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Issues list

runDLKcat(): _pickle.UnpicklingError: invalid load key, 'v'. bug
#396 by edkerk was closed Oct 20, 2024
3 tasks done
3
runDLKcat(): use DLKcat.tsv in a different directory fixed in develop Has already been addressed in develop branch
#392 by edkerk was closed Oct 15, 2024
2
new in GECKO 3.2.0: protein usage reactions always draw from protein pool, also when proteomics is integrated enhancement question
#375 by edkerk was closed May 27, 2024
2 tasks done
4
error: DLKcat Docker invalid reference format error fixed in develop Has already been addressed in develop branch
#351 by edkerk was closed Dec 2, 2023
1
10
doc: renumber steps in tutorials documentation fixed in develop Has already been addressed in develop branch
#348 by edkerk was closed Dec 2, 2023
3 tasks
3.1.2
protocol for ecEcoli, and GECKO light protocol for Human-GEM enhancement
#314 by edkerk was closed Jun 30, 2023
1 task
@edkerk @Yu-sysbio
3
fill in ecModel.eccodes from ecModel.ec.eccodes enhancement
#309 by edkerk was closed Jun 30, 2023
2 tasks done
1
feat: GECKOInstaller checks for latest release enhancement fixed in develop Has already been addressed in develop branch
#270 by edkerk was closed Dec 2, 2023
2 tasks
feat: getStandardKcat in model without subSystems bug
#258 by edkerk was closed Mar 3, 2023
1
@ae-tafur
5
fix: findMetSmiles warning if many API queries fail bug
#257 by edkerk was closed Mar 5, 2023
3
feat: getStandardKcat should replace zeros in model.ec.kcat enhancement
#232 by edkerk was closed Feb 25, 2023
@edkerk
1
bug: makeEcModel if cytosol is not 'c' bug
#231 by edkerk was closed Feb 27, 2023
@edkerk
5
chore: consistent names and terminology enhancement
#229 opened Feb 22, 2023 by edkerk
1
GitHub Action that runs core function tests with each PR enhancement
#223 by edkerk was closed Feb 27, 2023
4 tasks done
@mihai-sysbio
2
store model-specific files away from GECKO code
#187 by edkerk was closed Dec 22, 2022
1
@ae-tafur
21
store ec-model in yml format
#178 by edkerk was closed Jan 22, 2023
2
assign and use EC codes from model.eccodes
#175 by edkerk was closed Dec 23, 2022
3 tasks
1
4
applyKcatConstraints: uses model.ec.kcat to constrain in S-matrix
#172 by edkerk was closed Dec 21, 2022
@edkerk
1
runDLKcat: I/O of DLKcat
#171 by edkerk was closed Jan 22, 2023
@edkerk @feiranl @le-yuan
1
refactor: prepare model for ec-extension enhancement
#161 by edkerk was closed Jul 8, 2022
2 of 4 tasks
3
loadComplexData: read Complex Portal or similar input for subunit numbers
#160 by edkerk was closed Dec 19, 2022
1
@ae-tafur
6
readKcatTable: for loading curated kcat data
#159 by edkerk was closed Mar 5, 2023
2 tasks
@Yu-sysbio
11
fuzzyKcatMatching: refactoring of BRENDA-based approach
#158 by edkerk was closed Dec 23, 2022
3 tasks
1
@IVANDOMENZAIN
1
refactor: update general kcat database
#157 opened May 25, 2022 by edkerk
6
makeEcModel: model-specific kcat data in dedicated structure enhancement
#156 by edkerk was closed Feb 14, 2023
5 tasks
@edkerk
6
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