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opencobra

5 indexed repositories · View on GitHub

cobrapy
COBRApy is a package for constraint-based modeling of metabolic networks.

Python · 587 stars
cobratoolbox
The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

MATLAB · 288 stars
swiglpk
Simple swig bindings for the GNU Linear Programming Kit

Python · 30 stars
COBRA.tutorials
Repository of tutorials for The COBRA Toolbox

MATLAB · 25 stars
COBRA.papers
Repository for scripts related to reproducing the results of an individual publication

MATLAB · 10 stars

Beginner friendly Everything

Open All

GNU Octave native GLPK is detected as unavailable and solveCobraLP misinterprets glpk status Open

Difficulty 4/5 3-5 days Newbie friendliness 68/100

opencobra/cobratoolbox#2687 · Opened Jul 28, 2026
Uninformative Error when reading excel models Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

opencobra/cobratoolbox#2670 · Opened Jun 22, 2026
Question about submodule handling for historical COBRA Toolbox commits Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

opencobra/cobratoolbox#2669 · Opened Jun 20, 2026
Issue with FastGapFill Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobratoolbox#2663 · Opened May 22, 2026
test for unmet dependencies Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

opencobra/cobratoolbox#2631 · Opened Mar 16, 2026
predictMicrobeContributions not filtering flux spans below tol Open

Difficulty 2/5 1-3 hours Newbie friendliness 50/100

opencobra/cobratoolbox#2619 · 1 comment · Opened Mar 3, 2026
Output argument "signifRxns" (and maybe others) not assigned during call to "mapExpressionToReactions" Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

opencobra/cobratoolbox#2601 · 2 comments · Opened Dec 26, 2025
[BUG] build_reaction_from_string wipes reaction's bounds Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 50/100

opencobra/cobrapy#1463 · 2 comments · Opened Nov 20, 2025
[BUG] SVD did not converge while trying to sample flux solutions Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

opencobra/cobrapy#1461 · 2 comments · Opened Nov 3, 2025
Adding a reaction that is already part of a model to another model creates an alias (not a copy) Open

opencobra/cobrapy#1456 · 3 comments · 1 assignee · Opened Aug 13, 2025
[BUG] test_load fails if Biomodels website happens to be down. Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 48/100

opencobra/cobrapy#1455 · 1 comment · Opened Aug 3, 2025
[BUG] SBO terms incorrectly handled if multiple exist Open

bug

Difficulty 5/5 Over a week Newbie friendliness 25/100

opencobra/cobrapy#1454 · Opened Jul 11, 2025
[Feature] Fast Gapfill Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

opencobra/cobrapy#1449 · Opened Jun 27, 2025
[BUG] Restrictions on Gene IDs? Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobrapy#1448 · Opened Jun 27, 2025
[BUG] Reaction and gene essentiality not completing when multiple processes are specified Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 25/100

opencobra/cobrapy#1447 · Opened Jun 26, 2025
The 'prepareFastGapFill' function runs incorrectly Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

opencobra/cobratoolbox#2499 · 1 comment · Opened Jun 25, 2025
[BUG] Adding unnecessary exchange reactions Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobrapy#1446 · 4 comments · 1 reaction · Opened Jun 19, 2025
Documentation Link Broken Open

Difficulty 1/5 Under an hour Newbie friendliness 55/100

opencobra/cobrapy#1441 · 1 comment · Opened May 19, 2025
Issue with converting .mat into json and sbml Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

opencobra/cobratoolbox#2475 · Opened May 12, 2025
Inquiry on Best Practices for Integrating automated GEMs from CarveMe and ModelSEED Open

Difficulty 5/5 Over a week Newbie friendliness 15/100

opencobra/cobratoolbox#2463 · 1 comment · Opened Apr 4, 2025
[BUG] Gene equality outside of models Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobrapy#1434 · Opened Apr 4, 2025
[BUG] Reaction addition/subtraction is unaware of reaction direction Open

bug

Difficulty 5/5 Over a week Newbie friendliness 30/100

opencobra/cobrapy#1433 · 2 comments · Opened Mar 20, 2025
[BUG] I can not open validated model for pseudomonas putida Open

needs information

Difficulty 3/5 1-2 days Newbie friendliness 25/100

opencobra/cobrapy#1430 · 6 comments · Opened Mar 14, 2025
[BUG] Gene.functional attribute not saved in SBML model Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

