{"id":"https://openalex.org/W2476171611","doi":"https://doi.org/10.2390/biecoll-jib-2016-284","title":"PetriScape - A plugin for discrete Petri net simulations in Cytoscape","display_name":"PetriScape - A plugin for discrete Petri net simulations in Cytoscape","publication_year":2016,"publication_date":"2016-01-01","ids":{"openalex":"https://openalex.org/W2476171611","doi":"https://doi.org/10.2390/biecoll-jib-2016-284","mag":"2476171611","pmid":"https://pubmed.ncbi.nlm.nih.gov/27402693"},"language":"en","primary_location":{"id":"pmid:27402693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27402693","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":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://portal.findresearcher.sdu.dk/da/publications/14a4ae2e-27e0-46e0-93c5-fcf1627b73af","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025615159","display_name":"Diogo Almeida","orcid":null},"institutions":[{"id":"https://openalex.org/I4210143403","display_name":"Norwegian Institute of Bioeconomy Research","ror":"https://ror.org/04aah1z61","country_code":"NO","type":"funder","lineage":["https://openalex.org/I4210143403"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Almeida, Diogo","raw_affiliation_strings":["Institut for Biokemi og Molekyl\u00e6r Biologi"],"affiliations":[{"raw_affiliation_string":"Institut for Biokemi og Molekyl\u00e6r Biologi","institution_ids":["https://openalex.org/I4210143403"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090969979","display_name":"Vasco Azevedo","orcid":"https://orcid.org/0000-0002-4775-2280"},"institutions":[{"id":"https://openalex.org/I59606676","display_name":"Universidade Federal do Par\u00e1","ror":"https://ror.org/03q9sr818","country_code":"BR","type":"education","lineage":["https://openalex.org/I59606676"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Azevedo, Vasco","raw_affiliation_strings":["FEDERAL UNIVERSITY OF PARA"],"affiliations":[{"raw_affiliation_string":"FEDERAL UNIVERSITY OF PARA","institution_ids":["https://openalex.org/I59606676"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100635120","display_name":"Artur Silva","orcid":"https://orcid.org/0000-0002-4082-1132"},"institutions":[{"id":"https://openalex.org/I110200422","display_name":"Universidade Federal de Minas Gerais","ror":"https://ror.org/0176yjw32","country_code":"BR","type":"education","lineage":["https://openalex.org/I110200422"]}],"countries":["BR"],"is_corresponding":false,"raw_author_name":"Silva, Artur","raw_affiliation_strings":["FEDERAL UNIVERSITY OF MINAS GERAIS"],"affiliations":[{"raw_affiliation_string":"FEDERAL UNIVERSITY OF MINAS GERAIS","institution_ids":["https://openalex.org/I110200422"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5073222532","display_name":"Jan Baumbach","orcid":"https://orcid.org/0000-0002-0282-0462"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Baumbach, Jan","raw_affiliation_strings":["Institut for Matematik og Datalogi"],"affiliations":[{"raw_affiliation_string":"Institut for Matematik og Datalogi","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5025615159"],"corresponding_institution_ids":["https://openalex.org/I4210143403"],"apc_list":null,"apc_paid":null,"fwci":0.1743,"has_fulltext":true,"cited_by_count":4,"citation_normalized_percentile":{"value":0.64513441,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"13","issue":"1","first_page":"284","last_page":"284"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9908000230789185,"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":0.9908000230789185,"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/T11986","display_name":"Scientific Computing and Data Management","score":0.9778000116348267,"subfield":{"id":"https://openalex.org/subfields/1802","display_name":"Information Systems and Management"},"field":{"id":"https://openalex.org/fields/18","display_name":"Decision Sciences"},"domain":{"id":"https://openalex.org/domains/2","display_name":"Social Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9767000079154968,"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/petri-net","display_name":"Petri net","score":0.8492588400840759},{"id":"https://openalex.org/keywords/sbml","display_name":"SBML","score":0.8446247577667236},{"id":"https://openalex.org/keywords/plug-in","display_name":"Plug-in","score":0.8342688679695129},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.776627242565155},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.6227683424949646},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.5473634004592896},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.5446982979774475},{"id":"https://openalex.org/keywords/graph-drawing","display_name":"Graph drawing","score":0.4260382354259491},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.4257136583328247},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.38042622804641724},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.36122214794158936},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3088182806968689},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16176098585128784},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.15044227242469788},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.11172658205032349},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.08823013305664062}],"concepts":[{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.8492588400840759},{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.8446247577667236},{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.8342688679695129},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.776627242565155},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6227683424949646},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5473634004592896},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.5446982979774475},{"id":"https://openalex.org/C112953755","wikidata":"https://www.wikidata.org/wiki/Q739462","display_name":"Graph