Package: fbc-curation
fbc_curation: FROG analysis in PythonThe projectfbc_curationimplements the FROG analysis for reproducibility of constraint-based models in Python.
FROG can be runprogrammatically in pythonusing therunfrogcommand line tool available in this packagevia the websitehttps://runfrog.devia the REST APIhttps://runfrog.de/docsThe FROG analysis creates standardized reference files for a given constraint-based computational model.
The FROG files can be used in the model curation process for validating the model behavior, e.g., when
submitting the model toBioModels.
The latest version supportsfbc_curationprovides two implementations of FROG usingcobrapybased on COBRApy (Constraint-Based Reconstruction and Analysis in Python)cameocameo based on Cameo (Computer Aided Metabolic Engineering and Optimization)For more information see the following resourcesDocumentation:https://fbc-curation.readthedocs.ioWebsite:https://runfrog.deREST API:https://runfrog.de/docsFROG format:FROG version 1FROG JSON schema:frog-schema-version-1.json.Code:https://github.com/matthiaskoenig/fbc_curationFROG BioModels submission:https://www.ebi.ac.uk/biomodels/curation/fbc.If you have any questions or issues pleaseopen an issue.How to citeIf you usefbc_curationorrunfrogplease cite us viaInstallationfbc_curationis available frompypiand
can be installed via:pip install fbc-curationThe latest develop version can be installed via:pip install git+https://github.com/matthiaskoenig/fbc-curation.git@developRun FROGCommand line toolAfter installation FROG analysis can be performed using therunfrogcommand line tool$runfrog──────────────────────────────────────────────────────────────────────────────────🐸FBCCURATIONFROGANALYSIS🐸Version0.2.1(https://github.com/matthiaskoenig/fbc_curation)Citationhttps://doi.org/10.5281/zenodo.3708271──────────────────────────────────────────────────────────────────────────────────Usage:runfrog[options]Options:-h,--helpshowthishelpmessageandexit-iINPUT_PATH,--input=INPUT_PATH(required)pathtoCOMBINEarchive(OMEX)withSBMLmodeloranSBMLmodel-oOUTPUT_PATH,--output=OUTPUT_PATH(required)omexoutputpathtowriteFROG──────────────────────────────────────────────────────────────────────────────────WebsiteFROG can be easily executed via the websitehttps://runfrog.deREST APIFROG can be execute via the REST APIhttps://runfrog.de/docsPythonTo run FROG programmatically via python use therun_frogfunctionfromfbc_curation.workerimportrun_frogrun_frog(model_path,omex_path)Here a complete example with comparison of the FROG results"""FROG example using `fbc_curation`."""frompathlibimportPathfromfbc_curation.compareimportFrogComparisonfromfbc_curation.workerimportrun_frogdefcreate_frog(model_path:Path,omex_path:Path)->None:"""Create FROG report and writes OMEX for given model."""# create FROG and write to COMBINE archiverun_frog(source_path=model_path,omex_path=omex_path,)# compare FROG results in created COMBINE archivemodel_reports=FrogComparison.read_reports_from_omex(omex_path=omex_path)for_,reportsinmodel_reports.items():FrogComparison.compare_reports(reports=reports)if__name__=="__main__":base_path=Path(".")create_frog(model_path=base_path/"e_coli_core.xml",omex_path=base_path/"e_coli_core_FROG.omex",)The typically output of a FROG analysis is depicted belowrunfrog-ie_coli_core.xml-oe_coli_core.omex───────────────────────────────────────────────────────────────────────────────────────🐸FBCCURATIONFROGANALYSIS🐸Version0.2.3(https://github.com/matthiaskoenig/fbc_curation)Citationhttps://doi.org/10.5281/zenodo.3708271───────────────────────────────────────────────────────────────────────────────────────INFOLoading'e_coli_core.xml'worker.py:70WARNINGOmexpath'e_coli_core.xml'isnotaziparchive.omex.py:500─────────────────────────────────FROGCuratorCobrapy─────────────────────────────────INFO*metadatacurator.py:107INFO*objectivescurator.py:110INFO*fvacurator.py:113INFO*reactiondeletionscurator.py:116INFO*genedeletionscurator.py:119INFOFROGcreatedin'0.977'[s]worker.py:178──────────────────────────────────FROGCuratorCameo──────────────────────────────────INFO*metadatacurator.py:107INFO*objectivescurator.py:110INFO*fvacurator.py:113INFO*reactiondeletionscurator.py:116INFO*genedeletionscurator.py:119INFOFROGcreatedin'1.219'[s]worker.py:178─────────────────────────────────────WriteOMEX──────────────────────────────────────WARNINGExistingomexisoverwritten:'e_coli_core.omex'omex.py:680INFOReportsinomex:compare.py:60{'./e_coli_core.xml':['cobrapy','cobrapy_tsv','cameo','cameo_tsv']}──────────────────────────────ComparisonofFROGReports──────────────────────────────---objective---cobrapycobrapy_tsvcameocameo_tsvcobrapy1111cobrapy_tsv1111cameo1111cameo_tsv1111---fva---cobrapycobrapy_tsvcameocameo_tsvcobrapy1111cobrapy_tsv1111cameo1111cameo_tsv1111---reaction_deletion---cobrapycobrapy_tsvcameocameo_tsvcobrapy1111cobrapy_tsv1111cameo1111cameo_tsv1111---gene_deletion---cobrapycobrapy_tsvcameocameo_tsvcobrapy1111cobrapy_tsv1111cameo1111cameo_tsv1111───────────────────────────────────────────────────────────────────────────────────────Equal:True───────────────────────────────────────────────────────────────────────────────────────LicenseSource Code:LGPLv3Documentation:CC BY-SA 4.0Thefbc_curationsource is released under both the GPL and LGPL licenses version 2 or
later. You may choose which license you choose to use the software under.This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License or the GNU Lesser General Public
License as published by the Free Software Foundation, either version 2 of the
License, or (at your option) any later version.This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE. See the GNU General Public License for more details.FundingMatthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany)
within the research network Systems Medicine of the Liver (LiSyM, grant number 031L0054)
and by the German Research Foundation (DFG) within the Research Unit Programme FOR 5151
“QuaLiPerF(Quantifying Liver Perfusion-Function Relationship in Complex Resection -
A Systems Medicine Approach)” by grant number 436883643 and by grant number 465194077
(Priority Programme SPP 2311, Subproject SimLivA).© 2020-2022 Matthias König