Ecosyste.ms: Issues
An open API service for providing issue and pull request metadata for open source projects.
GitHub / SysBioChalmers/GECKO issues and pull requests
#396 - `runDLKcat()`: _pickle.UnpicklingError: invalid load key, 'v'.
Issue -
State: closed - Opened by edkerk 3 months ago
- 3 comments
Labels: bug
#395 - chore/feat: dlkcat docker multiarch
Pull Request -
State: open - Opened by mihai-sysbio 3 months ago
- 2 comments
#394 - feat: support for alternative location of DLKcat in/output
Pull Request -
State: closed - Opened by edkerk 3 months ago
- 1 comment
#393 - DLKcat on Mac with Apple Silicon (arm64 architecture)
Issue -
State: open - Opened by SilentWaveSW 4 months ago
- 15 comments
Labels: enhancement
#392 - runDLKcat(): use DLKcat.tsv in a different directory
Issue -
State: closed - Opened by edkerk 4 months ago
- 2 comments
Labels: fixed in develop
#391 - fix: compatibility with RAVEN 2.10.0
Pull Request -
State: closed - Opened by edkerk 4 months ago
- 1 comment
#388 - GECKO 3.2.2
Pull Request -
State: closed - Opened by edkerk 6 months ago
- 1 comment
#385 - feat: keep track of kcat curations
Pull Request -
State: closed - Opened by edkerk 6 months ago
- 1 comment
#383 - GECKO 3.2.1
Pull Request -
State: closed - Opened by edkerk 8 months ago
- 1 comment
#382 - fix/feat: various, including ecFVA, enzymeUsage, constrainEnzConcs, constrainFluxData
Pull Request -
State: closed - Opened by edkerk 8 months ago
- 1 comment
#381 - GECKO 3.2.0
Pull Request -
State: closed - Opened by edkerk 8 months ago
- 1 comment
#380 - revert #372
Pull Request -
State: closed - Opened by edkerk 8 months ago
- 1 comment
#379 - feat: prot_usage always draws from prot_pool
Pull Request -
State: closed - Opened by edkerk 8 months ago
- 1 comment
#376 - enzyme usage unit
Issue -
State: closed - Opened by HossFir 9 months ago
- 1 comment
Labels: fixed in develop
#375 - new in GECKO 3.2.0: protein usage reactions always draw from protein pool, also when proteomics is integrated
Issue -
State: closed - Opened by edkerk 9 months ago
- 4 comments
Labels: enhancement, question
#374 - fix: minor patches
Pull Request -
State: closed - Opened by edkerk 9 months ago
- 1 comment
#372 - Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes
Pull Request -
State: closed - Opened by HossFir 9 months ago
- 4 comments
#368 - Bug detected: model.summary does not match expected phenotype for ecYeastGEM.xml for different carbon sources
Issue -
State: open - Opened by Caseses100 10 months ago
- 2 comments
Labels: bug
#365 - GECKO 3.1.3
Pull Request -
State: closed - Opened by mihai-sysbio 12 months ago
- 1 comment
#363 - feat: clearer mac docker error
Pull Request -
State: closed - Opened by mihai-sysbio almost 1 year ago
- 1 comment
#362 - chore: update-doi
Pull Request -
State: closed - Opened by mihai-sysbio almost 1 year ago
- 1 comment
#361 - fix: save ec model xml
Pull Request -
State: closed - Opened by mihai-sysbio about 1 year ago
- 1 comment
#359 - fix: getSubsetEcModel check for reaction presence
Pull Request -
State: closed - Opened by edkerk about 1 year ago
- 1 comment
#358 - GECKO 3.1.2
Pull Request -
State: closed - Opened by edkerk about 1 year ago
- 2 comments
#357 - doc: move installations instructions to wiki
Pull Request -
State: closed - Opened by edkerk about 1 year ago
- 1 comment
#356 - refactor: FSEOF
Pull Request -
State: closed - Opened by ae-tafur over 1 year ago
- 2 comments
Labels: enhancement
#353 - bug: full ecHumanGEM has multiple usage reactions for the same proteins
Issue -
State: closed - Opened by wshao1 over 1 year ago
- 6 comments
Labels: bug, fixed in develop
#352 - fix: runDLKcat if path has spaces
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#351 - error: DLKcat Docker invalid reference format error
Issue -
State: closed - Opened by edkerk over 1 year ago
- 10 comments
Labels: fixed in develop
#349 - fix: loadDatabases check for duplicate protIDs
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 3 comments
#348 - doc: renumber steps in tutorials
Issue -
State: closed - Opened by edkerk over 1 year ago
Labels: fixed in develop, documentation
#347 - fix: calculateFfactor if paxDB has taxID !4 digits
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 2 comments
#346 - fix: applyKcatConstraints prevent NaN in light ecModels
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#345 - bug: correctly parse PaxDB if taxonomic ID > 4 digits
Issue -
State: closed - Opened by Soratake-HirotakaYajima over 1 year ago
- 1 comment
Labels: fixed in develop
#344 - bug: applyKcatConstraints may give NaN in S-matrix of light ecModel
Issue -
