COSYS: a computational infrastructure for systems biology

Fabio Cumbo, Marco S. Nobile, Chiara Damiani, Riccardo Colombo, Giancarlo Mauri, Paolo Cazzaniga

Research output: Chapter in Book/Report/Conference proceedingConference contributionAcademicpeer-review

4 Citations (Scopus)

Abstract

Computational models are essential in order to integrate and extract knowledge from the large amount of -omics data that are increasingly being collected thanks to high-throughput technologies. Unfortunately, the definition of an appropriate mathematical model is typically inaccessible to scientists with a poor computational background, whereas expert users often lack the proficiency required for biologically grounded models. Although many efforts have been put in software packages intended to bridge the gap between the two communities, once a model is defined, the problem of simulating and analyzing it within a reasonable time still persists. We here present COSYS, a web-based infrastructure for Systems Biology that guides the user through the definition, simulation and analysis of reaction-based models, including the deterministic and stochastic description of the temporal dynamics, and the Flux Balance Analysis. In the case of computationally demanding analyses, COSYS can exploit GPU-accelerated algorithms to speed up the computation, thereby making critical tasks, as for instance an exhaustive scan of parameter values, attainable to a large audience.

Original languageEnglish
Title of host publicationComputational Intelligence Methods for Bioinformatics and Biostatistics - 13th International Meeting, CIBB 2016, Revised Selected Papers
EditorsGiulio Caravagna, Roberto Tagliaferri, David Gilbert, Andrea Bracciali
Place of PublicationCham
PublisherSpringer
Pages82-92
Number of pages11
ISBN (Electronic)978-3-319-67834-4
ISBN (Print)978-3-319-67833-7
DOIs
Publication statusPublished - 1 Jan 2017
Event13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016 - Stirling, United Kingdom
Duration: 1 Sep 20163 Sep 2016

Publication series

NameLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Volume10477 LNBI
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Conference

Conference13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016
Country/TerritoryUnited Kingdom
CityStirling
Period1/09/163/09/16

Keywords

  • Flux balance analysis
  • GPGPU computing
  • High-performance computing
  • Modeling and simulation
  • Systems biology

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