{"id":"https://openalex.org/W2044327544","doi":"https://doi.org/10.1007/s40484-014-0036-4","title":"Construction, visualization, and analysis of biological network models in Dynetica","display_name":"Construction, visualization, and analysis of biological network models in Dynetica","publication_year":2015,"publication_date":"2015-02-06","ids":{"openalex":"https://openalex.org/W2044327544","doi":"https://doi.org/10.1007/s40484-014-0036-4","mag":"2044327544"},"language":"en","primary_location":{"id":"doi:10.1007/s40484-014-0036-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-014-0036-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-014-0036-4.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"diamond","oa_url":"https://link.springer.com/content/pdf/10.1007/s40484-014-0036-4.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5049790356","display_name":"Derek M. Eidum","orcid":"https://orcid.org/0000-0003-2651-6534"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Derek Eidum","raw_affiliation_strings":["<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA"],"affiliations":[{"raw_affiliation_string":"<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047591738","display_name":"Kanishk Asthana","orcid":"https://orcid.org/0009-0005-2973-6614"},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kanishk Asthana","raw_affiliation_strings":["<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA"],"affiliations":[{"raw_affiliation_string":"<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045592143","display_name":"Samir Unni","orcid":null},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Samir Unni","raw_affiliation_strings":["<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA"],"affiliations":[{"raw_affiliation_string":"<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069089615","display_name":"Michael Deng","orcid":null},"institutions":[{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Deng","raw_affiliation_strings":["<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA"],"affiliations":[{"raw_affiliation_string":"<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100401842","display_name":"Lingchong You","orcid":"https://orcid.org/0000-0003-3725-4007"},"institutions":[{"id":"https://openalex.org/I4210155419","display_name":"Center for Systems Biology","ror":"https://ror.org/05r3dyn47","country_code":"US","type":"facility","lineage":["https://openalex.org/I136199984","https://openalex.org/I4210087915","https://openalex.org/I4210155419","https://openalex.org/I48633490"]},{"id":"https://openalex.org/I170897317","display_name":"Duke University","ror":"https://ror.org/00py81415","country_code":"US","type":"education","lineage":["https://openalex.org/I170897317"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lingchong You","raw_affiliation_strings":["<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","<!--2--> Center for Systems Biology Duke University Durham NC 27708 USA","<!--3--> Center for Genomic and Computational Biology Duke University Durham NC 27708 USA","2. Center for Systems Biology, Duke University, Durham, NC 27708, USA","3. Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA","1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA"],"affiliations":[{"raw_affiliation_string":"<!--1--> Department of Biomedical Engineering Duke University Durham NC 27708 USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"<!--2--> Center for Systems Biology Duke University Durham NC 27708 USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I170897317"]},{"raw_affiliation_string":"<!--3--> Center for Genomic and Computational Biology Duke University Durham NC 27708 USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"2. Center for Systems Biology, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I4210155419","https://openalex.org/I170897317"]},{"raw_affiliation_string":"3. Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]},{"raw_affiliation_string":"1. Department of Biomedical Engineering, Duke University, Durham, NC 27708, USA","institution_ids":["https://openalex.org/I170897317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5049790356"],"corresponding_institution_ids":["https://openalex.org/I170897317"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.0463085,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":96},"biblio":{"volume":"2","issue":"4","first_page":"142","last_page":"150"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9994999766349792,"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":0.9994999766349792,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9940999746322632,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9940000176429749,"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/sbml","display_name":"SBML","score":0.9115559458732605},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8376399278640747},{"id":"https://openalex.org/keywords/modular-design","display_name":"Modular