Package: geckopy
Please refer tohttp://geckotoolbox.readthedocs.ioHistory2.0.2 (2021-02-17)Features:FSEOF implementation for ecModels in/geckomat/utilities/(PR #119).Routines for quickly generating context-specific ecModels from a general ecModel, also in/geckomat/utilities/(PR #120).Fixes:Closes #116: Migrated CI toTravis-CI.com(PR #118).prot_abundance.txtcan now be an empty file without the pipeline erroring (PR #124).Removes storage of metabolite notes in the ecModel, which were causing an error in COBRA (PR #125).Documentation/Styling/Others:Added contributing guidelines, code of conduct and PR/issue templates (PR #115).Closes #123: Simplified GECKO pipeline log (PR #128).2.0.1 (2020-11-19)Fixes:UBs are only changed for strictly required proteins (PR #103).Solves #101: All yeast models in the toolbox are built on the same yeast-GEM version8.1.3(PR #105).Solved bug ingenerate_protModels.mthat constrained both the biomass and growth reactions (PR #107).Updated env. list after release of pandas 1.0 (PR #110).A folder for ecModels is added in case it doesn’t exist already (PR #111).Solves #112: Avoid using the variable nameversionfor potential conflicts with Matlab (PR #113).Style:Solves #102: All UBs in repo changed from +Inf to +1000 (PR #109).2.0.0 (2020-05-18)Features:A main utility for constraining an ecModel with proteomics data stored in data files, and ensuring the model can grow at the provided conditions (PR #82).More constraining options in FVA utility (PR #95).An option for reducing display offitGAM.m(PR #82).A chemostat simulation utility (PR #82).Fixes:Fixes #73: Bug ingetKcat.m(PR #75).Fixes #78: Updated BRENDA URL (PR #91).FVA utility: Fixed directionality bugs inMAX_min_Optimizer.m(PRs #69 & #95) & optimization bug incomparativeFVA.m(PR #95).geckopy: Updated csv reader in geckopy test (PR #83) and met id parsing (PR #93).Fixed subfolder bug inmodifyKcats.m(PR #80).Refactoring:IntroducedgetModelParameters.mfor defining all input parameters, for streamlining the main ecModel generation pipeline (PR #76).Simplified constraining procedure in the FVA utility (PR #95).Documentation:Improved documentation of several main functions (PR #76).Updated Matlab requirements (PR #96).1.3.5 (2019-05-03)Features:Additional options for output tables frommodifyKcats.m&topUsedEnzymes.m(PR #61).keggIDis now an input forupdateDatabases.m(PR #62).Backwards compatibility with any yeastGEM from 8.0.0 onwards (PR #66).New utilities:getSubset_ecModel.m, for getting context-specific ecModels (PR #64).getKcat.m, for retrieving kcats (PR #67).Fixes:Fixed bug in aconitase kcat & misc. error handling (PR #62).Refactoring:Speed improvements intopUsedEnzymes.m(PR #61).Reduced display of several functions (PR #62).SimplifiedchangeMedia_batch.mand made more genericconstrainEnzymes.m&flexibilizeProteins.m(PR #63).Style:Changed EOL to LF (unix default) (PR #68).Documentation:Documented input/output oftopUsedEnzymes.m&truncateValues.m(PR #61).Added/updated documentation ofchangeMedia_batch.m,constrainEnzymes.m,flexibilizeProteins.m&getConstrainedModel.m(PR #63).1.3.4 (2018-12-04)Features:Generalization ofmeasureAbundance.mto receive any PaxDB file, a relative proteomics dataset, or even nothing at all (PR #58).New utility: Comparative FVA between a model and its enzyme-constrained version (PR #57).Fixes:Consistent definition of what data is inuniprot.tab(PR #48).Proper use ofmeasureAbundance.mfrom withinconstrainEnzymes.m(PR #56).Refactoring:Switch all functions that add/change rxns/genes from COBRA to RAVEN (PR #48).Avoid any functions from Simulink (PR #48).1.3.3 (2018-11-02)Fixes:Fixes #15: Binary results from the model (ecModel.mat,ecModel_batch.mat&enzData.mat) are no longer stored in repo (PR #52).Misc. fixes in the biomass composition + GAM calculations (PR #53).Refactoring:Speed improvement in misc. functions (PR #49).AddedsumProtein.mfor easier use when creating new ecModels (PR #53).Documentation:Documented better which scripts/data should be changed and which are optional when adapting geckomat to produce a new ecModel (PR #53).1.3.2 (2018-10-12)Features:Name & version of the model are now read/stored from/as model fields (PR #42).Pipeline now works for any objective function (PR #47).Fixes:Fixed bug from #39 that saved the.matfile with the wrong name (PR #42).Adapted pipeline to deal with multiple gene IDs for 1 protein / multiple protein IDs for 1 gene, for dealing with human-based GEMs (PR #43).changeMedia_batch.mmodified to reflect the Y6 minimal media composition (PR #47).Refactoring:Performance improvements togetConstrainedModel.mandsigmaFitter.m(PR #47).fitGAM.mis now only called from insidescaleBioMass.m(PR #47).1.3.1 (2018-08-28)Features:Adapted the pipeline to work withyeast-GEM, including loading, processing and saving the model. Current model is constructed from yeastv8.1.3(PR #39).When constructingecModel_batch, lipid fraction is now scaled together with protein and carbohydrate fractions (PR #39).Fixes:geckopytests flexibilized to comply with yeast-GEM (PR #39).Refactoring:Reorganized the repo, making a division betweengeckomat(Matlab part for generation + simulation of ecModels) andgeckopy(Python part for simulations of ecYeastGEM) (PR #40).Parametersf(mass fraction of enzymes in model),Pbase,Cbase,Lbase(biomass composition) andGAM(growth-associated ATP maintenance) are now automatically computed (PR #39).AddedRAVENas a dependency forgeckomat(PR #38).Changed most COBRA functions in pipeline to RAVEN functions (PR #39).1.3.0 (2018-08-01)Features:Protein flexibilization: When proteomic measurements are provided, individual protein levels will now be iteratively flexibilized by the pipeline if the model results to be overconstrained, based on a provided growth rate. After this, flexibilized protein exchange pseudoreaction upper bounds will be set to the their flux values from a parsimonious FBA simulation (PR #34).Utilities: Included a folder with useful functions (PR #34).Fixes:Fixes #14: CI is no longer failing, as model location, model naming and metabolite ID naming were corrected.test_adjust_pool_boundswas simplified to test with only 1 essential protein (PR #28).1.2.1 (2018-05-30)Features:All genes from the original yeast model now included in the.xmlfile. Genes connected to enzyme constraints are now stored inmodel.enzGenesin the.matstructure.Docs badge in README.Fixes:FieldsgrRulesandrulesfixed in a consistent way:grRulesfor the backwards reactions are the same as for the forward ones.For reactions catalyzed by just 1 enzyme (or complex),grRulesof the original reactions are assigned to them.For reactions catalyzed by more than 1 enzyme (or more than 1 complex),grRulesof the original reactions are assigned to the arm reactions, and the corresponding sub-rules are assigned to the isozyme-controlled reactions.For enzyme exchange reactions,grRulesare assigned as thecorresponding gene ID.Therulesfield is set equal togrRulesfor providing consistency with different toolboxes.Inter-OS compatibility:
* Numbers in scientific notation are stored in the.xmlfiles with formatXe-0N, notXe-00N, or with formatXe-1N, notXe-01N, regardless of the OS used for generating them.
* Numbers in all files are shown with up to 6 significant figures.Refactoring:Updated to new COBRA standards foraddReactionusage.NOTE: Not available in pypi (issue #14 unresolved)1.2.0 (2018-04-12)Implemented automatickcatflexibilization for over-constrained models:Based on a maximum growth rate specified by the user, the algorithm iteratively identifies the top growth-limitingkcatvalue and changes it for the highest one in BRENDA (same EC number)Once that the model is growing close to the set value, the average enzyme saturation factor is refittedFor non-feasible/zero-growth models, sensitivity analysis is performed on a reaction and enzyme basis rather than on individualkcatvaluesThe outputs of this step are stored intopUsedEnzymes.txtandkcatModification.txtand can be used for further manual curationAll databases updated (BRENDA, swissprot, KEGG, PaxDB)More generic gene/protein matching for compatibility with other modelsRe-organization of all output files in a single folderNew badges + styling of websiteNOTE: Not available in pypi (issue #14 unresolved)1.1.2 (2018-03-20)Improved kcat matching to BRENDA with:Specific activityPhylogenetic distance, when data for organism of choice is not availableSwitched to readthedocs for documentation:http://geckotoolbox.readthedocs.ioAdded a Gitter room for discussion:https://gitter.im/SysBioChalmers/GECKOSwitched to a simplified GitFlow structure (master+devel+ feature branches)Python 3.4 environment dropped in CI (no longer supported by pandas)NOTE: Not available in pypi (issue #14 unresolved)1.1.1 (2017-12-08)Model and data are now also deployed.Changes in license and readme.1.1.0 (2017-09-07)First release on PyPI.1.0.0 (2017-09-07)First release of GECKO in Github.