{"id":"https://openalex.org/W2011257065","doi":"https://doi.org/10.1145/2633461","title":"Graphical Modeling Tools for Systems Biology","display_name":"Graphical Modeling Tools for Systems Biology","publication_year":2014,"publication_date":"2014-07-31","ids":{"openalex":"https://openalex.org/W2011257065","doi":"https://doi.org/10.1145/2633461","mag":"2011257065"},"language":"en","primary_location":{"id":"doi:10.1145/2633461","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2633461","pdf_url":null,"source":{"id":"https://openalex.org/S157921468","display_name":"ACM Computing Surveys","issn_l":"0360-0300","issn":["0360-0300","1557-7341"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Computing Surveys","raw_type":"journal-article"},"type":"review","indexed_in":["crossref"],"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/A5072105363","display_name":"Roswitha Gostner","orcid":null},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Roswitha Gostner","raw_affiliation_strings":["The Microsoft Research - University of Trento Centre for Computational and Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027793378","display_name":"Bianca Baldacci","orcid":null},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Bianca Baldacci","raw_affiliation_strings":["The Microsoft Research - University of Trento Centre for Computational and Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031554670","display_name":"Melissa J. Morine","orcid":null},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Melissa J. Morine","raw_affiliation_strings":["Dept of Mathematics, University of Trento and The Microsoft Research - University of Trento Centre for Computational and Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Mathematics, University of Trento and The Microsoft Research - University of Trento Centre for Computational and Systems Biology","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5028775661","display_name":"Corrado Priami","orcid":"https://orcid.org/0000-0002-3261-6235"},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]},{"id":"https://openalex.org/I2802934434","display_name":"The Microsoft Research - University of Trento Centre for Computational and Systems Biology","ror":"https://ror.org/04kcgyj43","country_code":"IT","type":"nonprofit","lineage":["https://openalex.org/I1290206253","https://openalex.org/I193223587","https://openalex.org/I2802934434","https://openalex.org/I4210164937"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Corrado Priami","raw_affiliation_strings":["Dept of Mathematics, University of Trento and The Microsoft Research - University of Trento Centre for Computational and Systems Biology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dept of Mathematics, University of Trento and The Microsoft Research - University of Trento Centre for Computational and Systems Biology","institution_ids":["https://openalex.org/I2802934434","https://openalex.org/I193223587"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":1.4233,"has_fulltext":false,"cited_by_count":16,"citation_normalized_percentile":{"value":0.80612645,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"47","issue":"2","first_page":"1","last_page":"21"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9998000264167786,"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":0.9998000264167786,"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":0.9994000196456909,"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":0.998199999332428,"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/rotation-formalisms-in-three-dimensions","display_name":"Rotation formalisms in three dimensions","score":0.9674288034439087},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8171616196632385},{"id":"https://openalex.org/keywords/usability","display_name":"Usability","score":0.6662531495094299},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.45523881912231445},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.431770920753479},{"id":"https://openalex.org/keywords/graphical-model","display_name":"Graphical model","score":0.4171534478664398},{"id":"https://openalex.org/keywords/human\u2013computer-interaction","display_name":"Human\u2013computer interaction","score":0.4053216278553009},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.370799720287323},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.23235145211219788}],"concepts":[{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.9674288034439087},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8171616196632385},{"id":"https://openalex.org/C170130773","wikidata":"https://www.wikidata.org/wiki/Q216378","display_name":"Usability","level":2,"score":0.6662531495094299},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.45523881912231445},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.431770920753479},{"id":"https://openalex.org/C155846161","wikidata":"https://www.wikidata.org/wiki/Q1143367","display_name":"Graphical model","level":2,"score":0.4171534478664398},{"id":"https://openalex.org/C107457646","wikidata":"https://www.wikidata.org/wiki/Q207434","display_name":"Human\u2013computer interaction","level":1,"score":0.4053216278553009},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.370799720287323},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.23235145211219788},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.0},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1145/2633461","is_oa":false,"landing_page_url":"https://doi.org/10.1145/2633461","pdf_url":null,"source":{"id":"https://openalex.org/S157921468","display_name":"ACM