State: closed - Opened by johan-gson over 1 year ago
- 4 comments
Labels: fixed in develop
#342 - Fix: get flux target at different alphas
Pull Request -
State: closed - Opened by ae-tafur over 1 year ago
- 1 comment
#341 - doc: clarify PR merge strategies in contrib guide
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 2 comments
#340 - GECKO 3.1.1
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 2 comments
#339 - refactor: rename ProtConcs to EnzConcs
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#338 - Bug detected in Step 4
Issue -
State: closed - Opened by Yu-sysbio over 1 year ago
- 3 comments
Labels: bug
#337 - feat: Add new rxns to ecModel & fix: ecFSEOF
Pull Request -
State: closed - Opened by ae-tafur over 1 year ago
- 5 comments
Labels: enhancement
#336 - feat: flexEnz instead of flexProt + more detailed errors
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#335 - docs: futher polishing
Pull Request -
State: closed - Opened by mihai-sysbio over 1 year ago
- 6 comments
#334 - readDLKcatOutput reports non-matching metabolites
Issue -
State: closed - Opened by HossFir over 1 year ago
- 1 comment
#333 - GECKO 3.1.0
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 2 comments
#332 - Flux comparison using GLPK & CPLEX
Issue -
State: closed - Opened by Yu-sysbio over 1 year ago
- 4 comments
Labels: enhancement
#331 - chore: rerun light_ecModel tutorial
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 3 comments
#330 - Name of the subfolder in GECKO/tutorials/
Issue -
State: closed - Opened by Yu-sysbio over 1 year ago
- 2 comments
Labels: enhancement
#329 - Error running makeEcModel in full_ecModel protocol
Issue -
State: closed - Opened by Yu-sysbio over 1 year ago
- 2 comments
Labels: bug
#328 - feat: compare light vs full ecModel
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#327 - Bug detected in `getSubsetEcModel`
Issue -
State: closed - Opened by mihai-sysbio over 1 year ago
- 3 comments
Labels: bug
#326 - docs: add link to tutorials in README
Pull Request -
State: closed - Opened by mihai-sysbio over 1 year ago
- 4 comments
#325 - feat: parameters format, phylDist.mat file and yeast-GEM.yml
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#324 - RAVEN version
Issue -
State: closed - Opened by Yu-sysbio over 1 year ago
- 5 comments
#323 - refactor: applyComplexData
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#322 - feat: light_ecModel tutorial getSubsetEcModel
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 6 comments
#321 - fix: full_ecModel tutorial ecFVA
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 3 comments
#320 - fix: getStandardKcat and applyKcatConstraints
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#319 - feat: updates related to tutorials
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 7 comments
#318 - feat: online docs
Pull Request -
State: closed - Opened by mihai-sysbio over 1 year ago
- 1 comment
Labels: documentation
#317 - online documentation
Issue -
State: closed - Opened by mihai-sysbio over 1 year ago
- 2 comments
Labels: enhancement
#316 - fix: minor bugs identified
Pull Request -
State: closed - Opened by ae-tafur over 1 year ago
- 1 comment
Labels: bug, enhancement
#315 - Fix: id entry in databases can be duplicated (kegg.tsv and uniprot.tsv)
Issue -
State: closed - Opened by ae-tafur over 1 year ago
- 1 comment
Labels: fixed in develop
#314 - protocol for ecEcoli, and GECKO light protocol for Human-GEM
Issue -
State: closed - Opened by edkerk over 1 year ago
- 3 comments
Labels: enhancement
#313 - feat: currencyMets and pseudoreactions handling
Pull Request -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
#312 - feat: a function that creates a the project structure an adapter class
Pull Request -
State: closed - Opened by ae-tafur over 1 year ago
- 3 comments
Labels: enhancement
#311 - failing tests
Issue -
State: closed - Opened by mihai-sysbio over 1 year ago
- 3 comments
Labels: bug
#310 - chore: restructure tutorials
Pull Request -
State: closed - Opened by mihai-sysbio over 1 year ago
- 4 comments
#309 - fill in ecModel.eccodes from ecModel.ec.eccodes
Issue -
State: closed - Opened by edkerk over 1 year ago
- 1 comment
Labels: enhancement
#308 - restructure tutorials
Issue -
State: closed - Opened by mihai-sysbio over 1 year ago
- 7 comments
#307 - verify Zenodo releases
Issue -
State: closed - Opened by mihai-sysbio over 1 year ago
- 3 comments
#306 - Feat: ignore in tunning kcats user defined proteins
Pull Request -
State: closed - Opened by ae-tafur over 1 year ago
- 3 comments
Labels: enhancement
#305 - protocol gives non-functional model after step 22.
