MetMAP: an integrated Matlab package for analysis and optimization of metabolic systems

In previous works we have presented and applied a method to predict the parameter profile that optimizes biochemical systems regarding either a single or a set of metabolic responses within physiological constraints Vera et al., 2003a]. This optimization technique requires a previous model definition and a translation to S-system form and the use of widely available linear programming packages. However, in dealing with these issues the interested researcher has to confront additional difficulties because of a lack of connectivity among available software packages or routines specifically designed to perform different tasks. In addition to this difficulty is the unavailability of any automated package which is capable of performing such optimizations and the previous required analysis. This situation prompted us to develop an integrated software package able to deal with these tasks in a single program environment. In this paper we present a software package for the model definition, analysis and optimization of a biochemical system. It starts with a given model definition that is directly translated to its equivalent S-system form. Once the model quality assessment is performed (stability and sensitivity analysis) the program determines the parameter profile that yields the optimized response compatible with a predefined set of constraints. Moreover the package finds the set of solutions obtained when more than one system's responses are to be optimized (multiobjective optimization).