{"id":"https://openalex.org/W3121429485","doi":"https://doi.org/10.1371/journal.pcbi.1008208","title":"MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics","display_name":"MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics","publication_year":2021,"publication_date":"2021-01-28","ids":{"openalex":"https://openalex.org/W3121429485","doi":"https://doi.org/10.1371/journal.pcbi.1008208","mag":"3121429485","pmid":"https://pubmed.ncbi.nlm.nih.gov/33507922"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008208","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008208","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008208&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.1008208&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5046266224","display_name":"Zachary B. Haiman","orcid":"https://orcid.org/0000-0001-6175-5050"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Zachary B. Haiman","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America"],"raw_orcid":"https://orcid.org/0000-0001-6175-5050","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070567302","display_name":"Daniel C. Zielinski","orcid":"https://orcid.org/0000-0001-6452-483X"},"institutions":[{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Daniel C. Zielinski","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034020037","display_name":"Yuko Koike","orcid":null},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuko Koike","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","Institute for Systems Biology, Seattle, Washington, United States of America"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082126398","display_name":"James T. Yurkovich","orcid":"https://orcid.org/0000-0002-9403-509X"},"institutions":[{"id":"https://openalex.org/I3148997608","display_name":"Institute for Systems Biology","ror":"https://ror.org/02tpgw303","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I3148997608"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James T. Yurkovich","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","Institute for Systems Biology, Seattle, Washington, United States of America"],"raw_orcid":"https://orcid.org/0000-0002-9403-509X","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Institute for Systems Biology, Seattle, Washington, United States of America","institution_ids":["https://openalex.org/I3148997608"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5051097609","display_name":"Bernhard \u00d8. Palsson","orcid":"https://orcid.org/0000-0003-2357-6785"},"institutions":[{"id":"https://openalex.org/I2801134892","display_name":"Novo Nordisk Foundation","ror":"https://ror.org/04txyc737","country_code":"DK","type":"facility","lineage":["https://openalex.org/I2801134892"]},{"id":"https://openalex.org/I36258959","display_name":"University of California San Diego","ror":"https://ror.org/0168r3w48","country_code":"US","type":"education","lineage":["https://openalex.org/I36258959"]},{"id":"https://openalex.org/I96673099","display_name":"Technical University of Denmark","ror":"https://ror.org/04qtj9h94","country_code":"DK","type":"education","lineage":["https://openalex.org/I96673099"]}],"countries":["DK","US"],"is_corresponding":true,"raw_author_name":"Bernhard O. Palsson","raw_affiliation_strings":["Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark"],"raw_orcid":"https://orcid.org/0000-0003-2357-6785","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of California San Diego, La Jolla, California, United States of America","institution_ids":["https://openalex.org/I36258959"]},{"raw_affiliation_string":"Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Kongens Lyngby, Denmark","institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I96673099"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5051097609"],"corresponding_institution_ids":["https://openalex.org/I2801134892","https://openalex.org/I36258959","https://openalex.org/I96673099"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.7755,"has_fulltext":true,"cited_by_count":45,"citation_normalized_percentile":{"value":0.91600978,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":100},"biblio":{"volume":"17","issue":"1","first_page":"e1008208","last_page":"e1008208"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9950000047683716,"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":0.9950000047683716,"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":0.9746999740600586,"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/T13539","display_name":"thermodynamics and calorimetric analyses","score":0.9230999946594238,"subfield":{"id":"https://openalex.org/subfields/1606","display_name":"Physical and Theoretical Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/python","display_name":"Python (programming