MEIGO

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. Optimization is key to solve many problems in computational biology. Global optimization methods provide a robust methodology, and metaheuristics in particular have proven to be the most ecient methods for many applications. Despite their utility, there is limited availability of metaheuristic tools. We present MEIGO, an R and Matlab optimization toolbox (also available in Python via a wrapper of the R version), that implements metaheuristics capable of solving diverse problems arising in systems biology and bioinformatics: enhanced scatter search method (eSS) for continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems, and variable neighborhood search (VNS) for Integer Programming (IP) problems. Both methods can be run on a single-thread or in parallel using a cooperative strategy. The code is supplied under GPLv3 and is available at http://www.iim.csic.es/ gingproc/meigo.html. Documentation and examples are included. The R package has been submitted to Bioconductor. We evaluate MEIGO against optimization benchmarks, and illustrate its applicability to a series of case studies in bioinformatics and systems biology, outperforming other state-of-the-art methods. MEIGO provides a free, open-source platform for optimization, that can be applied to multiple domains of systems biology and bioinformatics. It includes ecient state of the art metaheuristics, and its open and modular structure allows the addition of further methods


References in zbMATH (referenced in 6 articles )

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  1. Leonard Schmiester, Yannik Schälte, Frank T. Bergmann, Tacio Camba, Erika Dudkin, Janine Egert, Fabian Fröhlich, Lara Fuhrmann, Adrian L. Hauber, Svenja Kemmer, Polina Lakrisenko, Carolin Loos, Simon Merkt, Wolfgang Müller, Dilan Pathirana, Elba Raimúndez, Lukas Refisch, Marcus Rosenblatt, Paul L. Stapor, Philipp Städter, Dantong Wang, Franz-Georg Wieland, Julio R. Banga, Jens Timmer, Alejandro F. Villaverde, Sven Sahle, Clemens Kreutz, Jan Hasenauer, Daniel Weindl: PEtab - interoperable specification of parameter estimation problems in systems biology (2020) arXiv
  2. Eshan D. Mitra, Ryan Suderman, Joshua Colvin, Alexander Ionkov, Andrew Hu, Herbert M. Sauro, Richard G. Posner, William S. Hlavacek: PyBioNetFit and the Biological Property Specification Language (2019) arXiv
  3. Sanguinetti, Guido (ed.); Huynh-Thu, Vân Anh (ed.): Gene regulatory networks. Methods and protocols (2019)
  4. Joao Paulo Papa, Gustavo Henrique Rosa, Douglas Rodrigues, Xin-She Yang: LibOPT: An Open-Source Platform for Fast Prototyping Soft Optimization Techniques (2017) arXiv
  5. Jose A Egea, David Henriques, Thomas Cokelaer, Alejandro F Villaverde, Julio R Banga, Julio Saez-Rodriguez: MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics (2013) arXiv
  6. Egea, Jose A.; Martí, Rafael; Banga, Julio R.: An evolutionary method for complex-process optimization (2010)