{"id":"https://openalex.org/W2109041166","doi":"https://doi.org/10.1186/1471-2105-15-345","title":"Interactively illustrating polymerization using three-level model fusion","display_name":"Interactively illustrating polymerization using three-level model fusion","publication_year":2014,"publication_date":"2014-10-14","ids":{"openalex":"https://openalex.org/W2109041166","doi":"https://doi.org/10.1186/1471-2105-15-345","mag":"2109041166","pmid":"https://pubmed.ncbi.nlm.nih.gov/25315282"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-15-345","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-345","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-345","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-345","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5006962854","display_name":"Ivan Koles\u00e1r","orcid":null},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"Ivan Kolesar","raw_affiliation_strings":["Department of Informatics, University of Bergen, N-5020 Bergen, Norway. Ivan.Kolesar@UiB.no","Department\u00a0of Informatics, University of Bergen, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Bergen, N-5020 Bergen, Norway. Ivan.Kolesar@UiB.no","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Department\u00a0of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025345988","display_name":"J\u00falius Parulek","orcid":null},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Julius Parulek","raw_affiliation_strings":["Department of Informatics, University of Bergen, N-5020, Bergen, Norway","Department\u00a0of Informatics, University of Bergen, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Bergen, N-5020, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Department\u00a0of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022294742","display_name":"Ivan Viola","orcid":"https://orcid.org/0000-0003-4248-6574"},"institutions":[{"id":"https://openalex.org/I145847075","display_name":"TU Wien","ror":"https://ror.org/04d836q62","country_code":"AT","type":"education","lineage":["https://openalex.org/I145847075"]},{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["AT","NO"],"is_corresponding":false,"raw_author_name":"Ivan Viola","raw_affiliation_strings":["Department of Informatics, University of Bergen, N-5020, Bergen, Norway","Vienna University of Technology, Vienna, Austria","Department of Informatics, University of Bergen, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Bergen, N-5020, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Vienna University of Technology, Vienna, Austria","institution_ids":["https://openalex.org/I145847075"]},{"raw_affiliation_string":"Department of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063965880","display_name":"Stefan Br\u00fcckner","orcid":"https://orcid.org/0000-0002-0885-8402"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Stefan Bruckner","raw_affiliation_strings":["Department of Informatics, University of Bergen, N-5020, Bergen, Norway","Department\u00a0of Informatics, University of Bergen, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Bergen, N-5020, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Department\u00a0of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072933480","display_name":"Anne-Kristin Stavrum","orcid":"https://orcid.org/0000-0002-5482-1141"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Anne-Kristin Stavrum","raw_affiliation_strings":["Department of Informatics, University of Bergen, N-5020, Bergen, Norway","Department\u00a0of Informatics, University of Bergen, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Bergen, N-5020, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Department\u00a0of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000755776","display_name":"Helwig Hauser","orcid":"https://orcid.org/0000-0003-0395-3192"},"institutions":[{"id":"https://openalex.org/I4432739","display_name":"University of Bergen","ror":"https://ror.org/03zga2b32","country_code":"NO","type":"education","lineage":["https://openalex.org/I4432739"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"Helwig Hauser","raw_affiliation_strings":["Department of Informatics, University of Bergen, N-5020, Bergen, Norway","Department\u00a0of Informatics, University of Bergen, Bergen, Norway"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, University of Bergen, N-5020, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]},{"raw_affiliation_string":"Department\u00a0of Informatics, University of Bergen, Bergen, Norway","institution_ids":["https://openalex.org/I4432739"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5006962854"],"corresponding_institution_ids":["https://openalex.org/I4432739"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":1723,"currency":"EUR","value_usd":1858},"fwci":2.4437,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.89463835,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"15","issue":"1","first_page":"345","last_page":"345"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13286","display_name":"Modeling and Simulation Systems","score":0.14980000257492065,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T13286","display_name":"Modeling and Simulation Systems","score":0.14980000257492065,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.14010000228881836,"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/T12093","display_name":"Greenhouse Technology and Climate Control","score":0.03060000017285347,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5118398070335388},{"id":"https://openalex.org/keywords/fusion","display_name":"Fusion","score":0.45201289653778076},{"id":"https://openalex.org/keywords/polymerization","display_name":"Polymerization","score":0.4181111752986908},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.39629244804382324},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.22917988896369934},{"id":"https://openalex.org/keywords/materials-science","display_name":"Materials science","score":0.1759999692440033},{"id":"https://openalex.org/keywords/polymer","display_name":"Polymer","score":0.08646911382675171}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5118398070335388},{"id":"https://openalex.org/C158525013","wikidata":"https://www.wikidata.org/wiki/Q2593739","display_name":"Fusion","level":2,"score":0.45201289653778076},{"id":"https://openalex.org/C44228677","wikidata":"https://www.wikidata.org/wiki/Q181898","display_name":"Polymerization","level":3,"score":0.4181111752986908},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.39629244804382324},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.22917988896369934},{"id":"https://openalex.org/C192562407","wikidata":"https://www.wikidata.org/wiki/Q228736","display_name":"Materials