{"id":"https://openalex.org/W2045182523","doi":"https://doi.org/10.1177/109434200101500304","title":"Distributing MCell Simulations on the Grid","display_name":"Distributing MCell Simulations on the Grid","publication_year":2001,"publication_date":"2001-08-01","ids":{"openalex":"https://openalex.org/W2045182523","doi":"https://doi.org/10.1177/109434200101500304","mag":"2045182523"},"language":"en","primary_location":{"id":"doi:10.1177/109434200101500304","is_oa":false,"landing_page_url":"https://doi.org/10.1177/109434200101500304","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/A5022674890","display_name":"Henri Casanova","orcid":"https://orcid.org/0000-0001-6310-0365"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Henri Casanova","raw_affiliation_strings":["CSE Department, University of California, San Diego"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CSE Department, University of California, San Diego","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027860030","display_name":"Thomas M. Bartol","orcid":"https://orcid.org/0009-0002-2598-0052"},"institutions":[{"id":"https://openalex.org/I1307098950","display_name":"Salk Institute for Biological Studies","ror":"https://ror.org/03xez1567","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I1307098950"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Thomas M. Bartol","raw_affiliation_strings":["Computational Neurobiology Laboratory, Salk Institute","Computational Neurobiology Laboratory, Salk Institute#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational Neurobiology Laboratory, Salk Institute","institution_ids":["https://openalex.org/I1307098950"]},{"raw_affiliation_string":"Computational Neurobiology Laboratory, Salk Institute#TAB#","institution_ids":["https://openalex.org/I1307098950"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007448715","display_name":"Joel R. Stiles","orcid":null},"institutions":[{"id":"https://openalex.org/I35765314","display_name":"Pittsburgh Supercomputing Center","ror":"https://ror.org/04tac1482","country_code":"US","type":"facility","lineage":["https://openalex.org/I35765314"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Joel Stiles","raw_affiliation_strings":["Biomedical Applications Group, Pittsburgh Supercomputing Center"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Biomedical Applications Group, Pittsburgh Supercomputing Center","institution_ids":["https://openalex.org/I35765314"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5046731611","display_name":"Francine Berman","orcid":"https://orcid.org/0000-0001-8505-1752"},"institutions":[{"id":"https://openalex.org/I181653535","display_name":"San Diego Supercomputer Center","ror":"https://ror.org/04mg3nk07","country_code":"US","type":"facility","lineage":["https://openalex.org/I181653535","https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Francine Berman","raw_affiliation_strings":["San Diego Supercomputer Center","SAN DIEGO SUPERCOMPUTER CENTER#TAB#"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"San Diego Supercomputer Center","institution_ids":["https://openalex.org/I181653535"]},{"raw_affiliation_string":"SAN DIEGO SUPERCOMPUTER CENTER#TAB#","institution_ids":["https://openalex.org/I181653535"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":3.6853,"has_fulltext":false,"cited_by_count":39,"citation_normalized_percentile":{"value":0.94023784,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"15","issue":"3","first_page":"243","last_page":"257"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9998999834060669,"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"}},"topics":[{"id":"https://openalex.org/T10715","display_name":"Distributed and Parallel Computing Systems","score":0.9998999834060669,"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/T10054","display_name":"Parallel Computing and Optimization Techniques","score":0.9976000189781189,"subfield":{"id":"https://openalex.org/subfields/1708","display_name":"Hardware and Architecture"},"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/T11181","display_name":"Advanced Data Storage Technologies","score":0.991100013256073,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.8185570240020752},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8122501373291016},{"id":"https://openalex.org/keywords/software-deployment","display_name":"Software deployment","score":0.7809805870056152},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.7405679225921631},{"id":"https://openalex.org/keywords/grid-computing","display_name":"Grid