{"id":"https://openalex.org/W2952649401","doi":"https://doi.org/10.1145/3107411.3107471","title":"TRuML","display_name":"TRuML","publication_year":2017,"publication_date":"2017-08-20","ids":{"openalex":"https://openalex.org/W2952649401","doi":"https://doi.org/10.1145/3107411.3107471","mag":"2952649401"},"language":"en","primary_location":{"id":"doi:10.1145/3107411.3107471","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107471","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.osti.gov/servlets/purl/1392820","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5057558587","display_name":"Ryan Suderman","orcid":"https://orcid.org/0000-0001-5604-1387"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ryan Suderman","raw_affiliation_strings":["Los Alamos National Laboratory, Los Alamos, NM, USA"],"affiliations":[{"raw_affiliation_string":"Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016126519","display_name":"William S. Hlavacek","orcid":"https://orcid.org/0000-0003-4383-8711"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William S. Hlavacek","raw_affiliation_strings":["Los Alamos National Laboratory, Los Alamos, NM, USA"],"affiliations":[{"raw_affiliation_string":"Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5057558587"],"corresponding_institution_ids":["https://openalex.org/I1343871089"],"apc_list":null,"apc_paid":null,"fwci":0.5595,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.67649163,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":null,"issue":null,"first_page":"372","last_page":"377"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9959999918937683,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.9843000173568726,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8194677829742432},{"id":"https://openalex.org/keywords/modeling-language","display_name":"Modeling language","score":0.6032413244247437},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5877529382705688},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.5457467436790466},{"id":"https://openalex.org/keywords/automation","display_name":"Automation","score":0.4801042377948761},{"id":"https://openalex.org/keywords/key","display_name":"Key (lock)","score":0.437299907207489},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.4189775586128235},{"id":"https://openalex.org/keywords/domain-specific-language","display_name":"Domain-specific language","score":0.41875240206718445},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.37662649154663086},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3703081011772156},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3253953456878662}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8194677829742432},{"id":"https://openalex.org/C179603123","wikidata":"https://www.wikidata.org/wiki/Q1941921","display_name":"Modeling language","level":3,"score":0.6032413244247437},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5877529382705688},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.5457467436790466},{"id":"https://openalex.org/C115901376","wikidata":"https://www.wikidata.org/wiki/Q184199","display_name":"Automation","level":2,"score":0.4801042377948761},{"id":"https://openalex.org/C26517878","wikidata":"https://www.wikidata.org/wiki/Q228039","display_name":"Key (lock)","level":2,"score":0.437299907207489},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.4189775586128235},{"id":"https://openalex.org/C135257023","wikidata":"https://www.wikidata.org/wiki/Q691358","display_name":"Domain-specific language","level":2,"score":0.41875240206718445},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.37662649154663086},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3703081011772156},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3253953456878662},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0},{"id":"https://openalex.org/C38652104","wikidata":"https://www.wikidata.org/wiki/Q3510521","display_name":"Computer security","level":1,"score":0.0},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/3107411.3107471","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3107411.3107471","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 8th ACM International Conference on Bioinformatics, Computational Biology,and Health Informatics","raw_type":"proceedings-article"},{"id":"pmh:oai:osti.gov:1392820","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1392820","pdf_url":"https://www.osti.gov/servlets/purl/1392820","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null}],"best_oa_location":{"id":"pmh:oai:osti.gov:1392820","is_oa":true,"landing_page_url":"https://www.osti.gov/biblio/1392820","pdf_url":"https://www.osti.gov/servlets/purl/1392820","source":{"id":"https://openalex.org/S4306402487","display_name":"OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I139351228","host_organization_name":"Office of Scientific and Technical Information","host_organization_lineage":["https://openalex.org/I139351228"],"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":null},"sustainable_development_goals":[{"display_name":"Quality Education","score":0.5699999928474426,"id":"https://metadata.un.org/sdg/4"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320338304","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2952649401.pdf","grobid_xml":"https://content.openalex.org/works/W2952649401.grobid-xml"},"referenced_works_count":11,"referenced_works":["https://openalex.org/W9952812","https://openalex.org/W1563071114","https://openalex.org/W1986649132","https://openalex.org/W2006466539","https://openalex.org/W2027857026","https://openalex.org/W2097240335","https://openalex.org/W2121490181","https://openalex.org/W2167154952","https://openalex.org/W2175715045","https://openalex.org/W2532622426","https://openalex.org/W4226316596"],"related_works":["https://openalex.org/W2161550557","https://openalex.org/W2065949834","https://openalex.org/W4387796988","https://openalex.org/W2150010249","https://openalex.org/W2303430181","https://openalex.org/W2071356121","https://openalex.org/W2924405342","https://openalex.org/W2107238869","https://openalex.org/W2396093860","https://openalex.org/W98267493"],"abstract_inverted_index":{"Rule-based":[0],"modeling":[1,15],"languages,":[2],"such":[3],"as":[4],"the":[5,16,60,71,86,96,100],"Kappa":[6,56,129],"and":[7,32,89,105,121,130],"BioNetGen":[8],"languages":[9,73],"(BNGL),":[10],"are":[11],"powerful":[12],"frameworks":[13],"for":[14],"dynamics":[17],"of":[18,39,99,118,124],"complex":[19,77],"biochemical":[20],"reaction":[21],"networks.":[22],"Each":[23],"language":[24,98],"is":[25],"distributed":[26],"with":[27],"a":[28,45,81,91,116],"distinct":[29],"software":[30],"suite":[31],"modelers":[33],"may":[34],"wish":[35],"to":[36],"take":[37],"advantage":[38],"both":[40,128],"toolsets.":[41],"This":[42],"paper":[43],"introduces":[44],"practical":[46],"application":[47],"called":[48],"TRuML":[49,84],"that":[50,78],"translates":[51],"models":[52,126],"written":[53],"in":[54,65,95,109,127],"either":[55],"or":[57],"BNGL":[58],"into":[59],"other":[61,111],"language.":[62],"While":[63],"similar":[64],"many":[66],"respects,":[67],"key":[68],"differences":[69],"between":[70],"two":[72],"makes":[74],"translation":[75],"sufficiently":[76],"automation":[79],"becomes":[80],"useful":[82],"tool.":[83],"accommodates":[85],"languages'":[87],"complexities":[88,120],"produces":[90],"semantically":[92],"equivalent":[93,125],"model":[94,102,108],"alternate":[97],"input":[101],"when":[103],"possible":[104],"an":[106],"approximate":[107],"certain":[110],"cases.":[112],"Here,":[113],"we":[114],"discuss":[115],"number":[117],"these":[119],"provide":[122],"examples":[123],"BNGL.":[131]},"counts_by_year":[{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2019-06-27T00:00:00"}
