SysBioChalmers/GECKO

Issues

• protocol gives non-functional model after step 22.

  #305 opened a year ago by Champion-GuanWang
  11

• new in GECKO 3.2.0: protein usage reactions always draw from protein pool, also when proteomics is integrated

  #375 opened 6 months ago by edkerk
  4

• enzyme usage unit

  #376 opened 6 months ago by HossFir
  1

• Bug detected: model.summary does not match expected phenotype for ecYeastGEM.xml for different carbon sources

  #368 opened 8 months ago by Caseses100
  2

• doc: renumber steps in tutorials

  #348 opened a year ago by edkerk
  0

• error: DLKcat Docker invalid reference format error

  #351 opened a year ago by edkerk
  10

• bug: correctly parse PaxDB if taxonomic ID > 4 digits

  #345 opened a year ago by Soratake-HirotakaYajima
  1

• bug: applyKcatConstraints may give NaN in S-matrix of light ecModel

  #344 opened a year ago by johan-gson
  4

• Fix: id entry in databases can be duplicated (kegg.tsv and uniprot.tsv)

  #315 opened a year ago by ae-tafur
  1

• feat: GECKOInstaller checks for latest release

  #270 opened a year ago by edkerk
  0

• bug: full ecHumanGEM has multiple usage reactions for the same proteins

  #353 opened a year ago by wshao1
  6

• Bug detected in Step 4

  #338 opened a year ago by Yu-sysbio
  3

• Flux comparison using GLPK & CPLEX

  #332 opened a year ago by Yu-sysbio
  4

• readDLKcatOutput reports non-matching metabolites

  #334 opened a year ago by HossFir
  1

• feat: universal DLKcat.tsv for both light and full ecModels

  #248 opened 2 years ago by Yu-sysbio
  8

• verify Zenodo releases

  #307 opened a year ago by mihai-sysbio
  3

• work with multiple models in one MATLAB session

  #298 opened a year ago by HossFir
  1

• applyCustomKcats with customKcats structure input

  #303 opened a year ago by adimadkaikar
  1

• model with proteomics is overconstrained to reach maximum growth rate

  #296 opened a year ago by ae-tafur
  8

• RAVEN version

  #324 opened a year ago by Yu-sysbio
  5

• Name of the subfolder in GECKO/tutorials/

  #330 opened a year ago by Yu-sysbio
  2

• Bug detected in `getSubsetEcModel`

  #327 opened a year ago by mihai-sysbio
  3

• Error running makeEcModel in full_ecModel protocol

  #329 opened a year ago by Yu-sysbio
  2

• protocol for ecEcoli, and GECKO light protocol for Human-GEM

  #314 opened a year ago by edkerk
  3

• fill in ecModel.eccodes from ecModel.ec.eccodes

  #309 opened a year ago by edkerk
  1

• online documentation

  #317 opened a year ago by mihai-sysbio
  2

• restructure tutorials

  #308 opened a year ago by mihai-sysbio
  7

• chore: clean up stale branches

  #243 opened 2 years ago by mihai-sysbio
  5

• sensitivityTuning can introduce changes in undesired reactions

  #294 opened 2 years ago by ae-tafur
  0

• bug: refactor ecFSEOF for GECKO3 model format

  #300 opened 2 years ago by ae-tafur
  0

• failing tests

  #311 opened 2 years ago by mihai-sysbio
  3

• Bug detected

  #290 opened 2 years ago by HossFir
  0

• Error in matching the custom Kcats

  #291 opened 2 years ago by HossFir
  4

• Error in minimizing protein pool usage

  #287 opened 2 years ago by Yu-sysbio
  3

• ec.source in getStandardKcat

  #286 opened 2 years ago by Yu-sysbio
  2

• Bug detected getECfromDatabase

  #281 opened 2 years ago by Yu-sysbio
  0

• New feature sensitivityTuning

  #285 opened 2 years ago by Yu-sysbio
  1

• getStandardKcat assigns protein costs to pseudo-reactions

  #280 opened 2 years ago by Yu-sysbio
  3

• Minor enhancement in protocol.m

  #279 opened 2 years ago by Yu-sysbio
  4

• Bug: check if DLKcat.tsv has actually been run through DLKcat

  #278 opened 2 years ago by HossFir
  1

• Bug: Looks for the taxonomically closest organism for matching the Kcats

  #277 opened 2 years ago by HossFir
  8

• Bug: incorrect definition of input

  #267 opened 2 years ago by ae-tafur
  0

• convert the manual tests to run with GH actions

  #269 opened 2 years ago by mihai-sysbio
  0

• Bug detected using getECfromGEM

  #246 opened 2 years ago by Yu-sysbio
  7

• fix: findMetSmiles warning if many API queries fail

  #257 opened 2 years ago by edkerk
  3

• feat: getStandardKcat in model without subSystems

  #258 opened 2 years ago by edkerk
  5

• Bug detected in applyComplexData (line 77)

  #262 opened 2 years ago by Yu-sysbio
  5

• no error reported when customKcats file is missing

  #255 opened 2 years ago by mihai-sysbio
  1

• bug for applyComplexData for rat-GEM

  #249 opened 2 years ago by feiranl
  2

• Bug: Filter proteomics only return one column, despite there are 3 conditions

  #250 opened 2 years ago by ae-tafur
  2