{"id":"https://openalex.org/W2063102049","doi":"https://doi.org/10.1093/bioinformatics/btp405","title":"DYNAMIK: a software environment for cell DYNAmics, Motility, and Information tracKing, with an application to Ras pathways","display_name":"DYNAMIK: a software environment for cell DYNAmics, Motility, and Information tracKing, with an application to Ras pathways","publication_year":2009,"publication_date":"2009-07-04","ids":{"openalex":"https://openalex.org/W2063102049","doi":"https://doi.org/10.1093/bioinformatics/btp405","mag":"2063102049","pmid":"https://pubmed.ncbi.nlm.nih.gov/19578170"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btp405","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp405","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/18/2383/48994407/bioinformatics_25_18_2383.pdf","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":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/25/18/2383/48994407/bioinformatics_25_18_2383.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035100758","display_name":"Stefan Jaeger","orcid":"https://orcid.org/0000-0001-6877-4318"},"institutions":[{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Stefan Jaeger","raw_affiliation_strings":["Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China"],"affiliations":[{"raw_affiliation_string":"Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101741895","display_name":"Qingfeng Song","orcid":"https://orcid.org/0000-0002-3494-8436"},"institutions":[{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingfeng Song","raw_affiliation_strings":["Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China"],"affiliations":[{"raw_affiliation_string":"Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5069755055","display_name":"Su\u2010Shing Chen","orcid":null},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Su-Shing Chen","raw_affiliation_strings":["Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China"],"affiliations":[{"raw_affiliation_string":"Partner Institute of Computational Biology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Max-Planck Society, Shanghai 200031, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5035100758"],"corresponding_institution_ids":["https://openalex.org/I19820366","https://openalex.org/I4210106477"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.1185,"has_fulltext":false,"cited_by_count":11,"citation_normalized_percentile":{"value":0.83667048,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"25","issue":"18","first_page":"2383","last_page":"2388"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9995999932289124,"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"}},"topics":[{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9995999932289124,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9894000291824341,"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/T13114","display_name":"Image Processing Techniques and Applications","score":0.9884999990463257,"subfield":{"id":"https://openalex.org/subfields/2214","display_name":"Media Technology"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7373104095458984},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.7203866839408875},{"id":"https://openalex.org/keywords/focus","display_name":"Focus (optics)","score":0.6700892448425293},{"id":"https://openalex.org/keywords/tracking","display_name":"Tracking (education)","score":0.60396808385849},{"id":"https://openalex.org/keywords/segmentation","display_name":"Segmentation","score":0.47829538583755493},{"id":"https://openalex.org/keywords/variety","display_name":"Variety (cybernetics)","score":0.4756079316139221},{"id":"https://openalex.org/keywords/plot","display_name":"Plot (graphics)","score":0.475501149892807},{"id":"https://openalex.org/keywords/trajectory","display_name":"Trajectory","score":0.4626868963241577},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4469538927078247},{"id":"https://openalex.org/keywords/biological-data","display_name":"Biological data","score":0.4318932890892029},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.302386075258255},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2123379111289978},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.15187713503837585},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.08420643210411072}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7373104095458984},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.7203866839408875},{"id":"https://openalex.org/C192209626","wikidata":"https://www.wikidata.org/wiki/Q190909","display_name":"Focus (optics)","level":2,"score":0.6700892448425293},{"id":"https://openalex.org/C2775936607","wikidata":"https://www.wikidata.org/wiki/Q466845","display_name":"Tracking (education)","level":2,"score":0.60396808385849},{"id":"https://openalex.org/C89600930","wikidata":"https://www.wikidata.org/wiki/Q1423946","display_name":"Segmentation","level":2,"score":0.47829538583755493},{"id":"https://openalex.org/C136197465","wikidata":"https://www.wikidata.org/wiki/Q1729295","display_name":"Variety (cybernetics)","level":2,"score":0.4756079316139221},{"id":"https://openalex.org/C167651023","wikidata":"https://www.wikidata.org/wiki/Q1474611","display_name":"Plot (graphics)","level":2,"score":0.475501149892807},{"id":"https://openalex.org/C13662910","wikidata":"https://www.wikidata.org/wiki/Q193139","display_name":"Trajectory","level":2,"score":0.4626868963241577},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4469538927078247},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.4318932890892029},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.302386075258255},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2123379111289978},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.15187713503837585},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.08420643210411072},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C1276947","wikidata":"https://www.wikidata.org/wiki/Q333","display_name":"Astronomy","level":1,"score":0.0},{"id":"https://openalex.org/C19417346","wikidata":"https://www.wikidata.org/wiki/Q7922","display_name":"Pedagogy","level":1,"score":0.0},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.0},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C120665830","wikidata":"https://www.wikidata.org/wiki/Q14620","display_name":"Optics","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D002465","descriptor_name":"Cell Movement","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002465","descriptor_name":"Cell Movement","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002465","descriptor_name":"Cell Movement","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004023","descriptor_name":"Dictyostelium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004023","descriptor_name":"Dictyostelium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D004023","descriptor_name":"Dictyostelium","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007091","descriptor_name":"Image Processing, Computer-Assisted","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D018631","descriptor_name":"ras Proteins","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bioinformatics/btp405","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp405","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/18/2383/48994407/bioinformatics_25_18_2383.pdf","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:19578170","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19578170","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}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btp405","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btp405","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/25/18/2383/48994407/bioinformatics_25_18_2383.pdf","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"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2063102049.pdf","grobid_xml":"https://content.openalex.org/works/W2063102049.grobid-xml"},"referenced_works_count":23,"referenced_works":["https://openalex.org/W18096758","https://openalex.org/W400660352","https://openalex.org/W1562012334","https://openalex.org/W1889969990","https://openalex.org/W2013268726","https://openalex.org/W2017038627","https://openalex.org/W2038922801","https://openalex.org/W2044599041","https://openalex.org/W2055551670","https://openalex.org/W2076476329","https://openalex.org/W2102938423","https://openalex.org/W2104095591","https://openalex.org/W2110347960","https://openalex.org/W2146749791","https://openalex.org/W2153504150","https://openalex.org/W2155296963","https://openalex.org/W2158939069","https://openalex.org/W2161179221","https://openalex.org/W2411207881","https://openalex.org/W2911849323","https://openalex.org/W3023913994","https://openalex.org/W6639739270","https://openalex.org/W6714766686"],"related_works":["https://openalex.org/W2084534438","https://openalex.org/W2373557848","https://openalex.org/W2088970451","https://openalex.org/W2002488624","https://openalex.org/W2157008402","https://openalex.org/W2384910134","https://openalex.org/W2020120615","https://openalex.org/W4283071714","https://openalex.org/W2347965233","https://openalex.org/W3140650048"],"abstract_inverted_index":{"The":[0],"emergence":[1],"of":[2,12,40,56,64,84,90,124,131,137],"new":[3],"microscopy":[4],"techniques":[5],"in":[6,31],"combination":[7],"with":[8,186],"the":[9,48,54,81,88,129,174,187],"increasing":[10],"resource":[11],"bioimaging":[13],"data":[14,65,175],"has":[15],"given":[16],"fresh":[17],"impetus":[18],"to":[19,69,80,120,155,167],"utilizing":[20],"image":[21],"processing":[22],"methods":[23],"for":[24,36,75,101],"studying":[25],"biological":[26,41,85],"processes.":[27],"Cell":[28],"tracking":[29,103,183],"studies":[30,59],"particular,":[32],"which":[33],"are":[34,67],"important":[35],"a":[37,122,135],"wide":[38],"range":[39],"processes":[42],"such":[43],"as":[44,144],"embryonic":[45],"development":[46],"or":[47,99],"immune":[49],"system,":[50],"have":[51],"recently":[52],"become":[53],"focus":[55],"attention.":[57],"These":[58],"typically":[60],"produce":[61],"large":[62,82],"volumes":[63],"that":[66,117,179],"hard":[68],"investigate":[70],"manually":[71],"and":[72,87,127,141,161,165,182],"therefore":[73],"call":[74],"an":[76,145],"automated":[77],"approach.":[78],"Due":[79],"variety":[83],"cells":[86,133],"inhomogeneity":[89],"applications,":[91],"however,":[92],"there":[93],"exists":[94],"no":[95],"widely":[96],"accepted":[97],"method":[98],"system":[100],"cell":[102,125,159,163],"until":[104],"today.":[105],"In":[106],"this":[107],"article,":[108],"we":[109,147],"present":[110],"our":[111,153],"publicly":[112],"available":[113],"DYNAMIK":[114],"software":[115,154,192],"environment":[116],"allows":[118],"users":[119,150],"compute":[121,156],"suit":[123],"features":[126],"plot":[128],"trajectory":[130],"multiple":[132],"over":[134],"sequence":[136],"frames.":[138],"Using":[139],"chemotaxis":[140],"Ras":[142],"pathways":[143],"example,":[146],"show":[148],"how":[149,166],"can":[151],"employ":[152],"statistics":[157],"about":[158],"motility":[160],"other":[162,191],"information,":[164],"evaluate":[168],"their":[169],"test":[170],"series":[171],"based":[172],"on":[173],"computed.":[176],"We":[177],"see":[178],"DYNAMIK's":[180],"segmentation":[181],"compares":[184],"favorably":[185],"output":[188],"produced":[189],"by":[190],"packages.":[193]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
