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PNNL-CompBio
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CONCERTO
Continuous integration and validation for genome-scale metabolic model consortia
Apache License 2.0
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Reworked to find metabolite placement bug
#114
JamesPino
closed
9 months ago
0
Obtain data from Pavlo where metabolomics and transcriptomics was measured in the same conditions
#113
djinnome
opened
11 months ago
1
Concerto Discussion
#112
djinnome
opened
12 months ago
0
Concerto Results
#111
djinnome
opened
12 months ago
0
Concerto Methods
#110
djinnome
opened
12 months ago
0
Concerto Introduction
#109
djinnome
opened
12 months ago
0
Concerto Abstract
#108
djinnome
opened
12 months ago
0
Test whether Azo grows on Glycolate with and without ammonium
#107
djinnome
opened
12 months ago
0
Set up overleaf for milestone 6a. Concerto publication
#106
djinnome
opened
12 months ago
0
Bayesian MCA Discussion
#105
djinnome
opened
1 year ago
0
Bayesian MCA Results
#104
djinnome
opened
1 year ago
0
Bayesian MCA Methods
#103
djinnome
opened
1 year ago
0
Bayesian MCA Abstract
#102
djinnome
opened
1 year ago
0
Create FluxViz method
#101
ShantMahserejian
opened
1 year ago
0
Select dual carbon source for Azo-Rhodo consortia
#100
djinnome
opened
1 year ago
5
visualization-friendly version of Carbon dioxide flux
#99
djinnome
opened
1 year ago
6
simulate ternary consortium model to confirm no growth under tested media conditions
#98
djinnome
opened
1 year ago
0
Generate Memote pull request for github actions compatibility
#97
djinnome
opened
1 year ago
1
predict all secreted metabolites under 20 Rhodo+ Azo- biolog conditions and intersect with Azo+ biolog conditions
#96
djinnome
closed
1 year ago
3
Update LICENSE
#95
djinnome
closed
1 year ago
0
Updating the Cyano confusion matrix with the new model
#94
djinnome
closed
1 year ago
4
Get binary azo-rhodo working with a carbon source that only rhodo grows on
#93
djinnome
opened
1 year ago
6
Get binary rhodo-cyano working with CO2 as sole carbon (ammonia is fine as a nitrogen source)
#92
djinnome
opened
1 year ago
1
Get binary azo-cyano working with CO2 and N2 as sole carbon and nitrogen sources
#91
djinnome
opened
1 year ago
1
Flux viz
#90
djinnome
closed
1 year ago
2
Adding function to add biolog exchange reactions to model if missing
#89
JamesPino
closed
1 year ago
0
Swap colors between Azoto and Cyano
#88
djinnome
closed
1 year ago
2
ternary consortium does not have a dinitrogen flux
#87
djinnome
closed
1 year ago
9
Try loading cyano, rhodo, and azoto in Kbase prior to Monday meeting with Chris Henry
#86
djinnome
closed
1 year ago
3
explore if there is a way to run dynamic FBA for microbial consortia
#85
vladpetyuk
opened
1 year ago
1
Convert Pavlo's cyano-rhodo data to binary consortia unit tests
#84
djinnome
opened
1 year ago
1
Removing models from repo.
#83
JamesPino
closed
1 year ago
0
Review additional community modeling frameworks
#82
djinnome
opened
1 year ago
0
updated the name of the sucrose transporter
#81
vladpetyuk
closed
1 year ago
0
Adding load_model_from_git.py helper function and universal model
#80
mcnaughtonadm
closed
1 year ago
1
Get working BioCyc model
#79
djinnome
opened
1 year ago
0
Adding Notebooks to explore Binary Consortium Models
#78
mcnaughtonadm
closed
1 year ago
2
Removing models from repo. Moving tools used in each to concerto sour…
#77
JamesPino
closed
1 year ago
0
Fix MiCOM leaks
#76
djinnome
opened
1 year ago
0
Add exchange reactions for each Biolog nutrient to each model.
#75
djinnome
closed
1 year ago
1
get information about genetic modifications of the azobacter strain so we can incorporate them into the model
#74
vladpetyuk
opened
1 year ago
0
Plan for designing Azo to depend on Rhodo for carbon
#73
djinnome
opened
1 year ago
1
start the axenic samples
#72
vladpetyuk
opened
1 year ago
0
Write rxn files to sbml
#71
vladpetyuk
opened
1 year ago
0
simulate rhodo on those rhodo+ azoto- carbon sources to see if anything it excretes can be ingested by azoto
#70
vladpetyuk
opened
1 year ago
1
Removing models from repo.
#69
JamesPino
closed
1 year ago
0
manuscript for describing good practices for microbial community modeling
#68
vladpetyuk
opened
1 year ago
0
Visualization for Exchange Metabolites in Ternary Model
#67
ShantMahserejian
closed
1 year ago
1
Visualization of Exchange Metabolites for Binary Models
#66
ShantMahserejian
closed
1 year ago
2
designed media for sustained growth of ternary consortium
#65
vladpetyuk
opened
1 year ago
0
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