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SysBioChalmers
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GECKO
Toolbox for including enzyme constraints on a genome-scale model.
http://sysbiochalmers.github.io/GECKO/
MIT License
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`runDLKcat()`: _pickle.UnpicklingError: invalid load key, 'v'.
#396
edkerk
closed
1 month ago
3
chore/feat: dlkcat docker multiarch
#395
mihai-sysbio
opened
1 month ago
2
feat: support for alternative location of DLKcat in/output
#394
edkerk
closed
1 month ago
1
DLKcat on Mac with Apple Silicon (arm64 architecture)
#393
Mengzhensw
opened
1 month ago
15
runDLKcat(): use DLKcat.tsv in a different directory
#392
edkerk
closed
1 month ago
2
fix: compatibility with RAVEN 2.10.0
#391
edkerk
closed
2 months ago
1
GECKO 3.2.2
#388
edkerk
closed
1 month ago
1
feat: keep track of kcat curations
#385
edkerk
closed
3 months ago
1
GECKO 3.2.1
#383
edkerk
closed
5 months ago
1
fix/feat: various, including ecFVA, enzymeUsage, constrainEnzConcs, constrainFluxData
#382
edkerk
closed
5 months ago
1
GECKO 3.2.0
#381
edkerk
closed
6 months ago
1
revert #372
#380
edkerk
closed
6 months ago
1
feat: prot_usage always draws from prot_pool
#379
edkerk
closed
6 months ago
1
enzyme usage unit
#376
HossFir
closed
6 months ago
1
new in GECKO 3.2.0: protein usage reactions always draw from protein pool, also when proteomics is integrated
#375
edkerk
closed
6 months ago
4
fix: minor patches
#374
edkerk
closed
6 months ago
1
Update ProtPool Calculation by Including usage_prot_ Reaction Fluxes
#372
HossFir
closed
6 months ago
4
Bug detected: model.summary does not match expected phenotype for ecYeastGEM.xml for different carbon sources
#368
Caseses100
opened
8 months ago
2
GECKO 3.1.3
#365
mihai-sysbio
closed
9 months ago
1
feat: clearer mac docker error
#363
mihai-sysbio
closed
10 months ago
1
chore: update-doi
#362
mihai-sysbio
closed
10 months ago
1
fix: save ec model xml
#361
mihai-sysbio
closed
10 months ago
1
fix: getSubsetEcModel check for reaction presence
#359
edkerk
closed
11 months ago
1
GECKO 3.1.2
#358
edkerk
closed
11 months ago
2
doc: move installations instructions to wiki
#357
edkerk
closed
11 months ago
1
refactor: FSEOF
#356
ae-tafur
closed
12 months ago
2
bug: full ecHumanGEM has multiple usage reactions for the same proteins
#353
wshao1
closed
11 months ago
6
fix: runDLKcat if path has spaces
#352
edkerk
closed
1 year ago
1
error: DLKcat Docker invalid reference format error
#351
edkerk
closed
11 months ago
10
fix: loadDatabases check for duplicate protIDs
#349
edkerk
closed
1 year ago
3
doc: renumber steps in tutorials
#348
edkerk
closed
11 months ago
0
fix: calculateFfactor if paxDB has taxID !4 digits
#347
edkerk
closed
1 year ago
2
fix: applyKcatConstraints prevent NaN in light ecModels
#346
edkerk
closed
1 year ago
1
bug: correctly parse PaxDB if taxonomic ID > 4 digits
#345
Soratake-HirotakaYajima
closed
11 months ago
1
bug: applyKcatConstraints may give NaN in S-matrix of light ecModel
#344
johan-gson
closed
11 months ago
4
Fix: get flux target at different alphas
#342
ae-tafur
closed
1 year ago
1
doc: clarify PR merge strategies in contrib guide
#341
edkerk
closed
1 year ago
2
GECKO 3.1.1
#340
edkerk
closed
1 year ago
2
refactor: rename ProtConcs to EnzConcs
#339
edkerk
closed
1 year ago
1
Bug detected in Step 4
#338
Yu-sysbio
closed
1 year ago
3
feat: Add new rxns to ecModel & fix: ecFSEOF
#337
ae-tafur
closed
1 year ago
5
feat: flexEnz instead of flexProt + more detailed errors
#336
edkerk
closed
1 year ago
1
docs: futher polishing
#335
mihai-sysbio
closed
1 year ago
6
readDLKcatOutput reports non-matching metabolites
#334
HossFir
closed
1 year ago
1
GECKO 3.1.0
#333
edkerk
closed
1 year ago
2
Flux comparison using GLPK & CPLEX
#332
Yu-sysbio
closed
1 year ago
4
chore: rerun light_ecModel tutorial
#331
edkerk
closed
1 year ago
3
Name of the subfolder in GECKO/tutorials/
#330
Yu-sysbio
closed
1 year ago
2
Error running makeEcModel in full_ecModel protocol
#329
Yu-sysbio
closed
1 year ago
2
feat: compare light vs full ecModel
#328
edkerk
closed
1 year ago
1
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