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Title: DistributedFBA.jl: High-level, high-performance flux balance analysis in Julia

Journal Article · · Bioinformatics
 [1];  [1];  [1]
  1. University of Luxembourg, Esch-sur-Alzette (Luxembourg). Luxembourg Centre for Systems Biomedicine
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Flux balance analysis and its variants are widely used methods for predicting steady-state reaction rates in biochemical reaction networks. The exploration of high dimensional networks with such methods is currently hampered by software performance limitations. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes. DistributedFBA.jl is a high-level, high-performance, open-source implementation of flux balance analysis in Julia. It is tailored to solve multiple flux balance analyses on a subset or all the reactions of large and huge-scale networks, on any number of threads or nodes.

Research Organization:
University of Luxembourg, Esch-sur-Alzette (Luxembourg)
Sponsoring Organization:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; USDOE Office of Science (SC), Advanced Scientific Computing Research (ASCR)
Grant/Contract Number:
SC0010429
OSTI ID:
1424909
Journal Information:
Bioinformatics, Vol. 33, Issue 9; ISSN 1367-4803
Publisher:
Oxford University PressCopyright Statement
Country of Publication:
United States
Language:
English
Citation Metrics:
Cited by: 18 works
Citation information provided by
Web of Science

References (9)

Global reconstruction of the human metabolic network based on genomic and bibliomic data journal January 2007
COBRApy: COnstraints-Based Reconstruction and Analysis for Python journal January 2013
Computationally efficient flux variability analysis journal September 2010
Systematic prediction of health-relevant human-microbial co-metabolism through a computational framework journal February 2015
Computing in Operations Research Using Julia journal April 2015
Reconstruction and Use of Microbial Metabolic Networks: the Core Escherichia coli Metabolic Model as an Educational Guide journal September 2010
Systems Biology book January 2015
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0 journal August 2011
A community-driven global reconstruction of human metabolism journal March 2013

Cited By (2)

Systematic assessment of secondary bile acid metabolism in gut microbes reveals distinct metabolic capabilities in inflammatory bowel disease journal May 2019
Dynamic load balancing enables large-scale flux variability analysis posted_content October 2018

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Related Subjects

59 BASIC BIOLOGICAL SCIENCES
97 MATHEMATICS AND COMPUTING