{"id":"https://openalex.org/W2148672014","doi":"https://doi.org/10.1093/bib/bbt040","title":"Parallel stochastic systems biology in the cloud","display_name":"Parallel stochastic systems biology in the cloud","publication_year":2013,"publication_date":"2013-06-18","ids":{"openalex":"https://openalex.org/W2148672014","doi":"https://doi.org/10.1093/bib/bbt040","mag":"2148672014","pmid":"https://pubmed.ncbi.nlm.nih.gov/23780997"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbt040","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbt040","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"http://hdl.handle.net/2318/140080","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5089092418","display_name":"Marco Aldinucci","orcid":"https://orcid.org/0000-0001-8788-0829"},"institutions":[{"id":"https://openalex.org/I4210142764","display_name":"Healing Foundation","ror":"https://ror.org/041kwj007","country_code":"AU","type":"other","lineage":["https://openalex.org/I4210142764"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["AU","IT"],"is_corresponding":false,"raw_author_name":"M. Aldinucci","raw_affiliation_strings":["Marco Aldinucci is an assistant professor at Computer Science Department of the University of Torino, Italy, since 2008. Previously, he has been researcher at University of Pisa and Italian National Research Agency. He is the author of over a hundred articles in international journals and conference proceeding. He has been participating in >20 research projects concerning parallel computing. He is the recipient of the HPC Advisory Council University Award 2011, and NVidia CUDA Research centre award 2013. He has been leading the \u2018Low-Level Virtualization and Platform-Specific Deployment\u2019 workpackage within the EU-STREP FP7 ParaPhrase project. His research is focused on parallel and distributed computing","Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Marco Aldinucci is an assistant professor at Computer Science Department of the University of Torino, Italy, since 2008. Previously, he has been researcher at University of Pisa and Italian National Research Agency. He is the author of over a hundred articles in international journals and conference proceeding. He has been participating in >20 research projects concerning parallel computing. He is the recipient of the HPC Advisory Council University Award 2011, and NVidia CUDA Research centre award 2013. He has been leading the \u2018Low-Level Virtualization and Platform-Specific Deployment\u2019 workpackage within the EU-STREP FP7 ParaPhrase project. His research is focused on parallel and distributed computing","institution_ids":["https://openalex.org/I4210142764"]},{"raw_affiliation_string":"Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053667707","display_name":"Massimo Torquati","orcid":"https://orcid.org/0000-0001-6323-3459"},"institutions":[{"id":"https://openalex.org/I108290504","display_name":"University of Pisa","ror":"https://ror.org/03ad39j10","country_code":"IT","type":"education","lineage":["https://openalex.org/I108290504"]},{"id":"https://openalex.org/I16718484","display_name":"Hess (United States)","ror":"https://ror.org/00zbk1w77","country_code":"US","type":"company","lineage":["https://openalex.org/I16718484"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"M. Torquati","raw_affiliation_strings":["Massimo Torquati is a researcher at the Computer Science Department of the University of Pisa, Italy. He has >15 years experience in software design; he participated to the design and the implementation of several compilers and frameworks for parallel programming both in academic and industrial settings, inter-alia SkIE, ASSIST, VirtuaLinux and FastFlow. He co-authored >30 articles appeared in proceedings of international conferences and journals. His main research area is language and algorithms for parallel computing","Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","Computer Science Department, University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Massimo Torquati is a researcher at the Computer Science Department of the University of Pisa, Italy. He has >15 years experience in software design; he participated to the design and the implementation of several compilers and frameworks for parallel programming both in academic and industrial settings, inter-alia SkIE, ASSIST, VirtuaLinux and FastFlow. He co-authored >30 articles appeared in proceedings of international conferences and journals. His main research area is language and algorithms for parallel computing","institution_ids":["https://openalex.org/I16718484"]},{"raw_affiliation_string":"Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Computer Science Department, University of Pisa, Largo B. Pontecorvo 3, 56127 Pisa, Italy","institution_ids":["https://openalex.org/I108290504"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075815307","display_name":"Concetto Spampinato","orcid":"https://orcid.org/0000-0001-6653-2577"},"institutions":[{"id":"https://openalex.org/I16718484","display_name":"Hess (United States)","ror":"https://ror.org/00zbk1w77","country_code":"US","type":"company","lineage":["https://openalex.org/I16718484"]},{"id":"https://openalex.org/I39063666","display_name":"University of Catania","ror":"https://ror.org/03a64bh57","country_code":"IT","type":"education","lineage":["https://openalex.org/I39063666"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"C. Spampinato","raw_affiliation_strings":["Concetto