{"id":"https://openalex.org/W2103173634","doi":"https://doi.org/10.1093/bioinformatics/btl497","title":"Cell++\u2014simulating biochemical pathways","display_name":"Cell++\u2014simulating biochemical pathways","publication_year":2006,"publication_date":"2006-10-11","ids":{"openalex":"https://openalex.org/W2103173634","doi":"https://doi.org/10.1093/bioinformatics/btl497","mag":"2103173634","pmid":"https://pubmed.ncbi.nlm.nih.gov/17038347"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btl497","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl497","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/23/2918/16851740/btl497.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/22/23/2918/16851740/btl497.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041455841","display_name":"Chris Sanford","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Chris Sanford","raw_affiliation_strings":["Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada","Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5073321157","display_name":"Matthew L.K. Yip","orcid":null},"institutions":[{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Matthew L.K. Yip","raw_affiliation_strings":["Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112490540","display_name":"Carl A. White","orcid":null},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":false,"raw_author_name":"Carl White","raw_affiliation_strings":["Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada","Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada","institution_ids":["https://openalex.org/I2801317318"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5085182984","display_name":"John Parkinson","orcid":"https://orcid.org/0000-0001-9815-1189"},"institutions":[{"id":"https://openalex.org/I185261750","display_name":"University of Toronto","ror":"https://ror.org/03dbr7087","country_code":"CA","type":"education","lineage":["https://openalex.org/I185261750"]},{"id":"https://openalex.org/I2801317318","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57","country_code":"CA","type":"healthcare","lineage":["https://openalex.org/I2801317318"]}],"countries":["CA"],"is_corresponding":true,"raw_author_name":"John Parkinson","raw_affiliation_strings":["Department of Biochemistry, University of Toronto 3 \u00a0 3 \u00a0 \u00a0 ON, Canada","Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada","Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biochemistry, University of Toronto 3 \u00a0 3 \u00a0 \u00a0 ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada","institution_ids":["https://openalex.org/I185261750"]},{"raw_affiliation_string":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada","institution_ids":["https://openalex.org/I2801317318"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5085182984"],"corresponding_institution_ids":["https://openalex.org/I185261750","https://openalex.org/I2801317318"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.363,"has_fulltext":true,"cited_by_count":55,"citation_normalized_percentile":{"value":0.79325855,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":100},"biblio":{"volume":"22","issue":"23","first_page":"2918","last_page":"2925"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.436599999666214,"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":0.436599999666214,"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":0.23250000178813934,"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/T13362","display_name":"Slime Mold and Myxomycetes Research","score":0.12120000272989273,"subfield":{"id":"https://openalex.org/subfields/2204","display_name":"Biomedical Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5131924748420715},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.45551979541778564},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25925326347351074}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5131924748420715},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.45551979541778564},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25925326347351074}],"mesh":[{"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":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D002468","descriptor_name":"Cell Physiological Phenomena","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":"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":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011381","descriptor_name":"Programming Languages","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"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":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"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":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","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":2,"locations":[{"id":"doi:10.1093/bioinformatics/btl497","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl497","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/23/2918/16851740/btl497.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17038347","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17038347","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":"Bioinformatics (Oxford, England)","raw_type":null}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btl497","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btl497","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/22/23/2918/16851740/btl497.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320323654","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57"},{"id":"https://openalex.org/F4320334593","display_name":"Natural Sciences and Engineering Research Council of Canada","ror":"https://ror.org/01h531d29"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2103173634.pdf","grobid_xml":"https://content.openalex.org/works/W2103173634.grobid-xml"},"referenced_works_count":34,"referenced_works":["https://openalex.org/W1485297825","https://openalex.org/W1589291832","https://openalex.org/W1811488600","https://openalex.org/W1873506857","https://openalex.org/W1971805158","https://openalex.org/W1978911766","https://openalex.org/W1984699863","https://openalex.org/W1986528647","https://openalex.org/W1986606329","https://openalex.org/W1998342535","https://openalex.org/W2003807928","https://openalex.org/W2010575732","https://openalex.org/W2013947447","https://openalex.org/W2017260253","https://openalex.org/W2034085191","https://openalex.org/W2065439398","https://openalex.org/W2068359975","https://openalex.org/W2069981259","https://openalex.org/W2089930561","https://openalex.org/W2113972438","https://openalex.org/W2117364474","https://openalex.org/W2130687290","https://openalex.org/W2131067724","https://openalex.org/W2132898564","https://openalex.org/W2139125300","https://openalex.org/W2142003218","https://openalex.org/W2150908245","https://openalex.org/W2155723007","https://openalex.org/W2159628188","https://openalex.org/W2166633151","https://openalex.org/W2171539493","https://openalex.org/W2791260982","https://openalex.org/W6635491538","https://openalex.org/W6643410447"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W2358668433","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2382290278","https://openalex.org/W2478288626","https://openalex.org/W2350741829","https://openalex.org/W2530322880","https://openalex.org/W1596801655"],"abstract_inverted_index":{"MOTIVATION:":[0],"With":[1],"the":[2,22,48,70,77,100,110],"generation":[3],"of":[4,7,24,29,55,73,81,102],"a":[5,18,42,52,59,131],"wealth":[6],"information,":[8],"detailing":[9],"cellular":[10],"components,":[11],"their":[12],"functions":[13],"and":[14,35,79,83,91,116,123],"interactions,":[15],"there":[16],"is":[17,107,134],"growing":[19],"need":[20],"for":[21],"development":[23],"new":[25],"computational":[26],"tools":[27],"capable":[28],"interpreting":[30],"these":[31],"data":[32],"within":[33,58],"spatial":[34,60,74],"dynamic":[36],"contexts.":[37],"Here,":[38],"we":[39,68],"introduce":[40],"Cell++,":[41],"novel":[43],"stochastic":[44],"simulation":[45],"environment":[46],"with":[47,99,130],"capacity":[49],"to":[50,88],"study":[51],"wide":[53],"variety":[54],"biochemical":[56],"processes":[57],"context.":[61],"RESULTS:":[62],"Focusing":[63],"on":[64],"three":[65],"case":[66],"studies,":[67],"highlight":[69],"potential":[71],"impact":[72],"organization":[75],"in":[76],"evolution":[78],"engineering":[80],"signaling":[82,90],"metabolic":[84,92,103],"pathways.":[85],"In":[86],"addition":[87],"altering":[89],"efficiency,":[93],"simulations":[94],"also":[95],"demonstrated":[96],"features":[97],"consistent":[98],"phenomenon":[101],"channeling.":[104],"AVAILABILITY:":[105],"Cell++":[106],"licensed":[108],"under":[109,121],"GNU":[111],"general":[112],"public":[113],"license":[114],"(GPL)":[115],"has":[117],"been":[118],"successfully":[119],"implemented":[120],"Linux":[122],"IRIX":[124],"operating":[125],"systems.":[126],"Source":[127],"code":[128],"together":[129],"simple":[132],"tutorial":[133],"available":[135],"at":[136],"http://www.compsysbio.org/CellSim/.":[137]},"counts_by_year":[{"year":2024,"cited_by_count":17},{"year":2023,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":3},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":2},{"year":2012,"cited_by_count":2}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
