{"id":"https://openalex.org/W2047377602","doi":"https://doi.org/10.3390/computation3020197","title":"Simulation Frameworks for Morphogenetic Problems","display_name":"Simulation Frameworks for Morphogenetic Problems","publication_year":2015,"publication_date":"2015-04-24","ids":{"openalex":"https://openalex.org/W2047377602","doi":"https://doi.org/10.3390/computation3020197","mag":"2047377602"},"language":"en","primary_location":{"id":"doi:10.3390/computation3020197","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3020197","pdf_url":"https://www.mdpi.com/2079-3197/3/2/197/pdf?version=1429859412","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","datacite","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2079-3197/3/2/197/pdf?version=1429859412","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054714993","display_name":"Simon Tanaka","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"]},{"id":"https://openalex.org/I12708293","display_name":"SIB Swiss Institute of Bioinformatics","ror":"https://ror.org/002n09z45","country_code":"CH","type":"funder","lineage":["https://openalex.org/I12708293"]}],"countries":["CH"],"is_corresponding":true,"raw_author_name":"Simon Tanaka","raw_affiliation_strings":["Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland","Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland\u00a0"],"affiliations":[{"raw_affiliation_string":"Department for Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, Basel 4058, Switzerland","institution_ids":["https://openalex.org/I35440088"]},{"raw_affiliation_string":"Swiss Institute of Bioinformatics (SIB), Basel 4058, Switzerland\u00a0","institution_ids":["https://openalex.org/I12708293"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054714993"],"corresponding_institution_ids":["https://openalex.org/I12708293","https://openalex.org/I35440088"],"apc_list":{"value":1400,"currency":"CHF","value_usd":1515},"apc_paid":{"value":1400,"currency":"CHF","value_usd":1515},"fwci":4.0948,"has_fulltext":false,"cited_by_count":58,"citation_normalized_percentile":{"value":0.94205974,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":100},"biblio":{"volume":"3","issue":"2","first_page":"197","last_page":"221"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.9980999827384949,"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"}},"topics":[{"id":"https://openalex.org/T10379","display_name":"Cellular Mechanics and Interactions","score":0.9980999827384949,"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"}},{"id":"https://openalex.org/T11190","display_name":"3D Printing in Biomedical Research","score":0.9889000058174133,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11829","display_name":"Mathematical Biology Tumor Growth","score":0.9882000088691711,"subfield":{"id":"https://openalex.org/subfields/2611","display_name":"Modeling and Simulation"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6812840104103088},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.6134310364723206},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.42706042528152466},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3544614315032959},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3488522171974182},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2824808359146118},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.2032850682735443},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.12061873078346252},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.10198694467544556}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6812840104103088},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.6134310364723206},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.42706042528152466},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3544614315032959},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3488522171974182},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2824808359146118},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.2032850682735443},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.12061873078346252},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.10198694467544556}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3390/computation3020197","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3020197","pdf_url":"https://www.mdpi.com/2079-3197/3/2/197/pdf?version=1429859412","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},{"id":"pmh:oai:doaj.org/article:f9332fda6a684eb2bac046f9fc5f3d68","is_oa":true,"landing_page_url":"https://doaj.org/article/f9332fda6a684eb2bac046f9fc5f3d68","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Computation, Vol 