{"id":"https://openalex.org/W1595961914","doi":"https://doi.org/10.1186/1471-2105-7-129","title":"SNA \u2013 a toolbox for the stoichiometric analysis of metabolic networks","display_name":"SNA \u2013 a toolbox for the stoichiometric analysis of metabolic networks","publication_year":2006,"publication_date":"2006-03-13","ids":{"openalex":"https://openalex.org/W1595961914","doi":"https://doi.org/10.1186/1471-2105-7-129","mag":"1595961914","pmid":"https://pubmed.ncbi.nlm.nih.gov/16533403"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-7-129","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-129","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-129","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/10.1186/1471-2105-7-129","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032338878","display_name":"Robert Urbanczik","orcid":null},"institutions":[{"id":"https://openalex.org/I118564535","display_name":"University of Bern","ror":"https://ror.org/02k7v4d05","country_code":"CH","type":"education","lineage":["https://openalex.org/I118564535"]},{"id":"https://openalex.org/I130692619","display_name":"Bern University of Applied Sciences","ror":"https://ror.org/02bnkt322","country_code":"CH","type":"education","lineage":["https://openalex.org/I130692619"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Robert Urbanczik","raw_affiliation_strings":["Institute of Pharmacology, University of Bern, Friedb\u00fchlstr. 49, CH-3010 Bern, Switzerland. urbanczik@physik.uni-wuerzburg.de","Institute of Pharmacology, University of Bern, Friedb\u00fchlstr. 49, CH-3010 Bern, Switzerland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Pharmacology, University of Bern, Friedb\u00fchlstr. 49, CH-3010 Bern, Switzerland. urbanczik@physik.uni-wuerzburg.de","institution_ids":["https://openalex.org/I118564535"]},{"raw_affiliation_string":"Institute of Pharmacology, University of Bern, Friedb\u00fchlstr. 49, CH-3010 Bern, Switzerland","institution_ids":["https://openalex.org/I118564535","https://openalex.org/I130692619"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5032338878"],"corresponding_institution_ids":["https://openalex.org/I118564535","https://openalex.org/I130692619"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.2715,"has_fulltext":true,"cited_by_count":40,"citation_normalized_percentile":{"value":0.7653595,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"7","issue":"1","first_page":"129","last_page":"129"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9883999824523926,"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":0.9883999824523926,"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/T12643","display_name":"Sustainability and Ecological Systems Analysis","score":0.003000000026077032,"subfield":{"id":"https://openalex.org/subfields/2305","display_name":"Environmental Engineering"},"field":{"id":"https://openalex.org/fields/23","display_name":"Environmental Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12915","display_name":"Biochemical Acid Research Studies","score":0.0008999999845400453,"subfield":{"id":"https://openalex.org/subfields/1303","display_name":"Biochemistry"},"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/toolbox","display_name":"Toolbox","score":0.8681579828262329},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7289983630180359},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.683411180973053},{"id":"https://openalex.org/keywords/license","display_name":"License","score":0.5932006239891052},{"id":"https://openalex.org/keywords/metabolic-network","display_name":"Metabolic network","score":0.5135312676429749},{"id":"https://openalex.org/keywords/mit-license","display_name":"MIT License","score":0.4784281849861145},{"id":"https://openalex.org/keywords/computation","display_name":"Computation","score":0.47639599442481995},{"id":"https://openalex.org/keywords/network-analysis","display_name":"Network analysis","score":0.44288474321365356},{"id":"https://openalex.org/keywords/metabolic-flux-analysis","display_name":"Metabolic flux analysis","score":0.43143048882484436},{"id":"https://openalex.org/keywords/flux-balance-analysis","display_name":"Flux balance analysis","score":0.41374847292900085},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.38272976875305176},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3327251076698303},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.22601163387298584},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1943715214729309},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10654321312904358},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09875255823135376}],"concepts":[{"id":"https://openalex.org/C2777655017","wikidata":"https://www.wikidata.org/wiki/Q1501161","display_name":"Toolbox","level":2,"score":0.8681579828262329},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7289983630180359},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.683411180973053},{"id":"https://openalex.org/C2780560020","wikidata":"https://www.wikidata.org/wiki/Q79719","display_name":"License","level":2,"score":0.5932006239891052},{"id":"https://openalex.org/C101810790","wikidata":"https://www.wikidata.org/wiki/Q2263094","display_name":"Metabolic network","level":2,"score":0.5135312676429749},{"id":"https://openalex.org/C174183944","wikidata":"https://www.wikidata.org/wiki/Q334661","display_name":"MIT License","level":3,"score":0.4784281849861145},{"id":"https://openalex.org/C45374587","wikidata":"https://www.wikidata.org/wiki/Q12525525","display_name":"Computation","level":2,"score":0.47639599442481995},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.44288474321365356},{"id":"https://openalex.org/C160941953","wikidata":"https://www.wikidata.org/wiki/Q6822342","display_name":"Metabolic