{"id":"https://openalex.org/W2147438495","doi":"https://doi.org/10.1109/biovis.2013.6664345","title":"From biochemical reaction networks to 3D dynamics in the cell: The ZigCell3D modeling, simulation and visualisation framework","display_name":"From biochemical reaction networks to 3D dynamics in the cell: The ZigCell3D modeling, simulation and visualisation framework","publication_year":2013,"publication_date":"2013-10-01","ids":{"openalex":"https://openalex.org/W2147438495","doi":"https://doi.org/10.1109/biovis.2013.6664345","mag":"2147438495"},"language":"en","primary_location":{"id":"doi:10.1109/biovis.2013.6664345","is_oa":true,"landing_page_url":"https://doi.org/10.1109/biovis.2013.6664345","pdf_url":"https://ieeexplore.ieee.org/ielx7/6648474/6664331/06664345.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE Symposium on Biological Data Visualization (BioVis)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://ieeexplore.ieee.org/ielx7/6648474/6664331/06664345.pdf","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5000822492","display_name":"Pablo de Heras Ciechomski","orcid":null},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Pablo de Heras Ciechomski","raw_affiliation_strings":["ScienceVisuals Sarl Lausanne, Switzerland","ScienceVisuals Sarl, Lausanne, Switzerland"],"affiliations":[{"raw_affiliation_string":"ScienceVisuals Sarl Lausanne, Switzerland","institution_ids":[]},{"raw_affiliation_string":"ScienceVisuals Sarl, Lausanne, Switzerland","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5032056161","display_name":"Michael Klann","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Michael Klann","raw_affiliation_strings":["ETH, Zurich, Switzerland","ETH Z\u00fcrich, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"ETH, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016316761","display_name":"Robin Mange","orcid":null},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Robin Mange","raw_affiliation_strings":["ETH, Zurich, Switzerland","ETH Z\u00fcrich, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"ETH, Zurich, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5070544702","display_name":"Heinz Koeppl","orcid":"https://orcid.org/0000-0002-8305-9379"},"institutions":[{"id":"https://openalex.org/I35440088","display_name":"ETH Zurich","ror":"https://ror.org/05a28rw58","country_code":"CH","type":"education","lineage":["https://openalex.org/I2799323385","https://openalex.org/I35440088"]},{"id":"https://openalex.org/I4210126328","display_name":"IBM Research - Zurich","ror":"https://ror.org/02js37d36","country_code":"CH","type":"facility","lineage":["https://openalex.org/I1341412227","https://openalex.org/I4210114115","https://openalex.org/I4210126328"]}],"countries":["CH"],"is_corresponding":false,"raw_author_name":"Heinz Koeppl","raw_affiliation_strings":["ETH Zurich, IBM Research, Zurich, Switzerland","ETH Z\u00fcrich, Z\u00fcrich, Switzerland"],"affiliations":[{"raw_affiliation_string":"ETH Zurich, IBM Research, Zurich, Switzerland","institution_ids":["https://openalex.org/I4210126328","https://openalex.org/I35440088"]},{"raw_affiliation_string":"ETH Z\u00fcrich, Z\u00fcrich, Switzerland","institution_ids":["https://openalex.org/I35440088"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5000822492"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.0481,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.77141687,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":null,"issue":null,"first_page":"41","last_page":"48"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9997000098228455,"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":0.9997000098228455,"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":0.996399998664856,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9941999912261963,"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":0.7667943239212036},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.7328043580055237},{"id":"https://openalex.org/keywords/virtual-reality","display_name":"Virtual reality","score":0.6004128456115723},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.4363325834274292},{"id":"https://openalex.org/keywords/animation","display_name":"Animation","score":0.4207327663898468},{"id":"https://openalex.org/keywords/zoom","display_name":"Zoom","score":0.4182093143463135},{"id":"https://openalex.org/keywords/computer-graphics","display_name":"Computer