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About FROG PAWS

Table of content

Tool description
Publications
External links

Tool description

FROG PAWS is an online tool to generate FROG reports using the FBCModelTests.jl package and COBREXA.jl constraint-based metabolic modeling toolkit. The FROG reports are designed to scrutinise and ensure the reproducibility of constraint-based metabolic modeling models and their generated results.

More information about FROG and its application to metabolic model curation is available from the FROG homepage at BioModels.

Current specification of FROG reports is maintained at github.com/LCSB-BioCore/frog-specification.

In summary, the FROG report contains base reproducibility information about:

Objective values
Flux variability in all reactions
Response of the model to single-reaction knockouts
Response of the model to gene knockouts

Publications

COBREXA.jl: constraint-based reconstruction and exascale analysis
Miroslav Kratochvíl, Laurent Heirendt, St. Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P. Satagopam, Oliver Ebenhöh, Reinhard Schneider, Christophe Trefois, and Wei Gu
Miroslav Kratochvíl, Laurent Heirendt, St Elmo Wilken, Taneli Pusa, Sylvain Arreckx, Alberto Noronha, Marvin van Aalst, Venkata P Satagopam, Oliver Ebenhöh, Reinhard Schneider, Christophe Trefois, Wei Gu, COBREXA.jl: constraint-based reconstruction and exascale analysis, Bioinformatics, Volume 38, Issue 4, February 2022, Pages 1171–1172, doi:10.1093/bioinformatics/btab782