{"id":"https://openalex.org/W2734824431","doi":"https://doi.org/10.1093/bioinformatics/btx456","title":"SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces","display_name":"SPATKIN: a simulator for rule-based modeling of biomolecular site dynamics on surfaces","publication_year":2017,"publication_date":"2017-07-14","ids":{"openalex":"https://openalex.org/W2734824431","doi":"https://doi.org/10.1093/bioinformatics/btx456","mag":"2734824431","pmid":"https://pubmed.ncbi.nlm.nih.gov/29036531"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btx456","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx456","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,"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"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860254","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041747421","display_name":"Marek Kocha\u0144czyk","orcid":"https://orcid.org/0000-0003-1215-3920"},"institutions":[{"id":"https://openalex.org/I4210119410","display_name":"Institute of Fundamental Technological Research","ror":"https://ror.org/03fs4aq04","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210119410","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":true,"raw_author_name":"Marek Kocha\u0144czyk","raw_affiliation_strings":["Institute of Fundamental Technological Research, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Fundamental Technological Research, Warsaw, Poland","institution_ids":["https://openalex.org/I4210119410"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016126519","display_name":"William S. Hlavacek","orcid":"https://orcid.org/0000-0003-4383-8711"},"institutions":[{"id":"https://openalex.org/I1343871089","display_name":"Los Alamos National Laboratory","ror":"https://ror.org/01e41cf67","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I1343871089","https://openalex.org/I198811213","https://openalex.org/I4210120050"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William S Hlavacek","raw_affiliation_strings":["Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA","institution_ids":["https://openalex.org/I1343871089"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5024103451","display_name":"Tomasz Lipniacki","orcid":"https://orcid.org/0000-0002-3488-2561"},"institutions":[{"id":"https://openalex.org/I4210119410","display_name":"Institute of Fundamental Technological Research","ror":"https://ror.org/03fs4aq04","country_code":"PL","type":"facility","lineage":["https://openalex.org/I4210119410","https://openalex.org/I99542240"]}],"countries":["PL"],"is_corresponding":false,"raw_author_name":"Tomasz Lipniacki","raw_affiliation_strings":["Institute of Fundamental Technological Research, Warsaw, Poland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Fundamental Technological Research, Warsaw, Poland","institution_ids":["https://openalex.org/I4210119410"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5041747421"],"corresponding_institution_ids":["https://openalex.org/I4210119410"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":0.3037,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.56149926,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":96},"biblio":{"volume":"33","issue":"22","first_page":"3667","last_page":"3669"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.13490000367164612,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.13490000367164612,"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":0.11580000072717667,"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/T14135","display_name":"Cancer and biochemical research","score":0.04820000007748604,"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":0.8095114231109619},{"id":"https://openalex.org/keywords/source-code","display_name":"Source code","score":0.6360641717910767},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.47345560789108276},{"id":"https://openalex.org/keywords/code","display_name":"Code (set theory)","score":0.44502827525138855},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4356958866119385},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.40749573707580566},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3929244875907898},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3872218132019043},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.171311616897583}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8095114231109619},{"id":"https://openalex.org/C43126263","wikidata":"https://www.wikidata.org/wiki/Q128751","display_name":"Source