GrowMatch specifications

Information


Unique identifier OMICS_13370
Name GrowMatch
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Costas Maranas <>

Publications for GrowMatch

GrowMatch in publications

 (20)
PMCID: 5902709
PMID: 29692801
DOI: 10.3389/fgene.2018.00121

[…] filled gaps identified through topological gap analysis and flux-based functional tests. the pathway visualization tool, escher, was instrumental in this gap analysis (). we also utilized the growmatch algorithm to obtain potential reactions to fill identified gaps (). additionally, the recently published model of a. baumannii atcc 19606, ilp844, was used as an additional resource […]

PMCID: 5377334
PMID: 28367990
DOI: 10.1038/srep45557

[…] functionality. with the three input data, the tinit algorithm was implemented using the raven toolbox under matlab r2013a (mathworks inc., natick, ma) environment. after the reconstruction, the growmatch algorithm was performed to enable the cell type-specific gems to demonstrate growth under rpmi-1640 medium by adding a minimum number of reactions from the hmr 2.0 to the lcsc and non-lcsc […]

PMCID: 5288723
PMID: 28150713
DOI: 10.1038/srep41774

[…] of biolog™ microplates, for example) there is not sufficient data of growth profiles for eukaryotic organisms, which restricts the use of this method for gap filling. another well-known method, growmatch, makes use of gene essentiality data for analysis of gaps. although correct predictions of essential genes is very important for a metabolic network model to be considered reliable, […]

PMCID: 5282492
PMID: 28139686
DOI: 10.1038/srep41569

[…] were taken from those genes that were identified as essential or non-essential from the transposon library of synechococcus 7942 published by rubin et al.. these results were categorized using the growmatch terminology, where either the in silico and in vivo results for growth or no growth match (i.e. gg and ngng) or conflict (i.e. gng and ngg)., how to cite this article: mueller, t. j. et al. […]

PMCID: 5001716
PMID: 27563720
DOI: 10.1371/journal.pcbi.1005085

[…] all scores except sensitivity. this can be explained by one igsm (ibsu1103) being largely based on a predecessor (iyo844); in addition, ibsu1103 was optimized for correct growth predictions using growmatch [,]. information from iyo844 can thus include errors that were deliberately removed from ibsu1103 and it can reverse changes made by the performance optimization. thus, although […]


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GrowMatch institution(s)
Department of Industrial and Manufacturing Engineering, The Pennsylvania State University, University Park, PA, USA; Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA; King's College London, UK
GrowMatch funding source(s)
This work was supported by the Department of Energy grant DE-FG02-05ER25684.

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