{"id":"https://openalex.org/W2170405129","doi":"https://doi.org/10.1093/bioinformatics/bts659","title":"Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI","display_name":"Bridging the scales: semantic integration of quantitative SBML in graphical multi-cellular models and simulations with EPISIM and COPASI","publication_year":2012,"publication_date":"2012-11-18","ids":{"openalex":"https://openalex.org/W2170405129","doi":"https://doi.org/10.1093/bioinformatics/bts659","mag":"2170405129","pmid":"https://pubmed.ncbi.nlm.nih.gov/23162085"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts659","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts659","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/2/223/48889716/bioinformatics_29_2_223.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/29/2/223/48889716/bioinformatics_29_2_223.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5017276043","display_name":"Thomas S\u00fctterlin","orcid":"https://orcid.org/0000-0003-0126-4692"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210111460","display_name":"National Center for Tumor Diseases","ror":"https://ror.org/01txwsw02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I4210111460"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Thomas S\u00fctterlin","raw_affiliation_strings":["1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210111460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045094937","display_name":"Christoph Kolb","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210111460","display_name":"National Center for Tumor Diseases","ror":"https://ror.org/01txwsw02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I4210111460"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Christoph Kolb","raw_affiliation_strings":["1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210111460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091133949","display_name":"Hartmut Dickhaus","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210111460","display_name":"National Center for Tumor Diseases","ror":"https://ror.org/01txwsw02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I4210111460"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hartmut Dickhaus","raw_affiliation_strings":["1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210111460"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034918056","display_name":"Dirk J\u00e4ger","orcid":null},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210111460","display_name":"National Center for Tumor Diseases","ror":"https://ror.org/01txwsw02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I4210111460"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Dirk J\u00e4ger","raw_affiliation_strings":["1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210111460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039930487","display_name":"Niels Grabe","orcid":"https://orcid.org/0000-0003-1732-3706"},"institutions":[{"id":"https://openalex.org/I223822909","display_name":"Heidelberg University","ror":"https://ror.org/038t36y30","country_code":"DE","type":"education","lineage":["https://openalex.org/I223822909"]},{"id":"https://openalex.org/I2802164966","display_name":"University Hospital Heidelberg","ror":"https://ror.org/013czdx64","country_code":"DE","type":"healthcare","lineage":["https://openalex.org/I2802164966"]},{"id":"https://openalex.org/I4210111460","display_name":"National Center for Tumor Diseases","ror":"https://ror.org/01txwsw02","country_code":"DE","type":"funder","lineage":["https://openalex.org/I4210111460"]}],"countries":["DE"],"is_corresponding":true,"raw_author_name":"Niels Grabe","raw_affiliation_strings":["1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Department of Medical Oncology, National Center for Tumor Diseases (NCT), University Hospital Heidelberg, 2Hamamatsu Tissue Imaging and Analysis Center (TIGA), BIOQUANT, Heidelberg University and 3Department of Medical Informatics, Institute of Medical Biometry and Informatics, University Hospital Heidelberg, 69120 Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210111460"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5039930487"],"corresponding_institution_ids":["https://openalex.org/I223822909","https://openalex.org/I2802164966","https://openalex.org/I4210111460"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":2.4554,"has_fulltext":true,"cited_by_count":73,"citation_normalized_percentile":{"value":0.8982303,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"29","issue":"2","first_page":"223","last_page":"229"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.79339998960495,"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":0.79339998960495,"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/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.04500000178813934,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"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/T13286","display_name":"Modeling and Simulation Systems","score":0.03310000151395798,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/sbml","display_name":"SBML","score":0.9867742657661438},{"id":"https://openalex.org/keywords/executable","display_name":"Executable","score":0.9431228637695312},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.772891640663147},{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.7536090612411499},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.7340635061264038},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5545790791511536},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4742695093154907},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.47019562125205994},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3656314015388489},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.334184467792511},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.29647940397262573},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.24254709482192993},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23805701732635498},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15346339344978333},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.12186840176582336}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9867742657661438},{"id":"https://openalex.org/C160145156","wikidata":"https://www.wikidata.org/wiki/Q778586","display_name":"Executable","level":2,"score":0.9431228637695312},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.