{"id":"https://openalex.org/W2790019339","doi":"https://doi.org/10.1093/bioinformatics/bty107","title":"BEL2ABM: agent-based simulation of static models in Biological Expression Language","display_name":"BEL2ABM: agent-based simulation of static models in Biological Expression Language","publication_year":2018,"publication_date":"2018-02-21","ids":{"openalex":"https://openalex.org/W2790019339","doi":"https://doi.org/10.1093/bioinformatics/bty107","mag":"2790019339","pmid":"https://pubmed.ncbi.nlm.nih.gov/29949955"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bty107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2316/25098444/bty107.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","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":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2316/25098444/bty107.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5029878448","display_name":"Michaela G\u00fcndel","orcid":null},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Michaela G\u00fcndel","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]},{"raw_affiliation_string":"Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164149"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065488553","display_name":"Charles Tapley Hoyt","orcid":"https://orcid.org/0000-0003-4423-4370"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Charles Tapley Hoyt","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany"],"raw_orcid":"https://orcid.org/0000-0003-4423-4370","affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]},{"raw_affiliation_string":"Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164149"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5003139478","display_name":"Martin Hofmann\u2010Apitius","orcid":"https://orcid.org/0000-0001-9012-6720"},"institutions":[{"id":"https://openalex.org/I135140700","display_name":"University of Bonn","ror":"https://ror.org/041nas322","country_code":"DE","type":"education","lineage":["https://openalex.org/I135140700"]},{"id":"https://openalex.org/I4210098248","display_name":"Fraunhofer Institute for Algorithms and Scientific Computing","ror":"https://ror.org/00trw9c49","country_code":"DE","type":"facility","lineage":["https://openalex.org/I4210098248","https://openalex.org/I4923324"]},{"id":"https://openalex.org/I4210164149","display_name":"Bonn Aachen International Center for Information Technology","ror":"https://ror.org/054zhq066","country_code":"DE","type":"facility","lineage":["https://openalex.org/I135140700","https://openalex.org/I155417937","https://openalex.org/I4210164149","https://openalex.org/I4923324"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Hofmann-Apitius","raw_affiliation_strings":["Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics, Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), Sankt Augustin, Germany","institution_ids":["https://openalex.org/I4210098248"]},{"raw_affiliation_string":"Department of Life Science Informatics, Bonn-Aachen International Center for IT, Rheinische Friedrich-Wilhelms-Universit\u00e4t Bonn, Bonn, Germany","institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210164149"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5029878448"],"corresponding_institution_ids":["https://openalex.org/I135140700","https://openalex.org/I4210098248","https://openalex.org/I4210164149"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.01071064,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"34","issue":"13","first_page":"2316","last_page":"2318"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5152999758720398,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.5152999758720398,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.021900000050663948,"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/T12072","display_name":"Machine Learning and Algorithms","score":0.019700000062584877,"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/executable","display_name":"Executable","score":0.8292126059532166},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8067693710327148},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.6963464617729187},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.6874017715454102},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.5555188059806824},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5178049802780151},{"id":"https://openalex.org/keywords/tracing","display_name":"Tracing","score":0.4949116110801697},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.4822045564651489},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.4563468396663666},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.43972456455230713},{"id":"https://openalex.org/keywords/template","display_name":"Template","score":0.43306222558021545},{"id":"https://openalex.org/keywords/netlogo","display_name":"NetLogo","score":0.4218188226222992},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4095233380794525}],"concepts":[{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.8292126059532166},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8067693710327148},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.6963464617729187},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.6874017715454102},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.5555188059806824},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5178049802780151},{"id":"https://openalex.org/C138673069","wikidata":"https://www.wikidata.org/wiki/Q322229","display_name":"Tracing","level":2,"score":0.4949116110801697},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.4822045564651489},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.4563468396663666},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.43972456455230713},{"id":"https://openalex.org/C82714645","wikidata":"https://www.wikidata.org/wiki/Q438331","display_name":"Template","level":2,"score":0.43306222558021545},{"id":"https://openalex.org/C167221231","wikidata":"https://www.wikidata.org/wiki/Q672307","display_name":"NetLogo","level":2,"score":0.4218188226222992},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4095233380794525},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007802","descriptor_name":"Language","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":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":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}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/bty107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2316/25098444/bty107.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:29949955","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29949955","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:4991131","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6022644","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:fraunhofer.de:N-525144","is_oa":true,"landing_page_url":"http://publica.fraunhofer.de/documents/N-525144.html","pdf_url":null,"source":{"id":"https://openalex.org/S4306400801","display_name":"Publikationsdatenbank der Fraunhofer-Gesellschaft (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"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":"Fraunhofer SCAI","raw_type":"Journal Article"},{"id":"pmh:oai:publica.fraunhofer.de:publica/255399","is_oa":false,"landing_page_url":"https://publica.fraunhofer.de/handle/publica/255399","pdf_url":null,"source":{"id":"https://openalex.org/S4306400318","display_name":"Fraunhofer-Publica (Fraunhofer-Gesellschaft)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4923324","host_organization_name":"Fraunhofer-Gesellschaft","host_organization_lineage":["https://openalex.org/I4923324"],"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":"journal article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bty107","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bty107","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/34/13/2316/25098444/bty107.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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education","score":0.5299999713897705}],"awards":[],"funders":[{"id":"https://openalex.org/F4320324287","display_name":"B-IT Foundation","ror":"https://ror.org/054zhq066"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2790019339.pdf","grobid_xml":"https://content.openalex.org/works/W2790019339.grobid-xml"},"referenced_works_count":7,"referenced_works":["https://openalex.org/W1799481352","https://openalex.org/W1989842786","https://openalex.org/W2085093793","https://openalex.org/W2150908245","https://openalex.org/W2187969747","https://openalex.org/W2766482558","https://openalex.org/W6682497444"],"related_works":["https://openalex.org/W3023917853","https://openalex.org/W4224013512","https://openalex.org/W4252443692","https://openalex.org/W2557308315","https://openalex.org/W27898408","https://openalex.org/W2598672065","https://openalex.org/W1993817217","https://openalex.org/W3120610872","https://openalex.org/W1638297612","https://openalex.org/W2523911541"],"abstract_inverted_index":{"Summary:":[0],"While":[1],"cause-and-effect":[2],"knowledge":[3],"assembly":[4],"models":[5,42],"encoded":[6],"in":[7,24,54],"Biological":[8],"Expression":[9],"Language":[10],"are":[11,20,62,75],"able":[12],"to":[13,27],"support":[14],"generation":[15],"of":[16],"mechanistic":[17],"hypotheses,":[18],"they":[19],"static":[21],"and":[22,47,56,60],"limited":[23],"their":[25],"ability":[26],"encode":[28],"temporality.":[29],"Here,":[30],"we":[31],"present":[32],"BEL2ABM,":[33],"a":[34],"software":[35],"for":[36],"producing":[37],"continuous,":[38],"dynamic,":[39],"executable":[40],"agent-based":[41],"from":[43],"BEL":[44],"templates.":[45],"Availability":[46],"implementation:":[48],"The":[49],"tool":[50],"has":[51],"been":[52],"developed":[53],"Java":[55],"NetLogo.":[57],"Code,":[58],"data":[59,74],"documentation":[61],"available":[63,76],"under":[64],"the":[65],"Apache":[66],"2.0":[67],"License":[68],"at":[69,77],"https://github.com/pybel/bel2abm.":[70],"Supplementary":[71,73],"information:":[72],"Bioinformatics":[78],"online.":[79]},"counts_by_year":[],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