design","score":0.6482908725738525},{"id":"https://openalex.org/keywords/debugging","display_name":"Debugging","score":0.632266640663147},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.5787839293479919},{"id":"https://openalex.org/keywords/graphical-user-interface","display_name":"Graphical user interface","score":0.5184921026229858},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.4988386631011963},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.48759832978248596},{"id":"https://openalex.org/keywords/biological-network","display_name":"Biological network","score":0.48507753014564514},{"id":"https://openalex.org/keywords/java","display_name":"Java","score":0.4536459147930145},{"id":"https://openalex.org/keywords/matlab","display_name":"MATLAB","score":0.4404248595237732},{"id":"https://openalex.org/keywords/process","display_name":"Process (computing)","score":0.4393463134765625},{"id":"https://openalex.org/keywords/markup-language","display_name":"Markup language","score":0.37768951058387756},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.37611839175224304},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3305779695510864},{"id":"https://openalex.org/keywords/xml","display_name":"XML","score":0.11397579312324524},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.11383405327796936}],"concepts":[{"id":"https://openalex.org/C87186988","wikidata":"https://www.wikidata.org/wiki/Q452197","display_name":"SBML","level":4,"score":0.9115559458732605},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8376399278640747},{"id":"https://openalex.org/C101468663","wikidata":"https://www.wikidata.org/wiki/Q1620158","display_name":"Modular design","level":2,"score":0.6482908725738525},{"id":"https://openalex.org/C168065819","wikidata":"https://www.wikidata.org/wiki/Q845566","display_name":"Debugging","level":2,"score":0.632266640663147},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.5787839293479919},{"id":"https://openalex.org/C37789001","wikidata":"https://www.wikidata.org/wiki/Q782543","display_name":"Graphical user interface","level":2,"score":0.5184921026229858},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.4988386631011963},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.48759832978248596},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.48507753014564514},{"id":"https://openalex.org/C548217200","wikidata":"https://www.wikidata.org/wiki/Q251","display_name":"Java","level":2,"score":0.4536459147930145},{"id":"https://openalex.org/C2780365114","wikidata":"https://www.wikidata.org/wiki/Q169478","display_name":"MATLAB","level":2,"score":0.4404248595237732},{"id":"https://openalex.org/C98045186","wikidata":"https://www.wikidata.org/wiki/Q205663","display_name":"Process (computing)","level":2,"score":0.4393463134765625},{"id":"https://openalex.org/C45874996","wikidata":"https://www.wikidata.org/wiki/Q37045","display_name":"Markup language","level":3,"score":0.37768951058387756},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.37611839175224304},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3305779695510864},{"id":"https://openalex.org/C8797682","wikidata":"https://www.wikidata.org/wiki/Q2115","display_name":"XML","level":2,"score":0.11397579312324524},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.11383405327796936},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1007/s40484-014-0036-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-014-0036-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-014-0036-4.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1007/s40484-014-0036-4","is_oa":true,"landing_page_url":"https://doi.org/10.1007/s40484-014-0036-4","pdf_url":"https://link.springer.com/content/pdf/10.1007/s40484-014-0036-4.pdf","source":{"id":"https://openalex.org/S4210172333","display_name":"Quantitative Biology","issn_l":"2095-4689","issn":["2095-4689","2095-4697"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310319900","host_organization_name":"Springer Science+Business Media","host_organization_lineage":["https://openalex.org/P4310319900","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Springer Science+Business Media","Springer Nature"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Quantitative Biology","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1441707171","display_name":null,"funder_award_id":"Fellow","funder_id":"https://openalex.org/F4320306079","funder_display_name":"David and Lucile Packard Foundation"},{"id":"https://openalex.org/G4641068160","display_name":null,"funder_award_id":"Packard","funder_id":"https://openalex.org/F4320306079","funder_display_name":"David