{"id":"https://openalex.org/W2131684839","doi":"https://doi.org/10.1186/1471-2105-12-196","title":"Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface","display_name":"Acorn: A grid computing system for constraint based modeling and visualization of the genome scale metabolic reaction networks via a web interface","publication_year":2011,"publication_date":"2011-05-24","ids":{"openalex":"https://openalex.org/W2131684839","doi":"https://doi.org/10.1186/1471-2105-12-196","mag":"2131684839","pmid":"https://pubmed.ncbi.nlm.nih.gov/21609434"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-12-196","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-196","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-196","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-196","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5091346096","display_name":"Jacek Sroka","orcid":"https://orcid.org/0000-0002-1714-9667"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Jacek Sroka","raw_affiliation_strings":["Institute of Informatics University of Warsaw, Poland","[Institute of Informatics, University of Warsaw, Poland]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"[Institute of Informatics, University of Warsaw, Poland]","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5074815708","display_name":"\u0141ukasz Bieniasz-Krzywiec","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"\u0141ukasz Bieniasz-Krzywiec","raw_affiliation_strings":["Institute of Informatics University of Warsaw, Poland","[Institute of Informatics, University of Warsaw, Poland]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"[Institute of Informatics, University of Warsaw, Poland]","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5043356589","display_name":"Szymon Gw\u00f3\u017ad\u017a","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Szymon Gw\u00f3\u017ad\u017a","raw_affiliation_strings":["Institute of Informatics University of Warsaw, Poland","[Institute of Informatics, University of Warsaw, Poland]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"[Institute of Informatics, University of Warsaw, Poland]","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086944842","display_name":"Dariusz Leniowski","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Dariusz Leniowski","raw_affiliation_strings":["Institute of Informatics University of Warsaw, Poland","[Institute of Informatics, University of Warsaw, Poland]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"[Institute of Informatics, University of Warsaw, Poland]","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044510135","display_name":"Jakub \u0141\u0105cki","orcid":"https://orcid.org/0000-0001-9347-0041"},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Jakub \u0141\u0105cki","raw_affiliation_strings":["Institute of Informatics University of Warsaw, Poland","[Institute of Informatics, University of Warsaw, Poland]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"[Institute of Informatics, University of Warsaw, Poland]","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5064299061","display_name":"Mateusz Markowski","orcid":null},"institutions":[{"id":"https://openalex.org/I4654613","display_name":"University of Warsaw","ror":"https://ror.org/039bjqg32","country_code":"PL","type":"education","lineage":["https://openalex.org/I4654613"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Mateusz Markowski","raw_affiliation_strings":["Institute of Informatics University of Warsaw, Poland","[Institute of Informatics, University of Warsaw, Poland]"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Informatics University of Warsaw, Poland","institution_ids":["https://openalex.org/I4654613"]},{"raw_affiliation_string":"[Institute of Informatics, University of Warsaw, Poland]","institution_ids":["https://openalex.org/I4654613"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085212686","display_name":"Claudio Avignone\u2013Rossa","orcid":"https://orcid.org/0000-0002-1625-6487"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Claudio Avignone-Rossa","raw_affiliation_strings":["Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","institution_ids":["https://openalex.org/I28290843"]},{"raw_affiliation_string":"Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088161465","display_name":"Michael E. Bushell","orcid":"https://orcid.org/0000-0001-9544-6686"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Michael E Bushell","raw_affiliation_strings":["Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","institution_ids":["https://openalex.org/I28290843"]},{"raw_affiliation_string":"Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028497882","display_name":"Johnjoe McFadden","orcid":"https://orcid.org/0000-0003-2145-0046"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Johnjoe McFadden","raw_affiliation_strings":["Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","institution_ids":["https://openalex.org/I28290843"]},{"raw_affiliation_string":"Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;","institution_ids":["https://openalex.org/I28290843"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5015589509","display_name":"Andrzej Kierzek","orcid":"https://orcid.org/0000-0002-2605-9057"},"institutions":[{"id":"https://openalex.org/I28290843","display_name":"University of Surrey","ror":"https://ror.org/00ks66431","country_code":"GB","type":"education","lineage":["https://openalex.org/I28290843"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Andrzej M Kierzek","raw_affiliation_strings":["Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Health and Medical Sciences, University of Surrey, Guildford, GU2 7XH, UK","institution_ids":["https://openalex.org/I28290843"]},{"raw_affiliation_string":"Faculty of Health & Medical Sciences, University of