{"id":"https://openalex.org/W4319460934","doi":"https://doi.org/10.1093/bioinformatics/btad083","title":"APL@voro\u2014interactive visualization and analysis of cell membrane simulations","display_name":"APL@voro\u2014interactive visualization and analysis of cell membrane simulations","publication_year":2023,"publication_date":"2023-02-01","ids":{"openalex":"https://openalex.org/W4319460934","doi":"https://doi.org/10.1093/bioinformatics/btad083","pmid":"https://pubmed.ncbi.nlm.nih.gov/36752505"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btad083","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad083","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad083/49345183/btad083.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","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":"gold","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad083/49345183/btad083.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030873380","display_name":"Martin Kern","orcid":null},"institutions":[{"id":"https://openalex.org/I189712700","display_name":"University of Konstanz","ror":"https://ror.org/0546hnb39","country_code":"DE","type":"education","lineage":["https://openalex.org/I189712700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Martin Kern","raw_affiliation_strings":["Department of Computer and Information Science, University of Konstanz , Konstanz 76484, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Konstanz , Konstanz 76484, Germany","institution_ids":["https://openalex.org/I189712700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058097371","display_name":"Sabrina Jaeger-Honz","orcid":"https://orcid.org/0000-0003-1144-7468"},"institutions":[{"id":"https://openalex.org/I189712700","display_name":"University of Konstanz","ror":"https://ror.org/0546hnb39","country_code":"DE","type":"education","lineage":["https://openalex.org/I189712700"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Sabrina Jaeger-Honz","raw_affiliation_strings":["Department of Computer and Information Science, University of Konstanz , Konstanz 76484, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Konstanz , Konstanz 76484, Germany","institution_ids":["https://openalex.org/I189712700"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003441276","display_name":"Falk Schreiber","orcid":"https://orcid.org/0000-0002-9307-3254"},"institutions":[{"id":"https://openalex.org/I189712700","display_name":"University of Konstanz","ror":"https://ror.org/0546hnb39","country_code":"DE","type":"education","lineage":["https://openalex.org/I189712700"]},{"id":"https://openalex.org/I56590836","display_name":"Monash University","ror":"https://ror.org/02bfwt286","country_code":"AU","type":"education","lineage":["https://openalex.org/I56590836"]}],"countries":["AU","DE"],"is_corresponding":true,"raw_author_name":"Falk Schreiber","raw_affiliation_strings":["Department of Computer and Information Science, University of Konstanz , Konstanz 76484, Germany","Faculty of Information Technology, Monash University , Clayton, VIC 3800, Australia"],"raw_orcid":"https://orcid.org/0000-0002-9307-3254","affiliations":[{"raw_affiliation_string":"Department of Computer and Information Science, University of Konstanz , Konstanz 76484, Germany","institution_ids":["https://openalex.org/I189712700"]},{"raw_affiliation_string":"Faculty of Information Technology, Monash University , Clayton, VIC 3800, Australia","institution_ids":["https://openalex.org/I56590836"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5059487495","display_name":"Bj\u00f6rn Sommer","orcid":"https://orcid.org/0000-0003-1514-9898"},"institutions":[{"id":"https://openalex.org/I165526535","display_name":"Royal College of Art","ror":"https://ror.org/01egahc47","country_code":"GB","type":"education","lineage":["https://openalex.org/I165526535"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Bjorn Sommer","raw_affiliation_strings":["Royal College of Art, School of Design , London SW7 2EU, UK"],"raw_orcid":"https://orcid.org/0000-0003-1514-9898","affiliations":[{"raw_affiliation_string":"Royal College of Art, School of Design , London SW7 2EU, UK","institution_ids":["https://openalex.org/I165526535"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5003441276","https://openalex.org/A5059487495"],"corresponding_institution_ids":["https://openalex.org/I165526535","https://openalex.org/I189712700","https://openalex.org/I56590836"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":1.1075,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.75080187,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":100},"biblio":{"volume":"39","issue":"2","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.4043999910354614,"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/T10407","display_name":"Lipid