pnnl-predictive-phenomics syn_bmca issues

pnnl-predictive-phenomics / syn_bmca

Code for implementing BMCA for Synechococcus elongatus

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Run Bayesian MCA on proteomics data + Eflux + metabolomics

#36 djinnome opened 2 months ago
1
Renormalize proteomics and metabolomics using L_T2_B

#35 djinnome closed 2 months ago
1
30 add proteomics to circadian experiments

#34 CJohnsonPnnl closed 3 months ago
0
Refactoring to follow proper python package structure with formatting.

#33 mcnaughtonadm closed 3 months ago
0
Linting

#32 mcnaughtonadm closed 3 months ago
0
test_create_Issue_CJ

#31 CJohnsonPnnl closed 4 months ago
0
Add proteomics to circadian experiments

#30 djinnome closed 3 months ago
0
Completed running Eflux on model with no biomass cofactor

#29 ShantMahserejian closed 4 months ago
0
rescale fluxes to logscale

#28 augeorge opened 4 months ago
4
24 create function to calculate fluxes from metabolomics data

#27 ShantMahserejian opened 4 months ago
0
Add fluxomics data from GAPDH strain

#26 djinnome opened 4 months ago
0
enzyme constrained fluxes and the notebook that runs Eflux with slack…

#25 djinnome closed 4 months ago
0
Create function to calculate fluxes from metabolomics data

#24 ShantMahserejian opened 4 months ago
1
Run Eflux on external metabolites and circadian data

#23 djinnome closed 4 months ago
0
18 prepare and share circadian data

#22 mcnaughtonadm closed 4 months ago
0
Fix model flipping

#21 mcnaughtonadm closed 4 months ago
0
Adding new flipped no zero model

#20 mcnaughtonadm closed 4 months ago
0
18 prepare and share circadian data

#19 djinnome closed 5 months ago
0
Prepare and Share Circadian Data

#18 ShantMahserejian closed 5 months ago
0
Add disclaimer and license

#17 mcnaughtonadm closed 5 months ago
0
11 prepare dataframes for pathway tools smart tables

#16 djinnome closed 5 months ago
0
5 eflux2 is run on the transcriptomics data to get condition specific flux predictions

#15 djinnome closed 5 months ago
0
Add data

#14 djinnome closed 5 months ago
2
Add disclaimer and license for public release

#13 djinnome closed 5 months ago
0
Get fluxes constrained on observed data

#12 ShantMahserejian opened 5 months ago
0
Prepare dataframes for Pathway-Tools Smart-Tables

#11 ShantMahserejian closed 5 months ago
1
Adding Code for Syn BMCA PyMC Model

#10 mcnaughtonadm closed 5 months ago
0
Find out how to include missing metabolites

#9 mcnaughtonadm opened 6 months ago
0
Update the compartment in `build.py` for metabolomics

#8 mcnaughtonadm opened 6 months ago
1
Generate Proteomics Data from Transcriptomics Data

#7 mcnaughtonadm opened 6 months ago
1
Create PyMC BMCA Skeleton for running with processed data

#6 mcnaughtonadm closed 5 months ago
0
EFlux2 is run on the transcriptomics data to get condition-specific flux predictions

#5 mcnaughtonadm closed 5 months ago
2
Calculate Growth Rate from Cell Numbers

#4 mcnaughtonadm opened 6 months ago
5
Handle missing data for input into Bayesian MCA

#3 djinnome opened 8 months ago
4
Adding raw data zipfile

#2 mcnaughtonadm closed 6 months ago
3
Load in Pavlo's Data

#1 mcnaughtonadm closed 6 months ago
1