opencobra/cobratoolbox

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The COnstraint-Based Reconstruction and Analysis Toolbox. Documentation:

Stars: 288
Forks: 336
Open beginner issues: 0
Indexed issues: 65
Avg merge: 4d 5h
Merged PRs (30d): 1

Dominant language: MATLAB
License: No license data
Last GitHub push: Jul 21, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: help wanted

Beginner friendly Everything

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65 open issues indexed

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
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
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
findStoichConsistentSubset error in minCardinalityConservationRelaxationVector Open

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

opencobra/cobratoolbox#2337 · Opened Oct 3, 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
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
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
sphinxcontrib-matlabdomain 0.19.0 pre-release Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

opencobra/cobratoolbox#2112 · Opened Apr 28, 2023
No Results from GDLS in latest version Open

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

opencobra/cobratoolbox#2110 · Opened Mar 10, 2023
bqmodel and bqbiol annotations merged. Open

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

opencobra/cobratoolbox#2080 · Opened Nov 28, 2022
Error when running chrrSampler, "x0 not interior" Open

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

opencobra/cobratoolbox#2069 · 2 comments · Opened Nov 14, 2022
documentation seems outdated and broken Open

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

opencobra/cobratoolbox#2056 · 2 comments · Opened Nov 1, 2022
Warning in prepareFastgapfill Open

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

opencobra/cobratoolbox#2055 · 2 comments · Opened Oct 30, 2022
essentialRxnsTasks in checkMetabolicTasks gives wrong results due to minimizeModelFlux design Open

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

opencobra/cobratoolbox#2048 · 2 comments · Opened Oct 6, 2022
unable to run optimizeCbModel with error of "unrecongnized field name "dual" Open

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

opencobra/cobratoolbox#2047 · 2 comments · Opened Oct 4, 2022
FastGapFill not working- file missing Open

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

opencobra/cobratoolbox#2011 · 2 comments · Opened Aug 5, 2022
COBRA tool box add to path Open

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

opencobra/cobratoolbox#2000 · Opened Jun 11, 2022
Cobra path add Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

opencobra/cobratoolbox#1999 · 1 comment · Opened Jun 11, 2022
FindExcRxn returns non-Exc reactions Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

opencobra/cobratoolbox#1990 · 2 comments · Opened May 12, 2022
three folders are empty in the downloaded cobratoolbox Open

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

opencobra/cobratoolbox#1971 · 5 comments · Opened Mar 30, 2022
error in initializing submodules Open

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

opencobra/cobratoolbox#1955 · 1 comment · Opened Mar 10, 2022
mapExpressionToReactions returning NaN array Open

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

opencobra/cobratoolbox#1942 · 4 comments · Opened Feb 23, 2022
uFBA : error when testing it (testuFBA) Open

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

opencobra/cobratoolbox#1922 · 1 comment · Opened Jan 23, 2022
most of https://opencobra.github.io/cobratoolbox/stable/tutorials/ website section is broken/ loading very slow Open

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

opencobra/cobratoolbox#1867 · 2 comments · Opened Nov 12, 2021
Error in Microbiome Modelling Toolbox related to Gurobi solver Open

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

opencobra/cobratoolbox#1863 · 8 comments · Opened Nov 3, 2021
initialization of cobratoolbox failed Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

opencobra/cobratoolbox#1800 · 32 comments · Opened Sep 15, 2021
Error in generateMexFastFVA depends on CPLEX1210 and MATLAB R2021a Open

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

opencobra/cobratoolbox#1794 · 1 comment · Opened Aug 30, 2021
OptGene Tutorial error and crash Open

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

opencobra/cobratoolbox#1792 · 1 comment · Opened Aug 25, 2021
Certificates issue within postMINERVArequest Open

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

opencobra/cobratoolbox#1775 · 1 comment · Opened May 22, 2021
FindMustLL never finishes with E coli standard model Open

Difficulty 4/5 3-5 days Newbie friendliness 20/100

opencobra/cobratoolbox#1770 · 4 comments · Opened May 13, 2021
Construction of microbial growth model Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

opencobra/cobratoolbox#1724 · Opened Feb 26, 2021

opencobra/cobratoolbox

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