{"id":"https://openalex.org/W2162544362","doi":"https://doi.org/10.1093/bioinformatics/bts267","title":"GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization","display_name":"GEMSiRV: a software platform for GEnome-scale metabolic model simulation, reconstruction and visualization","publication_year":2012,"publication_date":"2012-05-04","ids":{"openalex":"https://openalex.org/W2162544362","doi":"https://doi.org/10.1093/bioinformatics/bts267","mag":"2162544362","pmid":"https://pubmed.ncbi.nlm.nih.gov/22563070"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/bts267","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts267","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1752/48866589/bioinformatics_28_13_1752.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1752/48866589/bioinformatics_28_13_1752.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032462579","display_name":"Yu-Chieh Liao","orcid":"https://orcid.org/0000-0002-4360-7932"},"institutions":[{"id":"https://openalex.org/I165441096","display_name":"National Health Research Institutes","ror":"https://ror.org/02r6fpx29","country_code":"TW","type":"nonprofit","lineage":["https://openalex.org/I165441096"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Yu-Chieh Liao","raw_affiliation_strings":["1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C","institution_ids":["https://openalex.org/I165441096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039538599","display_name":"Ming-Hsin Tsai","orcid":null},"institutions":[{"id":"https://openalex.org/I165441096","display_name":"National Health Research Institutes","ror":"https://ror.org/02r6fpx29","country_code":"TW","type":"nonprofit","lineage":["https://openalex.org/I165441096"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Ming-Hsin Tsai","raw_affiliation_strings":["1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C","institution_ids":["https://openalex.org/I165441096"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5054373289","display_name":"Feng\u2010Chi Chen","orcid":"https://orcid.org/0000-0002-1437-4420"},"institutions":[{"id":"https://openalex.org/I165441096","display_name":"National Health Research Institutes","ror":"https://ror.org/02r6fpx29","country_code":"TW","type":"nonprofit","lineage":["https://openalex.org/I165441096"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Feng-Chi Chen","raw_affiliation_strings":["1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C","institution_ids":["https://openalex.org/I165441096"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5016184067","display_name":"Chao A. Hsiung","orcid":"https://orcid.org/0000-0003-1427-6641"},"institutions":[{"id":"https://openalex.org/I165441096","display_name":"National Health Research Institutes","ror":"https://ror.org/02r6fpx29","country_code":"TW","type":"nonprofit","lineage":["https://openalex.org/I165441096"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chao A. Hsiung","raw_affiliation_strings":["1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C"],"affiliations":[{"raw_affiliation_string":"1 Division of Biostatistics and Bioinformatics, Institute of Population Health Sciences, National Health Research Institutes, Zhunan 350 and 2Department of Computer Science, National Tsing Hua University, Hsinchu, Taiwan, R.O.C","institution_ids":["https://openalex.org/I165441096"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5032462579"],"corresponding_institution_ids":["https://openalex.org/I165441096"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.7479,"has_fulltext":false,"cited_by_count":43,"citation_normalized_percentile":{"value":0.84596257,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"28","issue":"13","first_page":"1752","last_page":"1758"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":1.0,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9958000183105469,"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/visualization","display_name":"Visualization","score":0.7641447186470032},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.7571974992752075},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7170811891555786},{"id":"https://openalex.org/keywords/software-visualization","display_name":"Software visualization","score":0.6294972896575928},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.6166673898696899},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5764681696891785},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.5717079639434814},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.513827383518219},{"id":"https://openalex.org/keywords/data-visualization","display_name":"Data visualization","score":0.4521487057209015},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"Metabolic flux analysis","score":0.4456169605255127},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.43821296095848083},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.42626819014549255},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.39631593227386475},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3170212209224701},{"id":"https://openalex.org/keywords/software-system","display_name":"Software system","score":0.3082652688026428},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.24688270688056946},{"id":"https://openalex.org/keywords/component-based-software-engineering","display_name":"Component-based software