Spampinato received the PhD in Computer Engineering from University of Catania, Italy, in 2008 where he is a Research Assistant. He has worked actively on object detection, tracking, behaviour understanding and even detection in complex and noisy environments. He has been working to EU-STREP FP7 Fish4Knowledge project and the AQUACAM research program. He also worked on machine-learning atlas-guided approaches for 2D medical image segmentation and knowledge discovery in biomedicine. He has published >90 articles in international journals and refereed conference proceedings","Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","Department of Electrical, Electronics and Computer Engineering, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Concetto Spampinato received the PhD in Computer Engineering from University of Catania, Italy, in 2008 where he is a Research Assistant. He has worked actively on object detection, tracking, behaviour understanding and even detection in complex and noisy environments. He has been working to EU-STREP FP7 Fish4Knowledge project and the AQUACAM research program. He also worked on machine-learning atlas-guided approaches for 2D medical image segmentation and knowledge discovery in biomedicine. He has published >90 articles in international journals and refereed conference proceedings","institution_ids":["https://openalex.org/I16718484"]},{"raw_affiliation_string":"Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Department of Electrical, Electronics and Computer Engineering, University of Catania, Viale Andrea Doria 6, 95125 Catania, Italy","institution_ids":["https://openalex.org/I39063666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5015548694","display_name":"Maurizio Drocco","orcid":"https://orcid.org/0000-0001-6500-7607"},"institutions":[{"id":"https://openalex.org/I4210158944","display_name":"Heifer International","ror":"https://ror.org/04pmfqr73","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210158944"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"M. Drocco","raw_affiliation_strings":["Maurizio Drocco is a master student and software engineer at the University of Torino, Italy. He has been participating to the FastFlow project and BioBITs project projects. He is the main developer of the CWC simulator. He has co-authored >10 articles in international journals and refereed conference proceedings","Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Maurizio Drocco is a master student and software engineer at the University of Torino, Italy. He has been participating to the FastFlow project and BioBITs project projects. He is the main developer of the CWC simulator. He has co-authored >10 articles in international journals and refereed conference proceedings","institution_ids":["https://openalex.org/I4210158944"]},{"raw_affiliation_string":"Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007904705","display_name":"Claudia Misale","orcid":"https://orcid.org/0000-0003-3737-7373"},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"C. Misale","raw_affiliation_strings":["Claudia Misale received her MSc degree cum laude in Computer Science at University of Calabria in 2012 and is currently a PhD student at Computer Science Department of the University of Torino, Italy. She has been participating to the FastFlow project. Her research is focused on high-performance tools for bioinformatics","Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Claudia Misale received her MSc degree cum laude in Computer Science at University of Calabria in 2012 and is currently a PhD student at Computer Science Department of the University of Torino, Italy. She has been participating to the FastFlow project. Her research is focused on high-performance tools for bioinformatics","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075511258","display_name":"C. Calcagno","orcid":null},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"C. Calcagno","raw_affiliation_strings":["Cristina Calcagno received her MSc degree cum laude in Plant Biology at University of Torino, Italy, in 2007, and the PhD in Science and High Technology\u2013Biology and Biotechnology of fungi at the same university. From February 2011 to July 2012 she has been postdoctoral researcher at the Department of Computer Science within the project BioBITs project. Her main research interests are molecular biology, plant biology, systems biology, nutrigenetic and nutrigenomic","Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","Department of Life Sciences and Systems Biology, University of Torino, Viale P. A. Mattioli 25, 10125 Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Cristina Calcagno received her MSc degree cum laude in Plant Biology at University of Torino, Italy, in 2007, and the PhD in Science and High Technology\u2013Biology and Biotechnology of fungi at the same university. From February 2011 to July 2012 she has been postdoctoral researcher at the Department of Computer Science within the project BioBITs project. Her main research interests are molecular biology, plant biology, systems biology, nutrigenetic and nutrigenomic","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Department of Life Sciences and Systems Biology, University of Torino, Viale P. A. Mattioli 25, 10125 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5018907550","display_name":"Massimiliano