OptCom statistics

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Citations per year

Number of citations per year for the bioinformatics software tool OptCom
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Tool usage distribution map

This map represents all the scientific publications referring to OptCom per scientific context
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OptCom specifications

Information


Unique identifier OMICS_16105
Name OptCom
Software type Framework/Library
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Costas Maranas

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Publications for OptCom

OptCom citations

 (5)
library_books

Linking soil biology and chemistry in biological soil crust using isolate exometabolomics

2018
Nat Commun
PMCID: 5750228
PMID: 29296020
DOI: 10.1038/s41467-017-02356-9

[…] oundary constraints for flux-balance analysis in metabolic models and to inform trait-based models,] providing a genome-scale approach for linking soil metabolites with metagenomic data. For example, OptCom, a multi-level and multi-objective flux balance analysis framework to understand metabolism within microbial communities, which currently primarily relies on genomic information, could be used […]

library_books

Parametric studies of metabolic cooperativity in Escherichia coli colonies: Strain and geometric confinement effects

2017
PLoS One
PMCID: 5562313
PMID: 28820904
DOI: 10.1371/journal.pone.0182570

[…] rnal constraints (e.g. limited availability of a molecule needed for growth). Several FBA methods designed to examine communities of microorganisms have been developed including community FBA (cFBA), OptCom, dynamic multi-scale FBA (dmsFBA) and population FBA [, –]. cFBA compartmentalizes different organisms but allows them to compete for and exchange metabolites through an extracellular compartme […]

library_books

Metabolic Network Modeling of Microbial Interactions in Natural and Engineered Environmental Systems

2016
Front Microbiol
PMCID: 4870247
PMID: 27242701
DOI: 10.3389/fmicb.2016.00673

[…] mmunity culturing applications. None of our current computational tools can simultaneously capture the dynamics in all the mentioned scales. However, modeling approaches such as COMETS, HYDROGEOCHEM, OptCom, and MCM are pioneering tools to integrate different scale dynamics. […]

library_books

Genome scale metabolic reconstructions of Bifidobacterium adolescentis L2 32 and Faecalibacterium prausnitzii A2 165 and their interaction

2014
BMC Syst Biol
PMCID: 4108055
PMID: 24708835
DOI: 10.1186/1752-0509-8-41

[…] ibution of metabolite d to the different microorganisms in the community and the second being different transport reactions, where each reaction represents transport of glucose to one organism []. In OptCom, g d became two variables: uptake variable for growth medium metabolite d, uval d k , or/and export variable for growth media, eval d k , where k = bif or fap  [] and where bif is B. adolesc […]

library_books

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

2012
Brief Bioinform
PMCID: 3505041
PMID: 23175748
DOI: 10.1093/bib/bbs070

[…] examples can be found in the excellent review of Klitgord and Segrè []. Importantly, increasing interest in microbial community metabolic simulations is evident, as shown by the recent development of OptCom, a microbial community-addressed FBA framework [].Metagenomics offers the possibility of complementing existing whole genome sequences by determining, after appropriate processing and through a […]


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OptCom institution(s)
Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA
OptCom funding source(s)
This work was supported by the DOE grant DE-FG02-05ER25684.

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