GECKO 3.1.3

• Fixes:
  • resolve a bug when saving the ecModel in xml format #361
• Documentation:
  • update DOI in code and Readme #362
• Features:
  • clearer error message for use of Docker in Matlab #363

Full Changelog: v3.1.2...v3.1.3

GECKO 3.1.2

• Fixes:
  • makeEcModel prevent duplicated protein pseudometabolites
  • applyKcatConstraints occassionally fills S-matrix with NaN in light ecModels (solves #344)
  • calculateFfactor handle data from PAXdb if the taxonomic ID is not 4 digits long (solves #345)
  • runDLKcat correctly handles param.path if the folder name has spaces (solves #351)
  • loadDatabases throws error if duplicate protein IDs are found
  • getSubsetEcModel requires both bigEcModel and smallGEM to have derived from the same starting GEM, and will therefore check whether all reactions from smallGEM are also present in bigEcModel. (solves #353)
• Documentation:
  • Installation instructions are moved to the Wiki
  • Mention correct human-GEM version in HumanGEMAdapter.m
  • Replace Gitter with GitHub Discussions for asking support
• Refactor:
  • Have ecFSEOF follow the original implementation of FSEOF (PR #356)
• Features:
  • Navigate into new project folder after running startGECKOproject

GECKO 3.1.1

• Features:
  • addNewRxnsToEC to add new enzyme-catalyzed metabolic reactions to an ecModel. (PR #337)
  • readDLKcatOutput reports which metabolites or reactions are not matching. (solves #334)
  • mapRxnsToConv throws error if empty flux vector is used as input. (solves #332)
• Fixes:
  • getComplexData does not write empty complex data. (solves #338)
• Refactor:
  • Rename Prot to Enz to give the new function names flexibilizeEnzConcs, fillEnzConcs and constraintEnzConcs.
  • ecFSEOF as one combined function to run FSEOF simulations on ecModels.
• Documentation:
  • Minor edits in protocol.m files.

GECKO 3.1.0

Main improvements in this PR:

• Features:

  • Renamed various parameters in model adapter.
  • getComplexData uses taxonomic ID instead of species name.
  • GECKOInstaller checks if correct RAVEN version is installed (release 2.8.3+).
  • Tutorials are moved to tutorials, and userData is removed as default location for model files. Users are encouraged to make their model folders outside the GECKO directory, facilitated by startGECKOproject().
  • full_ecModel tutorial:
    • more detailed discussions around kcat curation, protein usage etc.
    • plotCrabtree makes plot that demonstrates Crabtree effect in ecModels
    • plotlightVSfull makes plot comparing flux distribution in light and full ecModels
  • light_ecModel:
    • minimum code to make a light ecModel based on human-GEM 1.15.0
    • make contextualized ecModel based on a cell-line specific tINIT model with getSubsetEcModel
  • ecFSEOF is compatible with GECKO3.
  • makeEcModel can use pseudoRxns.tsv to filter out pseudoreactions.
  • various functions show progress bar that indicates estimated remaining time.
  • reportEnzymeUsage can make report of top-10 used enzymes.
  • loadConventionalGEM can load yaml model files.
  • enzymeUsage reports as positive values.
  • flexibilizeProtConcs also keeps track of the ratio of protein concentration change.
  • fillProtConcs allows for selection of column from protData, if it contains multiple datasets.
  • setKcatForReactions can directly modify a kcat for all associated reactions, useful for manual curation on existing ecModels.
  • getReactionsFromEnzyme gives which reactions are catalyzed by a particular enzyme, from a provided Uniprot ID.
  • copyECtoGEM to copy ecModel.ec.eccodes to ecModel.eccodes.

• Documentation:

  • All function documentation is available from /doc/ and online (becomes available upon PR commit).
  • sensitivityTuning allows for ignoring selected reactions.

• Fix / refactor:

  • Numerous fixes and refactoring of code in many functions.
  • Note that various functions have had their input parameters changed.

GECKO 3.0.2

• Documentation:
  • Clarifications and fixes in protocol.m (solves #279, #287).
  • Protein concentrations (in model.ec.concs and proteomics data) are in mg/gDCW.
• Fix:
  • Correct calculation of new protein pool if constrained with proteomics, by considering the total amount of measured protein.
  • getStandardKcat can use data/pseudoRxns.tsv as input of reactions to ignore, it overwrites previous standard Kcat definitions, and specifies model.ec.source{i} = 'standard' if a standard kcat is assigned to a zero-kcat reaction (solves #280, #286)
  • Various bugfixes in fuzzyKcatMatching (solves #277), readDLKcatOutput (solves #278), getECfromDatabase (solves #281), sensitivityTuning (solves #285), & applyCustomKcats (solves #291).

GECKO 3.0.1

• Fix:
  • getECfromDatabase incorrect definition of ecRxns and action input parameters.
• Features:
  • flexibilizeProtConcs prevent infinite runs in no (more) proteins are limiting and check if protein pool is constraining growth.
• Documentation:
  • Updated Issues and PR templates.
  • Updated contributor guidelines.
  • Updated README.md.
  • Updated protocol.m.
  • GitHub Pages.

GECKO 3.0.0

After significant refactoring of the codebase, GECKO 3 is more user-friendly, flexibile and versatile than before.

Most notable changes:

• ecModels have an .ec structure containing all enzyme and kcat information.
• Enzymes are incorporated in the S-matrix as MW/kcat (previously this was 1/kcat, where the MW was instead considered in the protein exchange reactions).
• ecModels can be stored in YAML file format that retains all model content.
• The model-provided list of EC numbers can be used.
• Various kcat sources can easily be combined.
• DLKcat is distributed as part of GECKO, as alternative kcat source.
• Enzyme complex data can be gathered and considered.
• All model-specific files and scripts are kept in the userData subfolder.
• Model-specific modelAdapter files contain parameters that are used in model reconstruction and analysis.
• Because of the above, there is virtually no backwards compatibility with GECKO versions 1 and 2, regarding both models and code.

GECKO 2.0.3

• Refactor:
  • speed improvements around matchKcats and getEnzymesCodes (PR #154)

GECKO 2.0.2

• 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 to Travis-CI.com (PR #118).
  • prot_abundance.txt can now be an empty file (for organisms not present in pax-db) 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).

GECKO 2.0.1

• Fixes:
  • UBs are only changed for strictly required proteins (PR #103).
  • Closes #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).
  • Closes #112: Avoid using the variable name version for potential conflicts with Matlab (PR #113).
• Style:
  • Closes #102: All UBs in repo changed from +Inf to +1000 (PR #109).