flux analysis","level":3,"score":0.43143048882484436},{"id":"https://openalex.org/C167091322","wikidata":"https://www.wikidata.org/wiki/Q5463029","display_name":"Flux balance analysis","level":2,"score":0.41374847292900085},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.38272976875305176},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3327251076698303},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.22601163387298584},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1943715214729309},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10654321312904358},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09875255823135376},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"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/C119599485","wikidata":"https://www.wikidata.org/wiki/Q43035","display_name":"Electrical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"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":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":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":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":6,"locations":[{"id":"doi:10.1186/1471-2105-7-129","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-129","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-129","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:16533403","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/16533403","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:boris.unibe.ch:18528","is_oa":true,"landing_page_url":"https://boris.unibe.ch/18528/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401086","display_name":"Bern Open Repository and Information System (University of Bern)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I118564535","host_organization_name":"University of Bern","host_organization_lineage":["https://openalex.org/I118564535"],"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":"Urbanczik, Robert (2006). SNA--a toolbox for the stoichiometric analysis of metabolic networks. BMC bioinformatics, 7, p. 129. London: BioMed Central 10.1186/1471-2105-7-129 <http://dx.doi.org/10.1186/1471-2105-7-129>","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:b00a1a4cca484a849b1a8b7cef10f82d","is_oa":false,"landing_page_url":"https://doaj.org/article/b00a1a4cca484a849b1a8b7cef10f82d","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 7, Iss 1, p 129 (2006)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:185754","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC1431567","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:1431567","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1431567","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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-7-129","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-7-129","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-7-129","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":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1595961914.pdf","grobid_xml":"https://content.openalex.org/works/W1595961914.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W1537437230","https://openalex.org/W1758395617","https://openalex.org/W1964491374","https://openalex.org/W1996529795","https://openalex.org/W2004159793","https://openalex.org/W2025663053","https://openalex.org/W2048214825","https://openalex.org/W2068065441","https://openalex.org/W2094399313","https://openalex.org/W2116324021","https://openalex.org/W2170576111","https://openalex.org/W4249667877"],"related_works":["https://openalex.org/W1999460937","https://openalex.org/W2113329733","https://openalex.org/W2133150343","https://openalex.org/W2341681417","https://openalex.org/W1984242440","https://openalex.org/W1983989854","https://openalex.org/W2070388085","https://openalex.org/W2047334633","https://openalex.org/W2350881169","https://openalex.org/W2613838074"],"abstract_inverted_index":{"BACKGROUND:":[0],"Despite":[1],"recent":[2],"algorithmic":[3],"and":[4,42,48,68,88,115],"conceptual":[5],"progress,":[6],"the":[7,30,40,55,102,112,118],"stoichiometric":[8],"network":[9],"analysis":[10,114],"of":[11,35,45,117],"large":[12],"metabolic":[13,36,99],"models":[14],"remains":[15],"a":[16,23,107],"computationally":[17],"challenging":[18],"problem.":[19],"RESULTS:":[20],"SNA":[21,91],"is":[22,63,74,92],"interactive,":[24],"high":[25],"performance":[26,87],"toolbox":[27,62],"for":[28,111],"analysing":[29,54,96],"possible":[31],"steady":[32,56],"state":[33],"behaviour":[34],"networks":[37],"by":[38,58],"computing":[39],"generating":[41],"elementary":[43],"vectors":[44],"their":[46],"flux":[47],"conversions":[49],"cones.":[50],"It":[51,73],"also":[52],"supports":[53],"states":[57],"linear":[59],"programming.":[60],"The":[61],"implemented":[64],"mainly":[65],"in":[66,95],"Mathematica":[67,105],"returns":[69],"numerically":[70],"exact":[71],"results.":[72,119],"available":[75],"under":[76],"an":[77],"open":[78],"source":[79],"license":[80],"from:":[81],"http://bioinformatics.org/project/?group_id=546.":[82],"CONCLUSION:":[83],"Thanks":[84],"to":[85],"its":[86],"modular":[89],"design,":[90],"demonstrably":[93],"useful":[94],"genome":[97],"scale":[98],"networks.":[100],"Further,":[101],"integration":[103],"into":[104],"provides":[106],"very":[108],"flexible":[109],"environment":[110],"subsequent":[113],"interpretation":[116]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":4}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}