{"id":"https://openalex.org/W2123089646","doi":"https://doi.org/10.1186/1752-0509-8-22","title":"GraTeLPy: graph-theoretic linear stability analysis","display_name":"GraTeLPy: graph-theoretic linear stability analysis","publication_year":2014,"publication_date":"2014-01-01","ids":{"openalex":"https://openalex.org/W2123089646","doi":"https://doi.org/10.1186/1752-0509-8-22","mag":"2123089646","pmid":"https://pubmed.ncbi.nlm.nih.gov/24572152"},"language":"en","primary_location":{"id":"doi:10.1186/1752-0509-8-22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-22","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-22","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-22","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000935471","display_name":"Georg R. Walther","orcid":null},"institutions":[{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]},{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Georg R Walther","raw_affiliation_strings":["Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK. gratelpy@gmail.com","Computational & Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK. gratelpy@gmail.com","institution_ids":[]},{"raw_affiliation_string":"Computational & Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055606383","display_name":"Matthew Hartley","orcid":"https://orcid.org/0000-0001-6178-2884"},"institutions":[{"id":"https://openalex.org/I100288624","display_name":"John Innes Centre","ror":"https://ror.org/055zmrh94","country_code":"GB","type":"facility","lineage":["https://openalex.org/I100288624","https://openalex.org/I2799693246","https://openalex.org/I4210087105"]},{"id":"https://openalex.org/I2799300731","display_name":"Norwich Research Park","ror":"https://ror.org/0062dz060","country_code":"GB","type":"archive","lineage":["https://openalex.org/I2799300731"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Matthew Hartley","raw_affiliation_strings":["Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK","Computational & Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computational and Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]},{"raw_affiliation_string":"Computational & Systems Biology, John Innes Centre, Norwich Research Park, Norwich, UK","institution_ids":["https://openalex.org/I2799300731","https://openalex.org/I100288624"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034736452","display_name":"Maya Mincheva","orcid":null},"institutions":[{"id":"https://openalex.org/I102502594","display_name":"Northern Illinois University","ror":"https://ror.org/012wxa772","country_code":"US","type":"education","lineage":["https://openalex.org/I102502594"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Maya Mincheva","raw_affiliation_strings":["Department of Mathematical Sciences, Northern Illinois University, DeKalb, IL 60115, USA","Department of Mathematical Sciences, Northern Illinois University, DeKalb, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematical Sciences, Northern Illinois University, DeKalb, IL 60115, USA","institution_ids":["https://openalex.org/I102502594"]},{"raw_affiliation_string":"Department of Mathematical Sciences, Northern Illinois University, DeKalb, USA","institution_ids":["https://openalex.org/I102502594"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000935471"],"corresponding_institution_ids":["https://openalex.org/I100288624","https://openalex.org/I2799300731"],"apc_list":null,"apc_paid":null,"fwci":0.996,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.757803,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"8","issue":"1","first_page":"22","last_page":"22"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.8485999703407288,"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":0.8485999703407288,"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/T12772","display_name":"Control and Stability of Dynamical Systems","score":0.07450000196695328,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11187","display_name":"Nonlinear Dynamics and Pattern Formation","score":0.02070000022649765,"subfield":{"id":"https://openalex.org/subfields/1705","display_name":"Computer Networks and Communications"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/bipartite-graph","display_name":"Bipartite graph","score":0.7989692687988281},{"id":"https://openalex.org/keywords/digraph","display_name":"Digraph","score":0.7225638628005981},{"id":"https://openalex.org/keywords/multistability","display_name":"Multistability","score":0.49360764026641846},{"id":"https://openalex.org/keywords/correctness","display_name":"Correctness","score":0.4922991991043091},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4538699984550476},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.40710434317588806},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.39804741740226746},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.34885525703430176},{"id":"https://openalex.org/keywords/discrete-mathematics","display_name":"Discrete mathematics","score":0.2946879267692566},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.2173764705657959},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.16181281208992004},{"id":"https://openalex.org/keywords/nonlinear-system","display_name":"Nonlinear system","score":0.11264210939407349}],"concepts":[{"id":"https://openalex.org/C197657726","wikidata":"https://www.wikidata.org/wiki/Q174733","display_name":"Bipartite graph","level":3,"score":0.7989692687988281},{"id":"https://openalex.org/C2779145032","wikidata":"https://www.wikidata.org/wiki/Q191494","display_name":"Digraph","level":2,"score":0.7225638628005981},{"id":"https://openalex.org/C2776966350","wikidata":"https://www.wikidata.org/wiki/Q6935096","display_name":"Multistability","level":3,"score":0.49360764026641846},{"id":"https://openalex.org/C55439883","wikidata":"https://www.wikidata.org/wiki/Q360812","display_name":"Correctness","level":2,"score":0.4922991991043091},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4538699984550476},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.40710434317588806},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.39804741740226746},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.34885525703430176},{"id":"https://openalex.org/C118615104","wikidata":"https://www.wikidata.org/wiki/Q121416","display_name":"Discrete