SBRG cobrame issues - Githubissues

SBRG / cobrame

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

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issues

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Adding translation reaction without utility function

#40 FH96 opened 2 months ago
0
Cannot build docker image

#39 mheydasch opened 3 months ago
0
CobraPy version not being correctly detected

#38 geno-nvenayak closed 1 year ago
2
Cannot convert expression to float in build_me_model.ipynb

#37 bigsuicideparty opened 2 years ago
1
Changing objective function for optimization in COBRAME

#36 sumanasri opened 4 years ago
0
biomass constituents

#35 weif000 opened 5 years ago
1
In algorithms.py,function binary_search()

#34 weif000 closed 5 years ago
2
[question] Auxotroph E. coli

#33 emarquezz closed 5 years ago
0
COBRAme workshop

#32 fairquestion opened 5 years ago
0
Tiny fix in docs

#31 tiermak closed 5 years ago
2
Access to MiniME or pickled version of iJL965_ME that does not depend on MiniME?

#30 djinnome opened 5 years ago
9
Runtime error when attempting to remove genes from model

#29 djinnome opened 6 years ago
3
Allow lower case nucleotide sequences or make error explicit

#28 coltonlloyd opened 6 years ago
0
Issues that need to be fixed to run Docker version successfully

#27 djinnome closed 6 years ago
11
FVA in COBRAme

#26 Mzohrabi closed 6 years ago
1
knockout gene

#25 Mzohrabi closed 6 years ago
3
[subreaction].enzyme should always be a list or None

#24 coltonlloyd opened 6 years ago
0
Add docker script

#23 coltonlloyd closed 6 years ago
1
Remove <metabolite>.mass handling

#22 coltonlloyd closed 6 years ago
1
Specify metabolite compartments in JSON

#21 coltonlloyd closed 6 years ago
1
Acetate production prediction

#20 emarquezz closed 6 years ago
1
processdata.py met does not have formula

#19 emarquezz closed 7 years ago
1
Model dictlist attributes should only include process_data

#18 coltonlloyd closed 7 years ago
1
MetabolicReaction should include complex.id

#17 coltonlloyd opened 7 years ago
0
[question] steps to add a new gene + product

#16 cdiener closed 7 years ago
2
Allow changing StoichiometricData stoichiometry without changing hidden attribute

#15 coltonlloyd closed 7 years ago
1
Compatibility with COBRApy versions > 0.6.0

#14 coltonlloyd opened 7 years ago
0
Implement and test full model JSON saving/loading

#13 coltonlloyd closed 7 years ago
0
Combine ModificationData and SubreactionData

#12 coltonlloyd closed 7 years ago
1
Save and load ME-models using JSON

#11 coltonlloyd closed 7 years ago
0
Linking enzymes to keffs

#10 coltonlloyd opened 7 years ago
0
model.update() intention

#9 hvdinh16 closed 6 years ago
0
Flag to allow expression of pseudo genes; fixed bug with iteritems

#8 zakandrewking closed 6 years ago
0
Flag to allow expression of pseudo genes; fixed bug with iteritems

#7 zakandrewking closed 7 years ago
0
Flag to allow expression of pseudo genes; fixed bug with iteritems

#6 zakandrewking closed 7 years ago
0
Method to make Escher-compatible JSON

#5 zakandrewking opened 7 years ago
0
Get translation flux for metabolic reaction

#4 zakandrewking opened 7 years ago
0
COBRAme JSON loading

#3 zakandrewking closed 7 years ago
1
Allow prune to skip objects

#2 avsastry closed 7 years ago
0
Separate check mass balance functions for each MEReaction subclass

#1 coltonlloyd closed 7 years ago
1