{"id":"https://openalex.org/W2147015829","doi":"https://doi.org/10.1142/s0219720011005410","title":"VISUALIZATION IN SIMULATION TOOLS: REQUIREMENTS AND A TOOL SPECIFICATION TO SUPPORT THE TEACHING OF DYNAMIC BIOLOGICAL PROCESSES","display_name":"VISUALIZATION IN SIMULATION TOOLS: REQUIREMENTS AND A TOOL SPECIFICATION TO SUPPORT THE TEACHING OF DYNAMIC BIOLOGICAL PROCESSES","publication_year":2011,"publication_date":"2011-03-08","ids":{"openalex":"https://openalex.org/W2147015829","doi":"https://doi.org/10.1142/s0219720011005410","mag":"2147015829","pmid":"https://pubmed.ncbi.nlm.nih.gov/21776610"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720011005410","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720011005410","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"review","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5076709079","display_name":"Katarina M. J\u00f8rgensen","orcid":"https://orcid.org/0000-0003-3158-3459"},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":true,"raw_author_name":"KATARINA M. J\u00d8RGENSEN","raw_affiliation_strings":["Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway"],"affiliations":[{"raw_affiliation_string":"Department of Biology, Norwegian University of Science and Technology, N-7491 Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5087467473","display_name":"Pauline C. Haddow","orcid":null},"institutions":[{"id":"https://openalex.org/I204778367","display_name":"Norwegian University of Science and Technology","ror":"https://ror.org/05xg72x27","country_code":"NO","type":"education","lineage":["https://openalex.org/I204778367"]}],"countries":["NO"],"is_corresponding":false,"raw_author_name":"PAULINE C. HADDOW","raw_affiliation_strings":["CRAB Lab, Department of Computer and Information Science, Norwegian University of Science and Technology, N-7491 Trondheim, Norway"],"affiliations":[{"raw_affiliation_string":"CRAB Lab, Department of Computer and Information Science, Norwegian University of Science and Technology, N-7491 Trondheim, Norway","institution_ids":["https://openalex.org/I204778367"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5076709079"],"corresponding_institution_ids":["https://openalex.org/I204778367"],"apc_list":null,"apc_paid":null,"fwci":0.2606,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.5885198,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"09","issue":"04","first_page":"579","last_page":"595"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.98089998960495,"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":0.98089998960495,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9778000116348267,"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/T11975","display_name":"Evolutionary Algorithms and Applications","score":0.9309999942779541,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6618071794509888},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.644578218460083},{"id":"https://openalex.org/keywords/field","display_name":"Field (mathematics)","score":0.5657097101211548},{"id":"https://openalex.org/keywords/curriculum","display_name":"Curriculum","score":0.5204175114631653},{"id":"https://openalex.org/keywords/limiting","display_name":"Limiting","score":0.5025789737701416},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4945840537548065},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.45078930258750916},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.37021586298942566},{"id":"https://openalex.org/keywords/management-science","display_name":"Management science","score":0.35034215450286865},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.3413105607032776},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.24148449301719666},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.17314261198043823},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.1004767119884491}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6618071794509888},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.644578218460083},{"id":"https://openalex.org/C9652623","wikidata":"https://www.wikidata.org/wiki/Q190109","display_name":"Field (mathematics)","level":2,"score":0.5657097101211548},{"id":"https://openalex.org/C47177190","wikidata":"https://www.wikidata.org/wiki/Q207137","display_name":"Curriculum","level":2,"score":0.5204175114631653},{"id":"https://openalex.org/C188198153","wikidata":"https://www.wikidata.org/wiki/Q1613840","display_name":"Limiting","level":2,"score":0.5025789737701416},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4945840537548065},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.45078930258750916},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37021586298942566},{"id":"https://openalex.org/C539667460","wikidata":"https://www.wikidata.org/wiki/Q2414942","display_name":"Management