mathematics","level":1,"score":0.2946879267692566},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.2173764705657959},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.16181281208992004},{"id":"https://openalex.org/C158622935","wikidata":"https://www.wikidata.org/wiki/Q660848","display_name":"Nonlinear system","level":2,"score":0.11264210939407349},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007700","descriptor_name":"Kinetics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016014","descriptor_name":"Linear Models","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1752-0509-8-22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-22","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-22","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},{"id":"pmid:24572152","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/24572152","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 systems biology","raw_type":null},{"id":"pmh:oai:europepmc.org:3005912","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4016541","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1752-0509-8-22","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1752-0509-8-22","pdf_url":"https://bmcsystbiol.biomedcentral.com/counter/pdf/10.1186/1752-0509-8-22","source":{"id":"https://openalex.org/S92363890","display_name":"BMC Systems Biology","issn_l":"1752-0509","issn":["1752-0509"],"is_oa":true,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Systems Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G8777311259","display_name":null,"funder_award_id":"BBS/E/J/000C0646","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":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2123089646.pdf","grobid_xml":"https://content.openalex.org/works/W2123089646.grobid-xml"},"referenced_works_count":32,"referenced_works":["https://openalex.org/W1530803355","https://openalex.org/W1974915811","https://openalex.org/W1985482228","https://openalex.org/W1987198995","https://openalex.org/W1996851382","https://openalex.org/W1999641688","https://openalex.org/W2008129880","https://openalex.org/W2008793553","https://openalex.org/W2009369602","https://openalex.org/W2009483875","https://openalex.org/W2011301426","https://openalex.org/W2016931470","https://openalex.org/W2049398671","https://openalex.org/W2053592662","https://openalex.org/W2062029454","https://openalex.org/W2064483836","https://openalex.org/W2083342911","https://openalex.org/W2091695815","https://openalex.org/W2094781369","https://openalex.org/W2105640293","https://openalex.org/W2112180211","https://openalex.org/W2127286352","https://openalex.org/W2132022337","https://openalex.org/W2133116903","https://openalex.org/W2134233117","https://openalex.org/W2135535700","https://openalex.org/W2137801186","https://openalex.org/W2150908245","https://openalex.org/W2599094605","https://openalex.org/W2799004609","https://openalex.org/W2963060498","https://openalex.org/W3101987991"],"related_works":["https://openalex.org/W1527571384","https://openalex.org/W2383189914","https://openalex.org/W2963840034","https://openalex.org/W4301445084","https://openalex.org/W1984975294","https://openalex.org/W99690574","https://openalex.org/W2790788195","https://openalex.org/W2962785705","https://openalex.org/W2121104987","https://openalex.org/W4293584096"],"abstract_inverted_index":{"BACKGROUND:":[0],"A":[1],"biochemical":[2,95,110,122,171],"mechanism":[3,123],"with":[4,173],"mass":[5,174],"action":[6,175],"kinetics":[7,176],"can":[8,32,71,163],"be":[9,164],"represented":[10],"as":[11,39,53],"a":[12,21,49,54,63,81,94,108,114,121],"directed":[13],"bipartite":[14,46,91,105],"graph":[15],"(bipartite":[16],"digraph),":[17],"and":[18,152,183],"modeled":[19],"by":[20,139,166],"system":[22],"of":[23,62,89,93,103,107,120,134],"differential":[24,28],"equations.":[25],"If":[26],"the":[27,45,60,68,86,90,104,118,135,156],"equations":[29],"(DE)":[30],"model":[31,70],"give":[33],"rise":[34],"to":[35,52,168],"some":[36,58,75,125],"instability":[37,126],"such":[38],"multistability":[40],"or":[41],"Turing":[42,184],"instability,":[43],"then":[44],"digraph":[47,92,106],"contains":[48],"structure":[50],"referred":[51],"critical":[55,64,87,101],"fragment.":[56],"In":[57],"cases":[59],"existence":[61],"fragment":[65],"indicates":[66],"that":[67,84],"DE":[69],"display":[72],"oscillations":[73,182],"for":[74,124,177,180],"parameter":[76],"values.":[77],"We":[78],"have":[79],"implemented":[80,145],"graph-theoretic":[82],"method":[83],"identifies":[85],"fragments":[88,102],"mechanism.":[96],"RESULTS:":[97],"GraTeLPy":[98,162],"lists":[99],"all":[100],"given":[109],"mechanism,":[111],"thus":[112],"enabling":[113],"preliminary":[115],"analysis":[116],"on":[117,128,149],"potential":[119],"based":[127],"its":[129],"topological":[130],"structure.":[131],"The":[132,142],"correctness":[133],"implementation":[136],"is":[137,144,153],"supported":[138],"multiple":[140],"examples.":[141],"code":[143],"in":[146],"Python,":[147],"relies":[148],"open":[150],"software,":[151],"available":[154],"under":[155],"GNU":[157],"General":[158],"Public":[159],"License.":[160],"CONCLUSIONS:":[161],"used":[165],"researchers":[167],"test":[169],"large":[170],"mechanisms":[172],"their":[178],"capacity":[179],"multistability,":[181],"instability.":[185]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3}],"updated_date":"2026-04-29T09:16:38.111599","created_date":"2025-10-10T00:00:00"}