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PNNL-CompBio
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CONCERTO
Continuous integration and validation for genome-scale metabolic model consortia
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develop and document the protocol for refinement of the ternary consortia
#64
vladpetyuk
opened
1 year ago
0
create ternary consortia GEM model
#62
vladpetyuk
closed
1 year ago
1
document the protocol for refining consortia
#61
vladpetyuk
opened
1 year ago
0
(OPTIONAL) Design an objective goodness-of-fit function for evaluating how well simulation fits the experimental data
#60
vladpetyuk
opened
1 year ago
0
compare, evaluate disagreement of the simulations with the growth experimental data
#59
vladpetyuk
opened
1 year ago
3
run simulation of the rhodo/syn co-culture under proper media conditions in MICOM
#58
vladpetyuk
closed
1 year ago
2
compile list of secreted metabolites for rhodo/syn co-culture
#57
vladpetyuk
closed
1 year ago
1
get individual species growth data from rhodo/syn co-culture
#56
vladpetyuk
opened
1 year ago
1
Talk to Bill and Ethan about getting access to modified rhodo model
#55
djinnome
closed
1 year ago
1
Write code that converts FBA model to biocyc
#54
djinnome
opened
1 year ago
0
develop experimental design for obtaining data on azotobacter secreted metabolites
#53
vladpetyuk
closed
1 year ago
1
find gene essentiality data for synecoccocus
#52
vladpetyuk
closed
1 year ago
0
find gene essentiality data for azotobacter
#51
vladpetyuk
closed
1 year ago
0
find gene essentiality data for rhodosporidium
#50
vladpetyuk
closed
1 year ago
0
derive the list of secreted metabolites for rhodosporidium and synecoccocus from various co-culture experiments
#49
vladpetyuk
closed
1 year ago
0
find biolog data for synecoccocus
#48
vladpetyuk
closed
1 year ago
2
find biolog data for azotobacter
#47
vladpetyuk
closed
1 year ago
0
find biolog data for rhodosporidium
#46
vladpetyuk
closed
1 year ago
0
Develop memote test for secreted metabolites within CONCERTO repo
#45
vladpetyuk
closed
1 year ago
0
Develop memote test for gene essentiality data within CONCERTO repo
#44
vladpetyuk
closed
1 year ago
0
Adding first concerto level module and removing RT model
#43
JamesPino
closed
1 year ago
0
Develop memote test for biolog data within CONCERTO repo
#42
vladpetyuk
closed
1 year ago
0
Create azotobacter repo under CONCERTO team
#41
vladpetyuk
closed
1 year ago
0
Create synechococcus elongatus repo under CONCERTO team
#40
vladpetyuk
closed
1 year ago
0
Create rhodosporidium repo under CONCERTO team
#39
vladpetyuk
closed
1 year ago
0
Create CONCERTO repo under CONCERTO team
#38
vladpetyuk
closed
1 year ago
0
create team named CONCERTO under PNNL CompBio
#37
vladpetyuk
closed
1 year ago
2
Create azo/rhodo binary coculture
#36
djinnome
closed
1 year ago
2
Create cyano/rhodo binary coculture
#35
djinnome
closed
1 year ago
2
Create cyano/azo binary coculture
#34
djinnome
closed
1 year ago
2
Dev
#33
mcnaughtonadm
closed
1 year ago
0
Add Biolog metabolites to every model that has Biolog plates
#32
djinnome
opened
1 year ago
0
Set up Biolog plates for RhodoCyc
#31
djinnome
opened
1 year ago
0
Set up Biolog plates for Azoto
#30
djinnome
opened
1 year ago
0
compare predicted excreted metabolites in rhodo in nitrogen replete vs deplete in sucrose carbon source
#29
djinnome
closed
1 year ago
1
explain cyano-rhodo coculture metabolite excretions based on computational simulations
#28
djinnome
opened
1 year ago
1
write test to ensure that rhodo can excrete each metabolite in Pavlo's list under sucrose conditions
#27
JamesPino
closed
1 year ago
2
Send externally excreted metabolites in excel and powerpoint
#26
djinnome
closed
1 year ago
0
2. Generate list of metabolites consumed and produced for each organism
#25
djinnome
closed
1 year ago
2
3. Create binary and ternary consortia GEM models. Explore a number of multi-scale modeling frameworks including Vivarium for GEM integration. Validate against the available experimental data on consortia growth and stability. (March, 2023)
#24
JamesPino
closed
1 year ago
0
get universal model to generate nonzero growth in rhodo nutrient medium
#23
djinnome
opened
1 year ago
2
Ensure universal stoichiometric matrix can run in cobra
#22
djinnome
closed
1 year ago
3
Reach out to Connah and get rhodo sbml into concerto
#21
djinnome
closed
1 year ago
1
Export sucrose from Synechococcus
#20
djinnome
closed
1 year ago
10
get CROP using the same universal matrix as gapfill
#19
djinnome
opened
1 year ago
0
gapfill one false negative in rhodosporidium
#18
djinnome
opened
1 year ago
3
Add invertase to Rhodo model
#17
djinnome
closed
1 year ago
3
Rebase
#16
JamesPino
closed
1 year ago
0
Adding syn elo essentiality tests.
#15
JamesPino
closed
1 year ago
0
Updating memote actions.
#14
JamesPino
closed
1 year ago
0
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