computing","score":0.7350493669509888},{"id":"https://openalex.org/keywords/middleware","display_name":"Middleware (distributed applications)","score":0.6418188214302063},{"id":"https://openalex.org/keywords/data-grid","display_name":"Data grid","score":0.5906639099121094},{"id":"https://openalex.org/keywords/semantic-grid","display_name":"Semantic grid","score":0.5259109735488892},{"id":"https://openalex.org/keywords/scheduling","display_name":"Scheduling (production processes)","score":0.4649113118648529},{"id":"https://openalex.org/keywords/drmaa","display_name":"DRMAA","score":0.4629894495010376},{"id":"https://openalex.org/keywords/domain","display_name":"Domain (mathematical analysis)","score":0.4299444556236267},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42322802543640137},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.4144400656223297},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.2855991721153259},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.18208399415016174},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10727551579475403},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09536194801330566}],"concepts":[{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.8185570240020752},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8122501373291016},{"id":"https://openalex.org/C105339364","wikidata":"https://www.wikidata.org/wiki/Q2297740","display_name":"Software deployment","level":2,"score":0.7809805870056152},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.7405679225921631},{"id":"https://openalex.org/C70429105","wikidata":"https://www.wikidata.org/wiki/Q249999","display_name":"Grid computing","level":3,"score":0.7350493669509888},{"id":"https://openalex.org/C169468491","wikidata":"https://www.wikidata.org/wiki/Q146923","display_name":"Middleware (distributed applications)","level":2,"score":0.6418188214302063},{"id":"https://openalex.org/C147639290","wikidata":"https://www.wikidata.org/wiki/Q56369138","display_name":"Data grid","level":4,"score":0.5906639099121094},{"id":"https://openalex.org/C103692084","wikidata":"https://www.wikidata.org/wiki/Q1765824","display_name":"Semantic grid","level":3,"score":0.5259109735488892},{"id":"https://openalex.org/C206729178","wikidata":"https://www.wikidata.org/wiki/Q2271896","display_name":"Scheduling (production processes)","level":2,"score":0.4649113118648529},{"id":"https://openalex.org/C192045728","wikidata":"https://www.wikidata.org/wiki/Q5206066","display_name":"DRMAA","level":4,"score":0.4629894495010376},{"id":"https://openalex.org/C36503486","wikidata":"https://www.wikidata.org/wiki/Q11235244","display_name":"Domain (mathematical analysis)","level":2,"score":0.4299444556236267},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42322802543640137},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.4144400656223297},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.2855991721153259},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.18208399415016174},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10727551579475403},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09536194801330566},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C21547014","wikidata":"https://www.wikidata.org/wiki/Q1423657","display_name":"Operations management","level":1,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C2129575","wikidata":"https://www.wikidata.org/wiki/Q54837","display_name":"Semantic Web","level":2,"score":0.0},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1177/109434200101500304","is_oa":false,"landing_page_url":"https://doi.org/10.1177/109434200101500304","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:CiteSeerX.psu:10.1.1.294.9810","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.294.9810","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://papers.cnl.salk.edu/PDFs/Distributing MCell Simulations on the Grid 2001-3099.