Membrane Structure and Behavior","score":0.4043999910354614,"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/T12859","display_name":"Cell Image Analysis Techniques","score":0.07090000063180923,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/T10540","display_name":"Advanced Fluorescence Microscopy Techniques","score":0.050700001418590546,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"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/visualization","display_name":"Visualization","score":0.7944693565368652},{"id":"https://openalex.org/keywords/membrane","display_name":"Membrane","score":0.6923854947090149},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.669124960899353},{"id":"https://openalex.org/keywords/visual-analytics","display_name":"Visual analytics","score":0.588691234588623},{"id":"https://openalex.org/keywords/interactive-visualization","display_name":"Interactive visualization","score":0.5336820483207703},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.5052247643470764},{"id":"https://openalex.org/keywords/open-source","display_name":"Open source","score":0.5023317337036133},{"id":"https://openalex.org/keywords/molecular-dynamics","display_name":"Molecular dynamics","score":0.44304734468460083},{"id":"https://openalex.org/keywords/open-source-software","display_name":"Open source software","score":0.425086110830307},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.37796884775161743},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2927846312522888},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.20095369219779968},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.08836296200752258},{"id":"https://openalex.org/keywords/biochemistry","display_name":"Biochemistry","score":0.08162632584571838},{"id":"https://openalex.org/keywords/computational-chemistry","display_name":"Computational chemistry","score":0.07249900698661804}],"concepts":[{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7944693565368652},{"id":"https://openalex.org/C41625074","wikidata":"https://www.wikidata.org/wiki/Q176088","display_name":"Membrane","level":2,"score":0.6923854947090149},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.669124960899353},{"id":"https://openalex.org/C59732488","wikidata":"https://www.wikidata.org/wiki/Q2528440","display_name":"Visual analytics","level":3,"score":0.588691234588623},{"id":"https://openalex.org/C64073096","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Interactive visualization","level":3,"score":0.5336820483207703},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.5052247643470764},{"id":"https://openalex.org/C3018397939","wikidata":"https://www.wikidata.org/wiki/Q3644502","display_name":"Open source","level":3,"score":0.5023317337036133},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.44304734468460083},{"id":"https://openalex.org/C2988343187","wikidata":"https://www.wikidata.org/wiki/Q1130645","display_name":"Open source software","level":3,"score":0.425086110830307},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.37796884775161743},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2927846312522888},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.20095369219779968},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.08836296200752258},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.08162632584571838},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.07249900698661804}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002462","descriptor_name":"Cell Membrane","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008051","descriptor_name":"Lipid Bilayers","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":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D046911","descriptor_name":"Macromolecular Substances","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D056004","descriptor_name":"Molecular Dynamics Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1093/bioinformatics/btad083","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad083","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad083/49345183/btad083.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:36752505","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/36752505","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:pubmedcentral.nih.gov:9969824","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/9969824","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC9969824/pdf/btad083.