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.

(2017). COSYS: A computational infrastructure for systems biology . Retrieved from http://hdl.handle.net/10446/108454

COSYS: A computational infrastructure for systems biology

Mauri, Giancarlo;Cazzaniga, Paolo
2017-01-01

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.
2017
Cumbo, Fabio; Nobile, Marco S.; Damiani, Chiara; Colombo, Riccardo; Mauri, Giancarlo; Cazzaniga, Paolo
File allegato/i alla scheda:
File Dimensione del file Formato  
cibb_paper_80.pdf

Solo gestori di archivio

Versione: postprint - versione referata/accettata senza referaggio
Licenza: Licenza default Aisberg
Dimensione del file 456.17 kB
Formato Adobe PDF
456.17 kB Adobe PDF   Visualizza/Apri
Pubblicazioni consigliate

Aisberg ©2008 Servizi bibliotecari, Università degli studi di Bergamo | Terms of use/Condizioni di utilizzo

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10446/108454
Citazioni
  • Scopus 4
  • ???jsp.display-item.citation.isi??? ND
social impact