graphics (images)","score":0.37276917695999146},{"id":"https://openalex.org/keywords/computational-science","display_name":"Computational science","score":0.3339655101299286},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2553701400756836},{"id":"https://openalex.org/keywords/lens","display_name":"Lens (geology)","score":0.12608188390731812}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7667943239212036},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.7328043580055237},{"id":"https://openalex.org/C194969405","wikidata":"https://www.wikidata.org/wiki/Q170519","display_name":"Virtual reality","level":2,"score":0.6004128456115723},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.4363325834274292},{"id":"https://openalex.org/C502989409","wikidata":"https://www.wikidata.org/wiki/Q11425","display_name":"Animation","level":2,"score":0.4207327663898468},{"id":"https://openalex.org/C124913957","wikidata":"https://www.wikidata.org/wiki/Q1232548","display_name":"Zoom","level":3,"score":0.4182093143463135},{"id":"https://openalex.org/C121684516","wikidata":"https://www.wikidata.org/wiki/Q7600677","display_name":"Computer graphics (images)","level":1,"score":0.37276917695999146},{"id":"https://openalex.org/C459310","wikidata":"https://www.wikidata.org/wiki/Q117801","display_name":"Computational science","level":1,"score":0.3339655101299286},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2553701400756836},{"id":"https://openalex.org/C15336307","wikidata":"https://www.wikidata.org/wiki/Q1766051","display_name":"Lens (geology)","level":2,"score":0.12608188390731812},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C78762247","wikidata":"https://www.wikidata.org/wiki/Q1273174","display_name":"Petroleum engineering","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1109/biovis.2013.6664345","is_oa":true,"landing_page_url":"https://doi.org/10.1109/biovis.2013.6664345","pdf_url":"https://ieeexplore.ieee.org/ielx7/6648474/6664331/06664345.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE Symposium on Biological Data Visualization (BioVis)","raw_type":"proceedings-article"},{"id":"pmh:oai:tubiblio.ulb.tu-darmstadt.de:64970","is_oa":false,"landing_page_url":"http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=6664345","pdf_url":null,"source":{"id":"https://openalex.org/S4377196390","display_name":"TUbilio (Technical University of Darmstadt)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I31512782","host_organization_name":"Technische Universit\u00e4t Darmstadt","host_organization_lineage":["https://openalex.org/I31512782"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Konferenzver\u00f6ffentlichung"}],"best_oa_location":{"id":"doi:10.1109/biovis.2013.6664345","is_oa":true,"landing_page_url":"https://doi.org/10.1109/biovis.2013.6664345","pdf_url":"https://ieeexplore.ieee.org/ielx7/6648474/6664331/06664345.pdf","source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2013 IEEE Symposium on Biological Data Visualization (BioVis)","raw_type":"proceedings-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1104884314","display_name":"Advanced algorithms and design principles for bio-molecular circuit analysis","funder_award_id":"128503","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G2651746407","display_name":"Nietzsche im Spannungsfeld zwischen historischer Kritik und Sprachkritik.","funder_award_id":"28503","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G580951548","display_name":null,"funder_award_id":"PP00P2","funder_id":"https://openalex.org/F4320320924","funder_display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung"},{"id":"https://openalex.org/G7260928730","display_name":null,"funder_award_id":"12850","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G848032724","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320320924","display_name":"Schweizerischer Nationalfonds zur F\u00f6rderung der Wissenschaftlichen Forschung","ror":"https://ror.org/00yjd3n13"},{"id":"https://openalex.org/F4320320998","display_name":"Kommission f\u00fcr Technologie und