and Lucile Packard Foundation"},{"id":"https://openalex.org/G6894402473","display_name":null,"funder_award_id":"Fellowship","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"},{"id":"https://openalex.org/G8832243575","display_name":null,"funder_award_id":"Fellowship","funder_id":"https://openalex.org/F4320306079","funder_display_name":"David and Lucile Packard Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320306079","display_name":"David and Lucile Packard Foundation","ror":"https://ror.org/032atxq54"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320338281","display_name":"Army Research Office","ror":"https://ror.org/05epdh915"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2044327544.pdf","grobid_xml":"https://content.openalex.org/works/W2044327544.grobid-xml"},"referenced_works_count":20,"referenced_works":["https://openalex.org/W1659842140","https://openalex.org/W1965725897","https://openalex.org/W1969727436","https://openalex.org/W1984263697","https://openalex.org/W2009307035","https://openalex.org/W2019916003","https://openalex.org/W2081781433","https://openalex.org/W2092724797","https://openalex.org/W2093514941","https://openalex.org/W2097319997","https://openalex.org/W2104484234","https://openalex.org/W2110232499","https://openalex.org/W2111420033","https://openalex.org/W2114124738","https://openalex.org/W2114228460","https://openalex.org/W2117364474","https://openalex.org/W2119017580","https://openalex.org/W2122000245","https://openalex.org/W2135879265","https://openalex.org/W2146212356"],"related_works":["https://openalex.org/W2082621456","https://openalex.org/W2150908245","https://openalex.org/W2981332207","https://openalex.org/W2159912904","https://openalex.org/W2211443823","https://openalex.org/W2100525485","https://openalex.org/W2040642413","https://openalex.org/W3048335229","https://openalex.org/W2146744007","https://openalex.org/W2890725831"],"abstract_inverted_index":{"Mathematical":[0],"modeling":[1],"has":[2],"become":[3],"an":[4,81],"increasingly":[5],"important":[6],"aspect":[7],"of":[8,18,25,44,88,128,139,164,175,182],"biological":[9],"research.":[10],"Computer":[11],"simulations":[12],"help":[13],"to":[14,71],"improve":[15],"our":[16],"understanding":[17],"complex":[19,129],"systems":[20,130],"by":[21,38],"testing":[22],"the":[23,39,89,110,113,125,176,183,196],"validity":[24],"proposed":[26],"mechanisms":[27],"and":[28,42,48,78,91,100,103,141,224],"generating":[29],"experimentally":[30],"testable":[31],"hypotheses.":[32],"However,":[33],"significant":[34],"overhead":[35],"is":[36,64,211,217],"generated":[37],"creation,":[40],"debugging,":[41],"perturbation":[43],"these":[45],"computational":[46],"models":[47],"their":[49],"parameters,":[50],"especially":[51],"for":[52,124,144,154,161,203,221],"researchers":[53],"who":[54],"are":[55,76],"unfamiliar":[56],"with":[57],"programming":[58],"or":[59,157,179,195,206],"numerical":[60],"methods.":[61],"Dynetica":[62,134,149,190,215],"2.0":[63,135,150,191,216],"a":[65,95,137,162],"user\u2010friendly":[66],"dynamic":[67],"network":[68],"simulator":[69],"designed":[70],"expedite":[72],"this":[73],"process.":[74],"Models":[75,118],"created":[77],"visualized":[79],"in":[80,94,213],"easy\u2010to\u2010use":[82],"graphical":[83],"interface,":[84],"which":[85],"displays":[86],"all":[87],"species":[90],"reactions":[92],"involved":[93],"graph":[96],"layout.":[97],"System":[98],"inputs":[99],"outputs,":[101],"indicators,":[102],"intermediate":[104],"expressions":[105],"may":[106],"be":[107,121,187],"incorporated":[108],"into":[109,192],"model":[111],"via":[112],"versatile":[114],"\u201cexpression":[115],"variable\u201d":[116],"entity.":[117],"can":[119,171,186],"also":[120],"modular,":[122],"allowing":[123,220],"quick":[126],"construction":[127],"from":[131,189],"simpler":[132],"components.":[133],"supports":[136],"number":[138,163],"deterministic":[140],"stochastic":[142],"algorithms":[143],"performing":[145,155],"time\u2010course":[146],"simulations.":[147],"Additionally,":[148],"provides":[151],"built\u2010in":[152],"tools":[153,170],"sensitivity":[156],"dose":[158,180],"response":[159,181],"analysis":[160,205],"different":[165],"metrics.":[166],"Its":[167],"parameter":[168],"searching":[169],"optimize":[172],"specific":[173],"objectives":[174],"time":[177],"course":[178],"system.":[184],"Systems":[185,197],"translated":[188],"MATLAB":[193],"code":[194],"Biology":[198],"Markup":[199],"Language":[200],"(SBML)":[201],"format":[202],"further":[204],"publication.":[207],"Finally,":[208],"since":[209],"it":[210],"written":[212],"Java,":[214],"platform":[218],"independent,":[219],"easy":[222],"sharing":[223],"collaboration":[225],"between":[226],"researchers.":[227]},"counts_by_year":[{"year":2019,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}