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:researchonline.rca.ac.uk:5286","is_oa":true,"landing_page_url":null,"pdf_url":"https://researchonline.rca.ac.uk/5286/1/btad083.pdf","source":{"id":"https://openalex.org/S4377196584","display_name":"Archive of research processes and output produced by RCA (Royal College of Art)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I165526535","host_organization_name":"Royal College of Art","host_organization_lineage":["https://openalex.org/I165526535"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"},{"id":"pmh:oai:kops.uni-konstanz.de:123456789/66056","is_oa":true,"landing_page_url":"http://nbn-resolving.de/urn:nbn:de:bsz:352-2-1o5fa52i6s5ut9","pdf_url":null,"source":{"id":"https://openalex.org/S4306401487","display_name":"KOPS (University of Konstanz)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189712700","host_organization_name":"University of Konstanz","host_organization_lineage":["https://openalex.org/I189712700"],"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":"Bioinformatics. Oxford University Press (OUP). 2023, 39(2), btad083. ISSN 1367-4803. eISSN 1367-4811. Verf\u00fcgbar unter: doi: 10.1093/bioinformatics/btad083","raw_type":"doc-type:article"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btad083","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btad083","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/39/2/btad083/49345183/btad083.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1616605873","display_name":null,"funder_award_id":"TRR 161","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G3146585569","display_name":null,"funder_award_id":"2,51654672 - TRR 161","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"},{"id":"https://openalex.org/G6401459825","display_name":"TRR 161: Quantitative Methoden f\u00fcr Visual Computing","funder_award_id":"251654672","funder_id":"https://openalex.org/F4320320879","funder_display_name":"Deutsche Forschungsgemeinschaft"}],"funders":[{"id":"https://openalex.org/F4320320879","display_name":"Deutsche Forschungsgemeinschaft","ror":"https://ror.org/018mejw64"}],"has_content":{"grobid_xml":false,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4319460934.pdf"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1031578623","https://openalex.org/W2011301426","https://openalex.org/W2028479107","https://openalex.org/W2029667189","https://openalex.org/W2062476751","https://openalex.org/W2068959787","https://openalex.org/W2119109208","https://openalex.org/W2132629607","https://openalex.org/W2170711116","https://openalex.org/W2171727742","https://openalex.org/W2507723354","https://openalex.org/W2909184263","https://openalex.org/W2911593691","https://openalex.org/W2911908713","https://openalex.org/W2976481502","https://openalex.org/W3104531408","https://openalex.org/W3160453752"],"related_works":["https://openalex.org/W4376877853","https://openalex.org/W1493891899","https://openalex.org/W4250928611","https://openalex.org/W4232280318","https://openalex.org/W166480398","https://openalex.org/W167327709","https://openalex.org/W4387839566","https://openalex.org/W4210922265","https://openalex.org/W4319870556","https://openalex.org/W2084742289"],"abstract_inverted_index":{"SUMMARY:":[0],"Molecular":[1],"dynamics":[2,37],"(MD)":[3],"simulations":[4,95],"of":[5,13,26,59,93,115],"cell":[6,34,60],"membranes":[7],"allow":[8],"for":[9,53],"a":[10,51],"better":[11],"understanding":[12],"complex":[14],"processes":[15],"such":[16,88],"as":[17,89],"changing":[18],"membrane":[19,35,61],"dynamics,":[20],"lipid":[21],"rafts":[22],"and":[23,32,38,57,86,96],"the":[24,54,66,90,103],"incorporation/passing":[25],"macromolecules":[27],"into/through":[28],"membranes.":[29],"To":[30],"explore":[31],"understand":[33],"compositions,":[36],"processes,":[39],"visual":[40],"analytics":[41],"can":[42,117],"help":[43],"to":[44,98,101],"interpret":[45],"MD":[46],"simulation":[47],"data.":[48],"APL@Voro":[49,116],"is":[50],"software":[52],"interactive":[55,91],"visualization":[56],"analysis":[58],"simulations.":[62],"Here,":[63],"we":[64],"present":[65],"new":[67],"APL@Voro,":[68],"which":[69],"has":[70],"been":[71],"continuously":[72],"developed":[73],"since":[74],"its":[75],"initial":[76],"release":[77],"in":[78],"2013.":[79],"We":[80],"discuss":[81],"newly":[82],"implemented":[83],"algorithms,":[84],"methodologies":[85],"features,":[87],"comparison":[92],"related":[94],"methods":[97],"assign":[99],"lipids":[100],"either":[102],"upper":[104],"or":[105],"lower":[106],"leaflet.":[107],"AVAILABILITY":[108],"AND":[109],"IMPLEMENTATION:":[110],"The":[111],"current":[112],"open-source":[113],"version":[114],"be":[118],"downloaded":[119],"from":[120],"http://aplvoro.com.":[121]},"counts_by_year":[{"year":2026,"cited_by_count":8},{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":2}],"updated_date":"2026-08-06T08:24:18.245995","created_date":"2025-10-10T00:00:00"}