engineering","score":0.20827925205230713},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.19837942719459534},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1666109263896942},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1305122673511505}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7641447186470032},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.7571974992752075},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7170811891555786},{"id":"https://openalex.org/C4379982","wikidata":"https://www.wikidata.org/wiki/Q1273511","display_name":"Software visualization","level":5,"score":0.6294972896575928},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.6166673898696899},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5764681696891785},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.5717079639434814},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.513827383518219},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.4521487057209015},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.4456169605255127},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.43821296095848083},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.42626819014549255},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.39631593227386475},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3170212209224701},{"id":"https://openalex.org/C149091818","wikidata":"https://www.wikidata.org/wiki/Q2429814","display_name":"Software system","level":3,"score":0.3082652688026428},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.24688270688056946},{"id":"https://openalex.org/C174683762","wikidata":"https://www.wikidata.org/wiki/Q609588","display_name":"Component-based software engineering","level":4,"score":0.20827925205230713},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.19837942719459534},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1666109263896942},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1305122673511505},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.0},{"id":"https://openalex.org/C62231903","wikidata":"https://www.wikidata.org/wiki/Q1057","display_name":"Metabolism","level":2,"score":0.0},{"id":"https://openalex.org/C134018914","wikidata":"https://www.wikidata.org/wiki/Q162606","display_name":"Endocrinology","level":1,"score":0.0},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.0},{"id":"https://openalex.org/C31258907","wikidata":"https://www.wikidata.org/wiki/Q1301371","display_name":"Computer network","level":1,"score":0.0}],"mesh":[{"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":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":"Q000379","qualifier_name":"methods","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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053858","descriptor_name":"Metabolic Networks and Pathways","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/bts267","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts267","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1752/48866589/bioinformatics_28_13_1752.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:22563070","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/22563070","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.1021.1737","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1021.1737","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://bioinformatics.oxfordjournals.org/content/early/2012/05/04/bioinformatics.bts267.full.pdf","raw_type":"text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/bts267","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/bts267","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/28/13/1752/48866589/bioinformatics_28_13_1752.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":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/9","score":0.5,"display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2162544362.pdf","grobid_xml":"https://content.openalex.org/works/W2162544362.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1516184414","https://openalex.org/W1543388089","https://openalex.org/W1946371345","https://openalex.org/W1996912752","https://openalex.org/W2015751324","https://openalex.org/W2021292622","https://openalex.org/W2048214825","https://openalex.org/W2070077734","https://openalex.org/W2072013780","https://openalex.org/W2072613143","https://openalex.org/W2075283200","https://openalex.org/W2078355959","https://openalex.org/W2083011190","https://openalex.org/W2085993965","https://openalex.org/W2098983518","https://openalex.org/W2100084634","https://openalex.org/W2106196417","https://openalex.org/W2117509624","https://openalex.org/W2127020923","https://openalex.org/W2128601422","https://openalex.org/W2131684839","https://openalex.org/W2140040278","https://openalex.org/W2143534289","https://openalex.org/W2147472054","https://openalex.org/W2150908245","https://openalex.org/W2151023149","https://openalex.org/W2156409537","https://openalex.org/W2170427655","https://openalex.org/W2172162746","https://openalex.org/W3101308120","https://openalex.org/W4237293127","https://openalex.org/W4238101851"],"related_works":["https://openalex.org/W2020641517","https://openalex.org/W2374260038","https://openalex.org/W2216418212","https://openalex.org/W1999460937","https://openalex.org/W2113329733","https://openalex.org/W2133150343","https://openalex.org/W2341681417","https://openalex.org/W2075919068","https://openalex.org/W1984242440","https://openalex.org/W1983989854"],"abstract_inverted_index":{"The":[0],"software":[1],"is":[2],"freely":[3],"available":[4],"on":[5],"the":[6],"web":[7],"at":[8],"http://sb.nhri.org.tw/GEMSiRV.":[9]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":5},{"year":2019,"cited_by_count":5},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":4},{"year":2014,"cited_by_count":6},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2025-10-10T00:00:00"}