{"id":"https://openalex.org/W4400344225","doi":"https://doi.org/10.1093/bib/bbae318","title":"Design patterns for the construction of computational biological models","display_name":"Design patterns for the construction of computational biological models","publication_year":2024,"publication_date":"2024-05-23","ids":{"openalex":"https://openalex.org/W4400344225","doi":"https://doi.org/10.1093/bib/bbae318","pmid":"https://pubmed.ncbi.nlm.nih.gov/38961813"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae318","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae318/58436638/bbae318.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae318/58436638/bbae318.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031918019","display_name":"Mostafa Herajy","orcid":"https://orcid.org/0000-0001-7181-6144"},"institutions":[{"id":"https://openalex.org/I88017793","display_name":"Port Said University","ror":"https://ror.org/01vx5yq44","country_code":"EG","type":"education","lineage":["https://openalex.org/I88017793"]}],"countries":["EG"],"is_corresponding":false,"raw_author_name":"Mostafa Herajy","raw_affiliation_strings":["Department of Mathematics and Computer Science, Faculty of Science, Port Said University , 42521 Port Said , Egypt"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mathematics and Computer Science, Faculty of Science, Port Said University , 42521 Port Said , Egypt","institution_ids":["https://openalex.org/I88017793"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100394589","display_name":"Fei Liu","orcid":"https://orcid.org/0000-0001-9415-0496"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fei Liu","raw_affiliation_strings":["School of Software Engineering, South China University of Technology , 510006 Guangzhou , China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology , 510006 Guangzhou , China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5002026696","display_name":"Monika Heiner","orcid":"https://orcid.org/0000-0003-1815-1205"},"institutions":[{"id":"https://openalex.org/I51783024","display_name":"Brandenburg University of Technology Cottbus-Senftenberg","ror":"https://ror.org/02wxx3e24","country_code":"DE","type":"education","lineage":["https://openalex.org/I51783024"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Monika Heiner","raw_affiliation_strings":["Computer Science Institute, Brandenburg University of Technology , 03013 Cottbus , Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Computer Science Institute, Brandenburg University of Technology , 03013 Cottbus , Germany","institution_ids":["https://openalex.org/I51783024"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":3,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.4288,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.81089241,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":99},"biblio":{"volume":"25","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9952999949455261,"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":0.9952999949455261,"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/T12029","display_name":"DNA and Biological Computing","score":0.9743000268936157,"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/T11450","display_name":"Model-Driven Software Engineering Techniques","score":0.9731000065803528,"subfield":{"id":"https://openalex.org/subfields/1712","display_name":"Software"},"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":0.828506350517273},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.719745397567749},{"id":"https://openalex.org/keywords/rotation-formalisms-in-three-dimensions","display_name":"Rotation formalisms in three dimensions","score":0.6971276998519897},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5554144978523254},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.5538830757141113},{"id":"https://openalex.org/keywords/petri-net","display_name":"Petri net","score":0.5207731127738953},{"id":"https://openalex.org/keywords/computational-model","display_name":"Computational model","score":0.5088860988616943},{"id":"https://openalex.org/keywords/software-engineering","display_name":"Software engineering","score":0.5005502700805664},{"id":"https://openalex.org/keywords/software","display_name":"Software","score":0.49606427550315857},{"id":"https://openalex.org/keywords/scratch","display_name":"Scratch","score":0.49542558193206787},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4079650640487671},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3347514867782593},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.3064344525337219},{"id":"https://openalex.org/keywords/systems-engineering","display_name":"Systems engineering","score":0.2718835175037384},{"id":"https://openalex.org/keywords/engineering","display_name":"Engineering","score":0.08597424626350403}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.828506350517273},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.719745397567749},{"id":"https://openalex.org/C171018156","wikidata":"https://www.wikidata.org/wiki/Q7370306","display_name":"Rotation formalisms in three dimensions","level":2,"score":0.6971276998519897},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5554144978523254},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.5538830757141113},{"id":"https://openalex.org/C38677869","wikidata":"https://www.wikidata.org/wiki/Q724168","display_name":"Petri net","level":2,"score":0.5207731127738953},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.5088860988616943},{"id":"https://openalex.org/C115903868","wikidata":"https://www.wikidata.org/wiki/Q80993","display_name":"Software engineering","level":1,"score":0.5005502700805664},{"id":"https://openalex.org/C2777904410","wikidata":"https://www.wikidata.org/wiki/Q7397","display_name":"Software","level":2,"score":0.49606427550315857},{"id":"https://openalex.org/C2781235140","wikidata":"https://www.wikidata.org/wiki/Q275131","display_name":"Scratch","level":2,"score":0.49542558193206787},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4079650640487671},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3347514867782593},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.3064344525337219},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.2718835175037384},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.08597424626350403},{"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":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"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":"D008954","descriptor_name":"Models, Biological","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae318","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae318/58436638/bbae318.