{"id":"https://openalex.org/W4284896622","doi":"https://doi.org/10.1093/bioinformatics/btac472","title":"DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia","display_name":"DelaySSAToolkit.jl: stochastic simulation of reaction systems with time delays in Julia","publication_year":2022,"publication_date":"2022-07-07","ids":{"openalex":"https://openalex.org/W4284896622","doi":"https://doi.org/10.1093/bioinformatics/btac472","pmid":"https://pubmed.ncbi.nlm.nih.gov/35799359"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btac472","doi":"https://doi.org/10.1093/bioinformatics/btac472","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac472","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.biorxiv.org/content/biorxiv/early/2022/01/23/2022.01.21.477236.full.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5060631280","display_name":"Xiaoming Fu","orcid":"https://orcid.org/0000-0003-4073-9822","observed_orcids":["https://orcid.org/0000-0003-4073-9822"]},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]},{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["CN","GB"],"is_corresponding":true,"raw_author_name":"Xiaoming Fu","raw_affiliation_strings":["MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China","School of Biological Sciences, The University of Edinburgh , Edinburgh, UK"],"raw_orcid":"https://orcid.org/0000-0003-4073-9822","affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China","institution_ids":["https://openalex.org/I143593769"]},{"raw_affiliation_string":"School of Biological Sciences, The University of Edinburgh , Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027605982","display_name":"Xinyi Zhou","orcid":"https://orcid.org/0000-0002-2862-7476","observed_orcids":["https://orcid.org/0000-0002-2862-7476","https://orcid.org/0009-0004-4576-4888","https://orcid.org/0000-0002-0189-8014"]},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xinyi Zhou","raw_affiliation_strings":["MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5008498739","display_name":"Dongyang Gu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Dongyang Gu","raw_affiliation_strings":["MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012669091","display_name":"Zhixing Cao","orcid":"https://orcid.org/0000-0003-2600-5806","observed_orcids":["https://orcid.org/0000-0003-2600-5806"]},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Zhixing Cao","raw_affiliation_strings":["MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China"],"raw_orcid":"https://orcid.org/0000-0003-2600-5806","affiliations":[{"raw_affiliation_string":"MOE Key Laboratory of Smart Manufacturing in Energy Chemical Process, East China University of Science and Technology , Shanghai, China","institution_ids":["https://openalex.org/I143593769"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029788536","display_name":"Ramon Grima","orcid":"https://orcid.org/0000-0002-1266-8169","observed_orcids":["https://orcid.org/0000-0002-1266-8169"]},"institutions":[{"id":"https://openalex.org/I98677209","display_name":"University of Edinburgh","ror":"https://ror.org/01nrxwf90","country_code":"GB","type":"education","lineage":["https://openalex.org/I98677209"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Ramon Grima","raw_affiliation_strings":["School of Biological Sciences, The University of Edinburgh , Edinburgh, UK"],"raw_orcid":"https://orcid.org/0000-0002-1266-8169","affiliations":[{"raw_affiliation_string":"School of Biological Sciences, The University of Edinburgh , Edinburgh, UK","institution_ids":["https://openalex.org/I98677209"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5012669091","https://openalex.org/A5029788536","https://openalex.org/A5060631280"],"corresponding_institution_ids":["https://openalex.org/I143593769","https://openalex.org/I98677209"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.6571,"has_fulltext":false,"cited_by_count":18,"citation_normalized_percentile":{"value":0.58677856,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":99},"biblio":{"volume":"38","issue":"17","first_page":"4243","last_page":"4245"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9599999785423279,"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":0.9599999785423279,"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/T11195","display_name":"Simulation Techniques and Applications","score":0.005400000140070915,"subfield":{"id":"https://openalex.org/subfields/1803","display_name":"Management Science and Operations Research"},"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/T11513","display_name":"stochastic dynamics and bifurcation","score":0.004100000020116568,"subfield":{"id":"https://openalex.org/subfields/3109","display_name":"Statistical and Nonlinear Physics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/time-delay","display_name":"time delay","score":0.7269999980926514},{"id":"https://openalex.org/keywords/reaction-systems","display_name":"reaction systems","score":0.7900000214576721},{"id":"https://openalex.org/keywords/non-markovian-dynamics","display_name":"non-Markovian dynamics","score":0.9879999756813049},{"id":"https://openalex.org/keywords/julia-package","display_name":"Julia package","score":0.6069999933242798},{"id":"https://openalex.org/keywords/model-reduction","display_name":"model reduction","score":0.8330000042915344},{"id":"https://openalex.org/keywords/chemical-reaction-networks","display_name":"chemical reaction networks","score":0.5789999961853027},{"id":"https://openalex.org/keywords/stochastic-simulation","display_name":"stochastic simulation","score":0.4259999990463257}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7020211219787598},{"id":"https://openalex.org/C56666940","wikidata":"https://www.wikidata.org/wiki/Q788790","display_name":"Documentation","level":2,"score":0.6642481088638306},{"id":"https://openalex.org/C2984074130","wikidata":"https://www.wikidata.org/wiki/Q73539779","display_name":"R