{"id":"https://openalex.org/W2119751370","doi":"https://doi.org/10.1093/bioinformatics/btv393","title":"<i>al3c</i>: high-performance software for parameter inference using Approximate Bayesian Computation","display_name":"<i>al3c</i>: high-performance software for parameter inference using Approximate Bayesian Computation","publication_year":2015,"publication_date":"2015-07-02","ids":{"openalex":"https://openalex.org/W2119751370","doi":"https://doi.org/10.1093/bioinformatics/btv393","mag":"2119751370","pmid":"https://pubmed.ncbi.nlm.nih.gov/26142186"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btv393","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv393","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3549/49035634/bioinformatics_31_21_3549.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3549/49035634/bioinformatics_31_21_3549.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5045605998","display_name":"Alexander Stram","orcid":"https://orcid.org/0000-0002-8278-6507"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Alexander H. Stram","raw_affiliation_strings":["1 Cancer Center - Research, USC, Los Angeles, CA 90089, USA and"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Cancer Center - Research, USC, Los Angeles, CA 90089, USA and","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079125457","display_name":"Paul Marjoram","orcid":"https://orcid.org/0000-0003-0824-7449"},"institutions":[{"id":"https://openalex.org/I1342924430","display_name":"LAC+USC Medical Center","ror":"https://ror.org/04xzj3x20","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328359107","https://openalex.org/I1342924430"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Paul Marjoram","raw_affiliation_strings":["2 Division of Biostatistics, Department of Preventive Medicine, USC, Los Angeles, CA 90033, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Division of Biostatistics, Department of Preventive Medicine, USC, Los Angeles, CA 90033, USA","institution_ids":["https://openalex.org/I1342924430"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5089243860","display_name":"Gary K. Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I1342924430","display_name":"LAC+USC Medical Center","ror":"https://ror.org/04xzj3x20","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1328359107","https://openalex.org/I1342924430"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Gary K. Chen","raw_affiliation_strings":["2 Division of Biostatistics, Department of Preventive Medicine, USC, Los Angeles, CA 90033, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"2 Division of Biostatistics, Department of Preventive Medicine, USC, Los Angeles, CA 90033, USA","institution_ids":["https://openalex.org/I1342924430"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5045605998"],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.0597,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.79940164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"31","issue":"21","first_page":"3549","last_page":"3551"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12056","display_name":"Markov Chains and Monte Carlo Methods","score":0.9890000224113464,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T12056","display_name":"Markov Chains and Monte Carlo Methods","score":0.9890000224113464,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10711","display_name":"Target Tracking and Data Fusion in Sensor Networks","score":0.0010000000474974513,"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"}},{"id":"https://openalex.org/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.0007999999797903001,"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":0.8447986841201782},{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.5918939113616943},{"id":"https://openalex.org/keywords/approximate-bayesian-computation","display_name":"Approximate Bayesian computation","score":0.5497430562973022},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4624142646789551},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.4347216486930847},{"id":"https://openalex.org/keywords/overhead","display_name":"Overhead (engineering)","score":0.4293966591358185},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.4168766438961029},{"id":"https://openalex.org/keywords/bayesian-inference","display_name":"Bayesian inference","score":0.4114660322666168},{"id":"https://openalex.org/keywords/bayesian-probability","display_name":"Bayesian probability","score":0.3980247974395752},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3888165354728699},{"id":"https://openalex.org/keywords/parallel-computing","display_name":"Parallel computing","score":0.3683710992336273},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34028691053390503},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3272734582424164},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1721072793006897},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.16522550582885742},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.16299447417259216}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8447986841201782},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.5918939113616943},{"id":"https://openalex.org/C2779377595","wikidata":"https://www.wikidata.org/wiki/Q21045424","display_name":"Approximate Bayesian computation","level":3,"score":0.5497430562973022},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4624142646789551},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.4347216486930847},{"id":"https://openalex.org/C2779960059","wikidata":"https://www.wikidata.org/wiki/Q7113681","display_name":"Overhead (engineering)","level":2,"score":0.4293966591358185},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.4168766438961029},{"id":"https://openalex.org/C160234255","wikidata":"https://www.wikidata.org/wiki/Q812535","display_name":"Bayesian inference","level":3,"score":0.4114660322666168},{"id":"https://openalex.org/C107673813","wikidata":"https://www.wikidata.org/wiki/Q812534","display_name":"Bayesian