3, Iss 2, Pp 197-221 (2015)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2079-3197/3/2/197/","is_oa":true,"landing_page_url":"http://dx.doi.org/10.3390/computation3020197","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Computation","raw_type":"Text"},{"id":"pmh:oai:www.research-collection.ethz.ch:20.500.11850/108956","is_oa":true,"landing_page_url":"http://hdl.handle.net/20.500.11850/108956","pdf_url":null,"source":{"id":"https://openalex.org/S4306402302","display_name":"Repository for Publications and Research Data (ETH Zurich)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I35440088","host_organization_name":"ETH Zurich","host_organization_lineage":["https://openalex.org/I35440088"],"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":"Computation, 3 (2)","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"doi:10.3929/ethz-b-000108956","is_oa":true,"landing_page_url":"https://doi.org/10.3929/ethz-b-000108956","pdf_url":null,"source":{"id":"https://openalex.org/S7407051236","display_name":"ETH Z\u00fcrich Research Collection","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.3390/computation3020197","is_oa":true,"landing_page_url":"https://doi.org/10.3390/computation3020197","pdf_url":"https://www.mdpi.com/2079-3197/3/2/197/pdf?version=1429859412","source":{"id":"https://openalex.org/S2738402919","display_name":"Computation","issn_l":"2079-3197","issn":["2079-3197"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Computation","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2047377602.pdf","grobid_xml":"https://content.openalex.org/works/W2047377602.grobid-xml"},"referenced_works_count":142,"referenced_works":["https://openalex.org/W115452890","https://openalex.org/W403615107","https://openalex.org/W1523948508","https://openalex.org/W1586920498","https://openalex.org/W1597510423","https://openalex.org/W1967487044","https://openalex.org/W1967735338","https://openalex.org/W1969709265","https://openalex.org/W1969732580","https://openalex.org/W1971389297","https://openalex.org/W1973226464","https://openalex.org/W1974673184","https://openalex.org/W1975416805","https://openalex.org/W1976925230","https://openalex.org/W1978502060","https://openalex.org/W1979084896","https://openalex.org/W1979488786","https://openalex.org/W1980122996","https://openalex.org/W1981778940","https://openalex.org/W1983690504","https://openalex.org/W1984763084","https://openalex.org/W1987164692","https://openalex.org/W1989184968","https://openalex.org/W1989562629","https://openalex.org/W1996198135","https://openalex.org/W1996269383","https://openalex.org/W1998818894","https://openalex.org/W2002785668","https://openalex.org/W2003933044","https://openalex.org/W2005063895","https://openalex.org/W2006033261","https://openalex.org/W2013580499","https://openalex.org/W2020561965","https://openalex.org/W2020642487","https://openalex.org/W2020644315","https://openalex.org/W2023327598","https://openalex.org/W2024857915","https://openalex.org/W2029048914","https://openalex.org/W2029203100","https://openalex.org/W2035257048","https://openalex.org/W2035528554","https://openalex.org/W2037592763","https://openalex.org/W2038882764","https://openalex.org/W2041197340","https://openalex.org/W2042892258","https://openalex.org/W2043456783","https://openalex.org/W2043875880","https://openalex.org/W2045480992","https://openalex.org/W2048836357","https://openalex.org/W2049721114","https://openalex.org/W2052318766","https://openalex.org/W2054877682","https://openalex.org/W2056760934","https://openalex.org/W2058324879","https://openalex.org/W2058706104","https://openalex.org/W2060099544","https://openalex.org/W2061220010","https://openalex.org/W2062043635","https://openalex.org/W2067510267","https://openalex.org/W2068674173","https://openalex.org/W2079059689","https://openalex.org/W2080540629","https://openalex.org/W2081347187","https://openalex.org/W2084131634","https://openalex.org/W2084899416","https://openalex.org/W2084962429","https://openalex.org/W2089662478","https://openalex.org/W2089922484","https://openalex.org/W2096021672","https://openalex.org/W2097090938","https://openalex.org/W2097543272","https://openalex.org/W2099772777","https://openalex.org/W2100345558","https://openalex.org/W2104124840","https://openalex.org/W2105458906","https://openalex.org/W2106199085","https://openalex.org/W2112479189","https://openalex.org/W2113085696","https://openalex.org/W2113777491","https://openalex.org/W2114074036","https://openalex.org/W2114124738","https://openalex.org/W2116161854","https://openalex.org/W2116549060","https://openalex.org/W2117079953","https://openalex.org/W2119139172","https://openalex.org/W2119410416","https://openalex.org/W2120629640","https://openalex.org/W2122752792","https://openalex.org/W2122969640","https://openalex.org/W2123783513","https://openalex.org/W2127225632","https://openalex.org/W2128785312","https://openalex.org/W2129379345","https://openalex.org/W2129391320","https://openalex.org/W2129604277","https://openalex.org/W2129960309","https://openalex.org/W2131645519","https://openalex.org/W2134047171","https://openalex.org/W2134519035","https://openalex.org/W2135789936","https://openalex.org/W2137700068","https://openalex.org/W2138571902","https://openalex.org/W2139915618","https://openalex.org/W2140753536","https://openalex.org/W2145851836","https://openalex.org/W2146435848","https://openalex.org/W2146583321","https://openalex.org/W2150908245","https://openalex.org/W2151487012","https://openalex.org/W2153717411","https://openalex.org/W2154050348","https://openalex.org/W2154289334","https://openalex.org/W2154435723","https://openalex.org/W2154474869","https://openalex.org/W2155154349","https://openalex.org/W2156447979","https://openalex.org/W2157546970","https://openalex.org/W2157904870","https://openalex.org/W2159094603","https://openalex.org/W2159793005","https://openalex.org/W2160135160","https://openalex.org/W2161590805","https://openalex.org/W2163415630","https://openalex.org/W2164712741","https://openalex.org/W2164782424","https://openalex.org/W2165477530","https://openalex.org/W2170122529","https://openalex.org/W2170405129","https://openalex.org/W2171996376","https://openalex.org/W2175332918","https://openalex.org/W2260313537","https://openalex.org/W2272546316","https://openalex.org/W2305004685","https://openalex.org/W2396740394","https://openalex.org/W2732014227","https://openalex.org/W2963701805","https://openalex.org/W4245397581","https://openalex.org/W4250979478","https://openalex.org/W6643261885","https://openalex.org/W6678141185","https://openalex.org/W6679614950","https://openalex.org/W6679700816"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W4385386698","https://openalex.org/W4388119604","https://openalex.org/W2954418080","https://openalex.org/W3121570353","https://openalex.org/W818235636","https://openalex.org/W4388119676","https://openalex.org/W1566913699","https://openalex.org/W2081328318","https://openalex.org/W2127574606"],"abstract_inverted_index":{"Morphogenetic":[0],"modelling":[1,37,53,71,119],"and":[2,13,18,32,44,81,92,118,122],"simulation":[3],"help":[4],"to":[5],"understand":[6],"the":[7,11,28,33,36,39,51,55,65,76,79,85,107],"processes":[8],"by":[9],"which":[10],"form":[12],"shapes":[14],"of":[15,38,49,54,84],"organs":[16],"(organogenesis)":[17],"organisms":[19],"(embryogenesis)":[20],"emerge.":[21],"This":[22],"requires":[23],"two":[24],"mutually":[25],"coupled":[26],"entities:":[27],"biomolecular":[29],"signalling":[30,40],"network":[31],"tissue.":[34],"Whereas":[35],"has":[41,57],"been":[42,111],"discussed":[43,97],"used":[45,116],"in":[46,64,98],"a":[47,61],"multitude":[48],"works,":[50],"realistic":[52],"tissue":[56,70],"only":[58],"started":[59],"on":[60],"larger":[62],"scale":[63],"last":[66],"decade.":[67],"Here,":[68],"common":[69],"techniques":[72],"are":[73,96,124],"reviewed.":[74],"Besides":[75],"continuum":[77],"approach,":[78],"principles":[80],"main":[82],"applications":[83],"spheroid,":[86],"vertex,":[87],"Cellular":[88],"Potts,":[89],"Immersed":[90],"Boundary":[91],"Subcellular":[93],"Element":[94],"models":[95],"detail.":[99],"In":[100],"recent":[101],"years,":[102],"many":[103],"software":[104],"frameworks,":[105],"implementing":[106],"aforementioned":[108],"methods,":[109],"have":[110],"developed.":[112],"The":[113],"most":[114],"widely":[115],"frameworks":[117],"markup":[120],"languages":[121],"standards":[123],"presented.":[125]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":3},{"year":2023,"cited_by_count":4},{"year":2022,"cited_by_count":5},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":8},{"year":2018,"cited_by_count":14},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":4},{"year":2015,"cited_by_count":3}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}