolic models is a fundamental part of the integrated study of microbial communities; however, two of the most widely used frameworks for building and analyzing models use different metabolic network representations. Here we describe Mackinac, a Python package that combines ModelSEED's ability to automatically reconstruct metabolic models with COBRApy's advanced analysis capabilities to bridge the differences between the two frameworks and facilitate the study of the metabolic potential of microorganisms.

Original languageEnglish (US)
Pages (from-to)2416-2418
Number of pages3
JournalBioinformatics
Volume33
Issue number15
DOIs
StatePublished - Aug 1 2017

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Boidae
Metabolic Networks and Pathways
Genome
Genes
Python
Metabolic Network
Microorganisms
Model
Framework

ASJC Scopus subject areas

  • Statistics and Probability
  • Medicine(all)
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

Mackinac : A bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models. / Mundy, Michael; Mendes-Soares, Helena; Chia, Nicholas D.

In: Bioinformatics, Vol. 33, No. 15, 01.08.2017, p. 2416-2418.

Research output: Contribution to journalArticle

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