MEIGOR

MEIGO (MEtaheuristics for systems biology and bIoinformatics Global Optimization) is a free, open-source optimization toolbox available in R, Matlab, and Python (via a wrapper of the R version). The toolbox implements metaheuristic algorithms that can efficiently solve various optimization problems in systems biology and bioinformatics.

Key features of MEIGO include:

1. The Enhanced Scatter Search (eSS) method is used to solve continuous nonlinear programming (cNLP) and mixed-integer programming (MINLP) problems.

2. Variable Neighborhood Search (VNS) for solving Integer Programming (IP) problems.

3. BayesFit for parameter estimation by Bayesian inference (available in the R version).

4. Single-thread and parallel execution using a cooperative strategy for eSS and VNS methods.

5. Open and modular structure, allowing the addition of new optimization methods.

Topic

Systems biology;Data quality management

Detail

  • Operation: Optimisation and refinement

  • Software interface: Command-line user interface, Library

  • Language: R

  • License: The GNU General Public License v3.0

  • Cost: Free

  • Version name: 1.38.0

  • Credit: The EU through projects “BioPreDyn” and “NICHE”, Ministerio de Economía y Competitividad (and the FEDER) through the projects “Multi-Scales”, the CSIC intramural project “BioREDES”.

  • Input: -

  • Output: -

  • Contact: Jose A. Egea josea.egea@gmail.com

  • Collection: -

  • Maturity: Stable

Publications

  • MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics
  • Egea JA, Henriques D, Cokelaer T, Villaverde AF, MacNamara A, Danciu DP, Banga JR, Saez-Rodriguez J. MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics. BMC Bioinformatics. 2014 May 10;15:136. doi: 10.1186/1471-2105-15-136. PMID: 24885957; PMCID: PMC4025564.
  • https://doi.org/10.1186/1471-2105-15-136
  • PMID: 24885957
  • PMC: PMC4025564

Download and documentation

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