Metabolica: a statistical research tool for analyzing metabolic networks.
Steady state flux balance analysis (FBA) for cellular metabolism is used, e.g., to seek information on the activity of the different pathways under equilibrium conditions, or as a basis for kinetic models. In metabolic models, the stoichiometry of the system, commonly completed with bounds on some of the variables, is used as the constraint in the search of a meaningful solution. As model complexity and number of constraints increase, deterministic approach to FBA is no longer viable: a multitude of very different solutions may exist, or the constraints may be in conflict, implying that no precise solution can be found. Moreover, the solution may become overly sensitive to parameter values defining the constraints. Bayesian FBA treats the unknowns as random variables and provides estimates of their probability density functions. This stochastic setting naturally represents the variability which can be expected to occur over a population and helps to circumvent the drawbacks of the classical approach, but its implementation can be quite tedious for users without background in statistical computations. This article presents a software package called Metabolica for performing Bayesian FBA for complex multi-compartment models and visualization of the results.
Heino
Jenni
J
Department of Mathematics, Helsinki University of Technology, PO Box 1100, FIN-02015 TKK, Finland.
Calvetti
Daniela
D
Somersalo
Erkki
E
D000465:Algorithms; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D020869:Gene Expression Profiling / Q000379:methods*; D055442:Metabolome / Q000502:physiology*; D008954:Models, Biological; D011381:Programming Languages; D020543:Proteome / Q000502:physiology*; D012107:Research Design; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
D020543:Proteome