geckopy 2.0.1

Methods for using the GECKO model with cobrapy

Please refer to http://geckotoolbox.readthedocs.io

History

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 version 8.1.3 (PR #105).

  • Solved bug in generate_protModels.m that 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 name version for 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 of fitGAM.m (PR #82).

  • A chemostat simulation utility (PR #82).

• Fixes:

  • Fixes #73: Bug in getKcat.m (PR #75).

  • Fixes #78: Updated BRENDA URL (PR #91).

  • FVA utility: Fixed directionality bugs in MAX_min_Optimizer.m (PRs #69 & #95) & optimization bug in comparativeFVA.m (PR #95).

  • geckopy: Updated csv reader in geckopy test (PR #83) and met id parsing (PR #93).

  • Fixed subfolder bug in modifyKcats.m (PR #80).

• Refactoring:

  • Introduced getModelParameters.m for 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 from modifyKcats.m & topUsedEnzymes.m (PR #61).

  • keggID is now an input for updateDatabases.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 in topUsedEnzymes.m (PR #61).

  • Reduced display of several functions (PR #62).

  • Simplified changeMedia_batch.m and made more generic constrainEnzymes.m & flexibilizeProteins.m (PR #63).

• Style:

  • Changed EOL to LF (unix default) (PR #68).

• Documentation:

  • Documented input/output of topUsedEnzymes.m & truncateValues.m (PR #61).

  • Added/updated documentation of changeMedia_batch.m, constrainEnzymes.m, flexibilizeProteins.m & getConstrainedModel.m (PR #63).

1.3.4 (2018-12-04)

• Features:

  • Generalization of measureAbundance.m to 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 in uniprot.tab (PR #48).

  • Proper use of measureAbundance.m from within constrainEnzymes.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).

  • Added sumProtein.m for 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 .mat file 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.m modified to reflect the Y6 minimal media composition (PR #47).

• Refactoring:

  • Performance improvements to getConstrainedModel.m and sigmaFitter.m (PR #47).

  • fitGAM.m is now only called from inside scaleBioMass.m (PR #47).

1.3.1 (2018-08-28)

• Features:

  • Adapted the pipeline to work with yeast-GEM, including loading, processing and saving the model. Current model is constructed from yeast v8.1.3 (PR #39).

  • When constructing ecModel_batch, lipid fraction is now scaled together with protein and carbohydrate fractions (PR #39).

• Fixes:

  • geckopy tests flexibilized to comply with yeast-GEM (PR #39).

• Refactoring:

  • Reorganized the repo, making a division between geckomat (Matlab part for generation + simulation of ecModels) and geckopy (Python part for simulations of ecYeastGEM) (PR #40).

  • Parameters f (mass fraction of enzymes in model), Pbase, Cbase, Lbase (biomass composition) and GAM (growth-associated ATP maintenance) are now automatically computed (PR #39).

  • Added RAVEN as a dependency for geckomat (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_bounds was 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 .xml file. Genes connected to enzyme constraints are now stored in model.enzGenes in the .mat structure.

  • Docs badge in README.

• Fixes:

  • Fields grRules and rules fixed in a consistent way:

    • grRules for the backwards reactions are the same as for the forward ones.

    • For reactions catalyzed by just 1 enzyme (or complex), grRules of the original reactions are assigned to them.

    • For reactions catalyzed by more than 1 enzyme (or more than 1 complex), grRules of 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, grRules are assigned as thecorresponding gene ID.

    • The rules field is set equal to grRules for providing consistency with different toolboxes.

  • Inter-OS compatibility: * Numbers in scientific notation are stored in the .xml files with format Xe-0N, not Xe-00N, or with format Xe-1N, not Xe-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 for addReaction usage.

• NOTE: Not available in pypi (issue #14 unresolved)

1.2.0 (2018-04-12)

• Implemented automatic kcat flexibilization for over-constrained models:

  • Based on a maximum growth rate specified by the user, the algorithm iteratively identifies the top growth-limiting kcat value 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 refitted

  • For non-feasible/zero-growth models, sensitivity analysis is performed on a reaction and enzyme basis rather than on individual kcat values

  • The outputs of this step are stored in topUsedEnzymes.txt and kcatModification.txt and can be used for further manual curation

• All databases updated (BRENDA, swissprot, KEGG, PaxDB)

• More generic gene/protein matching for compatibility with other models

• Re-organization of all output files in a single folder

• New badges + styling of website

• NOTE: Not available in pypi (issue #14 unresolved)

1.1.2 (2018-03-20)

• Improved kcat matching to BRENDA with:

  1. Specific activity

  2. Phylogenetic distance, when data for organism of choice is not available

• Switched to readthedocs for documentation: http://geckotoolbox.readthedocs.io

• Added a Gitter room for discussion: https://gitter.im/SysBioChalmers/GECKO

• Switched 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.