Innovation","ror":"https://ror.org/012y9zp98"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2147438495.pdf","grobid_xml":"https://content.openalex.org/works/W2147438495.grobid-xml"},"referenced_works_count":35,"referenced_works":["https://openalex.org/W102033946","https://openalex.org/W255011565","https://openalex.org/W1963654595","https://openalex.org/W1965998139","https://openalex.org/W1969049442","https://openalex.org/W1971644094","https://openalex.org/W1974974415","https://openalex.org/W1976776824","https://openalex.org/W1986789040","https://openalex.org/W1993244675","https://openalex.org/W2004950702","https://openalex.org/W2017371931","https://openalex.org/W2025042015","https://openalex.org/W2030125944","https://openalex.org/W2033528502","https://openalex.org/W2091050840","https://openalex.org/W2097319997","https://openalex.org/W2101506009","https://openalex.org/W2102936861","https://openalex.org/W2107444296","https://openalex.org/W2114870653","https://openalex.org/W2117364474","https://openalex.org/W2117462302","https://openalex.org/W2123817333","https://openalex.org/W2125493690","https://openalex.org/W2127732571","https://openalex.org/W2153969663","https://openalex.org/W2157696144","https://openalex.org/W2157989234","https://openalex.org/W2165187344","https://openalex.org/W2175715045","https://openalex.org/W2227599634","https://openalex.org/W2618229491","https://openalex.org/W2944782266","https://openalex.org/W6609609171"],"related_works":["https://openalex.org/W2788595494","https://openalex.org/W2244676099","https://openalex.org/W3172556642","https://openalex.org/W3157456843","https://openalex.org/W1990150827","https://openalex.org/W2036676347","https://openalex.org/W1589307369","https://openalex.org/W3165790285","https://openalex.org/W3144351989","https://openalex.org/W201739634"],"abstract_inverted_index":{"Systems-oriented":[0],"research":[1,135],"accelerates":[2],"our":[3,21],"understanding":[4],"of":[5,17,40,88,155,179,203],"biological":[6,27],"processes":[7],"and":[8,20,58,141,151,184],"helps":[9],"in":[10,38,43,210,212],"identifying":[11],"novel":[12],"drug":[13],"candidates.":[14],"However,":[15],"development":[16],"good":[18],"models":[19,36],"intuition":[22],"is":[23,54,69,114,136,162,197,208],"hampered":[24],"by":[25],"the":[26,41,66,89,96,103,180,188,204,222],"complexity.":[28],"To":[29],"be":[30,227],"able":[31,77,100],"to":[32,78,101,120,126,187],"see":[33,82],"how":[34,83],"candidate":[35],"evolve":[37],"front":[39],"user":[42],"an":[44],"interactive":[45,130],"virtual":[46,116,219,223],"3D":[47,86,117,143,176],"cell":[48,90],"at":[49,91,95],"various":[50],"zoom":[51],"levels,":[52,93],"therefore":[53],"a":[55,59,71,107,115,128,139,156,165,174,213,218],"crucial":[56],"aspect":[57],"challenging":[60],"problem.":[61],"The":[62,145,159,194],"motivation":[63],"for":[64],"creating":[65],"ZigCell3D":[67,113],"software,":[68],"thus":[70],"holistic":[72],"view":[73],"ranging":[74],"from":[75],"being":[76,99],"change":[79],"model":[80,105,178],"parameters,":[81],"they":[84],"affect":[85],"versions":[87],"molecular":[92],"while":[94],"same":[97],"time":[98],"verify":[102],"simulated":[104],"against":[106,229],"real":[108,230],"experimental":[109,232],"fluorescence":[110,220],"microscopy":[111],"image.":[112],"whiteboard":[118],"approach":[119],"chemical":[121],"reaction":[122],"modelling.":[123],"It":[124],"aims":[125],"provide":[127],"realtime":[129],"environment,":[131],"where":[132],"complex":[133],"biophysics":[134],"turned":[137],"into":[138],"creative":[140],"game-like":[142],"environment.":[144],"complete":[146,175],"system":[147],"entails":[148],"modelling,":[149],"simulation":[150,224],"visualisation":[152,161],"as":[153],"part":[154],"unified":[157],"framework.":[158],"core":[160],"based":[163,198],"on":[164,199],"multi-core":[166],"parallel":[167],"C/C++":[168],"ray":[169],"tracing":[170],"engine,":[171],"that":[172],"builds":[173],"iso-surface":[177],"cell,":[181],"its":[182],"organelles":[183],"molecules":[185],"down":[186],"atomic":[189],"level":[190],"using":[191],"PDB":[192],"files.":[193],"simulator":[195],"itself":[196],"coarse-grained":[200],"Brownian":[201],"motion":[202],"individual":[205],"molecules,":[206],"which":[207],"visualised":[209],"detail":[211],"tightly":[214],"coupled":[215],"manner.":[216],"Using":[217],"microscope":[221],"environment":[225],"can":[226],"benchmarked":[228],"life":[231],"data.":[233]},"counts_by_year":[{"year":2022,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":2},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2016-06-24T00:00:00"}