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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

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Maintainer


  • person_outline Costas Maranas <>

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Publications for OptCom

OptCom in publications

 (14)
PMCID: 5906705
PMID: 29540507
DOI: 10.1042/BST20170265

[…] framework to couple the cbms of a geobacter and a rhodoferax with a groundwater environment and simulate bacterial competition; then zomorrodi et al. [] proposed a multi-objective framework, d-optcom, that introduced individual- and community-level fitness principles as inner and outer optimization problems, respectively; going a step further, harcombe et al. [] added spatial dynamics […]

PMCID: 5840735
PMID: 29556373
DOI: 10.1186/s12263-018-0594-6

[…] or parasitic relationships can exist in an ecosystem and often the objective is not to maximize the biomass of the competitors in the surrounding. therefore, more sophisticated methods like d-optcom [] have been developed, which break the community optimization problem into multiple single problems. these consist of smaller optimization problems for each community member, and the main […]

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

[…] 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 […]

PMCID: 5134014
PMID: 28334697
DOI: 10.1098/rsif.2016.0627

[…] by iteratively fixing the growth rate of one organism and optimizing the other species' growth rate, whereby the resulting pareto frontiers revealed four different types of interactions. in the optcom framework, a nested objective function is used whereby a community-level objective is optimized (e.g. maximizing the total biomass of the community) subject to the single-species objectives […]

PMCID: 4870247
PMID: 27242701
DOI: 10.3389/fmicb.2016.00673

[…] between estimated rates define new community stoichiometry's which are then used to define inter-guild interactions (taffs et al., ). the bi-level optimization approach, like that developed as the optcom algorithm (zomorrodi and maranas, ), postulates a separate biomass maximization problem for each species as initial (inner) optimization problems, consequently capturing driving forces […]


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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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