opencobra/cobrapy#1422 · 6 comments · Opened Jan 8, 2025
[BUG] Setting model.compartments asymmetric with getting Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobrapy#1416 · 2 comments · 1 reaction · Opened Nov 28, 2024
[Feature] Equality of metabolites and reactions Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

opencobra/cobrapy#1414 · 4 comments · Opened Nov 26, 2024
[BUG] FVA doesn work on windows 11 and Python 3.12.7 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobrapy#1410 · 2 comments · Opened Oct 23, 2024
Not clear how to run tests Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

opencobra/swiglpk#108 · 5 comments · Opened Oct 21, 2024
findStoichConsistentSubset error in minCardinalityConservationRelaxationVector Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

opencobra/cobratoolbox#2337 · Opened Oct 3, 2024
`write_to_sbml()` fails with `TypeError` Open

Difficulty 2/5 1-3 hours Newbie friendliness 45/100

opencobra/cobrapy#1408 · Opened Sep 26, 2024
[Feature] Verbosity Option in `read_sbml_model` or similar. Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

opencobra/cobrapy#1405 · 1 comment · Opened Sep 9, 2024
Question - regarding the expectation of mcc ctf compile Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

opencobra/cobratoolbox#2275 · 3 comments · Opened Aug 21, 2024
[Feature] Handle reaction removal in the objective Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

opencobra/cobrapy#1396 · Opened Jul 5, 2024
How to use the toolkit to calculate rates Open

Difficulty 2/5 1-3 hours Newbie friendliness 25/100

opencobra/cobratoolbox#2267 · Opened Jun 29, 2024
mgPipe > fastSetupCreator + createPersonalizedModel Interaction causes errors due to rmfield Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

opencobra/cobratoolbox#2265 · 1 comment · Opened Jun 11, 2024
Gapfilling failed in context manager (infeasible) Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobrapy#1392 · 3 comments · Opened May 28, 2024
I cannot install Cobrapy in Anacoda I get this error "chr(c) # raise ValueError for invalid code error: incomplete escape \U at position 28" What should I do? Open

needs information stale

Difficulty 3/5 1-2 days Newbie friendliness 18/100

opencobra/cobrapy#1391 · 1 comment · Opened May 21, 2024
mgPipe PART2 issue Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobratoolbox#2261 · 3 comments · Opened May 15, 2024
refactor how solver parameters are handled Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

opencobra/cobratoolbox#2257 · Opened Apr 29, 2024
`optimizeCbModel` returning `NaN` for solution Open

Difficulty 4/5 3-5 days Newbie friendliness 38/100

opencobra/cobratoolbox#2255 · Opened Apr 12, 2024
Function out of work findRxnsFromMets.m Open

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

opencobra/cobratoolbox#2248 · 1 comment · Opened Mar 7, 2024
Combining metabolite lists: Error using mergeTwoModels (line 164) Open

Difficulty 3/5 1-2 days Newbie friendliness 25/100

opencobra/cobratoolbox#2247 · 1 comment · Opened Mar 5, 2024
unrecongnized field name "annotation" Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

opencobra/cobratoolbox#2244 · 1 comment · Opened Mar 1, 2024
Gurobi error 10010: Model too large for size-limited license Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

opencobra/cobratoolbox#2239 · 6 comments · Opened Feb 28, 2024
Missing function "findTranscriptionValue" Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

opencobra/cobratoolbox#2235 · Opened Feb 23, 2024
Unrecognized function or variable 'TranslateSBML'. Open

Difficulty 2/5 1-3 hours Newbie friendliness 30/100

opencobra/cobratoolbox#2233 · 3 comments · Opened Feb 18, 2024
Tutorial revision Open

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

opencobra/cobratoolbox#2218 · Opened Jan 25, 2024
Invalid MEX-file Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

opencobra/cobratoolbox#2210 · 2 comments · Opened Dec 31, 2023
"FVAOptForce" function Error Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

opencobra/cobratoolbox#2153 · Opened Jun 15, 2023
AGORA2 Open

Difficulty 1/5 Under an hour Newbie friendliness 25/100

opencobra/COBRA.papers#118 · Opened May 30, 2023

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