probability","level":2,"score":0.3980247974395752},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3888165354728699},{"id":"https://openalex.org/C173608175","wikidata":"https://www.wikidata.org/wiki/Q232661","display_name":"Parallel computing","level":1,"score":0.3683710992336273},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34028691053390503},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3272734582424164},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1721072793006897},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.16522550582885742},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.16299447417259216}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001499","descriptor_name":"Bayes Theorem","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009010","descriptor_name":"Monte Carlo Method","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btv393","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv393","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3549/49035634/bioinformatics_31_21_3549.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:26142186","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/26142186","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:4033820","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4626746","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:open-archive.highwire.org:bioinfo:31/21/3549","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/21/3549","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btv393","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btv393","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/21/3549/49035634/bioinformatics_31_21_3549.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2528367832","display_name":null,"funder_award_id":"U01 GM103804","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G2992560931","display_name":null,"funder_award_id":"R01 MH100879","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G4704487691","display_name":null,"funder_award_id":"MH100879","funder_id":"https://openalex.org/F4320337346","funder_display_name":"National Institute of Mental Health"},{"id":"https://openalex.org/G5491323521","display_name":null,"funder_award_id":"U01 GM10380","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320337346","display_name":"National Institute of Mental Health","ror":"https://ror.org/04xeg9z08"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":13,"referenced_works":["https://openalex.org/W1964547306","https://openalex.org/W2020684750","https://openalex.org/W2031134376","https://openalex.org/W2077033024","https://openalex.org/W2096791516","https://openalex.org/W2146803704","https://openalex.org/W2151729750","https://openalex.org/W2152246075","https://openalex.org/W2165141658","https://openalex.org/W2165974744","https://openalex.org/W2167030304","https://openalex.org/W2324359847","https://openalex.org/W4214499534"],"related_works":["https://openalex.org/W2226294016","https://openalex.org/W4297145487","https://openalex.org/W3012988968","https://openalex.org/W4287824571","https://openalex.org/W2971727066","https://openalex.org/W3113268434","https://openalex.org/W4362583294","https://openalex.org/W2966726156","https://openalex.org/W4242918646","https://openalex.org/W4289242714"],"abstract_inverted_index":{"MOTIVATION:":[0],"The":[1,190],"development":[2,51],"of":[3,27,36,52,66,136,142],"Approximate":[4],"Bayesian":[5,83],"Computation":[6],"(ABC)":[7],"algorithms":[8,53],"for":[9,106,164,184,201],"parameter":[10],"inference":[11,84],"which":[12,205],"are":[13,71,206,241],"both":[14,133],"computationally":[15],"efficient":[16],"and":[17,124,139,186,197,225],"scalable":[18],"in":[19,95,109,160,229],"parallel":[20,96,137,161],"computing":[21,97,162,188],"environments":[22,163],"is":[23,39,47,153,178],"an":[24,193],"important":[25],"area":[26],"research.":[28],"Monte":[29,58],"Carlo":[30,59],"rejection":[31,67],"sampling,":[32,68],"a":[33,80,103,181],"fundamental":[34],"component":[35],"ABC":[37,56],"algorithms,":[38],"trivial":[40],"to":[41,93,155,210],"distribute":[42],"over":[43],"multiple":[44,77],"processors":[45],"but":[46],"inherently":[48],"inefficient.":[49],"While":[50],"such":[54,69,119],"as":[55,73,120,180],"Sequential":[57],"(ABC-SMC)":[60],"help":[61],"address":[62],"the":[63,91,121,130,134,140,143,148,151,157,202,212,218],"inherent":[64],"inefficiencies":[65],"approaches":[70],"not":[72],"easily":[74],"scaled":[75],"on":[76],"processors.":[78],"As":[79],"result,":[81],"current":[82],"software":[85],"offerings":[86],"that":[87,114],"use":[88],"ABC-SMC":[89,108,144,158],"lack":[90],"ability":[92],"scale":[94,156],"environments.":[98,189],"RESULTS:":[99],"We":[100],"present":[101],"al3c,":[102],"C++":[104,198],"framework":[105],"implementing":[107],"parallel.":[110],"By":[111,146],"requiring":[112],"only":[113],"users":[115],"define":[116],"essential":[117],"functions":[118],"simulation":[122],"model":[123],"prior":[125],"distribution":[126],"function,":[127],"al3c":[128,149,177,209],"abstracts":[129],"user":[131,152,191],"from":[132],"complexities":[135],"programming":[138,172],"details":[141],"algorithm.":[145],"using":[147],"framework,":[150],"able":[154],"algorithm":[159],"his":[165],"or":[166],"her":[167],"specific":[168,203],"application,":[169,204],"with":[170],"minimal":[171],"overhead.":[173],"AVAILABILITY":[174],"AND":[175],"IMPLEMENTATION:":[176],"offered":[179],"static":[182,219],"binary":[183],"Linux":[185],"OS-X":[187],"completes":[192],"XML":[194],"configuration":[195],"file":[196],"plug-in":[199],"template":[200],"used":[207],"by":[208,232],"obtain":[211],"desired":[213],"results.":[214],"Users":[215],"can":[216],"download":[217],"binaries,":[220],"source":[221],"code,":[222],"reference":[223],"documentation":[224],"examples":[226],"(including":[227],"those":[228],"this":[230],"article)":[231],"visiting":[233],"https://github.com/ahstram/al3c.":[234],"CONTACT:":[235],"astram@usc.edu":[236],"SUPPLEMENTARY":[237],"INFORMATION:":[238],"Supplementary":[239],"data":[240],"available":[242],"at":[243],"Bioinformatics":[244],"online.":[245]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2}],"updated_date":"2026-06-23T06:36:01.041984","created_date":"2016-06-24T00:00:00"}