{"id":"https://openalex.org/W3205057869","doi":"https://doi.org/10.1371/journal.pcbi.1009513","title":"Modular assembly of dynamic models in systems biology","display_name":"Modular assembly of dynamic models in systems biology","publication_year":2021,"publication_date":"2021-10-13","ids":{"openalex":"https://openalex.org/W3205057869","doi":"https://doi.org/10.1371/journal.pcbi.1009513","mag":"3205057869","pmid":"https://pubmed.ncbi.nlm.nih.gov/34644304"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1009513","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009513","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009513&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009513&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5059730193","display_name":"Michael Pan","orcid":"https://orcid.org/0000-0002-8978-7350"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":true,"raw_author_name":"Michael Pan","raw_affiliation_strings":["ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Parkville, Victoria, Australia","School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia","Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0002-8978-7350","affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085191745","display_name":"P.J. Gawthrop","orcid":"https://orcid.org/0000-0002-6029-515X"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Peter J. Gawthrop","raw_affiliation_strings":["Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0002-6029-515X","affiliations":[{"raw_affiliation_string":"Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048486605","display_name":"Joseph Cursons","orcid":"https://orcid.org/0000-0002-5053-4540"},"institutions":[{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Joseph Cursons","raw_affiliation_strings":["Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia"],"raw_orcid":"https://orcid.org/0000-0002-5053-4540","affiliations":[{"raw_affiliation_string":"Department of Biochemistry and Molecular Biology, Monash Biomedicine Discovery Institute, Monash University, Melbourne, Victoria, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5083478373","display_name":"Edmund J. Crampin","orcid":"https://orcid.org/0000-0001-6569-9543"},"institutions":[{"id":"https://openalex.org/I165779595","display_name":"The University of Melbourne","ror":"https://ror.org/01ej9dk98","country_code":"AU","type":"education","lineage":["https://openalex.org/I165779595"]}],"countries":["AU"],"is_corresponding":false,"raw_author_name":"Edmund J. Crampin","raw_affiliation_strings":["ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Parkville, Victoria, Australia","School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia","School of Medicine, University of Melbourne, Parkville, Victoria, Australia","Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Faculty of Engineering and Information Technology, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"School of Mathematics and Statistics, Faculty of Science, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"School of Medicine, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]},{"raw_affiliation_string":"Systems Biology Laboratory, School of Mathematics and Statistics, and Department of Biomedical Engineering, University of Melbourne, Parkville, Victoria, Australia","institution_ids":["https://openalex.org/I165779595"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5059730193"],"corresponding_institution_ids":["https://openalex.org/I165779595"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.2795,"has_fulltext":true,"cited_by_count":38,"citation_normalized_percentile":{"value":0.89293159,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"17","issue":"10","first_page":"e1009513","last_page":"e1009513"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9983999729156494,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9941999912261963,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/reusability","display_name":"Reusability","score":0.7798224687576294},{"id":"https://openalex.org/keywords/modularity","display_name":"Modularity (biology)","score":0.771666944026947},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.7244575619697571},{"id":"https://openalex.org/keywords/abstraction","display_name":"Abstraction","score":0.6816336512565613},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6395021677017212},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5867429971694946},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5623431205749512},{"id":"https://openalex.org/keywords/granularity","display_name":"Granularity","score":0.5470803380012512},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.506327748298645},{"id":"https://openalex.org/keywords/synthetic-biology","display_name":"Synthetic