CGXII comparison shows that some metabolites cannot be used because of missing exchanges

[famosab]

EX_ni2_e, EX_na1_e, EX_34dhbz_e and EX_btn_e are not present in any of the strains. More research into whether these metabolites should be consumed by the model is necessary since we add all of those to the medium mixture in the wetlab. While ni2, 34dhbz and btn can be removed in the wetlab, na1 is not removable since NaOH is being used to adjust the pH of the medium. This also relates to issue #5 in C_striatum_wetlab.

• [x] determine whether cobalt2, nmn, ala_B, pnto__R and cgly can be put into wetlab stock solutions or replaced by related metabolites
• [x] check for na1 uptake / transport reactions
• [x] research ni2 usage
• [x] research 34dhbz usage -> seems to be carbon source for C. glutamicum
• [x] research btn usage
• [x] compare fluxes of 'good' additives to other used metabolites for hints on concentration

[famosab]

A new simulation approach is to iterate through all exchanges and see if opening those would lead to higher growth rates on the same medium. With this approach I was able to identify a couple of metabolites that are also available in the chemical storage in the lab. I will now research appropriate concentrations and then test whether growth is improved (higher final ODs / higher growth rates).

[famosab]

All these 'unavailable' exchanges need to be added to the models, so that the metabolites are at least able to exist in the extracellular region. Only 34dhbz is a special case since its not available in some of the models, we will need to add the extracellular metabolite as well. This will lead to an extra orphan metabolite but might be a good starting point for investigations in the future.