language)","score":0.7358394861221313},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5161052942276001},{"id":"https://openalex.org/keywords/kinetics","display_name":"Kinetics","score":0.5021121501922607},{"id":"https://openalex.org/keywords/biological-system","display_name":"Biological system","score":0.3211175203323364},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1860136091709137},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16831663250923157},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.1631525456905365}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.7358394861221313},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5161052942276001},{"id":"https://openalex.org/C148898269","wikidata":"https://www.wikidata.org/wiki/Q1108792","display_name":"Kinetics","level":2,"score":0.5021121501922607},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.3211175203323364},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1860136091709137},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16831663250923157},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.1631525456905365},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":5,"locations":[{"id":"doi:10.1371/journal.pcbi.1008208","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008208","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008208&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:33507922","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33507922","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:3846a1961c114a0ab1c5d9e49137eaf3","is_oa":true,"landing_page_url":"https://doaj.org/article/3846a1961c114a0ab1c5d9e49137eaf3","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 1, p e1008208 (2021)","raw_type":"article"},{"id":"pmh:oai:escholarship.org:ark:/13030/qt12j2878v","is_oa":true,"landing_page_url":"https://escholarship.org/uc/item/12j2878v","pdf_url":null,"source":{"id":"https://openalex.org/S4306400115","display_name":"eScholarship (California Digital Library)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I2801248553","host_organization_name":"California Digital Library","host_organization_lineage":["https://openalex.org/I2801248553"],"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 Computational Biology, vol 17, iss 1","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7872247","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7872247","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.1008208","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008208","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008208&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":[],"awards":[{"id":"https://openalex.org/G5417901379","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320322436","funder_display_name":"Novo Nordisk"},{"id":"https://openalex.org/G6160741424","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320323153","funder_display_name":"Danmarks Tekniske Universitet"},{"id":"https://openalex.org/G7701966108","display_name":null,"funder_award_id":"NNF10CC1016517","funder_id":"https://openalex.org/F4320325957","funder_display_name":"Novo Nordisk Fonden"}],"funders":[{"id":"https://openalex.org/F4320322436","display_name":"Novo Nordisk","ror":"https://ror.org/0435rc536"},{"id":"https://openalex.org/F4320323153","display_name":"Danmarks Tekniske Universitet","ror":"https://ror.org/04qtj9h94"},{"id":"https://openalex.org/F4320325957","display_name":"Novo Nordisk Fonden","ror":"https://ror.org/04txyc737"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3121429485.pdf","grobid_xml":"https://content.openalex.org/works/W3121429485.grobid-xml"},"referenced_works_count":91,"referenced_works":["https://openalex.org/W147998453","https://openalex.org/W283102726","https://openalex.org/W627725698","https://openalex.org/W1490641033","https://openalex.org/W1493003385","https://openalex.org/W1665355332","https://openalex.org/W1860450641","https://openalex.org/W1862094217","https://openalex.org/W1869952022","https://openalex.org/W1972796370","https://openalex.org/W1978009694","https://openalex.org/W1988136571","https://openalex.org/W1991004166","https://openalex.org/W1992955330","https://openalex.org/W1997733142","https://openalex.org/W2000150815","https://openalex.org/W2003409413","https://openalex.org/W2003860267","https://openalex.org/W2011301426","https://openalex.org/W2011514820","https://openalex.org/W2017060799","https://openalex.org/W2019516978","https://openalex.org/W2022374283","https://openalex.org/W2030497958","https://openalex.org/W2034961255","https://openalex.org/W2044121023","https://openalex.org/W2048465561","https://openalex.org/W2061939373","https://openalex.org/W2064412842","https://openalex.org/W2068855150","https://openalex.org/W2082382448","https://openalex.org/W2090469606","https://openalex.org/W2091087653","https://openalex.org/W2096492216","https://openalex.org/W2097240335","https://openalex.org/W2098367419","