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.6299999952316284,"display_name":"Industry, innovation and infrastructure","id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":52,"referenced_works":["https://openalex.org/W69137203","https://openalex.org/W74322794","https://openalex.org/W74971858","https://openalex.org/W656531464","https://openalex.org/W1489252188","https://openalex.org/W1492040731","https://openalex.org/W1514217898","https://openalex.org/W1523826187","https://openalex.org/W1524149055","https://openalex.org/W1550091196","https://openalex.org/W1587962669","https://openalex.org/W1606342533","https://openalex.org/W1819660368","https://openalex.org/W1867704852","https://openalex.org/W1898830902","https://openalex.org/W1903036498","https://openalex.org/W1923643168","https://openalex.org/W1956351353","https://openalex.org/W1968526517","https://openalex.org/W1969524198","https://openalex.org/W1977153665","https://openalex.org/W2006312525","https://openalex.org/W2006523031","https://openalex.org/W2018867131","https://openalex.org/W2019693854","https://openalex.org/W2024048296","https://openalex.org/W2025828073","https://openalex.org/W2032930624","https://openalex.org/W2059312642","https://openalex.org/W2071075503","https://openalex.org/W2083956862","https://openalex.org/W2091257550","https://openalex.org/W2094186309","https://openalex.org/W2095629498","https://openalex.org/W2097025565","https://openalex.org/W2097863660","https://openalex.org/W2103440606","https://openalex.org/W2117540160","https://openalex.org/W2126831426","https://openalex.org/W2139126523","https://openalex.org/W2146438496","https://openalex.org/W2150075021","https://openalex.org/W2160348166","https://openalex.org/W2164230281","https://openalex.org/W2187867568","https://openalex.org/W2328255009","https://openalex.org/W2396699058","https://openalex.org/W2439240014","https://openalex.org/W2911607583","https://openalex.org/W3002421340","https://openalex.org/W4235381807","https://openalex.org/W4235762208"],"related_works":["https://openalex.org/W2145548705","https://openalex.org/W1541285588","https://openalex.org/W2181389252","https://openalex.org/W1580346733","https://openalex.org/W1590587551","https://openalex.org/W2049234965","https://openalex.org/W2115183957","https://openalex.org/W2021543546","https://openalex.org/W836263687","https://openalex.org/W1544823718"],"abstract_inverted_index":{"The":[0,194],"computational":[1],"Grid":[2,56,84,175,192],"is":[3,38,68,98],"a":[4,41,133,157,198],"promising":[5],"platform":[6],"for":[7,73,203],"the":[8,55,74,78,83,87,90,93,112,115,130,143,148,163,174],"deployment":[9,67],"of":[10,24,33,36,44,82,89,136],"large-scale":[11],"scientific":[12],"and":[13,26,28,58,80,92,114,125,165,176,185,218],"engineering":[14,27],"applications.":[15],"Parameter":[16,205],"sweep":[17],"applications":[18],"(PSAs)":[19],"arise":[20],"in":[21,222],"many":[22],"fields":[23],"science":[25,183],"are":[29,50],"structured":[30],"as":[31,107],"sets":[32],"\u201cexperiments,\u201d":[34],"each":[35],"which":[37],"executed":[39],"with":[40,132],"distinct":[42],"set":[43],"parameters.":[45],"Given":[46],"that":[47,105,223],"structure,":[48,167],"PSAs":[49],"particularly":[51],"well":[52],"suited":[53],"to":[54,71,101,128,156,213],"infrastructure":[57],"can":[59,210],"be":[60,211],"deployed":[61],"on":[62,142,151,173],"very":[63],"large":[64],"scales.":[65],"However,":[66],"not":[69],"easy":[70],"achieve":[72],"domain":[75],"scientist":[76],"given":[77,189],"complexity":[79],"multiplicity":[81],"software":[85],"infrastructure,":[86],"heterogeneity":[88],"resources,":[91],"dynamic":[94],"resource":[95],"availabilities.":[96],"It":[97],"therefore":[99],"necessary":[100],"provide":[102,129],"user-level":[103,200],"middleware":[104,118,153,201],"acts":[106],"an":[108],"intermediate":[109],"layer":[110],"between":[111],"application":[113,164],"Grid.":[116,144],"That":[117],"must":[119],"address":[120],"all":[121],"deployment,":[122],"data":[123],"movements,":[124],"scheduling":[126],"issues":[127],"user":[131,178],"transparent":[134],"way":[135],"running":[137],"his":[138],"or":[139],"her":[140],"simulation":[141],"In":[145],"this":[146],"paper,":[147],"authors":[149,195],"focus":[150],"such":[152],"specifically":[154],"targeted":[155],"biology":[158],"application:":[159],"MCell.":[160],"After":[161],"describing":[162],"its":[166],"they":[168],"describe":[169,197],"desired":[170],"usage":[171],"scenarios":[172],"identify":[177],"requirements,":[179,217],"discuss":[180],"relevant":[181],"computer":[182],"issues,":[184],"propose":[186],"suitable":[187],"solutions":[188],"currently":[190],"available":[191],"technologies.":[193],"then":[196],"general-purpose":[199],"project":[202],"PSAs\u2014AppLes":[204],"Sweep":[206],"Template\u2014explain":[207],"how":[208],"it":[209],"extended":[212],"accommodate":[214],"MCell\u2019s":[215],"specific":[216],"introduce":[219],"current":[220],"work":[221],"direction.":[224]},"counts_by_year":[{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3},{"year":2012,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