Surrey, Guildford, UK;","institution_ids":["https://openalex.org/I28290843"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5015589509"],"corresponding_institution_ids":["https://openalex.org/I28290843"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.9315,"has_fulltext":true,"cited_by_count":18,"citation_normalized_percentile":{"value":0.74339381,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"12","issue":"1","first_page":"196","last_page":"196"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9448999762535095,"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":0.9448999762535095,"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/T11882","display_name":"Plant biochemistry and biosynthesis","score":0.007300000172108412,"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":0.0038999998942017555,"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/computer-science","display_name":"Computer science","score":0.7481523156166077},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.6921083927154541},{"id":"https://openalex.org/keywords/grid","display_name":"Grid","score":0.5453625321388245},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5320181846618652},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.4945833384990692},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4880484342575073},{"id":"https://openalex.org/keywords/interface","display_name":"Interface (matter)","score":0.437645822763443},{"id":"https://openalex.org/keywords/user-interface","display_name":"User interface","score":0.427903950214386},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.4234659671783447},{"id":"https://openalex.org/keywords/constraint","display_name":"Constraint (computer-aided design)","score":0.41512852907180786},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3084558844566345},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.26822036504745483},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.24974000453948975},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18086302280426025},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.16552644968032837},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.13897395133972168},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1215423047542572},{"id":"https://openalex.org/keywords/operating-system","display_name":"Operating system","score":0.11584234237670898}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7481523156166077},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.6921083927154541},{"id":"https://openalex.org/C187691185","wikidata":"https://www.wikidata.org/wiki/Q2020720","display_name":"Grid","level":2,"score":0.5453625321388245},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5320181846618652},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.4945833384990692},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4880484342575073},{"id":"https://openalex.org/C113843644","wikidata":"https://www.wikidata.org/wiki/Q901882","display_name":"Interface (matter)","level":4,"score":0.437645822763443},{"id":"https://openalex.org/C89505385","wikidata":"https://www.wikidata.org/wiki/Q47146","display_name":"User interface","level":2,"score":0.427903950214386},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.4234659671783447},{"id":"https://openalex.org/C2776036281","wikidata":"https://www.wikidata.org/wiki/Q48769818","display_name":"Constraint (computer-aided design)","level":2,"score":0.41512852907180786},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3084558844566345},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.26822036504745483},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.24974000453948975},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18086302280426025},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.16552644968032837},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.13897395133972168},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1215423047542572},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.11584234237670898},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C157915830","wikidata":"https://www.wikidata.org/wiki/Q2928001","display_name":"Bubble","level":2,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0},{"id":"https://openalex.org/C129307140","wikidata":"https://www.wikidata.org/wiki/Q6795880","display_name":"Maximum bubble pressure method","level":3,"score":0.0}],"mesh":[{"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":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004926","descriptor_name":"Escherichia coli","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005716","descriptor_name":"Game Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005716","descriptor_name":"Game Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005716","descriptor_name":"Game Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D009169","descriptor_name":"Mycobacterium tuberculosis","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017433","descriptor_name":"Protein Structure, Secondary","qualifier_ui":null,"qualifier_name":null,"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}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-12-196","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-196","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-196","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:21609434","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21609434","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:alma.44SUR_INST:11139466940002346","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4210197018","display_name":"View","issn_l":"2688-268X","issn":["2688-268X","2688-3988"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320595","host_organization_name":"Wiley","host_organization_lineage":["https://openalex.org/P4310320595"],"host_organization_lineage_names":["Wiley"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:doaj.org/article:00f2babefdcf49639ec2c0ad213718fc","is_oa":false,"landing_page_url":"https://doaj.org/article/00f2babefdcf49639ec2c0ad213718fc","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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 12, Iss 1, p 196 (2011)","raw_type":"article"},{"id":"pmh:oai:epubs.surrey.ac.uk:185976","is_oa":false,"landing_page_url":"http://epubs.surrey.ac.uk/185976/1/acorn.