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Mackinac: a bridge between ModelSEED and COBRApy to generate and analyze genome-scale metabolic models
- Source :
- Bioinformatics
- Publication Year :
- 2017
- Publisher :
- Oxford University Press, 2017.
-
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. Availability and Implementation: This package works with Python 2.7, 3.4, and 3.5 on MacOS, Linux and Windows. The source code is available from https://github.com/mmundy42/mackinac. Contact: mundy.michael@mayo.edu or soares.maria@mayo.edu
- Subjects :
- 0301 basic medicine
Statistics and Probability
Source code
Computer science
media_common.quotation_subject
0206 medical engineering
Genome scale
Metabolic network
02 engineering and technology
Biochemistry
Genome
Models, Biological
Bridge (nautical)
03 medical and health sciences
Software
Metabolic potential
Molecular Biology
media_common
computer.programming_language
biology
Bacteria
business.industry
Systems Biology
Computational Biology
Python (programming language)
biology.organism_classification
Applications Notes
Computer Science Applications
Computational Mathematics
030104 developmental biology
Computational Theory and Mathematics
Software engineering
business
computer
020602 bioinformatics
Metabolic Networks and Pathways
Subjects
Details
- Language :
- English
- ISSN :
- 13674811 and 13674803
- Volume :
- 33
- Issue :
- 15
- Database :
- OpenAIRE
- Journal :
- Bioinformatics
- Accession number :
- edsair.doi.dedup.....7baaa9b68ba727073b9685fe9f93327b