{"id":"https://openalex.org/W2341934880","doi":"https://doi.org/10.1177/1094342015588565","title":"Porting bioinformatics applications from grid to cloud: A macromolecular surface analysis application case study","display_name":"Porting bioinformatics applications from grid to cloud: A macromolecular surface analysis application case study","publication_year":2015,"publication_date":"2015-06-02","ids":{"openalex":"https://openalex.org/W2341934880","doi":"https://doi.org/10.1177/1094342015588565","mag":"2341934880"},"language":"en","primary_location":{"id":"doi:10.1177/1094342015588565","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342015588565","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5026770450","display_name":"Ivan Merelli","orcid":"https://orcid.org/0000-0003-3587-3680"},"institutions":[{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Ivan Merelli","raw_affiliation_strings":["Institute of Biomedical Technologies, National Research Council of Italy, Segrate, Italy"],"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Technologies, National Research Council of Italy, Segrate, Italy","institution_ids":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5067286039","display_name":"Paolo Cozzi","orcid":"https://orcid.org/0000-0003-0388-6874"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Cozzi","raw_affiliation_strings":["Institute of Biomedical Technologies, National Research Council of Italy, Segrate, Italy"],"affiliations":[{"raw_affiliation_string":"Institute of Biomedical Technologies, National Research Council of Italy, Segrate, Italy","institution_ids":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078928700","display_name":"Elisabetta Ronchieri","orcid":"https://orcid.org/0000-0002-7341-6491"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Elisabetta Ronchieri","raw_affiliation_strings":["National Centre for Research and Development into the field of Information Technologies, National Institute of Nuclear Physics, Bologna, Italy"],"affiliations":[{"raw_affiliation_string":"National Centre for Research and Development into the field of Information Technologies, National Institute of Nuclear Physics, Bologna, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072687950","display_name":"Daniele Cesini","orcid":"https://orcid.org/0000-0002-1828-1715"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Daniele Cesini","raw_affiliation_strings":["National Centre for Research and Development into the field of Information Technologies, National Institute of Nuclear Physics, Bologna, Italy"],"affiliations":[{"raw_affiliation_string":"National Centre for Research and Development into the field of Information Technologies, National Institute of Nuclear Physics, Bologna, Italy","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002026919","display_name":"Daniele D\u2019Agostino","orcid":"https://orcid.org/0000-0003-2649-0071"},"institutions":[{"id":"https://openalex.org/I4210155236","display_name":"National Research Council","ror":"https://ror.org/04zaypm56","country_code":"IT","type":"funder","lineage":["https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniele D\u2019Agostino","raw_affiliation_strings":["Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy"],"affiliations":[{"raw_affiliation_string":"Institute for Applied Mathematics and Information Technologies, National Research Council of Italy, Genoa, Italy","institution_ids":["https://openalex.org/I4210155236"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5026770450"],"corresponding_institution_ids":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"],"apc_list":null,"apc_paid":null,"fwci":1.6059,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.90487468,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"31","issue":"3","first_page":"182","last_page":"195"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},"topics":[{"id":"https://openalex.org/T11986","display_name":"Scientific Computing and Data Management","score":0.9951000213623047,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9897000193595886,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11269","display_name":"Algorithms and Data Compression","score":0.9466000199317932,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.756066083908081},{"id":"https://openalex.org/keywords/cloud-computing","display_name":"Cloud computing","score":0.7430769801139832},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.7298348546028137},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7210946083068848},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.6585395336151123},{"id":"https://openalex.org/keywords/grid-computing","display_name":"Grid computing","score":0.5799369215965271},{"id":"https://openalex.org/keywords/installation","display_name":"Installation","score":0.5543569326400757},{"id":"https://openalex.org/keywords/porting","display_name":"Porting","score":0.5319462418556213},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.5097998976707458},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.4212588369846344},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3284042775630951},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.2254250943660736},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.18093350529670715},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.1696476936340332}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.756066083908081},{"id":"https://openalex.org/C79974875","wikidata":"https://www.wikidata.org/wiki/Q483639","display_name":"Cloud computing","level":2,"score":0.7430769801139832},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.7298348546028137},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7210946083068848},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.6585395336151123},{"id":"https://openalex.org/C70429105","wikidata":"https://www.wikidata.org/wiki/Q249999","display_name":"Grid computing","level":3,"score":0.5799369215965271},{"id":"https://openalex.org/C146778888","wikidata":"https://www.wikidata.org/wiki/Q836862","display_name":"Installation","level":2,"score":0.5543569326400757},{"id":"https://openalex.org/C106251023","wikidata":"https://www.wikidata.org/wiki/Q851989","display_name":"Porting","level":3,"score":0.5319462418556213},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.5097998976707458},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.4212588369846344},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3284042775630951},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.2254250943660736},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.18093350529670715},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.1696476936340332},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1177/1094342015588565","is_oa":false,"landing_page_url":"https://doi.org/10.1177/1094342015588565","pdf_url":null,"source":{"id":"https://openalex.org/S60606485","display_name":"The