{"id":"https://openalex.org/W2070311374","doi":"https://doi.org/10.1186/1471-2105-8-103","title":"Modeling biochemical transformation processes and information processing with Narrator","display_name":"Modeling biochemical transformation processes and information processing with Narrator","publication_year":2007,"publication_date":"2007-03-27","ids":{"openalex":"https://openalex.org/W2070311374","doi":"https://doi.org/10.1186/1471-2105-8-103","mag":"2070311374","pmid":"https://pubmed.ncbi.nlm.nih.gov/17389034"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-8-103","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-103","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-103","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-103","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5024009932","display_name":"Johannes Mandel","orcid":null},"institutions":[{"id":"https://openalex.org/I309496635","display_name":"Weihenstephan-Triesdorf University of Applied Sciences","ror":"https://ror.org/00gzkxz88","country_code":"DE","type":"education","lineage":["https://openalex.org/I309496635"]},{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["DE","GB"],"is_corresponding":true,"raw_author_name":"Johannes J Mandel","raw_affiliation_strings":["Dept, of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany. johannes.mandel@fh-weihenstephan.de","Dept. of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, Freising, Germany","School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland"],"affiliations":[{"raw_affiliation_string":"Dept, of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, 85350 Freising, Germany. johannes.mandel@fh-weihenstephan.de","institution_ids":["https://openalex.org/I309496635"]},{"raw_affiliation_string":"Dept. of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, Freising, Germany","institution_ids":["https://openalex.org/I309496635"]},{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Coleraine, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048168829","display_name":"Hendrik Fu\u00df","orcid":null},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Hendrik Fu\u00df","raw_affiliation_strings":["School of Biomedical Sciences, University of Ulster, Coleraine, BT52 1SA, Northern Ireland","School of Biomedical Sciences University of Ulster, Coleraine, Northern Ireland"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Coleraine, BT52 1SA, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Biomedical Sciences University of Ulster, Coleraine, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031724144","display_name":"Niall Palfreyman","orcid":"https://orcid.org/0000-0001-7033-2391"},"institutions":[{"id":"https://openalex.org/I309496635","display_name":"Weihenstephan-Triesdorf University of Applied Sciences","ror":"https://ror.org/00gzkxz88","country_code":"DE","type":"education","lineage":["https://openalex.org/I309496635"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Niall M Palfreyman","raw_affiliation_strings":["Dept. of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, 85350, Freising, Germany","Dept. of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, Freising, Germany"],"affiliations":[{"raw_affiliation_string":"Dept. of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, 85350, Freising, Germany","institution_ids":["https://openalex.org/I309496635"]},{"raw_affiliation_string":"Dept. of Biotechnology & Bioinformatics, Weihenstephan University of Applied Sciences, Freising, Germany","institution_ids":["https://openalex.org/I309496635"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5011609464","display_name":"Werner Dubitzky","orcid":null},"institutions":[{"id":"https://openalex.org/I138801177","display_name":"University of Ulster","ror":"https://ror.org/01yp9g959","country_code":"GB","type":"education","lineage":["https://openalex.org/I138801177"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Werner Dubitzky","raw_affiliation_strings":["School of Biomedical Sciences, University of Ulster, Coleraine, BT52 1SA, Northern Ireland","School of Biomedical Sciences University of Ulster, Coleraine, Northern Ireland"],"affiliations":[{"raw_affiliation_string":"School of Biomedical Sciences, University of Ulster, Coleraine, BT52 1SA, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]},{"raw_affiliation_string":"School of Biomedical Sciences University of Ulster, Coleraine, Northern Ireland","institution_ids":["https://openalex.org/I138801177"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5024009932"],"corresponding_institution_ids":["https://openalex.org/I138801177","https://openalex.org/I309496635"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.5359,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.65729705,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"8","issue":"1","first_page":"103","last_page":"103"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.987500011920929,"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":0.987500011920929,"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":0.9765999913215637,"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":0.9624000191688538,"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/transformation","display_name":"Transformation (genetics)","score":0.6268940567970276},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.573431134223938},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5189404487609863},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.500206708908081},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3601301312446594},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.33383506536483765},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19180813431739807},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.11264735460281372},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.0882863998413086}],"concepts":[{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.6268940567970276},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.573431134223938},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5189404487609863},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.500206708908081},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3601301312446594},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.33383506536483765},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19180813431739807},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.11264735460281372},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0882863998413086}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D001671","descriptor_name":"Biochemistry","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":true},{"descriptor_ui":"D003196","descriptor_name":"Computer Graphics","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":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":"D007257","descriptor_name":"Information Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007257","descriptor_name":"Information Theory","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007257","descriptor_name":"Information Theory","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":"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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D016247","descriptor_name":"Information Storage and Retrieval","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":4,"locations":[{"id":"doi:10.1186/1471-2105-8-103","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-103","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-103","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17389034","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17389034","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d4100a4a8dd24aabb4cd0bd046a7ce4a","is_oa":true,"landing_page_url":"https://doaj.org/article/d4100a4a8dd24aabb4cd0bd046a7ce4a","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 8, Iss 1, p 103 (2007)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1818257","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1847530","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-8-103","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-8-103","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-8-103","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2070311374.pdf","grobid_xml":"https://content.openalex.org/works/W2070311374.grobid-xml"},"referenced_works_count":38,"referenced_works":["https://openalex.org/W578108674","https://openalex.org/W1480692184","https://openalex.org/W1495660511","https://openalex.org/W1497710305","https://openalex.org/W1574796195","https://openalex.org/W1975385846","https://openalex.org/W1976101627","https://openalex.org/W1984208007","https://openalex.org/W1999866856","https://openalex.org/W2042321087","https://openalex.org/W2045478141","https://openalex.org/W2063219876","https://openalex.org/W2063389953","https://openalex.org/W2064442684","https://openalex.org/W2081873623","https://openalex.org/W2095766238","https://openalex.org/W2100525485","https://openalex.org/W2102653059","https://openalex.org/W2103563062","https://openalex.org/W2107062718","https://openalex.org/W2108896820","https://openalex.org/W2111420033","https://openalex.org/W2115343689","https://openalex.org/W2117364474","https://openalex.org/W2117822125","https://openalex.org/W2132232959","https://openalex.org/W2133429395","https://openalex.org/W2142206257","https://openalex.org/W2149991291","https://openalex.org/W2150599425","https://openalex.org/W2156906864","https://openalex.org/W2160751597","https://openalex.org/W2170543954","https://openalex.org/W2432517183","https://openalex.org/W2610191465","https://openalex.org/W2981264952","https://openalex.org/W4249884416","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W1971568933","https://openalex.org/W2013243191","https://openalex.org/W2117258802"],"abstract_inverted_index":{"Narrator":[0,46,53],"is":[1,10,54],"a":[2],"flexible":[3],"and":[4,18,38,60],"intuitive":[5],"systems":[6],"biology":[7,23],"tool.":[8],"It":[9],"specifically":[11],"intended":[12],"for":[13],"users":[14],"aiming":[15],"to":[16,26,34],"construct":[17],"simulate":[19],"dynamic":[20],"models":[21],"of":[22,43,50],"without":[24],"recourse":[25],"extensive":[27],"mathematical":[28],"detail.":[29],"Its":[30],"design":[31],"facilitates":[32],"mappings":[33],"different":[35],"formal":[36],"languages":[37],"frameworks.":[39],"The":[40],"combined":[41],"set":[42],"features":[44],"makes":[45],"unique":[47],"among":[48],"tools":[49],"its":[51],"kind.":[52],"implemented":[55],"as":[56,62],"Java":[57],"software":[58],"program":[59],"available":[61],"open-source":[63],"from":[64],"http://www.narrator-tool.org.":[65]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