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400680","display_name":"Surrey Research Insight Open Access (The University of Surrey)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28290843","host_organization_name":"University of Surrey","host_organization_lineage":["https://openalex.org/I28290843"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:3116490","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3116490","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-12-196","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-12-196","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-12-196","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1293619147","display_name":"Integration of modelling with transcription and gene essentiality profiling to study interaction of MTB bacillus with macrophages and dendritic cells.","funder_award_id":"BB/I00453X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"},{"id":"https://openalex.org/G2382994197","display_name":null,"funder_award_id":"BB/I00453X/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2131684839.pdf","grobid_xml":"https://content.openalex.org/works/W2131684839.grobid-xml"},"referenced_works_count":26,"referenced_works":["https://openalex.org/W1543388089","https://openalex.org/W1885034977","https://openalex.org/W1944107535","https://openalex.org/W1969067437","https://openalex.org/W1978928777","https://openalex.org/W1987622597","https://openalex.org/W1996529795","https://openalex.org/W2020916135","https://openalex.org/W2048214825","https://openalex.org/W2075283200","https://openalex.org/W2076262841","https://openalex.org/W2079531107","https://openalex.org/W2098983518","https://openalex.org/W2101127697","https://openalex.org/W2103950919","https://openalex.org/W2104108767","https://openalex.org/W2124536674","https://openalex.org/W2127257007","https://openalex.org/W2148895036","https://openalex.org/W2149829228","https://openalex.org/W2150908245","https://openalex.org/W2162237022","https://openalex.org/W2165554064","https://openalex.org/W2168465568","https://openalex.org/W2170427655","https://openalex.org/W2171437346"],"related_works":["https://openalex.org/W2150908245","https://openalex.org/W2211443823","https://openalex.org/W2097410126","https://openalex.org/W2136043941","https://openalex.org/W2735157934","https://openalex.org/W1869813392","https://openalex.org/W2043776573","https://openalex.org/W2026725606","https://openalex.org/W2020641517","https://openalex.org/W2136317480"],"abstract_inverted_index":{"BACKGROUND:":[0],"Constraint-based":[1],"approaches":[2,71],"facilitate":[3],"the":[4,16,22,83,94,98,151,195,235,243,255,276],"prediction":[5],"of":[6,15,18,54,57,60,93,117,134,153,175,208,275,282,313,327],"cellular":[7],"metabolic":[8,34,64,74,120,279,316],"capabilities,":[9],"based,":[10],"in":[11,21,63,97,194],"turn":[12],"on":[13],"predictions":[14,53],"repertoire":[17],"enzymes":[19],"encoded":[20],"genome.":[23],"Recently,":[24],"genome":[25,32,118,277,314],"annotations":[26],"have":[27,263],"been":[28],"used":[29,249],"to":[30,72,203,250,304,323],"reconstruct":[31],"scale":[33,119,278,315],"reaction":[35,121,201,280,317],"networks":[36,122,281],"for":[37,69,114,310],"numerous":[38],"species,":[39],"including":[40,52],"Homo":[41],"sapiens,":[42],"which":[43,144,163,297],"allow":[44],"simulations":[45,78,96,116,274,312],"that":[46,89],"provide":[47],"valuable":[48],"insights":[49],"into":[50,234],"topics,":[51],"gene":[55],"essentiality":[56],"pathogens,":[58],"interpretation":[59],"genetic":[61],"polymorphism":[62],"disease":[65],"syndromes":[66],"and":[67,168,172,185,199,212,221,231,266,287,325],"suggestions":[68],"novel":[70],"microbial":[73],"engineering.":[75],"These":[76],"constraint-based":[77,95,115],"are":[79,247],"being":[80],"integrated":[81,241],"with":[82],"functional":[84,205],"genomics":[85,206],"portals,":[86],"an":[87,106,124],"activity":[88],"requires":[90],"efficient":[91,132,165],"implementation":[92,174],"web-based":[99],"environment.":[100,127,257],"RESULTS:":[101],"Here,":[102],"we":[103,262],"present":[104],"Acorn,":[105],"open":[107],"source":[108],"(GNU":[109],"GPL)":[110],"grid":[111],"computing":[112],"system":[113],"within":[123,242,254],"interactive":[125],"web":[126,159,256,269,307],"The":[128,158],"grid-based":[129],"architecture":[130],"allows":[131],"execution":[133],"computationally":[135],"intensive,":[136],"iterative":[137],"protocols":[138],"such":[139],"as":[140,150],"Flux":[141],"Variability":[142],"Analysis,":[143],"can":[145,181,190,215,226,298],"be":[146,216,299],"readily":[147],"scaled":[148],"up":[149],"numbers":[152],"models":[154,193,211,324],"(and":[155],"users)":[156],"increase.":[157],"interface":[160],"uses":[161],"AJAX,":[162],"facilitates":[164,320],"model":[166],"browsing":[167],"other":[169],"search":[170],"functions,":[171],"intuitive":[173],"appropriate":[176],"simulation":[177,213],"conditions.":[178],"Research":[179],"groups":[180,303],"install":[182],"Acorn":[183,265,291],"locally":[184],"create":[186,305],"user":[187],"accounts.":[188],"Users":[189,225],"also":[191],"import":[192,232],"familiar":[196],"SBML":[197],"format":[198],"link":[200],"formulas":[202],"major":[204],"portals":[207],"choice.":[209],"Selected":[210],"results":[214,253],"shared":[217,321],"between":[218],"different":[219],"users":[220],"made":[222],"publically":[223],"available.":[224],"construct":[227],"pathway":[228],"map":[229],"layouts":[230],"them":[233],"server":[236,270],"using":[237],"a":[238,268,293,306],"desktop":[239],"editor":[240],"system.":[244],"Pathway":[245],"maps":[246],"then":[248],"visualise":[251],"numerical":[252],"To":[258],"illustrate":[259],"these":[260],"features":[261],"deployed":[264],"created":[267],"allowing":[271],"constraint":[272,330],"based":[273,308,331],"E.":[283],"coli,":[284],"S.":[285],"cerevisiae":[286],"M.":[288],"tuberculosis.":[289],"CONCLUSIONS:":[290],"is":[292],"free":[294],"software":[295],"package,":[296],"installed":[300],"by":[301],"research":[302],"environment":[309],"computer":[311],"networks.":[318],"It":[319],"access":[322],"creation":[326],"publicly":[328],"available":[329],"modelling":[332],"resources.":[333]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":3}],"updated_date":"2026-06-24T13:16:06.693445","created_date":"2025-10-10T00:00:00"}