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38961813","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38961813","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11222664","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11222664","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11222664/pdf/bbae318.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae318","pdf_url":"https://academic.oup.com/bib/article-pdf/25/4/bbae318/58436638/bbae318.pdf","source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"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":"cc-by-nc","license_id":"https://openalex.org/licenses/cc-by-nc","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2884727198","display_name":null,"funder_award_id":"2024A1515010900","funder_id":"https://openalex.org/F4320337111","funder_display_name":"Basic and Applied Basic Research Foundation of Guangdong Province"},{"id":"https://openalex.org/G301518385","display_name":null,"funder_award_id":"62273153","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320337111","display_name":"Basic and Applied Basic Research Foundation of Guangdong Province","ror":null}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4400344225.pdf"},"referenced_works_count":55,"referenced_works":["https://openalex.org/W67242188","https://openalex.org/W180888965","https://openalex.org/W1759934887","https://openalex.org/W1940417817","https://openalex.org/W1974161639","https://openalex.org/W1990043688","https://openalex.org/W2010900077","https://openalex.org/W2013336170","https://openalex.org/W2013484275","https://openalex.org/W2030945597","https://openalex.org/W2046855815","https://openalex.org/W2061245977","https://openalex.org/W2063773908","https://openalex.org/W2081828574","https://openalex.org/W2096601649","https://openalex.org/W2098579568","https://openalex.org/W2100193366","https://openalex.org/W2102434872","https://openalex.org/W2119571991","https://openalex.org/W2131295012","https://openalex.org/W2135249635","https://openalex.org/W2143784594","https://openalex.org/W2148895036","https://openalex.org/W2154045630","https://openalex.org/W2167154952","https://openalex.org/W2206783966","https://openalex.org/W2400137219","https://openalex.org/W2503470518","https://openalex.org/W2556034692","https://openalex.org/W2741871742","https://openalex.org/W2763427691","https://openalex.org/W2799055780","https://openalex.org/W2805549187","https://openalex.org/W2902000707","https://openalex.org/W2938329024","https://openalex.org/W2952884569","https://openalex.org/W3046591788","https://openalex.org/W3080133182","https://openalex.org/W3178965648","https://openalex.org/W3201132720","https://openalex.org/W4210730147","https://openalex.org/W4212938657","https://openalex.org/W4214594956","https://openalex.org/W4225552323","https://openalex.org/W4233292973","https://openalex.org/W4300591351","https://openalex.org/W4311218156","https://openalex.org/W4375946168","https://openalex.org/W4389472768","https://openalex.org/W6603878150","https://openalex.org/W6643786885","https://openalex.org/W6681451615","https://openalex.org/W6745199320","https://openalex.org/W6764563136","https://openalex.org/W6781905359"],"related_works":["https://openalex.org/W2475116013","https://openalex.org/W2770018148","https://openalex.org/W2358308169","https://openalex.org/W57206970","https://openalex.org/W2385135707","https://openalex.org/W2140315382","https://openalex.org/W2059109728","https://openalex.org/W3196191855","https://openalex.org/W322691623","https://openalex.org/W1981703794"],"abstract_inverted_index":{"Computational":[0],"biological":[1,18,90],"models":[2,33,135],"have":[3],"proven":[4],"to":[5,30,64,100],"be":[6,24,117,137],"an":[7],"invaluable":[8],"tool":[9],"for":[10,27,42,128],"understanding":[11],"and":[12,75,86,131],"predicting":[13],"the":[14,84,109,141,148],"behaviour":[15],"of":[16,61,88,105],"many":[17,156],"systems.":[19],"While":[20],"it":[21,36],"may":[22],"not":[23,38],"too":[25],"challenging":[26],"experienced":[28],"researchers":[29,157],"construct":[31],"such":[32],"from":[34,140],"scratch,":[35],"is":[37],"a":[39,59,97,102],"straightforward":[40],"task":[41],"early":[43],"stage":[44],"researchers.":[45],"Design":[46],"patterns":[47,78],"are":[48,80],"well-known":[49],"techniques":[50],"widely":[51],"applied":[52],"in":[53,67,112,151,158],"software":[54,68],"engineering":[55],"as":[56,96],"they":[57],"provide":[58,101,124],"set":[60],"typical":[62],"solutions":[63],"common":[65,77],"problems":[66],"design.":[69],"In":[70],"this":[71,113,152],"paper,":[72],"we":[73],"collect":[74],"discuss":[76],"that":[79,147],"usually":[81],"used":[82],"during":[83],"construction":[85],"execution":[87],"computational":[89],"models.":[91,163],"We":[92,123,145],"adopt":[93],"Petri":[94],"nets":[95],"modelling":[98,121],"language":[99],"visual":[103],"illustration":[104,129],"each":[106],"pattern;":[107],"however,":[108],"ideas":[110,149],"presented":[111,142],"paper":[114,153],"can":[115,136],"also":[116],"implemented":[118],"using":[119],"other":[120],"formalisms.":[122],"two":[125],"case":[126],"studies":[127],"purposes":[130],"show":[132],"how":[133],"these":[134],"built":[138],"up":[139],"smaller":[143],"modules.":[144],"hope":[146],"discussed":[150],"will":[154],"help":[155],"building":[159],"their":[160],"own":[161],"future":[162]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
