{"id":"https://openalex.org/W2950271351","doi":"https://doi.org/10.1016/j.biosystems.2018.05.008","title":"A portable structural analysis library for reaction networks","display_name":"A portable structural analysis library for reaction networks","publication_year":2018,"publication_date":"2018-05-29","ids":{"openalex":"https://openalex.org/W2950271351","doi":"https://doi.org/10.1016/j.biosystems.2018.05.008","mag":"2950271351","pmid":"https://pubmed.ncbi.nlm.nih.gov/29857031"},"language":"en","primary_location":{"id":"doi:10.1016/j.biosystems.2018.05.008","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.biosystems.2018.05.008","pdf_url":null,"source":{"id":"https://openalex.org/S99347777","display_name":"Biosystems","issn_l":"0303-2647","issn":["0303-2647","1872-8324"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biosystems","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6051435","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5063677284","display_name":"Yosef Bedaso","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Yosef Bedaso","raw_affiliation_strings":["Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA. Electronic address: bedasoy@uw.edu","Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA. Electronic address: bedasoy@uw.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076617999","display_name":"Frank Bergmann","orcid":"https://orcid.org/0000-0001-5553-4702"},"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"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Frank T. Bergmann","raw_affiliation_strings":["BioQuant/COS, Heidelberg University, Heidelberg, Germany. Electronic address: frank.bergmann@bioquant.uni-heidelberg.de","BioQuant/COS, Heidelberg University, Heidelberg, Germany"],"affiliations":[{"raw_affiliation_string":"BioQuant/COS, Heidelberg University, Heidelberg, Germany. Electronic address: frank.bergmann@bioquant.uni-heidelberg.de","institution_ids":[]},{"raw_affiliation_string":"BioQuant/COS, Heidelberg University, Heidelberg, Germany","institution_ids":["https://openalex.org/I223822909"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009998609","display_name":"Kiri Choi","orcid":"https://orcid.org/0000-0002-0156-8410"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kiri Choi","raw_affiliation_strings":["Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA. Electronic address: kirichoi@uw.edu","Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA. Electronic address: kirichoi@uw.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5035478017","display_name":"Kyle Medley","orcid":"https://orcid.org/0000-0002-9135-0844"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Kyle Medley","raw_affiliation_strings":["Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5044484291","display_name":"Herbert M. Sauro","orcid":"https://orcid.org/0000-0002-3659-6817"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Herbert M. Sauro","raw_affiliation_strings":["Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA. Electronic address: hsauro@u.washington.edu","Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA"],"affiliations":[{"raw_affiliation_string":"Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA. Electronic address: hsauro@u.washington.edu","institution_ids":[]},{"raw_affiliation_string":"Department of Bioengineering, William H. Foege Building, Box 355061, Seattle, WA 98195-5061, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5044484291"],"corresponding_institution_ids":[],"apc_list":{"value":2700,"currency":"USD","value_usd":2700},"apc_paid":null,"fwci":0.2793,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.58900279,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"169-170","issue":null,"first_page":"20","last_page":"25"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.996999979019165,"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":0.9807000160217285,"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/python","display_name":"Python (programming language)","score":0.8463256359100342},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7911690473556519},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6336507201194763},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.5934215188026428},{"id":"https://openalex.org/keywords/network-topology","display_name":"Network topology","score":0.524554967880249},{"id":"https://openalex.org/keywords/software-suite","display_name":"Software suite","score":0.503511369228363},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.5031608939170837},{"id":"https://openalex.org/keywords/suite","display_name":"Suite","score":0.48607924580574036},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.4535284638404846},{"id":"https://openalex.org/keywords/documentation","display_name":"Documentation","score":0.45084148645401},{"id":"https://openalex.org/keywords/mac-os","display_name":"Mac OS","score":0.4267060160636902},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.42560267448425293},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.4169427156448364},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3570745587348938},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.3248335123062134},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.12806618213653564},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.11561381816864014}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.8463256359100342},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7911690473556519},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6336507201194763},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.5934215188026428},{"id":"https://openalex.org/C199845137","wikidata":"https://www.wikidata.org/wiki/Q145490","display_name":"Network topology","level":2,"score":0.524554967880249},{"id":"https://openalex.org/C2778736646","wikidata":"https://www.wikidata.org/wiki/Q1143070","display_name":"Software suite","level":3,"score":0.503511369228363},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.5031608939170837},{"id":"https://openalex.org/C79581498","wikidata":"https://www.wikidata.org/wiki/Q1367530","display_name":"Suite","level":2,"score":0.48607924580574036},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.4535284638404846},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.45084148645401},{"id":"https://openalex.org/C522133331","wikidata":"https://www.wikidata.org/wiki/Q43627","display_name":"Mac OS","level":3,"score":0.4267060160636902},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.42560267448425293},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.4169427156448364},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3570745587348938},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.3248335123062134},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.12806618213653564},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.11561381816864014},{"id":"https://openalex.org/C166957645","wikidata":"https://www.wikidata.org/wiki/Q23498","display_name":"Archaeology","level":1,"score":0.0},{"id":"https://openalex.org/C95457728","wikidata":"https://www.wikidata.org/wiki/Q309","display_name":"History","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","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":"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","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":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013329","descriptor_name":"Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","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":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","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":true}],"locations_count":3,"locations":[{"id":"doi:10.1016/j.biosystems.2018.05.008","is_oa":false,"landing_page_url":"https://doi.org/10.1016/j.biosystems.2018.05.008","pdf_url":null,"source":{"id":"https://openalex.org/S99347777","display_name":"Biosystems","issn_l":"0303-2647","issn":["0303-2647","1872-8324"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Biosystems","raw_type":"journal-article"},{"id":"pmid:29857031","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29857031","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":"Bio Systems","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:6051435","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6051435","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Biosystems","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:6051435","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6051435","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Biosystems","raw_type":"Text"},"sustainable_development_goals":[{"display_name":"Life in Land","score":0.5600000023841858,"id":"https://metadata.un.org/sdg/15"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":30,"referenced_works":["https://openalex.org/W214924118","https://openalex.org/W1495660511","https://openalex.org/W1944909517","https://openalex.org/W1984378303","https://openalex.org/W2019512999","https://openalex.org/W2040890820","https://openalex.org/W2044935306","https://openalex.org/W2056090982","https://openalex.org/W2061364094","https://openalex.org/W2075283200","https://openalex.org/W2091793452","https://openalex.org/W2098367419","https://openalex.org/W2098494136","https://openalex.org/W2100334725","https://openalex.org/W2102653059","https://openalex.org/W2107306984","https://openalex.org/W2115343689","https://openalex.org/W2125615370","https://openalex.org/W2134221731","https://openalex.org/W2135535700","https://openalex.org/W2150908245","https://openalex.org/W2158069895","https://openalex.org/W2164111097","https://openalex.org/W2170032647","https://openalex.org/W2296033497","https://openalex.org/W2402354800","https://openalex.org/W2405441773","https://openalex.org/W2465211181","https://openalex.org/W2580869787","https://openalex.org/W2798909945"],"related_works":["https://openalex.org/W4225089214","https://openalex.org/W4309247532","https://openalex.org/W4308825558","https://openalex.org/W3096946169","https://openalex.org/W2172162746","https://openalex.org/W2113128227","https://openalex.org/W2144610372","https://openalex.org/W2927886090","https://openalex.org/W4312114021","https://openalex.org/W1988697672"],"abstract_inverted_index":null,"counts_by_year":[{"year":2023,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
