Impact of different atmosphere on gapseq adapt (growth medium and Biolog-like test)

[LucoDevro]

Hello there,
I have two questions regarding gapseq adapt.

(1) Atmosphere

I have been using gapseq adapt to refine my GEMs after Biolog phenotyping. My strains are strict anaerobes, so I was wondering how it is handling the different atmospheres.

It seems that it's hardcoded to use a minimal aerobic glucose medium (MM_glu.csv). For now, I solved this by removing the oxygen constraint from this medium file, but I'd like to have the option to specify the atmosphere conditions here.

gapseq/src/gf.adapt.R

Lines 29 to 31 in 846f5be

	media.org <- fread(paste0(script.dir,"/../dat/media/MM_glu.csv")) # use minimal medium
	#media.org <- fread(paste0(script.dir,"/../dat/media/MM_anaerobic_CO2_H2.csv")) # use minimal medium
	#media.org <- fread(paste0(script.dir,"/../dat/media/Mineral_salt.csv")) # use minimal medium

(2) Biolog-like test preparation

Since I'm working with strict anaerobes, I had to omit the Biolog dye and measure the plain OD instead. Wouldn't this impact the Biolog-like test gapseq adapt does (the esp.mode function)? Is this related to the Biolog dye acting on these electron transfer proteins? Is this special test actually necessary as I figure the gapfilling would work with the default biomass objective as well, won't it?

[Waschina]

@jotech , can you help with the two questions?