Figure 5

Screenshots illustrating FVA of M. tuberculosis using GSMN-TB. (a) Simulation set up. User specifies media conditions by setting minimal and maximal capacities of transport reactions in the 'Media conditions' field. The field contains specification of minimal glucose media and lists transport reactions that can be included by removing comment character. The page contains the link to the full model file, and the user may identify other reactions to be constrained. This adds additional flexibility to the simulation set up. The user may also choose one of the two objective functions used in our model to simulate in vitro or in vivo growth requirements. (b) Result of flux variability analysis (FVA) simulation. Maximal theoretical growth rate is displayed at the top of the page. Each row in the table contains reaction name maximal and minimal flux consistent with the maximal theoretical growth rate, reaction formula, and gene annotation. Gene names are linked to genome annotation pages of the TubercuList database. The rows of the table are loaded as computation progresses. The time of the simulation is about 10 min. GSMN-TB, genome-scale metabolic network of M. tuberculosis.