{"id":"https://openalex.org/W2146917917","doi":"https://doi.org/10.1007/978-3-642-02481-8_161","title":"A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems","display_name":"A Critical Review on Modelling Formalisms and Simulation Tools in Computational Biosystems","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W2146917917","doi":"https://doi.org/10.1007/978-3-642-02481-8_161","mag":"2146917917"},"language":"en","primary_location":{"id":"doi:10.1007/978-3-642-02481-8_161","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-02481-8_161","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"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":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},"type":"conference-paper","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://hdl.handle.net/1822/16627","any_repository_has_fulltext":null},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5028393749","display_name":"Daniel Machado","orcid":"https://orcid.org/0000-0002-2063-5383"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Daniel Machado","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026040695","display_name":"Rafael S. Costa","orcid":null},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Rafael S. Costa","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040524717","display_name":"Miguel Rocha","orcid":"https://orcid.org/0000-0001-8439-8172"},"institutions":[{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Miguel Rocha","raw_affiliation_strings":["Department of Informatics/CCTC, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics/CCTC, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal","institution_ids":["https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079343705","display_name":"Isabel Rocha","orcid":"https://orcid.org/0000-0001-9494-3410"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Isabel Rocha","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5028186526","display_name":"Bruce Tidor","orcid":null},"institutions":[{"id":"https://openalex.org/I63966007","display_name":"Massachusetts Institute of Technology","ror":"https://ror.org/042nb2s44","country_code":"US","type":"education","lineage":["https://openalex.org/I63966007"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Bruce Tidor","raw_affiliation_strings":["Department of Biological Engineering/Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biological Engineering/Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139, USA","institution_ids":["https://openalex.org/I63966007"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064824604","display_name":"Eug\u00e9nio C. Ferreira","orcid":"https://orcid.org/0000-0002-5400-3333"},"institutions":[{"id":"https://openalex.org/I4210167387","display_name":"Institute for Biotechnology and Bioengineering","ror":"https://ror.org/05ws8g470","country_code":"PT","type":"facility","lineage":["https://openalex.org/I4210167387"]},{"id":"https://openalex.org/I99682543","display_name":"University of Minho","ror":"https://ror.org/037wpkx04","country_code":"PT","type":"education","lineage":["https://openalex.org/I99682543"]}],"countries":["PT"],"is_corresponding":false,"raw_author_name":"Eug\u00e9nio C. Ferreira","raw_affiliation_strings":["IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"IBB-Institute for Biotechnology and Bioengineering/Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal","institution_ids":["https://openalex.org/I4210167387","https://openalex.org/I99682543"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":5000,"currency":"EUR","value_usd":5392},"apc_paid":{"value":5000,"currency":"EUR","value_usd":5392},"fwci":1.6971,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.8672467,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":94},"biblio":{"volume":null,"issue":null,"first_page":"1063","last_page":"1070"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9988999962806702,"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":0.9988999962806702,"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":0.9986000061035156,"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":0.9804999828338623,"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":0.9675446152687073},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7917842864990234},{"id":"https://openalex.org/keywords/formalism","display_name":"Formalism (music)","score":0.780720591545105},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.7423850297927856},{"id":"https://openalex.org/keywords/modelling-biological-systems","display_name":"Modelling biological systems","score":0.46095824241638184},{"id":"https://openalex.org/keywords/systems-biology","display_name":"Systems biology","score":0.4458044767379761},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.4092708230018616},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.39405179023742676},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.3449365496635437},{"id":"https://openalex.org/keywords/distributed-computing","display_name":"Distributed computing","score":0.28572511672973633},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.13252267241477966},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.09801730513572693},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.06976297497749329}],"concepts":[{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.9675446152687073},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7917842864990234},{"id":"https://openalex.org/C73301696","wikidata":"https://www.wikidata.org/wiki/Q5469984","display_name":"Formalism (music)","level":3,"score":0.780720591545105},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.7423850297927856},{"id":"https://openalex.org/C137866125","wikidata":"https://www.wikidata.org/wiki/Q4299308","display_name":"Modelling biological systems","level":3,"score":0.46095824241638184},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.4458044767379761},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.4092708230018616},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.39405179023742676},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.3449365496635437},{"id":"https://openalex.org/C120314980","wikidata":"https://www.wikidata.org/wiki/Q180634","display_name":"Distributed computing","level":1,"score":0.28572511672973633},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.13252267241477966},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.09801730513572693},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.06976297497749329},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.0},{"id":"https://openalex.org/C558565934","wikidata":"https://www.wikidata.org/wiki/Q2743","display_name":"Musical","level":2,"score":0.0},{"id":"https://openalex.org/C153349607","wikidata":"https://www.wikidata.org/wiki/Q36649","display_name":"Visual arts","level":1,"score":0.0},{"id":"https://openalex.org/C142362112","wikidata":"https://www.wikidata.org/wiki/Q735","display_name":"Art","level":0,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1007/978-3-642-02481-8_161","is_oa":false,"landing_page_url":"https://doi.org/10.1007/978-3-642-02481-8_161","pdf_url":null,"source":{"id":"https://openalex.org/S106296714","display_name":"Lecture notes in computer science","issn_l":"0302-9743","issn":["0302-9743","1611-3349"],"is_oa":false,"is_in_doaj":false,"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":"book series"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Lecture Notes in Computer Science","raw_type":"book-chapter"},{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/16627","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/16627","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null}],"best_oa_location":{"id":"pmh:oai:repositorium.sdum.uminho.pt:1822/16627","is_oa":true,"landing_page_url":"https://hdl.handle.net/1822/16627","pdf_url":null,"source":null,"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":null},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":41,"referenced_works":["https://openalex.org/W324637047","https://openalex.org/W333135988","https://openalex.org/W1514247755","https://openalex.org/W1518886905","https://openalex.org/W1591582819","https://openalex.org/W1606860353","https://openalex.org/W1740816575","https://openalex.org/W1964514022","https://openalex.org/W1971224531","https://openalex.org/W1973110798","https://openalex.org/W1984818254","https://openalex.org/W1986397618","https://openalex.org/W1986649132","https://openalex.org/W2000040887","https://openalex.org/W2007006124","https://openalex.org/W2011835017","https://openalex.org/W2053339983","https://openalex.org/W2082621456","https://openalex.org/W2103776834","https://openalex.org/W2106190666","https://openalex.org/W2108654339","https://openalex.org/W2119510512","https://openalex.org/W2120820364","https://openalex.org/W2120926795","https://openalex.org/W2122948231","https://openalex.org/W2126176298","https://openalex.org/W2131067724","https://openalex.org/W2132997183","https://openalex.org/W2143784594","https://openalex.org/W2146367686","https://openalex.org/W2148895036","https://openalex.org/W2162505680","https://openalex.org/W2163493106","https://openalex.org/W2169804422","https://openalex.org/W2412839122","https://openalex.org/W2489834657","https://openalex.org/W2913199219","https://openalex.org/W2940404124","https://openalex.org/W4248669983","https://openalex.org/W4251364655","https://openalex.org/W4299438414"],"related_works":["https://openalex.org/W1981703794","https://openalex.org/W2952249082","https://openalex.org/W2061420542","https://openalex.org/W2074343215","https://openalex.org/W2004465018","https://openalex.org/W4283799632","https://openalex.org/W659009177","https://openalex.org/W2949818316","https://openalex.org/W2149038841","https://openalex.org/W2259670429"],"abstract_inverted_index":{"Integration":[0],"of":[1,4,39,74],"different":[2,44],"kinds":[3],"biological":[5,45],"processes":[6],"is":[7,99],"an":[8,35,78],"ultimate":[9],"goal":[10],"for":[11,63,81],"whole-cell":[12],"modelling.":[13],"We":[14],"briefly":[15],"review":[16],"modelling":[17],"formalisms":[18],"that":[19,30,48],"have":[20],"been":[21],"used":[22],"in":[23],"Systems":[24],"Biology":[25],"and":[26,42,66,83,92,101],"identify":[27],"the":[28,72,95,102,108],"criteria":[29],"must":[31],"be":[32,105],"addressed":[33],"by":[34,90,94],"integrating":[36,79],"framework":[37,80],"capable":[38],"modelling,":[40],"analysing":[41],"simulating":[43],"networks.":[46,85],"Aware":[47],"no":[49],"formalism":[50,76],"can":[51],"fit":[52],"all":[53],"purposes":[54],"we":[55],"realize":[56],"Petri":[57],"nets":[58],"as":[59,77,107],"a":[60,68],"suitable":[61],"model":[62],"Metabolic":[64],"Engineering":[65],"take":[67],"deeper":[69],"perspective":[70],"on":[71],"role":[73],"this":[75],"regulatory":[82],"metabolic":[84],"These":[86],"keywords":[87,103],"were":[88],"added":[89],"machine":[91],"not":[93],"authors.":[96],"This":[97],"process":[98],"experimental":[100],"may":[104],"updated":[106],"learning":[109],"algorithm":[110],"improves.":[111]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2026-09-05T08:02:43.246662","created_date":"2025-10-10T00:00:00"}