biology","score":0.4364078640937805},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.4318177103996277},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4155893921852112},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.34747636318206787},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2637988328933716},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.23892319202423096},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19707855582237244}],"concepts":[{"id":"https://openalex.org/C137981799","wikidata":"https://www.wikidata.org/wiki/Q1369184","display_name":"Reusability","level":3,"score":0.7798224687576294},{"id":"https://openalex.org/C2779478453","wikidata":"https://www.wikidata.org/wiki/Q6889748","display_name":"Modularity (biology)","level":2,"score":0.771666944026947},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.7244575619697571},{"id":"https://openalex.org/C124304363","wikidata":"https://www.wikidata.org/wiki/Q673661","display_name":"Abstraction","level":2,"score":0.6816336512565613},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6395021677017212},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5867429971694946},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5623431205749512},{"id":"https://openalex.org/C177774035","wikidata":"https://www.wikidata.org/wiki/Q1246948","display_name":"Granularity","level":2,"score":0.5470803380012512},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.506327748298645},{"id":"https://openalex.org/C191908910","wikidata":"https://www.wikidata.org/wiki/Q862838","display_name":"Synthetic biology","level":2,"score":0.4364078640937805},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.4318177103996277},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4155893921852112},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.34747636318206787},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2637988328933716},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.23892319202423096},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19707855582237244},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"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":"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":"D014981","descriptor_name":"Xenopus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014981","descriptor_name":"Xenopus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014981","descriptor_name":"Xenopus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014981","descriptor_name":"Xenopus","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020935","descriptor_name":"MAP Kinase Signaling System","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1371/journal.pcbi.1009513","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009513","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009513&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:34644304","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34644304","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:doaj.org/article:4688ffc01167458e8271b1474bd0ae27","is_oa":true,"landing_page_url":"https://doaj.org/article/4688ffc01167458e8271b1474bd0ae27","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 17, Iss 10, p e1009513 (2021)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:7433563","is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC8544865","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/296783","is_oa":true,"landing_page_url":"http://hdl.handle.net/11343/296783","pdf_url":null,"source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8544865","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8544865","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1009513","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1009513","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1009513&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.44999998807907104,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G5980719551","display_name":null,"funder_award_id":"project number CE140100036","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"},{"id":"https://openalex.org/G8470230451","display_name":null,"funder_award_id":"CE140100036","funder_id":"https://openalex.org/F4320334704","funder_display_name":"Australian Research Council"}],"funders":[{"id":"https://openalex.org/F4320334704","display_name":"Australian Research Council","ror":"https://ror.org/05mmh0f86"},{"id":"https://openalex.org/F4320337223","display_name":"Faculty of Engineering and Information Technology, University of Technology