GECKO 3.1.1 #340
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GECKO 3.1.1 #340
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fix: getStandardKcat with multiple subSystems
* reverse: simulateGrowth for ecFSEOF * fix: consistency in terminology * refactor: fluxes for a target * refactor: compatibility to GECKO3 ecFlux_scanning * refactor: add compatibility to GECKO3 * fix: typo * fix: save file type file * fix: filter tolerance * fix: if not carbon uptake have been defined * fix: add toleracne to protein pool * refactor: spaces instead of tabs * fix: function input description * Update src/geckomat/utilities/ecFSEOF/run_ecFSEOF.m --------- Co-authored-by: edkerk <eduardk@chalmers.se>
* fix: applyCustomKcats should allow struct as input * fix: applyCustomKcats correct parse default param * fix: applyCustomKcats * applyCustomKcats doc and tests * refactor: reduce command window output testss * Apply suggestions from code review Co-authored-by: Albert Tafur Rangel <39610893+ae-tafur@users.noreply.github.com> --------- Co-authored-by: Albert Tafur Rangel <39610893+ae-tafur@users.noreply.github.com>
* fix: updateProtPool avoid correctinf for f twice * doc: flexibilizeProtConcs explain overconstraining * fix: loadProtData measuredProt if NaN exist * doc: protocol.m describe updateProtPool input * fix: updateProtPool simplified new pool calculation * chore: update protocol for updateProtPool --------- Co-authored-by: Mihail Anton <mihail.anton@chalmers.se>
#312) * feat: create structure project * feat: include empty .keep files --------- Co-authored-by: edkerk <eduardk@chalmers.se>
* fix: writeDLKcatInput currencyMets handling * fix: filter out pseudoreactions makeEcModel * fix: makeEcModel find pseudoreactions
* chore: rename userData to tutorials * chore: move protocol and adapters * chore: keep original in full under blankExample * chore: compact adapters for human and yeast * chore: cleanup protocol for yeast * feat: add a model adapter under blankExample * chore: rename adapter * feat: copy protocol from yeast to human * fix: typo * fix: new folder names in adapters * fix: update paths to tutorials * refactor: model adapter expects full adapter path and extension * fix: file paths for yeast-GEM tutorial * style: protocol in tutorial prints step * chore: rm doc * feat: compress outputs about downloading complexes * fix: full path to adapter in test * fix: full paths for adapters in tests * fix: undo bad path change * chore: remove blankExample, use startGECKOproject * chore: restore yeast-GEM protocol.m content * chore: run through yeast-GEM protocol * feat: simplify ModelAdapterManager commands * fix: allow to set empty default adapter * fix: tests refer to test adapter --------- Co-authored-by: edkerk <eduardk@chalmers.se>
by running updateGECKOdoc()
feat: online docs
* fix: getStandardKcat light model standard enzyme In light ecModels, even if standard enzyme is not a pseudo-substrate (it will always use prot_pool instesad), standard enzyme should still be in ecModel.ec.enzyme (and .rxnEnzMat etc.), to calculate MW/kcat. * refactor: applyKcatConstraints simplify light * refactor: getStandardKcat * fix: applyKcatConstraints zero-kcats light ecModel * feat: copyECtoGEM function
* fix: use logical vector to construct equations * fix: increase default tolerance * style: typo * style: use standard input names * fix: adaptar default method name * fix: set values under solver tol to zero * feat: run_ecFSEOF check alphaLims parameter --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
* feat: new/updated functions around enzyme usage * feat: install and adapter manager * feat: Crabtree plot and data * feat: updated protocol and model file * refactor: rename tutorials full_ and light_ecModel * feat: loadConventionalGEM can load YAML * feat: use progressbar to give time estimates * fix: ecFVA correct number of simulations * feat: sensitivityTuning reports eccodes * feat: fillProtConcs select column from protData * feat: flexibilizeProtConcs sort by highest ratio * feat: plotCrabtree plus graphs * feat: plot light vs full ecModel analysis * feat: GECKOInstaller checks RAVEN version * feat: update of full_ecModel protocol moved progressbar to RAVEN 2.8.2 * fix: getStandardKcat light model standard enzyme In light ecModels, even if standard enzyme is not a pseudo-substrate (it will always use prot_pool instesad), standard enzyme should still be in ecModel.ec.enzyme (and .rxnEnzMat etc.), to calculate MW/kcat. * refactor: applyKcatConstraints simplify light * refactor: getStandardKcat * feat: light_ecModel tutorial overhaul * fix: plot light vs full * fix: applyKcatConstraints zero-kcats light ecModel * feat: copyECtoGEM function * chore: updateDocumentation * fix: full_ecModel/protocol.m step 13 * full_ecModel misc small fixes * fix: full_ecModel/protocol.m step 15 * fix: full_ecModel/protocol.m install instructions * fix: findMetSmiles report success and handle prot_ * fix: full_ecModel customKcat non-funct. protein * fix: plotCrabtree avoid flux minimalization * fix: full_ecModel various minor changes * fix: GECKOInstaller RAVEN dep version bump * fix: full_ecModel and light_ecModel from review * fix: remove unused functions * feat: rerun light_ecModel pipeline * refactor: change vanHoek1998.csv to .tsv