code","level":2,"score":0.6360641717910767},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.47345560789108276},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.44502827525138855},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4356958866119385},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.40749573707580566},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3929244875907898},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3872218132019043},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.171311616897583}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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},{"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":"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":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/bioinformatics/btx456","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btx456","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,"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":"pmid:29036531","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29036531","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:5179161","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC5860254","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:5860254","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860254","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":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:5860254","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5860254","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":"Bioinformatics","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4293014701","display_name":null,"funder_award_id":"R01GM111510","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G8540799962","display_name":null,"funder_award_id":"2014/13/B/NZ2/03840","funder_id":"https://openalex.org/F4320322511","funder_display_name":"Narodowe Centrum Nauki"}],"funders":[{"id":"https://openalex.org/F4320322511","display_name":"Narodowe Centrum Nauki","ror":"https://ror.org/03ha2q922"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":15,"referenced_works":["https://openalex.org/W1563071114","https://openalex.org/W2005668417","https://openalex.org/W2014449669","https://openalex.org/W2030282707","https://openalex.org/W2041715593","https://openalex.org/W2047331390","https://openalex.org/W2055705064","https://openalex.org/W2104437669","https://openalex.org/W2121490181","https://openalex.org/W2145006655","https://openalex.org/W2185320462","https://openalex.org/W2271421556","https://openalex.org/W2303100661","https://openalex.org/W2419000639","https://openalex.org/W2593960650"],"related_works":["https://openalex.org/W323219885","https://openalex.org/W4292559016","https://openalex.org/W4231937131","https://openalex.org/W1589342014","https://openalex.org/W598950423","https://openalex.org/W4256673449","https://openalex.org/W2143331802","https://openalex.org/W2160964171","https://openalex.org/W2063928587","https://openalex.org/W3081644756"],"abstract_inverted_index":{"SUMMARY:":[0],"Rule-based":[1],"modeling":[2,21],"is":[3,29,57,86,104,150],"a":[4,16,30,78,90,108,182],"powerful":[5],"approach":[6],"for":[7,19,133,148,167,178],"studying":[8],"biomolecular":[9],"site":[10,93,199],"dynamics.":[11],"Here,":[12],"we":[13],"present":[14],"SPATKIN,":[15],"general-purpose":[17],"simulator":[18],"rule-based":[20],"in":[22],"two":[23],"spatial":[24,134],"dimensions.":[25],"The":[26,143,161,187],"simulation":[27],"algorithm":[28,56],"lattice-based":[31],"method":[32],"that":[33,60,94],"tracks":[34],"Brownian":[35],"motion":[36],"of":[37,44,84,106,111,125,136,156],"individual":[38],"molecules":[39],"and":[40,117,174,181,190],"the":[41,55,67,126,137,154,157,196],"stochastic":[42],"firing":[43],"rule-defined":[45],"reaction":[46,69],"events.":[47],"Because":[48],"rules":[49,73],"are":[50,120,185,193,207],"used":[51],"as":[52],"event":[53],"generators,":[54],"network-free,":[58],"meaning":[59],"it":[61],"does":[62],"not":[63],"require":[64],"to":[65,75,88,131],"generate":[66],"complete":[68],"network":[70],"implied":[71],"by":[72],"prior":[74],"simulation.":[76],"In":[77],"simulation,":[79],"each":[80],"molecule":[81,100],"(or":[82,101],"complex":[83],"molecules)":[85],"taken":[87],"occupy":[89],"single":[91],"lattice":[92],"cannot":[95],"be":[96,165],"shared":[97],"with":[98],"another":[99],"complex).":[102],"SPATKIN":[103,149,197],"capable":[105],"simulating":[107],"wide":[109],"array":[110],"membrane-associated":[112],"processes,":[113],"including":[114],"adsorption,":[115],"desorption":[116],"crowding.":[118],"Models":[119],"specified":[121],"using":[122],"an":[123],"extension":[124],"BioNetGen":[127],"language,":[128],"which":[129],"allows":[130],"account":[132],"features":[135],"simulated":[138],"process.":[139],"AVAILABILITY":[140],"AND":[141],"IMPLEMENTATION:":[142],"C":[144],"++":[145],"source":[146,162,188],"code":[147,163,189],"distributed":[151],"freely":[152],"under":[153],"terms":[155],"GNU":[158],"GPLv3":[159],"license.":[160],"can":[164],"compiled":[166],"execution":[168],"on":[169],"popular":[170],"platforms":[171],"(Windows,":[172],"Mac":[173],"Linux).":[175],"An":[176],"installer":[177],"64-bit":[179],"Windows":[180],"macOS":[183],"app":[184],"available.":[186],"precompiled":[191],"binaries":[192],"available":[194,208],"at":[195,209],"Web":[198],"(http://pmbm.ippt.pan.pl/software/spatkin).":[200],"CONTACT:":[201],"spatkin.simulator@gmail.com.":[202],"SUPPLEMENTARY":[203],"INFORMATION:":[204],"Supplementary":[205],"data":[206],"Bioinformatics":[210],"online.":[211]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2}],"updated_date":"2026-08-18T07:49:30.821534","created_date":"2025-10-10T00:00:00"}
