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SuBliMinaL Toolbox specifications


Unique identifier OMICS_20088
Name SuBliMinaL Toolbox
Software type Application/Script
Interface Command line interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Stability Stable
BioCyc Data File Licence
Maintained Yes




No version available


  • person_outline Neil Swainston

Publication for SuBliMinaL Toolbox

SuBliMinaL Toolbox citations


Insights from 20 years of bacterial genome sequencing

PMCID: 4361730
PMID: 25722247
DOI: 10.1007/s10142-015-0433-4

[…] ED ().There are other software platforms that are tailor made for semi-automated GEMs reconstruction like the Raven toolbox (Agren et al. ) which has a Web-based version (Garcia-Albornoz et al. ) and SuBliMinal toolbox (Swainston et al. ) which can be used for high-throughput GEM reconstruction. All mentioned platforms and software were compared in the recent review (Hamilton and Reed ) that can b […]


Computational Approaches for Microalgal Biofuel Optimization: A Review

Biomed Res Int
PMCID: 4189764
PMID: 25309916
DOI: 10.1155/2014/649453

[…] mited number of software tools for automated reconstruction are currently available (some examples are given in ); for instance, AUTOGRAPH [], GEMSiRV [], MicrobesFlux [], MetRxn [], Model SEED [, ], SuBliMinaL Toolbox [], FAME [], and RAVEN Toolbox [] can be named. A systematic comparison between some of these platforms can be found in []. While draft metabolic models can be generated through suc […]


Comparative evaluation of open source software for mapping between metabolite identifiers in metabolic network reconstructions: application to Recon 2

J Cheminform
PMCID: 3917611
PMID: 24468196
DOI: 10.1186/1758-2946-6-2

[…] th multiple identifiers each, is extremely laborious. Metabolites in early reconstructions were generally annotated manually. Today, reconstruction tools such as the Model SEED [], rBioNet [] and the SuBliMinaL Toolbox [] facilitate the process by populating new reconstructions with pre-annotated components from source databases. Metabolites in the source databases, however, may have incomplete or […]


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SuBliMinaL Toolbox institution(s)
Manchester Centre for Integrative Systems Biology, University of Manchester, Manchester, UK; Virginia Bioinformatics Institute, Virginia Tech, Blacksburg, VA, USA
SuBliMinaL Toolbox funding source(s)
Supported by Manchester Centre for Integrative Systems Biology funded by the BBSRC and EPSRC; BBSRC/EPSRC Grant BB/C008219/1.

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