* fix: remake ecFVA plot with generic plot function * fix: GECKOInstaller ignore doc subfolder * chore: updateGECKOdoc * fix: remove old ecFVA.tsv no purpose to write this file * refactor: speedup fuzzyKcatMatching & getECfromGEM * feat: saveEcModel more logical input * refactor: swap TIFF for PDF
* refactor: speed increase applyComplexData * feat: applyComplexData progressbar + code comments
* fix: remake ecFVA plot with generic plot function * fix: GECKOInstaller ignore doc subfolder * chore: updateGECKOdoc * fix: remove old ecFVA.tsv no purpose to write this file * fix: getStandardKcat no standard gene in light-ec * fix: light_ecModel until step 29 * feat: getSubsetEcModel + tutorial
* refactor: rename KEGG params to param.kegg. to param.kegg.geneID * refactor: rename Complex params to param.complex * refactor: rename UniProt params to param.uniprot. * fix: remove unused obj.params entries remnants of GECKO2 * refactor: add _id to uniprot taxonomy * refactor: use taxonomicID from complex portal easier to find than precise species name * feat: use RAVEN's phylDist.mat from RAVEN 2.8.3 includes species names * feat: tutorial yeast-GEM as yaml * feat: yeast-GEM file is for tutorial only * fix: remove unused manualModifications * fix: small fixes
…ment docs: add link to tutorials in README
* chore: rerun full_ecModel tutorial * feat: light vs full ecModel comparison * doc: swap step 29 and 30
* chore: rerun full_ecModel tutorial * feat: light vs full ecModel comparison * doc: swap step 29 and 30 * chore: rerun light_ecModel tutorial * refactor: consistent use of isozyme In agreement with manuscript * chore: updateDocumentation * doc: format of warning messages * fix: plotlightVSfull.m handle use of alt solvers * fix: consistent cutoff for low fluxes
docs: futher polishing
* refactor: rename to flexEnz and flexbilizeEnzConcs * feat: mapRxnsToConv report empty fluxVect * feat: readDLKcatOutput reports non-matches * doc: protocol.m small changes * chore: updateGECKOdoc
* feat: add new reactions to an ecModel * feat: return vector rxn added * fix: update function description * fix: validate if gene/enzymes are not in the model * fix: fix gene/enzyme validation * fix: gene/pathway validation * fix: function description * fix: functions name consistency * feat: add progressbar to ecFSEOF * fix: typo * fix: fixing uptake rate * fix: set alphas as optional * feat: only return minFlux if requested * refactor: ecFluxScanning is now part of ecFSEOF * fefactor: remove ecFSEOF sub-folder * chore: updateGECKOdoc and small change in addNewRxnsToEC error when genes are not found --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
* fix: getComplexData do not write empty complexes * refactor: rename ProtConcs to EnzConcs * chore: updateGECKOdoc
# Conflicts: # doc/index.html # doc/src/geckomat/change_model/getComplexData.html # doc/src/geckomat/gather_kcats/readDLKcatOutput.html # doc/src/geckomat/limit_proteins/getConcControlCoeffs.html # doc/src/geckomat/limit_proteins/index.html # doc/src/geckomat/utilities/getFluxTarget.html # doc/src/geckomat/utilities/index.html # doc/src/geckomat/utilities/mapRxnsToConv.html # doc/src/geckomat/utilities/updateGECKOdoc.html # src/geckomat/limit_proteins/fillEnzConcs.m # src/geckomat/limit_proteins/flexibilizeEnzConcs.m # src/geckomat/utilities/ecFSEOF/ecFlux_scanning.m # src/geckomat/utilities/ecFSEOF/run_ecFSEOF.m # src/geckomat/utilities/getFluxTarget.m # src/geckomat/utilities/updateGECKOdoc.m # test/unit_tests/geckoCoreFunctionTests.m # tutorials/full_ecModel/protocol.m # tutorials/light_ecModel/protocol.m
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This PR has been automatically tested with GH Actions. Here is the output of the tests:
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1 task
Yu-sysbio
reviewed
Jul 16, 2023
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Looks good. Both light and full protocols run very well. |
* fix: when to do protein usage minimization * refactor: remove unnecesary inputs * fix: alpha for WT flux * chore: updateGECKOdoc --------- Co-authored-by: Eduard Kerkhoven <eduardk@chalmers.se>
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Main improvements in this PR:
addNewRxnsToECto add new enzyme-catalyzed metabolic reactions to an ecModel. (PR feat: Add new rxns to ecModel & fix: ecFSEOF #337)readDLKcatOutputreports which metabolites or reactions are not matching. (solves readDLKcatOutput reports non-matching metabolites #334)mapRxnsToConvthrows error if empty flux vector is used as input. (solves Flux comparison using GLPK & CPLEX #332)getComplexDatadoes not write empty complex data. (solves Bug detected in Step 4 #338)ProttoEnzto give the new function namesflexibilizeEnzConcs,fillEnzConcsandconstraintEnzConcs.ecFSEOFas one combined function to run FSEOF simulations on ecModels.protocol.mfiles.I hereby confirm that I have:
mainas a target branch (top left drop-down menu)Note: merge from
developtomainshould be via merge commit, not squash merge.