772891640663147},{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.7536090612411499},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.7340635061264038},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5545790791511536},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4742695093154907},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.47019562125205994},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3656314015388489},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.334184467792511},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.29647940397262573},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.24254709482192993},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23805701732635498},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15346339344978333},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.12186840176582336}],"mesh":[{"descriptor_ui":"D000078404","descriptor_name":"Epidermal Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078404","descriptor_name":"Epidermal Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000078404","descriptor_name":"Epidermal Cells","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002453","descriptor_name":"Cell Cycle","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002454","descriptor_name":"Cell Differentiation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","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":"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":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012660","descriptor_name":"Semantics","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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057188","descriptor_name":"Workflow","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/bts659","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts659","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/2/223/48889716/bioinformatics_29_2_223.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:23162085","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23162085","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts659","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts659","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/2/223/48889716/bioinformatics_29_2_223.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":[],"funders":[{"id":"https://openalex.org/F4320321114","display_name":"Bundesministerium f\u00fcr Bildung und Forschung","ror":"https://ror.org/04pz7b180"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2170405129.pdf","grobid_xml":"https://content.openalex.org/works/W2170405129.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W1809480526","https://openalex.org/W1842201744","https://openalex.org/W1996195324","https://openalex.org/W1996198135","https://openalex.org/W2003909961","https://openalex.org/W2034834958","https://openalex.org/W2040163651","https://openalex.org/W2043875880","https://openalex.org/W2044765334","https://openalex.org/W2102653059","https://openalex.org/W2107062718","https://openalex.org/W2117364474","https://openalex.org/W2120629640","https://openalex.org/W2134648876","https://openalex.org/W2144244247","https://openalex.org/W2149193200","https://openalex.org/W2150908245","https://openalex.org/W2153355648","https://openalex.org/W2156571897","https://openalex.org/W2162144833","https://openalex.org/W2167931729","https://openalex.org/W2216895152","https://openalex.org/W3143164352"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2981332207","https://openalex.org/W2170405129","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2043776573"],"abstract_inverted_index":{"MOTIVATION:":[0],"Biological":[1],"reality":[2],"can":[3,118],"in":[4,10,76,100,167],"silico":[5],"only":[6],"be":[7,25,36,119],"comprehensively":[8],"represented":[9,105],"multi-scaled":[11,77],"models.":[12,31,90],"To":[13],"this":[14],"end,":[15],"cell":[16,101,164],"behavioural":[17,102],"models":[18,75,79,103,146],"addressing":[19],"the":[20,43,65,154,157,178,182],"multi-cellular":[21],"level":[22],"have":[23,34,149],"to":[24,35,85,122],"semantically":[26,98],"linked":[27,121],"with":[28],"mechanistic":[29],"molecular":[30],"These":[32],"requirements":[33],"met":[37],"by":[38,106,161],"flexible":[39,53],"software":[40,61,159],"workflows":[41],"solving":[42],"issues":[44],"of":[45,68,143,156,170,181],"different":[46,140,183],"time":[47,141],"scales,":[48],"inter-model":[49],"variable":[50],"referencing":[51],"and":[52,80,87,95,116,147,201],"sub-model":[54],"embedding.":[55],"RESULTS:":[56],"We":[57,152],"developed":[58],"a":[59,129],"novel":[60,158],"workflow":[62,83,160],"(EPISIM)":[63],"for":[64,198],"semantic":[66,179],"integration":[67],"Systems":[69],"Biology":[70],"Markup":[71],"Language":[72],"(SBML)-based":[73],"quantitative":[74],"tissue":[78,132,173,187],"simulations.":[81],"This":[82],"allows":[84],"import":[86],"access":[88],"SBML-based":[89],"SBML":[91,145],"model":[92,166,169],"species,":[93],"reactions":[94],"parameters":[96],"are":[97,209],"integrated":[99],"(CBM)":[104],"graphical":[107],"process":[108],"diagrams.":[109],"By":[110],"this,":[111],"cellular":[112],"states":[113],"like":[114],"proliferation":[115],"differentiation":[117],"flexibly":[120],"gene-regulatory":[123],"or":[124],"biochemical":[125],"reaction":[126],"networks.":[127],"For":[128],"multi-scale":[130],"agent-based":[131],"simulation":[133],"executable":[134],"code":[135],"is":[136,193],"automatically":[137],"generated":[138],"where":[139],"scales":[142,185],"imported":[144],"CBM":[148],"been":[150],"mapped.":[151],"demonstrate":[153],"capabilities":[155],"integrating":[162],"Tyson's":[163],"cycle":[165],"our":[168],"human":[171],"epidermal":[172],"homeostasis.":[174],"Finally,":[175],"we":[176],"show":[177],"interplay":[180],"biological":[184],"during":[186],"simulation.":[188],"AVAILABILITY:":[189],"The":[190],"EPISIM":[191],"platform":[192],"available":[194,210],"as":[195],"binary":[196],"executables":[197],"Windows,":[199],"Linux":[200],"Mac":[202],"OS":[203],"X":[204],"at":[205,211],"http://www.tiga.uni-hd.de.":[206],"Supplementary":[207],"data":[208],"http://www.tiga.uni-hd.de/supplements/SemSBMLIntegration.html.":[212],"CONTACT:":[213],"niels.grabe@bioquant.uni-heidelberg.de.":[214]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":7},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":5}],"updated_date":"2026-07-30T17:31:21.811387","created_date":"2025-10-10T00:00:00"}