Coppo","orcid":"https://orcid.org/0000-0002-1255-6263"},"institutions":[{"id":"https://openalex.org/I4210128445","display_name":"Torino e-district","ror":"https://ror.org/03cxxc369","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210128445"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"M. Coppo","raw_affiliation_strings":["Mario Coppo is a full professor of Computer Science at the Computer Science Department of the University of Torino, Italy, since 1987. He authored >70 articles appearing in journals and international conference proceedings. He has leading several research projects funded by National and European institutions and has been the Director of the Computer Science Department from 2004 to 2010. His main research topics are concurrency theory and programming language semantics","Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Mario Coppo is a full professor of Computer Science at the Computer Science Department of the University of Torino, Italy, since 1987. He authored >70 articles appearing in journals and international conference proceedings. He has leading several research projects funded by National and European institutions and has been the Director of the Computer Science Department from 2004 to 2010. His main research topics are concurrency theory and programming language semantics","institution_ids":["https://openalex.org/I4210128445"]},{"raw_affiliation_string":"Computer Science Department, University of Torino, Corso Svizzera 185, 10149 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":7,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":2.0649,"has_fulltext":false,"cited_by_count":19,"citation_normalized_percentile":{"value":0.87170123,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"15","issue":"5","first_page":"798","last_page":"813"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9979000091552734,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9915000200271606,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.85295569896698},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.7892203330993652},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7856874465942383},{"id":"https://openalex.org/keywords/interactivity","display_name":"Interactivity","score":0.7702937126159668},{"id":"https://openalex.org/keywords/merge","display_name":"Merge (version control)","score":0.637312114238739},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.518964946269989},{"id":"https://openalex.org/keywords/monte-carlo-method","display_name":"Monte Carlo method","score":0.4715172052383423},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.470964252948761},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"Stochastic simulation","score":0.4702813923358917},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.45111799240112305},{"id":"https://openalex.org/keywords/work-flow","display_name":"Work flow","score":0.4454791247844696},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3458464741706848},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3303235173225403},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.26828455924987793},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.19299748539924622},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.17568397521972656},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1563102900981903},{"id":"https://openalex.org/keywords/industrial-engineering","display_name":"Industrial engineering","score":0.12307432293891907}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.85295569896698},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.7892203330993652},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7856874465942383},{"id":"https://openalex.org/C144430266","wikidata":"https://www.wikidata.org/wiki/Q839721","display_name":"Interactivity","level":2,"score":0.7702937126159668},{"id":"https://openalex.org/C197129107","wikidata":"https://www.wikidata.org/wiki/Q1921621","display_name":"Merge (version control)","level":2,"score":0.637312114238739},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.518964946269989},{"id":"https://openalex.org/C19499675","wikidata":"https://www.wikidata.org/wiki/Q232207","display_name":"Monte Carlo method","level":2,"score":0.4715172052383423},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.470964252948761},{"id":"https://openalex.org/C25915931","wikidata":"https://www.wikidata.org/wiki/Q4180825","display_name":"Stochastic simulation","level":2,"score":0.4702813923358917},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.45111799240112305},{"id":"https://openalex.org/C2985179714","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Work flow","level":2,"score":0.4454791247844696},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3458464741706848},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3303235173225403},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.26828455924987793},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.19299748539924622},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.17568397521972656},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1563102900981903},{"id":"https://openalex.org/C13736549","wikidata":"https://www.wikidata.org/wiki/Q4489420","display_name":"Industrial engineering","level":1,"score":0.12307432293891907},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D013269","descriptor_name":"Stochastic