science","level":1,"score":0.35034215450286865},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.3413105607032776},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.24148449301719666},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.17314261198043823},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.1004767119884491},{"id":"https://openalex.org/C202444582","wikidata":"https://www.wikidata.org/wiki/Q837863","display_name":"Pure mathematics","level":1,"score":0.0},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"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/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C78519656","wikidata":"https://www.wikidata.org/wiki/Q101333","display_name":"Mechanical engineering","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D003194","descriptor_name":"Computer-Assisted Instruction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003194","descriptor_name":"Computer-Assisted Instruction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003194","descriptor_name":"Computer-Assisted Instruction","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003199","descriptor_name":"Computer Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000193","qualifier_name":"education","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false},{"descriptor_ui":"D049490","descriptor_name":"Systems Biology","qualifier_ui":"Q000706","qualifier_name":"statistics & numerical data","is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720011005410","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720011005410","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:21776610","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/21776610","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W18155658","https://openalex.org/W98222776","https://openalex.org/W1495660511","https://openalex.org/W1554939770","https://openalex.org/W1806544472","https://openalex.org/W2010861350","https://openalex.org/W2011835017","https://openalex.org/W2013522363","https://openalex.org/W2020616584","https://openalex.org/W2038264484","https://openalex.org/W2061425168","https://openalex.org/W2069157810","https://openalex.org/W2070311374","https://openalex.org/W2105771262","https://openalex.org/W2106814120","https://openalex.org/W2112656672","https://openalex.org/W2126153334","https://openalex.org/W2155843307","https://openalex.org/W2157573465","https://openalex.org/W2170543954","https://openalex.org/W2171594815","https://openalex.org/W2326127975","https://openalex.org/W4237910213"],"related_works":["https://openalex.org/W2068608913","https://openalex.org/W3124914020","https://openalex.org/W2141033859","https://openalex.org/W2077542787","https://openalex.org/W2071701083","https://openalex.org/W2348562106","https://openalex.org/W2370820329","https://openalex.org/W2383687187","https://openalex.org/W2370554813","https://openalex.org/W2156434174"],"abstract_inverted_index":{"Simulation":[0],"tools":[1,46,94,122,139,166],"are":[2,158,174],"playing":[3],"an":[4,83,130,153],"increasingly":[5],"important":[6],"role":[7],"behind":[8],"advances":[9],"in":[10,68,111],"the":[11,17,41,50,56,97,118,133,172],"field":[12],"of":[13,20,44,120,132,136],"systems":[14],"biology.":[15],"However,":[16,171],"current":[18],"generation":[19],"biological":[21,113,179],"science":[22,88,114],"students":[23],"has":[24,72,99],"either":[25],"little":[26,70],"or":[27],"no":[28],"experience":[29],"with":[30],"such":[31,45,121],"tools.":[32],"As":[33],"such,":[34],"this":[35],"educational":[36,84,155],"glitch":[37],"is":[38,109,162],"limiting":[39],"both":[40],"potential":[42,51],"use":[43,67],"as":[47,49,82],"well":[48],"for":[52,86,140,152,167],"tighter":[53],"cooperation":[54],"between":[55],"designers":[57],"and":[58,78,103],"users.":[59],"Although":[60],"some":[61],"simulation":[62,93,138,156,165,180],"tool":[63,85,157,181],"producers":[64],"encourage":[65],"their":[66,80],"teaching,":[69],"attempt":[71],"hitherto":[73],"been":[74],"made":[75],"to":[76,176],"analyze":[77],"discuss":[79],"suitability":[81],"noncomputing":[87],"students.":[89],"In":[90],"general,":[91],"today's":[92],"assume":[95],"that":[96,107],"user":[98],"a":[100,123,177],"stronger":[101],"mathematical":[102],"computing":[104],"background":[105],"than":[106],"which":[108],"found":[110],"most":[112],"curricula,":[115],"thus":[116],"making":[117],"introduction":[119],"considerable":[124],"pedagogical":[125,134],"challenge.":[126],"This":[127],"paper":[128],"provides":[129],"evaluation":[131],"attributes":[135],"existing":[137],"cell":[141,168],"signal":[142,169],"transduction":[143],"based":[144,163],"on":[145,164],"Cognitive":[146],"Load":[147],"theory.":[148],"Further,":[149],"design":[150],"recommendations":[151],"improved":[154],"provided.":[159],"The":[160],"study":[161],"transduction.":[170],"discussions":[173],"relevant":[175],"broader":[178],"set.":[182]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