Issue -
State: closed - Opened by Champion-GuanWang almost 2 years ago
- 11 comments
Labels: bug, fixed in develop
#304 - fix: applyCustomKcats with customKcats structure input
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 3 comments
#303 - applyCustomKcats with customKcats structure input
Issue -
State: closed - Opened by adimadkaikar almost 2 years ago
- 1 comment
Labels: bug, fixed in develop
#301 - Bug: Fix compatibility running ecFSEOF with GECKO3 models
Pull Request -
State: closed - Opened by ae-tafur almost 2 years ago
- 1 comment
Labels: bug
#300 - bug: refactor ecFSEOF for GECKO3 model format
Issue -
State: closed - Opened by ae-tafur almost 2 years ago
Labels: bug, fixed in develop
#299 - fix: getStandardKcat with multiple subSystems
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 5 comments
#298 - work with multiple models in one MATLAB session
Issue -
State: closed - Opened by HossFir almost 2 years ago
- 1 comment
Labels: help
#297 - doc: updateProtPool and flexibilizeProtConcs
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 1 comment
#296 - model with proteomics is overconstrained to reach maximum growth rate
Issue -
State: closed - Opened by ae-tafur almost 2 years ago
- 8 comments
Labels: bug, fixed in develop
#295 - fix: minor issues raised
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 1 comment
#294 - sensitivityTuning can introduce changes in undesired reactions
Issue -
State: closed - Opened by ae-tafur almost 2 years ago
Labels: enhancement, fixed in develop
#293 - GECKO 3.0.2
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 1 comment
#292 - fix: error if any match in customKcats
Pull Request -
State: closed - Opened by ae-tafur almost 2 years ago
- 1 comment
#291 - Error in matching the custom Kcats
Issue -
State: closed - Opened by HossFir almost 2 years ago
- 4 comments
Labels: fixed in develop
#290 - Bug detected
Issue -
State: closed - Opened by HossFir almost 2 years ago
Labels: bug
#289 - fix: if organism is in KEGG multiple times
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 5 comments
#288 - feat: getStandardKcat use custom list of non-enzyme reactions to ignore
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 1 comment
#287 - Error in minimizing protein pool usage
Issue -
State: closed - Opened by Yu-sysbio almost 2 years ago
- 3 comments
Labels: bug, fixed in develop
#286 - ec.source in getStandardKcat
Issue -
State: closed - Opened by Yu-sysbio almost 2 years ago
- 2 comments
Labels: enhancement, fixed in develop
#285 - New feature sensitivityTuning
Issue -
State: closed - Opened by Yu-sysbio almost 2 years ago
- 1 comment
Labels: enhancement, fixed in develop
#284 - fix: minor enhancements in protocol
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 1 comment
#283 - fix: read runDLKcat output
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 1 comment
#282 - fix: getECfromDatabase only change ecRxns entries
Pull Request -
State: closed - Opened by edkerk almost 2 years ago
- 2 comments
#281 - Bug detected getECfromDatabase
Issue -
State: closed - Opened by Yu-sysbio almost 2 years ago
Labels: bug, fixed in develop
#280 - getStandardKcat assigns protein costs to pseudo-reactions
Issue -
State: closed - Opened by Yu-sysbio almost 2 years ago
- 3 comments
Labels: enhancement, fixed in develop
#279 - Minor enhancement in protocol.m
Issue -
State: closed - Opened by Yu-sysbio almost 2 years ago
- 4 comments
Labels: fixed in develop
#278 - Bug: check if DLKcat.tsv has actually been run through DLKcat
Issue -
State: closed - Opened by HossFir almost 2 years ago
- 1 comment
Labels: fixed in develop
#277 - Bug: Looks for the taxonomically closest organism for matching the Kcats
Issue -
State: closed - Opened by HossFir almost 2 years ago
- 8 comments
Labels: fixed in develop