package","level":2,"score":0.572412371635437},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.5710334777832031},{"id":"https://openalex.org/C111335779","wikidata":"https://www.wikidata.org/wiki/Q3454686","display_name":"Reduction (mathematics)","level":2,"score":0.546876847743988},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.5044044256210327},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.47076085209846497},{"id":"https://openalex.org/C159886148","wikidata":"https://www.wikidata.org/wiki/Q176645","display_name":"Markov process","level":2,"score":0.4356396198272705},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3839004635810852},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2731727957725525},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1881209909915924},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.16235783696174622},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.12030684947967529},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btac472","doi":"https://doi.org/10.1093/bioinformatics/btac472","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btac472","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"is_in_doaj":true,"is_core":true,"listed_in":["abdc-a","anvur-class-a","anvur-scientific","ccf-a","cwts-core","doaj","dongbi-b","doyens","jufo-3","ki-jl-2","medline","norway-2","oarl","poland-200","russia-white-list-1","vabb-shw"],"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"doi:10.1101/2022.01.21.477236","doi":"https://doi.org/10.1101/2022.01.21.477236","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.01.21.477236","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/01/23/2022.01.21.477236.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},{"id":"pmid:35799359","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/35799359","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,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":"Journal Article"},{"id":"pmh:oai:pure.ed.ac.uk:openaire/e94a09a8-6438-4e47-9fad-86e725b786a7","doi":null,"is_oa":true,"landing_page_url":"https://www.research.ed.ac.uk/files/331030283/DelaySSAToolkit.jl.pdf","pdf_url":null,"source":{"id":"https://openalex.org/S4306400321","display_name":"Edinburgh Research Explorer (University of Edinburgh)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I98677209","host_organization_name":"University of Edinburgh","host_organization_lineage":["https://openalex.org/I98677209"],"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":"Fu, X, Zhou, X, Gu, D, Cao, Z & Grima, R 2022, 'DelaySSAToolkit.jl : Stochastic simulation of reaction systems with time delays in Julia', Bioinformatics, vol. 38, no. 17, btac472, pp. 4243-4245. https://doi.org/10.1093/bioinformatics/btac472","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1101/2022.01.21.477236","doi":"https://doi.org/10.1101/2022.01.21.477236","is_oa":true,"landing_page_url":"https://doi.org/10.1101/2022.01.21.477236","pdf_url":"https://www.biorxiv.org/content/biorxiv/early/2022/01/23/2022.01.21.477236.full.pdf","source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G4852710174","display_name":null,"funder_award_id":"62073137","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4284896622.pdf","grobid_xml":"https://content.openalex.org/works/W4284896622.grobid-xml"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W1970550298","https://openalex.org/W1987003260","https://openalex.org/W1996405985","https://openalex.org/W2005535920","https://openalex.org/W2062404235","https://openalex.org/W2066985627","https://openalex.org/W2078734278","https://openalex.org/W2089961542","https://openalex.org/W2090248212","https://openalex.org/W2125744693","https://openalex.org/W2155418451","https://openalex.org/W2162556737","https://openalex.org/W2240819236","https://openalex.org/W2619381903","https://openalex.org/W3133885705","https://openalex.org/W3137389997","https://openalex.org/W3160417254","https://openalex.org/W3163858189","https://openalex.org/W3193780421","https://openalex.org/W3198990520","https://openalex.org/W4306406786"],"related_works":["https://openalex.org/W4409249850","https://openalex.org/W2005535920","https://openalex.org/W2026933731","https://openalex.org/W4232519263","https://openalex.org/W2378873601","https://openalex.org/W7037067788","https://openalex.org/W1998793212","https://openalex.org/W2002540105","https://openalex.org/W1999325995","https://openalex.org/W2027506430"],"abstract_inverted_index":{"SUMMARY:":[0],"DelaySSAToolkit.jl":[1,67],"is":[2],"a":[3,47],"Julia":[4],"package":[5,45],"for":[6,35],"modelling":[7],"reaction":[8,24],"systems":[9,37],"with":[10,15],"non-Markovian":[11],"dynamics,":[12],"specifically":[13],"those":[14],"time":[16],"delays.":[17],"These":[18],"delays":[19],"implicitly":[20],"capture":[21],"multiple":[22],"intermediate":[23],"steps":[25],"and":[26,42,64],"hence":[27],"serve":[28],"as":[29],"an":[30],"effective":[31],"model":[32],"reduction":[33],"technique":[34],"complex":[36],"in":[38],"biology,":[39],"chemistry,":[40],"ecology":[41],"genetics.":[43],"The":[44,61],"implements":[46],"variety":[48],"of":[49,52,66],"exact":[50],"formulations":[51],"the":[53],"delay":[54],"stochastic":[55],"simulation":[56],"algorithm.":[57],"AVAILABILITY":[58],"AND":[59],"IMPLEMENTATION:":[60],"source":[62],"code":[63],"documentation":[65],"are":[68],"available":[69],"at":[70],"https://github.com/palmtree2013/DelaySSAToolkit.jl.":[71]},"counts_by_year":[{"year":2026,"cited_by_count":9},{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":1},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":1}],"updated_date":"2026-11-10T11:39:43.021295","created_date":"2022-07-09T00:00:00"}
