{"id":"https://openalex.org/W3185131596","doi":"https://doi.org/10.1093/bioinformatics/btab530","title":"Python interfaces for the Smoldyn simulator","display_name":"Python interfaces for the Smoldyn simulator","publication_year":2021,"publication_date":"2021-07-21","ids":{"openalex":"https://openalex.org/W3185131596","doi":"https://doi.org/10.1093/bioinformatics/btab530","mag":"3185131596","pmid":"https://pubmed.ncbi.nlm.nih.gov/34293100"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btab530","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab530","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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027475348","display_name":"Dilawar Singh","orcid":"https://orcid.org/0000-0002-4645-3211"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dilawar Singh","raw_affiliation_strings":["Subconscious Compute Pvt. Ltd. , Bangalore, Karnataka 560064, India"],"raw_orcid":"https://orcid.org/0000-0002-4645-3211","affiliations":[{"raw_affiliation_string":"Subconscious Compute Pvt. Ltd. , Bangalore, Karnataka 560064, India","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5079267168","display_name":"Steven S. Andrews","orcid":"https://orcid.org/0000-0002-4576-8107"},"institutions":[{"id":"https://openalex.org/I201448701","display_name":"University of Washington","ror":"https://ror.org/00cvxb145","country_code":"US","type":"education","lineage":["https://openalex.org/I201448701"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Steven S Andrews","raw_affiliation_strings":["Department of Bioengineering, University of Washington , Seattle, WA 98105, USA"],"raw_orcid":"https://orcid.org/0000-0002-4576-8107","affiliations":[{"raw_affiliation_string":"Department of Bioengineering, University of Washington , Seattle, WA 98105, USA","institution_ids":["https://openalex.org/I201448701"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5079267168"],"corresponding_institution_ids":["https://openalex.org/I201448701"],"apc_list":{"value":3478,"currency":"USD","value_usd":3478},"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.05982252,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":93,"max":97},"biblio":{"volume":"38","issue":"1","first_page":"291","last_page":"293"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.3133000135421753,"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":0.3133000135421753,"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":0.09189999848604202,"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/T10492","display_name":"Microtubule and mitosis dynamics","score":0.07150000333786011,"subfield":{"id":"https://openalex.org/subfields/1307","display_name":"Cell 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/python","display_name":"Python (programming language)","score":0.922335147857666},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6912841200828552},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.5639830827713013},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.5068932175636292},{"id":"https://openalex.org/keywords/simulation","display_name":"Simulation","score":0.42715027928352356},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.36399587988853455}],"concepts":[{"id":"https://openalex.org/C519991488","wikidata":"https://www.wikidata.org/wiki/Q28865","display_name":"Python (programming language)","level":2,"score":0.922335147857666},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6912841200828552},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.5639830827713013},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.5068932175636292},{"id":"https://openalex.org/C44154836","wikidata":"https://www.wikidata.org/wiki/Q45045","display_name":"Simulation","level":1,"score":0.42715027928352356},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.36399587988853455}],"mesh":[{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004282","descriptor_name":"Documentation","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":"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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btab530","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btab530","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:34293100","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34293100","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":"Journal Article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":12,"referenced_works":["https://openalex.org/W1493349649","https://openalex.org/W1971117579","https://openalex.org/W1974974415","https://openalex.org/W2104266030","https://openalex.org/W2109639508","https://openalex.org/W2150908245","https://openalex.org/W2210900609","https://openalex.org/W2593960650","https://openalex.org/W2795701150","https://openalex.org/W2928248997","https://openalex.org/W3034171991","https://openalex.org/W6629578927"],"related_works":["https://openalex.org/W2341492732","https://openalex.org/W3187193180","https://openalex.org/W106542691","https://openalex.org/W4287027380","https://openalex.org/W1699080303","https://openalex.org/W4297799326","https://openalex.org/W3116064965","https://openalex.org/W2207495067","https://openalex.org/W1906486629","https://openalex.org/W1486009489"],"abstract_inverted_index":{"MOTIVATION:":[0],"Smoldyn":[1,46,96],"is":[2,8,97,123],"a":[3,27,42],"particle-based":[4],"biochemical":[5],"simulator":[6],"that":[7,69,79],"frequently":[9],"used":[10],"for":[11],"systems":[12],"biology":[13],"and":[14,62,76,100,105,120,127],"biophysics":[15],"research.":[16],"Previously,":[17],"users":[18],"could":[19],"only":[20],"define":[21],"models":[22],"using":[23],"text-based":[24],"input":[25],"or":[26],"C/C++":[28,74],"application":[29],"programming":[30],"interface":[31],"(API),":[32],"which":[33],"were":[34],"convenient,":[35],"but":[36],"limited":[37],"extensibility.":[38],"RESULTS:":[39],"We":[40],"added":[41],"Python":[43,59,91,111],"API":[44,75],"to":[45,47,83],"improve":[48],"integration":[49],"with":[50,109],"other":[51,58,63],"software":[52],"tools,":[53],"such":[54],"as":[55],"Jupyter":[56],"notebooks,":[57],"code":[60],"libraries":[61],"simulators.":[64],"It":[65,115],"includes":[66],"low-level":[67],"functions":[68,78,87],"closely":[70],"mimic":[71],"the":[72,110],"existing":[73],"higher-level":[77],"are":[80],"more":[81],"convenient":[82],"use.":[84],"These":[85],"latter":[86],"follow":[88],"modern":[89],"object-oriented":[90],"conventions.":[92],"AVAILABILITY":[93],"AND":[94],"IMPLEMENTATION:":[95],"open":[98],"source":[99],"free,":[101],"available":[102,124],"at":[103,125],"http://www.smoldyn.org":[104],"can":[106],"be":[107],"installed":[108],"package":[112],"manager":[113],"pip.":[114],"runs":[116],"on":[117],"Mac,":[118],"Windows":[119],"Linux.":[121],"Documentation":[122],"http://www.smoldyn.org/SmoldynManual.pdf":[126],"https://smoldyn.readthedocs.io/en/latest/python/api.html.":[128]},"counts_by_year":[{"year":2026,"cited_by_count":1}],"updated_date":"2026-08-28T12:50:07.497085","created_date":"2025-10-10T00:00:00"}