International Journal of High Performance Computing Applications","issn_l":"1094-3420","issn":["1094-3420","1741-2846"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320017","host_organization_name":"SAGE Publishing","host_organization_lineage":["https://openalex.org/P4310320017"],"host_organization_lineage_names":["SAGE Publishing"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"The International Journal of High Performance Computing Applications","raw_type":"journal-article"},{"id":"pmh:oai:iris.unige.it:11567/1087335","is_oa":false,"landing_page_url":"https://hdl.handle.net/11567/1087335","pdf_url":null,"source":{"id":"https://openalex.org/S4377196291","display_name":"CINECA IRIS Institutial Research Information System (University of Genoa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I83816512","host_organization_name":"University of Genoa","host_organization_lineage":["https://openalex.org/I83816512"],"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"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6399999856948853,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W22745672","https://openalex.org/W164093228","https://openalex.org/W1505416946","https://openalex.org/W1530454533","https://openalex.org/W1589437951","https://openalex.org/W1596574250","https://openalex.org/W1602734977","https://openalex.org/W1827582277","https://openalex.org/W1921273830","https://openalex.org/W1934507398","https://openalex.org/W1968049950","https://openalex.org/W1968162858","https://openalex.org/W1980512811","https://openalex.org/W1991462891","https://openalex.org/W1993657374","https://openalex.org/W1996773532","https://openalex.org/W2003260632","https://openalex.org/W2013647284","https://openalex.org/W2018563675","https://openalex.org/W2050831357","https://openalex.org/W2071867759","https://openalex.org/W2075686162","https://openalex.org/W2084842674","https://openalex.org/W2088535827","https://openalex.org/W2094885948","https://openalex.org/W2097023032","https://openalex.org/W2099606917","https://openalex.org/W2100318434","https://openalex.org/W2105438341","https://openalex.org/W2105664606","https://openalex.org/W2107178875","https://openalex.org/W2108304242","https://openalex.org/W2113078179","https://openalex.org/W2113585410","https://openalex.org/W2123564600","https://openalex.org/W2124912619","https://openalex.org/W2139924275","https://openalex.org/W2148672014","https://openalex.org/W2150559991","https://openalex.org/W2154332114","https://openalex.org/W2155130419","https://openalex.org/W2156474553","https://openalex.org/W2162149523","https://openalex.org/W2276101994","https://openalex.org/W2500529989","https://openalex.org/W2800394774","https://openalex.org/W2994897625","https://openalex.org/W3092820992","https://openalex.org/W3197667449","https://openalex.org/W4248613739","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2356602486","https://openalex.org/W2351992668","https://openalex.org/W2324828474","https://openalex.org/W2374315191","https://openalex.org/W2391207559","https://openalex.org/W2384715785","https://openalex.org/W2349624418","https://openalex.org/W2064459023","https://openalex.org/W2384611437","https://openalex.org/W2347873412"],"abstract_inverted_index":{"In":[0],"this":[1],"paper":[2],"we":[3,232],"describe":[4],"our":[5],"experience":[6],"in":[7,34,236],"exploiting":[8],"different":[9],"cloud-based":[10,196,210],"environments":[11],"for":[12,96,126,182],"an":[13,135],"actual":[14],"use":[15,98,229],"case":[16,230],"taken":[17],"from":[18,67],"the":[19,23,35,59,79,139,151,155,170,174,188,214,225,234,245],"bioinformatics":[20],"domain":[21],"\u2013":[22],"molecular":[24,226],"surfaces":[25,42,61,227],"analysis":[26,39,62,184,228],"-":[27],"that":[28,57,81],"identifies":[29],"similarities":[30],"and":[31,63,100,145,157,177,220,231,241],"possible":[32],"complementarities":[33],"protein":[36,46],"surfaces.":[37],"The":[38],"of":[40,71,138,154,238],"macromolecular":[41,60],"is":[43,76,83,104,198],"important":[44,74],"since":[45],"surface":[47],"conformations":[48],"drive":[49],"many":[50],"biological":[51],"reactions.":[52],"We":[53,206],"developed":[54],"a":[55,68,92,101,112,195,202],"workflow":[56],"performs":[58],"provides":[64],"interesting":[65],"results":[66,235],"scientific":[69],"point":[70],"view.":[72],"An":[73],"issue":[75],"represented":[77,117],"by":[78,166],"fact":[80],"it":[82,87],"highly":[84],"compute-intensive,":[85],"therefore":[86,178],"cannot":[88],"be":[89],"run":[90,224],"on":[91,162,213,221],"single":[93],"CPU":[94],"system":[95],"meaningful":[97],"cases":[99],"parallel":[102],"infrastructure":[103],"required":[105],"to":[106,120,150,187,223,243,250],"obtain":[107],"reasonable":[108],"execution":[109],"time.":[110],"For":[111,192],"decade":[113],"grid":[114,190,204,251],"infrastructures":[115],"have":[116],"suitable":[118,200],"solutions":[119,131],"achieve":[121],"cost":[122],"effective":[123],"computational":[124,140,158],"power":[125],"Bioinformatics":[127],"applications.":[128],"However,":[129],"these":[130,193],"do":[132],"not":[133],"offer":[134],"adequate":[136],"customisation":[137],"environment":[141],"(e.g.":[142],"installing":[143],"databases":[144],"configuring":[146],"virtual":[147],"network)":[148],"due":[149],"rigid":[152],"organisation":[153],"storage":[156],"sites.":[159],"Running":[160],"applications":[161],"customised":[163],"machines":[164],"obtained":[165],"user-defined":[167],"images":[168],"simplifies":[169],"computing":[171,246],"model,":[172],"decreases":[173],"failure":[175],"rates":[176],"reduces":[179],"waiting":[180],"times":[181],"production":[183],"with":[185,248],"respect":[186,249],"canonical":[189],"computations.":[191],"reasons":[194],"approach":[197],"more":[199],"than":[201],"pure":[203],"paradigm.":[205],"experimented":[207],"using":[208],"two":[209],"approaches,":[211],"based":[212],"Worker":[215],"Node":[216],"On":[217],"Demand":[218],"Service":[219],"OpenStack,":[222],"compared":[233],"terms":[237],"performance,":[239],"efficiency":[240],"efforts":[242],"build":[244],"model":[247],"computing.":[252]},"counts_by_year":[{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2016-06-24T00:00:00"}