Sydney","ror":null}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3205057869.pdf","grobid_xml":"https://content.openalex.org/works/W3205057869.grobid-xml"},"referenced_works_count":93,"referenced_works":["https://openalex.org/W1521496944","https://openalex.org/W1576664335","https://openalex.org/W1592132377","https://openalex.org/W1982830461","https://openalex.org/W1985687822","https://openalex.org/W1986753065","https://openalex.org/W1991339919","https://openalex.org/W1994373703","https://openalex.org/W2000150815","https://openalex.org/W2000619385","https://openalex.org/W2008855387","https://openalex.org/W2016462601","https://openalex.org/W2042880070","https://openalex.org/W2053545034","https://openalex.org/W2066113694","https://openalex.org/W2070658593","https://openalex.org/W2075260598","https://openalex.org/W2081580266","https://openalex.org/W2081781433","https://openalex.org/W2097240335","https://openalex.org/W2098769288","https://openalex.org/W2102633175","https://openalex.org/W2102653059","https://openalex.org/W2105038431","https://openalex.org/W2110726849","https://openalex.org/W2114124738","https://openalex.org/W2115189047","https://openalex.org/W2116976883","https://openalex.org/W2123333705","https://openalex.org/W2123783513","https://openalex.org/W2134050761","https://openalex.org/W2146099270","https://openalex.org/W2148443868","https://openalex.org/W2152376294","https://openalex.org/W2164898811","https://openalex.org/W2166499263","https://openalex.org/W2168618155","https://openalex.org/W2171745314","https://openalex.org/W2171926758","https://openalex.org/W2186373804","https://openalex.org/W2219048344","https://openalex.org/W2229356245","https://openalex.org/W2275385930","https://openalex.org/W2328108594","https://openalex.org/W2346094579","https://openalex.org/W2411390783","https://openalex.org/W2413327964","https://openalex.org/W2441893520","https://openalex.org/W2472291363","https://openalex.org/W2489215644","https://openalex.org/W2551360187","https://openalex.org/W2553698069","https://openalex.org/W2578851857","https://openalex.org/W2610485937","https://openalex.org/W2742111569","https://openalex.org/W2767366948","https://openalex.org/W2771570772","https://openalex.org/W2786877773","https://openalex.org/W2807737529","https://openalex.org/W2810755205","https://openalex.org/W2884300959","https://openalex.org/W2898490408","https://openalex.org/W2916475656","https://openalex.org/W2950976461","https://openalex.org/W2952117952","https://openalex.org/W2980260871","https://openalex.org/W3008956387","https://openalex.org/W3043338671","https://openalex.org/W3044339796","https://openalex.org/W3099142114","https://openalex.org/W3099260878","https://openalex.org/W3102051271","https://openalex.org/W3104064088","https://openalex.org/W3105704522","https://openalex.org/W3105865579","https://openalex.org/W3111734200","https://openalex.org/W3127038835","https://openalex.org/W3134460489","https://openalex.org/W3137329076","https://openalex.org/W3159193180","https://openalex.org/W3163027238","https://openalex.org/W3194998279","https://openalex.org/W4210560508","https://openalex.org/W4225477695","https://openalex.org/W4231917197","https://openalex.org/W4237725837","https://openalex.org/W4241685680","https://openalex.org/W4242519561","https://openalex.org/W4244858075","https://openalex.org/W4246991885","https://openalex.org/W4247393540","https://openalex.org/W4253532831","https://openalex.org/W4298263761"],"related_works":["https://openalex.org/W4242697240","https://openalex.org/W2970353240","https://openalex.org/W2057769265","https://openalex.org/W2024161258","https://openalex.org/W1911418903","https://openalex.org/W2338895903","https://openalex.org/W3044523069","https://openalex.org/W2136248167","https://openalex.org/W2126646394","https://openalex.org/W2024722675"],"abstract_inverted_index":{"It":[0],"is":[1],"widely":[2],"acknowledged":[3],"that":[4,91],"the":[5,47,78,122,141,152,156],"construction":[6],"of":[7,49,62,80,124,132,143,148],"large-scale":[8,114],"dynamic":[9],"models":[10],"in":[11,46,99,103,127],"systems":[12,104],"biology":[13],"requires":[14],"complex":[15],"modelling":[16,30],"problems":[17],"to":[18,36,52,72,120,139,150,154],"be":[19,70],"broken":[20],"up":[21],"into":[22],"more":[23],"manageable":[24],"pieces.":[25],"To":[26],"this":[27,73,87,128],"end,":[28],"both":[29,81],"and":[31,83,101,106,145],"software":[32,50],"frameworks":[33],"are":[34,94,107],"required":[35],"enable":[37],"modular":[38],"modelling.":[39,85],"While":[40],"there":[41,56],"has":[42,57],"been":[43,58],"consistent":[44],"progress":[45],"development":[48],"tools":[51],"enhance":[53],"model":[54,131,147,157],"reusability,":[55],"a":[59,109,130,133,146],"relative":[60],"lack":[61],"consideration":[63],"for":[64,112],"how":[65],"underlying":[66],"biophysical":[67],"principles":[68],"can":[69],"applied":[71],"space.":[74],"Bond":[75],"graphs":[76,93,126],"combine":[77],"aspects":[79],"modularity":[82,100],"physics-based":[84],"In":[86],"paper,":[88],"we":[89],"argue":[90],"bond":[92,125],"compatible":[95],"with":[96],"recent":[97],"developments":[98],"abstraction":[102],"biology,":[105],"thus":[108],"desirable":[110],"framework":[111],"constructing":[113],"models.":[115],"We":[116],"use":[117],"two":[118],"examples":[119],"illustrate":[121,140,151],"utility":[123],"context:":[129],"mitogen-activated":[134],"protein":[135],"kinase":[136],"(MAPK)":[137],"cascade":[138],"reusability":[142],"modules":[144],"glycolysis":[149],"ability":[153],"modify":[155],"granularity.":[158]},"counts_by_year":[{"year":2025,"cited_by_count":10},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":10},{"year":2021,"cited_by_count":1}],"updated_date":"2026-05-21T09:19:25.381259","created_date":"2025-10-10T00:00:00"}