EFlux2 is run on the transcriptomics data to get condition-specific flux predictions

pnnl-predictive-phenomics / syn_bmca

Code for implementing BMCA for Synechococcus elongatus

Other

2 stars 0 forks source link

Closed mcnaughtonadm closed 6 months ago

mcnaughtonadm commented 8 months ago

We need to utilize sucrose production and growth rate along with the cobra model to generate fluxes for BMCA.

Get EFlux2 notebook running (solving infeasibility scenarios).

ShantMahserejian commented 8 months ago

I volunteer

djinnome commented 8 months ago

[x] Run flux variability analysis on the reference strain to get (reasonably) tight bounds on the fluxes.
[x] Next, convert the transcriptomics data to enzyme data (Take the min of subunits, take the sum of isozymes)
[ ] for each condition, normalize enzyme data with respect to the reference strain
[ ] for each condition, multiply the reference bounds by the normalized enzyme data.
[ ] Run FBA using the condition-specific bounds to compute the condition-specific fluxes