Analysis Methods - HelikarLab/cobra-app GitHub Wiki
Currently, the application supports the following simulations:
Flux Balance Analysis
Flux Balance Analysis is a type of popular Constraint-based Reconstruction and Analysis method for metabolic networks. These network contain all of the known metabolic reactions in an organism and the genes that encode each enzyme. It calculates the flux, i.e. flow of metabolites through the network.
Flux Variability Analysis
An FVA consists of getting the optimal value for the objective function, setting this value as a constraint and, given a list of entities, minimize and maximize their values. This analysis returns the objective value, and the minimum and maximum value for each entity desired.
Essentiality
The list of genes and reactions that are when removed will give a biomass objective function value of “0”. In terms of Reactions this can be calculated as: if Vi, which is associated with each particular reaction, is set to zero then Z = 0. For genes to be essential it means that if Gene gi is zero then Z = 0. Whether or not a gene is essential can be determined after the reactions are determined to be essential to minimize the number of calculations to be performed.
Synthetic Lethality
Synthetic Lethality is extremely similar to Essentiality, except instead of one gene or one reaction being deleted there will be pairs of genes or reactions deleted