Processes","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bib/bbt040","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbt040","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23780997","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23780997","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:arpi.unipi.it:11568/563669","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/563669","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:iris.unito.it:2318/140080","is_oa":true,"landing_page_url":"http://hdl.handle.net/2318/140080","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"pmh:oai:iris.unito.it:2318/140080","is_oa":true,"landing_page_url":"http://hdl.handle.net/2318/140080","pdf_url":null,"source":{"id":"https://openalex.org/S4306400637","display_name":"Institutional Research Information System University of Turin (University of Turin)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I55143463","host_organization_name":"University of Turin","host_organization_lineage":["https://openalex.org/I55143463"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.49000000953674316,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W192852513","https://openalex.org/W1457703051","https://openalex.org/W1535220465","https://openalex.org/W1568192366","https://openalex.org/W1579108863","https://openalex.org/W1588802060","https://openalex.org/W1597755753","https://openalex.org/W1895464354","https://openalex.org/W1964527851","https://openalex.org/W1965513001","https://openalex.org/W1977997149","https://openalex.org/W1983998787","https://openalex.org/W1990073900","https://openalex.org/W1996572185","https://openalex.org/W1997512351","https://openalex.org/W2002713790","https://openalex.org/W2011411346","https://openalex.org/W2013075149","https://openalex.org/W2032309817","https://openalex.org/W2038192316","https://openalex.org/W2039417226","https://openalex.org/W2041529497","https://openalex.org/W2047331390","https://openalex.org/W2061680337","https://openalex.org/W2062507172","https://openalex.org/W2065783627","https://openalex.org/W2085783269","https://openalex.org/W2091831308","https://openalex.org/W2093931624","https://openalex.org/W2099575742","https://openalex.org/W2101462174","https://openalex.org/W2101768141","https://openalex.org/W2108896820","https://openalex.org/W2111931353","https://openalex.org/W2113317262","https://openalex.org/W2121762798","https://openalex.org/W2124436671","https://openalex.org/W2125359798","https://openalex.org/W2130618526","https://openalex.org/W2131229759","https://openalex.org/W2132536544","https://openalex.org/W2134542242","https://openalex.org/W2136626795","https://openalex.org/W2138261199","https://openalex.org/W2147397672","https://openalex.org/W2149414426","https://openalex.org/W2150952308","https://openalex.org/W2155418451","https://openalex.org/W2157334579","https://openalex.org/W2160820250","https://openalex.org/W2162544437","https://openalex.org/W2162932599","https://openalex.org/W2167875025","https://openalex.org/W2173213060","https://openalex.org/W2256063247","https://openalex.org/W2336894004","https://openalex.org/W2978248818","https://openalex.org/W4237609491"],"related_works":["https://openalex.org/W2319020389","https://openalex.org/W2747851897","https://openalex.org/W1975913006","https://openalex.org/W4240086805","https://openalex.org/W1513662110","https://openalex.org/W2063506784","https://openalex.org/W2013411520","https://openalex.org/W2521348551","https://openalex.org/W2162688250","https://openalex.org/W3004636680"],"abstract_inverted_index":{"The":[0,20],"stochastic":[1],"modelling":[2],"of":[3,11,61,135,146],"biological":[4],"systems,":[5],"coupled":[6],"with":[7],"Monte":[8],"Carlo":[9],"simulation":[10,102,140],"models,":[12,100],"is":[13,70,78,90,141],"an":[14],"increasingly":[15],"popular":[16],"technique":[17],"in":[18,31,108,113,123],"bioinformatics.":[19],"simulation-analysis":[21],"workflow":[22,95,112,129],"may":[23],"result":[24],"computationally":[25],"expensive":[26],"reducing":[27],"the":[28,32,40,55,59,74,84,87,114,128,147,153],"interactivity":[29],"required":[30],"model":[33],"tuning.":[34],"In":[35,57],"this":[36],"work,":[37],"we":[38],"advocate":[39],"high-level":[41,94],"software":[42],"design":[43],"as":[44,92],"a":[45,93,109,125,133],"vehicle":[46],"for":[47,54,66],"building":[48],"efficient":[49],"and":[50,80,104,144],"portable":[51],"parallel":[52,111],"simulators":[53],"cloud.":[56,115],"particular,":[58],"Calculus":[60],"Wrapped":[62],"Components":[63],"(CWC)":[64],"simulator":[65,89,149],"systems":[67],"biology,":[68],"which":[69],"designed":[71,91],"according":[72],"to":[73,83,131],"FastFlow":[75,85],"pattern-based":[76],"approach,":[77],"presented":[79],"discussed.":[81],"Thanks":[82],"framework,":[86],"CWC":[88,99,148],"that":[96,127],"can":[97],"simulate":[98],"merge":[101],"results":[103,137],"statistically":[105],"analyse":[106],"them":[107],"single":[110],"To":[116],"improve":[117],"interactivity,":[118],"successive":[119],"phases":[120],"are":[121,150],"pipelined":[122],"such":[124],"way":[126],"begins":[130],"output":[132],"stream":[134],"analysis":[136],"immediately":[138],"after":[139],"started.":[142],"Performance":[143],"effectiveness":[145],"validated":[151],"on":[152],"Amazon":[154],"Elastic":[155],"Compute":[156],"Cloud.":[157]},"counts_by_year":[{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":3}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}
