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opencobra
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cobrapy
COBRApy is a package for constraint-based modeling of metabolic networks.
http://opencobra.github.io/cobrapy/
GNU General Public License v2.0
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[Feature] Handle reaction removal in the objective
#1396
cdiener
opened
1 day ago
0
SBML parsing fails on invalid GPRs
#1394
tamascogustavo
closed
1 month ago
2
[Feature] Nullspace calculation similar to COBRA (MATLAB)
#1393
dagl1
opened
1 month ago
11
Gapfilling failed in context manager (infeasible)
#1392
wshao1
opened
1 month ago
3
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?
#1391
zahraaaaaaaaaaaaaaaaaaaa
opened
1 month ago
1
Model optimization by integrating growth rate data from biolog
#1388
hites77
closed
2 months ago
0
[BUG] No biomass flux when another objective is added for FBA analysis
#1386
hites77
closed
3 months ago
3
Question about iCN900 from BiGG
#1384
amarsh26
closed
3 months ago
0
fix(core): catch missing reduced costs and shadow prices.
#1383
Palaract
closed
2 months ago
1
[BUG] using gurobi on non-linear optimization
#1381
lbugnon
closed
2 months ago
3
Stable release of docs broken [BUG]
#1379
gregmedlock
opened
4 months ago
1
Fix style
#1378
Midnighter
closed
4 months ago
0
fix: reaction bounds in _add_cycle_free function
#1375
alexpan00
closed
4 months ago
5
Error assigning the bounds in _add_cycle_free
#1374
alexpan00
closed
4 months ago
1
Introduction of general constraint in Gurobipy breaks Cobrapy assumption [BUG]
#1372
Palaract
closed
2 months ago
4
Adding new metabolites
#1371
amarsh26
closed
6 months ago
4
Use correct accessor for SBML group name
#1369
cdiener
closed
2 months ago
1
enable redirects for Biomodels download
#1368
cdiener
closed
8 months ago
1
[BUG] Biomodels web io access broekn due to redirects
#1367
cdiener
closed
8 months ago
0
Enable the hybrid solver interface
#1366
cdiener
closed
8 months ago
2
chore: allow broader range of pandas versions
#1364
Midnighter
closed
8 months ago
0
chore: update actions
#1363
Midnighter
closed
8 months ago
0
upgrading dependency to allow pandas>=2.0
#1362
eladnoor
closed
8 months ago
1
Update depinfo
#1361
Midnighter
closed
8 months ago
2
Hello I am new to python and Cobra, i would be grateful if you can provide me with steps to open an XML file from the computer and/or from online database, i tried the commands on Cobra documentation but i can't apply it.
#1356
Rahmaabubakr
closed
9 months ago
0
AttributeError: 'list' object has no attribute 'items'
#1354
QixingWei
closed
1 month ago
8
[Suggestion] drop suppport for Python 3.7
#1352
Midnighter
closed
10 months ago
1
find_gene_knockout_reactions error
#1351
Laminsecin
closed
1 month ago
1
gurobipy.Model.addConstr() DeprecationWarning
#1348
wshao1
closed
10 months ago
4
Make COBRApy compatible with pydantic version 2
#1346
teddygroves
closed
11 months ago
1
Incompatibility with pydantic version 2
#1345
teddygroves
closed
9 months ago
6
Flux-Samplig: Cannot escape sampling region, model seems to be numerically unstable. Reporting the model
#1344
brunorbqi
closed
1 month ago
2
Model valid but cannot be loaded
#1343
HASaunders
closed
9 months ago
2
how to handle mixed-integer programming (MIP) problems with the glpk, cplex or/and gurobi solvers in python/with cobrapy?
#1342
helehera
closed
11 months ago
3
fix the objective in CycleFreeFlux
#1341
cdiener
closed
10 months ago
4
Fix broken test for utils.solver with symengine
#1340
cdiener
closed
10 months ago
2
Cannot import cobra: import error involving numpy
#1339
CNelias
closed
1 year ago
4
How to perform relaxedFBA with cobrapy?
#1338
helehera
closed
11 months ago
1
SBML file not getting uploaded
#1337
ksingh371
closed
11 months ago
2
createMultipleSpeciesModel function can not find in cobrapy
#1336
wupeng1998
closed
1 year ago
4
ContainerAlreadyContains error with the fastcc()
#1334
Alvis-Jiang
closed
1 year ago
3
How to set the model solver
#1333
brunorbqi
closed
1 year ago
1
Improve backwards compatibility for pickled models
#1332
cdiener
closed
1 year ago
1
gapfilling.ipynb bug fix
#1331
pablodig
closed
1 year ago
3
Remove pin for numpy
#1330
cdiener
closed
1 year ago
1
Give parameters to model.optimize()
#1328
KurtzMarina
closed
1 year ago
0
Can Not Open the SBML File
#1327
xuejun1214
closed
1 year ago
4
problems reading certain AGORA2 models
#1326
eugenibc
opened
1 year ago
3
model.reactions.get_by_id error
#1325
dtusso2020
closed
1 year ago
1
fix broken IO with httpx>=0.24
#1324
cdiener
closed
1 year ago
1
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