Frequently Asked Questions
Q: How do I optimize for biomass?
A: One way is to include a reaction in the S matrix that consumes the biomass constituents from the network in the appropriate ratios and then optimize for this one flux.
Q: I don't get any growth from simulation. Why is that?
A: There could be several reasons for it. First, check that exchange fluxes are implemented correctly. Allow the input of SO4, O2, phosphate, water, proton, Fe2, csn, pro-L, thm, nac and the output of all other extracellular metabolites. Also allow the free input and output of small amounts of ahcys and glyclt (to/from the cytosol). Next, check if you can make basic precursors from glucose. Then, add a temporary reaction that drain each precursor and maximize for this temporary reaction. Finally, check that you can make each of the biomass constituents. Once you identify which ones you cannot make, you need to go through the metabolic routes and determine why.
Q: How come there are extracellular versions of compounds but not intracellular compounds?
A: It's because some transport reactions change the compound, for example, from galactitol to galactitol-1-phosphate.
Q: What is the difference between a transport reaction and an exchange reaction?
A: The difference lies in a boundary. Whereas the boundary of a transport reaction is a cell membrane, an exchange reaction's boundary is a system boundary.
Q: Are there any values available that I can compare my model's results with?
A: With 10 glc-D and 100 pro-L provided under aerobic conditions the flux through the biomass reactions is 0.012. The biomass should not be considered quantitatively accurate since it was generated without comprehensive data from S. aureus.