Capabilities

  • Software | AMIGO2: Advanced Modelling and Identification using Global Optimization, version 2

    AMIGO2 is a MATLAB-based multiplatform toolbox designed to solve mathematical optimization problems at the core of systems biology, within the context of parametric model identification, the underlying hypothesis for model development and the optimal control of biological systems to synthetically achieve the desired behavior.

    More information here.

  • Software | PREMER: fast network inference with information theory

    PREMER (Parallel Reverse Engineering with Mutual information & Entropy Reduction) is an open-source, multi-platform software tool for inferring network structures from data using information-theoretic measures. While this general purpose tool has been developed with biological networks in mind, it can be applied to other areas.

    More information here.

     

  • 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.

    More information here.

     

Active projects