drawing","level":3,"score":0.4260382354259491},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.4257136583328247},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.38042622804641724},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.36122214794158936},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3088182806968689},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16176098585128784},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.15044227242469788},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.11172658205032349},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.08823013305664062}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"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":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"pmid:27402693","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/27402693","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:sdu.dk:publications/14a4ae2e-27e0-46e0-93c5-fcf1627b73af","is_oa":true,"landing_page_url":"https://portal.findresearcher.sdu.dk/da/publications/14a4ae2e-27e0-46e0-93c5-fcf1627b73af","pdf_url":"https://portal.findresearcher.sdu.dk/da/publications/14a4ae2e-27e0-46e0-93c5-fcf1627b73af","source":{"id":"https://openalex.org/S4306400423","display_name":"University of Southern Denmark Research Portal (University of Southern Denmark)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177969490","host_organization_name":"University of Southern Denmark","host_organization_lineage":["https://openalex.org/I177969490"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Almeida , D , Azevedo , V , Silva , A &amp; Baumbach , J 2016 , ' PetriScape : A plugin for discrete Petri net simulations in Cytoscape ' , Journal of Integrative Bioinformatics , vol. 13 , no. 1 , 284 . https://doi.org/10.2390/biecoll-jib-2016-284","raw_type":"article"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:5423","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2016/5423/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=284","raw_type":"Journal Article"},{"id":"doi:10.2390/biecoll-jib-2016-284","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2016-284","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"pmh:oai:sdu.dk:publications/14a4ae2e-27e0-46e0-93c5-fcf1627b73af","is_oa":true,"landing_page_url":"https://portal.findresearcher.sdu.dk/da/publications/14a4ae2e-27e0-46e0-93c5-fcf1627b73af","pdf_url":"https://portal.findresearcher.sdu.dk/da/publications/14a4ae2e-27e0-46e0-93c5-fcf1627b73af","source":{"id":"https://openalex.org/S4306400423","display_name":"University of Southern Denmark Research Portal (University of Southern Denmark)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I177969490","host_organization_name":"University of Southern Denmark","host_organization_lineage":["https://openalex.org/I177969490"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Almeida , D , Azevedo , V , Silva , A &amp; Baumbach , J 2016 , ' PetriScape : A plugin for discrete Petri net simulations in Cytoscape ' , Journal of Integrative Bioinformatics , vol. 13 , no. 1 , 284 . https://doi.org/10.2390/biecoll-jib-2016-284","raw_type":"article"},"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[{"id":"https://openalex.org/G3938906640","display_name":null,"funder_award_id":"(CAPES)","funder_id":"https://openalex.org/F4320321091","funder_display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior"}],"funders":[{"id":"https://openalex.org/F4320314239","display_name":"Netherlands eScience Center","ror":"https://ror.org/00rbjv475"},{"id":"https://openalex.org/F4320321091","display_name":"Coordena\u00e7\u00e3o de Aperfei\u00e7oamento de Pessoal de N\u00edvel Superior","ror":"https://ror.org/00x0ma614"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2476171611.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W95898642","https://openalex.org/W156416472","https://openalex.org/W432429310","https://openalex.org/W1544455702","https://openalex.org/W1563476066","https://openalex.org/W1989277387","https://openalex.org/W2000860171","https://openalex.org/W2011835017","https://openalex.org/W2102263388","https://openalex.org/W2113665677","https://openalex.org/W2114124738","https://openalex.org/W2118934251","https://openalex.org/W2125810455","https://openalex.org/W2133730856","https://openalex.org/W2134784304","https://openalex.org/W2162144833","https://openalex.org/W2171594815"],"related_works":["https://openalex.org/W4385891864","https://openalex.org/W4321472021","https://openalex.org/W2141346699","https://openalex.org/W2045478141","https://openalex.org/W3091139413","https://openalex.org/W2118803783","https://openalex.org/W2115343689","https://openalex.org/W328975855","https://openalex.org/W2735157934","https://openalex.org/W1561795279"],"abstract_inverted_index":{"Systems":[0],"biology":[1],"plays":[2],"a":[3,129,159],"central":[4],"role":[5],"for":[6,26,46,80,154],"biological":[7,121,179],"network":[8,33,48,96],"analysis":[9,28],"in":[10,50,123,146,178],"the":[11,16,21,30,75,114,143,150,173],"post-genomic":[12],"era.":[13],"Cytoscape":[14,51,67,152],"is":[15,149],"standard":[17],"bioinformatics":[18],"tool":[19],"offering":[20],"community":[22],"an":[23],"extensible":[24],"platform":[25],"computational":[27],"of":[29,55,61,93,120,142,175],"emerging":[31],"cellular":[32],"together":[34],"with":[35,113,168],"experimental":[36],"omics":[37],"data":[38],"sets.":[39],"However,":[40],"only":[41],"few":[42],"apps/plugins/tools":[43],"are":[44,86,91,105],"available":[45],"simulating":[47,99],"dynamics":[49],"3.":[52],"Many":[53],"approaches":[54],"varying":[56],"complexity":[57],"exist":[58],"but":[59],"none":[60],"them":[62],"have":[63],"been":[64],"integrated":[65],"into":[66,128],"as":[68,134],"app/plugin":[69],"yet.":[70],"Here,":[71],"we":[72],"introduce":[73],"PetriScape,":[74],"first":[76,151],"Petri":[77,84,130,135,155,161],"net":[78,162],"simulator":[79],"Cytoscape.":[81,147],"Although":[82],"discrete":[83],"nets":[85],"quite":[87],"simplistic":[88],"models,":[89],"they":[90,104],"capable":[92],"modeling":[94],"global":[95],"properties":[97],"and":[98,108,137,140,166],"their":[100],"behaviour.":[101],"In":[102],"addition,":[103],"easily":[106],"understood":[107],"well":[109],"visualizable.":[110],"PetriScape":[111,148],"comes":[112],"following":[115],"main":[116],"functionalities:":[117],"(1)":[118],"import":[119],"networks":[122],"SBML":[124],"format,":[125],"(2)":[126],"conversion":[127],"net,":[131,136],"(3)":[132],"visualization":[133,141,167],"(4)":[138],"simulation":[139,165],"token":[144],"flow":[145],"plugin":[153],"nets.":[156],"It":[157],"allows":[158],"straightforward":[160],"model":[163],"creation,":[164],"Cytoscape,":[169],"providing":[170],"clues":[171],"about":[172],"activity":[174],"key":[176],"components":[177],"networks.":[180]},"counts_by_year":[{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
