Capabilities

  • Software | BioPreDyn-bench: a suite of benchmark problems for dynamic modeling in systems biology

    BioPreDyn-Bench is a suite of benchmark problems for dynamic modeling in systems biology. Currently, it contains six challenging parameter estimation problems, which aspire to serve as reference test cases in this area. This set includes medium- and large-scale kinetic models of E.coli, S. cerevisiae, D. melanogaster, Chinese Hamster Ovary (CHO) cells and a generic signaling network. The level of description includes metabolism, transcription, signal transduction and development.

    More information here.

  • Software | MIDER: a toolbox for network inference using mutual information distance and entropy reduction

    MIDER (mutual information distance and entropy reduction) is a general purpose software tool for inferring network structures. It has been developed with biological networks in mind but can be applied to other areas.

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  • Software | MEIGO: a multiplatform toolbox for Global Optimization using Metaheuristics

    MEIGO is a global optimization toolbox that includes a number of metaheuristic methods, as well as a Bayesian inference method for parameter estimation.

    More information here.

  • Software | DOTcvpSB: Matlab toolbox for Dynamic Optimization in Systems Biology

    DOTcvpSB is a toolbox written in MATLAB that uses the control vector parameterization (CVP) method to handle continuous and mixed integer dynamic optimization problems. DOTcvpSB has been successfully applied to several problems in systems biology and bioprocess engineering.

    More information here.

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