science","level":0,"score":0.1759999692440033},{"id":"https://openalex.org/C521977710","wikidata":"https://www.wikidata.org/wiki/Q81163","display_name":"Polymer","level":2,"score":0.08646911382675171},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C159985019","wikidata":"https://www.wikidata.org/wiki/Q181790","display_name":"Composite material","level":1,"score":0.0}],"mesh":[{"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":"D010829","descriptor_name":"Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010829","descriptor_name":"Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010829","descriptor_name":"Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058105","descriptor_name":"Polymerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058105","descriptor_name":"Polymerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D058105","descriptor_name":"Polymerization","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-15-345","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-345","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-345","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25315282","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25315282","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:4287442","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/4287442","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"},{"id":"pmh:oai:bora.uib.no:1956/8761","is_oa":true,"landing_page_url":"https://hdl.handle.net/1956/8761","pdf_url":null,"source":{"id":"https://openalex.org/S4306401716","display_name":"Duo Research Archive (University of Oslo)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184942183","host_organization_name":"University of Oslo","host_organization_lineage":["https://openalex.org/I184942183"],"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":"345","raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-15-345","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-15-345","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-15-345","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.5199999809265137,"id":"https://metadata.un.org/sdg/4","display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2196299318","display_name":null,"funder_award_id":"218023","funder_id":"https://openalex.org/F4320323299","funder_display_name":"Norges Forskningsr\u00e5d"},{"id":"https://openalex.org/G8424453579","display_name":"Visual Computing: Illustrative Visualization","funder_award_id":"VRG11-010","funder_id":"https://openalex.org/F4320321003","funder_display_name":"Vienna Science and Technology Fund"}],"funders":[{"id":"https://openalex.org/F4320321003","display_name":"Vienna Science and Technology Fund","ror":"https://ror.org/01f9mc681"},{"id":"https://openalex.org/F4320323299","display_name":"Norges Forskningsr\u00e5d","ror":"https://ror.org/00epmv149"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2109041166.pdf","grobid_xml":"https://content.openalex.org/works/W2109041166.grobid-xml"},"referenced_works_count":41,"referenced_works":["https://openalex.org/W102033946","https://openalex.org/W172217451","https://openalex.org/W817236362","https://openalex.org/W1481265772","https://openalex.org/W1505577908","https://openalex.org/W1507811735","https://openalex.org/W1576195516","https://openalex.org/W1586418342","https://openalex.org/W1601930706","https://openalex.org/W1903683453","https://openalex.org/W1967984011","https://openalex.org/W1975346450","https://openalex.org/W1981952333","https://openalex.org/W1985501881","https://openalex.org/W1986789040","https://openalex.org/W1989178848","https://openalex.org/W2000690667","https://openalex.org/W2010769244","https://openalex.org/W2021446134","https://openalex.org/W2029667189","https://openalex.org/W2030842498","https://openalex.org/W2047331390","https://openalex.org/W2080574968","https://openalex.org/W2080993455","https://openalex.org/W2083298149","https://openalex.org/W2086798521","https://openalex.org/W2111880327","https://openalex.org/W2117741646","https://openalex.org/W2121905328","https://openalex.org/W2133810181","https://openalex.org/W2139413502","https://openalex.org/W2145790759","https://openalex.org/W2159335259","https://openalex.org/W2165939338","https://openalex.org/W2169876309","https://openalex.org/W2177731497","https://openalex.org/W2296148643","https://openalex.org/W2799511660","https://openalex.org/W2908394422","https://openalex.org/W4205503054","https://openalex.org/W4244126043"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655","https://openalex.org/W2359140296"],"abstract_inverted_index":{"BACKGROUND:":[0],"Research":[1],"in":[2,42,120,154,157],"cell":[3],"biology":[4],"is":[5,111,181],"steadily":[6],"contributing":[7],"new":[8],"knowledge":[9],"about":[10],"many":[11],"aspects":[12],"of":[13,31,35,75,97,105,117,123,152,164,168],"physiological":[14,70],"processes,":[15],"both":[16],"with":[17,133],"respect":[18],"to":[19,68,88,183],"the":[20,32,73,93,109,115,121,150,172,176],"involved":[21,95],"molecular":[22],"structures":[23],"as":[24,26,50],"well":[25],"their":[27],"related":[28],"function.":[29],"Illustrations":[30],"spatio-temporal":[33],"development":[34],"such":[36],"processes":[37,71,126],"are":[38],"not":[39],"only":[40],"used":[41],"biomedical":[43],"education,":[44],"but":[45],"also":[46],"can":[47],"serve":[48],"scientists":[49],"an":[51],"additional":[52],"platform":[53],"for":[54,148],"in-silico":[55],"experiments.":[56],"RESULTS:":[57],"In":[58],"this":[59],"paper,":[60],"we":[61,100],"contribute":[62],"a":[63,103,130,143,158,165],"new,":[64,144],"three-level":[65],"modeling":[66,146,178],"approach":[67,90,119,141,147,163],"illustrate":[69],"from":[72,129,175],"class":[74],"polymerization":[76,125],"at":[77],"different":[78,94,177,185],"time":[79],"scales.":[80,189],"We":[81,113,137],"integrate":[82],"physical":[83],"and":[84,99,127,180,187],"empirical":[85],"modeling,":[86],"according":[87],"which":[89],"best":[91],"suits":[92],"levels":[96],"detail,":[98],"additionally":[101],"enable":[102],"form":[104],"interactive":[106],"steering,":[107],"while":[108],"process":[110,151],"illustrated.":[112],"demonstrate":[114],"suitability":[116],"our":[118,140],"context":[122],"several":[124],"report":[128],"first":[131],"evaluation":[132],"domain":[134],"experts.":[135],"CONCLUSION:":[136],"conclude":[138],"that":[139],"provides":[142],"hybrid":[145],"illustrating":[149],"emergence":[153],"physiology,":[155],"embedded":[156],"densely":[159],"filled":[160],"environment.":[161],"Our":[162],"complementary":[166],"fusion":[167],"three":[169],"systems":[170],"combines":[171],"strong":[173],"points":[174],"approaches":[179],"capable":[182],"bridge":[184],"spatial":[186],"temporal":[188]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":2}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}
