TY - GEN
T1 - COSYS
T2 - 13th International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, CIBB 2016
AU - Cumbo, Fabio
AU - Nobile, Marco S.
AU - Damiani, Chiara
AU - Colombo, Riccardo
AU - Mauri, Giancarlo
AU - Cazzaniga, Paolo
PY - 2017/1/1
Y1 - 2017/1/1
N2 - 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.
AB - 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.
KW - Flux balance analysis
KW - GPGPU computing
KW - High-performance computing
KW - Modeling and simulation
KW - Systems biology
UR - http://www.scopus.com/inward/record.url?scp=85032695238&partnerID=8YFLogxK
U2 - 10.1007/978-3-319-67834-4_7
DO - 10.1007/978-3-319-67834-4_7
M3 - Conference contribution
AN - SCOPUS:85032695238
SN - 978-3-319-67833-7
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 82
EP - 92
BT - Computational Intelligence Methods for Bioinformatics and Biostatistics - 13th International Meeting, CIBB 2016, Revised Selected Papers
A2 - Caravagna, Giulio
A2 - Tagliaferri, Roberto
A2 - Gilbert, David
A2 - Bracciali, Andrea
PB - Springer
CY - Cham
Y2 - 1 September 2016 through 3 September 2016
ER -