https://openalex.org/W2102653059","https://openalex.org/W2103795997","https://openalex.org/W2108141605","https://openalex.org/W2116976883","https://openalex.org/W2119642783","https://openalex.org/W2120167281","https://openalex.org/W2134221731","https://openalex.org/W2141053516","https://openalex.org/W2143861551","https://openalex.org/W2146292423","https://openalex.org/W2147472054","https://openalex.org/W2150583791","https://openalex.org/W2150908245","https://openalex.org/W2152540020","https://openalex.org/W2153373497","https://openalex.org/W2165612309","https://openalex.org/W2166751342","https://openalex.org/W2167919951","https://openalex.org/W2170032647","https://openalex.org/W2184314249","https://openalex.org/W2191824721","https://openalex.org/W2216418212","https://openalex.org/W2217402295","https://openalex.org/W2296335794","https://openalex.org/W2399769480","https://openalex.org/W2413327964","https://openalex.org/W2417863416","https://openalex.org/W2440036468","https://openalex.org/W2472803348","https://openalex.org/W2561266760","https://openalex.org/W2565927981","https://openalex.org/W2604657987","https://openalex.org/W2761155071","https://openalex.org/W2761502649","https://openalex.org/W2762019694","https://openalex.org/W2764202526","https://openalex.org/W2791048175","https://openalex.org/W2884300959","https://openalex.org/W2885674637","https://openalex.org/W2898731711","https://openalex.org/W2903675476","https://openalex.org/W2916475656","https://openalex.org/W2970732621","https://openalex.org/W2989997158","https://openalex.org/W3003257820","https://openalex.org/W3081478800","https://openalex.org/W3103145119","https://openalex.org/W3210886538","https://openalex.org/W4214933217","https://openalex.org/W4231917197","https://openalex.org/W4239049776","https://openalex.org/W4254747188","https://openalex.org/W4386373863","https://openalex.org/W6894202963","https://openalex.org/W6982728064"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W4287027380"],"abstract_inverted_index":{"Mathematical":[0],"models":[1,33,75,164],"of":[2,24,61,76,104,115,138,146,149,162,174,203,206,223],"metabolic":[3,25,105,224],"networks":[4,26],"utilize":[5],"simulation":[6,111,123,145],"to":[7,18,38,72,85,94,129,132,169,177,191,215],"study":[8,185],"system-level":[9],"mechanisms":[10,71,148],"and":[11,68,89,101,176,181,229],"functions.":[12],"Various":[13],"approaches":[14],"have":[15],"been":[16],"used":[17],"model":[19],"the":[20,46,86,117,139,201],"steady":[21],"state":[22],"behavior":[23],"using":[27,156,165],"genome-scale":[28],"reconstructions,":[29],"but":[30],"formulating":[31],"dynamic":[32,59,74,82,110,144,221],"from":[34],"such":[35],"reconstructions":[36],"continues":[37],"be":[39],"a":[40,136,153,157,183,212],"key":[41],"challenge.":[42],"Here,":[43],"we":[44],"present":[45],"Mass":[47],"Action":[48],"Stoichiometric":[49],"Simulation":[50],"Python":[51,91],"(MASSpy)":[52],"package,":[53],"an":[54,96],"open-source":[55],"computational":[56],"framework":[57,98],"for":[58,99,159],"modeling":[60,83,103,141,222],"metabolism.":[62],"MASSpy":[63,80,107,140,188,210],"utilizes":[64],"mass":[65],"action":[66],"kinetics":[67],"detailed":[69,147,207],"chemical":[70],"build":[73],"complex":[77],"biological":[78,179,208],"processes.":[79],"adds":[81],"tools":[84],"COnstraint-Based":[87],"Reconstruction":[88],"Analysis":[90],"(COBRApy)":[92],"package":[93],"provide":[95],"unified":[97],"constraint-based":[100],"kinetic":[102,163],"networks.":[106],"supports":[108],"high-performance":[109],"through":[112,143],"its":[113],"implementation":[114],"libRoadRunner:":[116],"Systems":[118],"Biology":[119],"Markup":[120],"Language":[121],"(SBML)":[122],"engine.":[124],"Three":[125],"examples":[126],"are":[127],"provided":[128],"demonstrate":[130],"how":[131],"use":[133],"MASSpy:":[134],"(1)":[135],"validation":[137],"tool":[142,214],"enzyme":[150],"regulation;":[151],"(2)":[152],"feature":[154],"demonstration":[155],"workflow":[158],"generating":[160],"ensemble":[161],"Monte":[166],"Carlo":[167],"sampling":[168],"approximate":[170],"missing":[171],"numerical":[172],"values":[173],"parameters":[175],"quantify":[178],"uncertainty,":[180],"(3)":[182],"case":[184],"in":[186,220],"which":[187],"is":[189],"utilized":[190],"overcome":[192],"issues":[193],"that":[194,218],"arise":[195,219],"when":[196],"integrating":[197],"experimental":[198],"data":[199],"with":[200],"computation":[202],"functional":[204],"states":[205],"mechanisms.":[209],"represents":[211],"powerful":[213],"address":[216],"challenges":[217],"networks,":[225],"both":[226],"at":[227],"small":[228],"large":[230],"scales.":[231]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":8},{"year":2024,"cited_by_count":15},{"year":2023,"cited_by_count":10},{"year":2022,"cited_by_count":4},{"year":2021,"cited_by_count":6},{"year":2020,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}