C-CoMP-STC GEM-mit1002 issues

C-CoMP-STC / GEM-mit1002

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Check biomass component producibility before and after adding Michelle's reaction

#68 hgscott opened 4 days ago
1
Compare biomass reaction to compositions of other models

#67 hgscott opened 4 days ago
10
Find/add maintenance reaction

#66 hgscott opened 1 month ago
0
Compare models made in KBase and with ModelSEEDpy

#65 hgscott opened 1 month ago
6
Compare genes where associated reactions do not match

#64 hgscott opened 5 months ago
0
Add Michelle's reactions

#63 hgscott opened 5 months ago
0
Add MACAW tests to the Action

#62 hgscott opened 5 months ago
5
KBase Gene Call IDs do not match Pangenome

#61 hgscott opened 6 months ago
7
Get a 1-to-1 comparison with pangenome reactions

#60 hgscott opened 6 months ago
1
Use OMEGGA to make model

#59 hgscott opened 7 months ago
22
Recreate model creation/gap filling using ModelSEEDpy

#58 hgscott opened 8 months ago
11
Leave some media out of gap filling for real validation

#57 hgscott opened 8 months ago
0
Use MetaNetX to get all annotations

#56 hgscott closed 6 months ago
1
Test/gapfill for new growth phenotypes

#55 hgscott opened 8 months ago
0
Growth on no carbon

#54 hgscott closed 7 months ago
4
False positives of growth

#53 hgscott opened 11 months ago
0
Use ReFill to gap fill

#52 hgscott opened 11 months ago
0
Check MEMOTE blocked biomass components

#51 hgscott opened 11 months ago
0
Connect RAST annotations to ModelSEED IDs

#50 hgscott opened 12 months ago
1
Export the RASTtk annotations to Anvio

#49 hgscott opened 12 months ago
8
Cycles

#48 hgscott closed 8 months ago
0
Make model using new gene calls

#47 hgscott closed 11 months ago
5
Add CheBI Keys for all metabolites

#46 hgscott closed 8 months ago
15
Do traditional gap filling on the model

#45 hgscott closed 11 months ago
25
Fix false proton gradient generating cycles.

#44 hgscott closed 11 months ago
3
Use Devlin's algorithm to identify even more cycles

#43 hgscott opened 1 year ago
6
Draw energy generating cycles

#42 hgscott closed 11 months ago
6
Why does MEMOTE give different numbers of energy generating cycle reactions?

#41 hgscott closed 11 months ago
7
Why is MEMOTE giving a different number of reactions than KBase

#40 hgscott closed 11 months ago
3
Make model with MS2 App

#39 hgscott closed 1 year ago
0
Gapfill model in KBase using only reactions present in the pangenome

#38 hgscott opened 1 year ago
0
Gapfill for production of a single biomass component

#37 hgscott opened 1 year ago
0
Look at biomass components one by one

#36 hgscott opened 1 year ago
1
Gapfill the new MS2 model

#35 hgscott closed 11 months ago
1
Write test for SBML validity

#34 hgscott closed 1 year ago
0
Run MEMOTE on new model before gap filling

#33 hgscott closed 1 year ago
3
Identify problematic reactions by adding dilution fluxes

#32 hgscott closed 1 year ago
19
Retrieve just the gap filled reactions

#31 hgscott opened 1 year ago
1
Come up with algorithm for iterative gap filling

#30 hgscott opened 1 year ago
3
SBML File is Not Valid

#29 hgscott closed 8 months ago
8
Talk to Claire and Carl (and Mary Ann) about

#28 hgscott closed 1 year ago
0
Fitting

#27 hgscott closed 1 year ago
0
Escher

#26 hgscott closed 1 year ago
0
Kbase models

#25 hgscott closed 1 year ago
0
Calculate maintenance using CO2 flux data

#24 hgscott opened 1 year ago
0
Pick high priority metabolites for experiments

#23 hgscott opened 1 year ago
0
Check maintenance reaction effects

#22 hgscott opened 1 year ago
12
Remake model with new KBase app

#21 hgscott closed 1 year ago
2
Check if Haroon's problem reactions are being added during gap filling

#20 hgscott opened 1 year ago
1
Revisit the biomass equation

#19 hgscott closed 4 days ago
7