Computing Surveys","issn_l":"0360-0300","issn":["0360-0300","1557-7341"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Computing Surveys","raw_type":"journal-article"},{"id":"pmh:oai:arpi.unipi.it:11568/881783","is_oa":false,"landing_page_url":"http://hdl.handle.net/11568/881783","pdf_url":null,"source":{"id":"https://openalex.org/S4377196265","display_name":"CINECA IRIS Institutial research information system (University of Pisa)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I108290504","host_organization_name":"University of Pisa","host_organization_lineage":["https://openalex.org/I108290504"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":72,"referenced_works":["https://openalex.org/W156086047","https://openalex.org/W582495273","https://openalex.org/W1509774833","https://openalex.org/W1534717118","https://openalex.org/W1582279759","https://openalex.org/W1593456738","https://openalex.org/W1857817679","https://openalex.org/W1963861745","https://openalex.org/W1974974415","https://openalex.org/W1978486653","https://openalex.org/W1993387100","https://openalex.org/W1995077427","https://openalex.org/W1995923922","https://openalex.org/W2003503318","https://openalex.org/W2008633581","https://openalex.org/W2010549653","https://openalex.org/W2012773975","https://openalex.org/W2013522363","https://openalex.org/W2016803695","https://openalex.org/W2022960516","https://openalex.org/W2031908202","https://openalex.org/W2034375827","https://openalex.org/W2038264484","https://openalex.org/W2040466333","https://openalex.org/W2045182523","https://openalex.org/W2049854874","https://openalex.org/W2058943257","https://openalex.org/W2061425168","https://openalex.org/W2064974862","https://openalex.org/W2065219357","https://openalex.org/W2065475665","https://openalex.org/W2069157810","https://openalex.org/W2081098704","https://openalex.org/W2081781433","https://openalex.org/W2086928685","https://openalex.org/W2094358340","https://openalex.org/W2095766238","https://openalex.org/W2097240335","https://openalex.org/W2097319997","https://openalex.org/W2099693848","https://openalex.org/W2101506009","https://openalex.org/W2102653059","https://openalex.org/W2103454055","https://openalex.org/W2110796675","https://openalex.org/W2111682035","https://openalex.org/W2113892406","https://openalex.org/W2114942707","https://openalex.org/W2118877187","https://openalex.org/W2121938758","https://openalex.org/W2124041499","https://openalex.org/W2130611503","https://openalex.org/W2136970290","https://openalex.org/W2137112190","https://openalex.org/W2138190671","https://openalex.org/W2138301803","https://openalex.org/W2144736357","https://openalex.org/W2146099270","https://openalex.org/W2149209973","https://openalex.org/W2150908245","https://openalex.org/W2154401739","https://openalex.org/W2157075780","https://openalex.org/W2157573465","https://openalex.org/W2157989234","https://openalex.org/W2160751597","https://openalex.org/W2164177637","https://openalex.org/W2166633151","https://openalex.org/W2170543954","https://openalex.org/W2178262931","https://openalex.org/W2416234265","https://openalex.org/W3148693409","https://openalex.org/W4285719527","https://openalex.org/W4300390001"],"related_works":["https://openalex.org/W57206970","https://openalex.org/W3196191855","https://openalex.org/W1950785758","https://openalex.org/W4235091896","https://openalex.org/W2023896637","https://openalex.org/W176020069","https://openalex.org/W3180766726","https://openalex.org/W2089263635","https://openalex.org/W2037309121","https://openalex.org/W2109325056"],"abstract_inverted_index":{"Modeling":[0],"biological":[1,59],"systems":[2,14,60],"to":[3,41,57,106,134],"understand":[4],"their":[5,66],"mechanistic":[6],"behavior":[7],"is":[8],"an":[9,100],"important":[10],"activity":[11],"in":[12,124,138],"molecular":[13],"biology.":[15],"Mathematical":[16],"modeling":[17,31,36,72],"typically":[18],"requires":[19],"deep":[20],"mathematical":[21],"or":[22],"computing":[23],"knowledge,":[24],"and":[25,95],"this":[26,43,115],"limits":[27],"the":[28,48,69,82,86,97,125],"spread":[29],"of":[30,71,85,99,109,131],"tools":[32],"among":[33,104],"biologists.":[34],"Graphical":[35],"languages":[37],"have":[38],"been":[39],"introduced":[40],"minimize":[42],"limit.":[44],"Here,":[45],"we":[46,89,122],"survey":[47,102],"main":[49,83],"graphical":[50,111,132],"formalisms":[51,133],"(supported":[52],"by":[53],"software":[54],"tools)":[55],"available":[56,110],"model":[58,135],"with":[61,75],"a":[62,91,117],"primary":[63],"focus":[64],"on":[65],"usability,":[67],"within":[68],"framework":[70],"reaction":[73,136],"pathways":[74,137],"two-dimensional":[76],"(2D)":[77],"(possibly":[78],"nested)":[79],"compartments.":[80],"Considering":[81],"characteristics":[84],"surveyed":[87],"formalisms,":[88],"synthesise":[90],"new":[92],"proposal":[93,116],"(Style)":[94],"report":[96],"results":[98],"online":[101],"conducted":[103],"biologists":[105],"assess":[107],"usability":[108],"formalisms.":[112],"We":[113],"consider":[114],"guideline":[118],"developed":[119],"from":[120],"what":[121],"learned":[123],"survey,":[126],"which":[127],"can":[128],"inform":[129],"development":[130],"2D":[139],"space.":[140]},"counts_by_year":[{"year":2021,"cited_by_count":3},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":1},{"year":2014,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2016-06-24T00:00:00"}
