jotech
Impact of different atmosphere on gapseq adapt (growth medium and Biolog-like test)
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.
https://github.com/jotech/gapseq/blob/846f5be51f6460346455c7f098e21b1f05b7a634/src/gf.adapt.R#L29-L31
(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?
