{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,8,12]],"date-time":"2025-08-12T22:42:37Z","timestamp":1755038557492,"version":"3.41.2"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"12","license":[{"start":{"date-parts":[[2023,12,9]],"date-time":"2023-12-09T00:00:00Z","timestamp":1702080000000},"content-version":"vor","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001321","name":"National Research Foundation","doi-asserted-by":"publisher","award":["CPPR 466624"],"award-info":[{"award-number":["CPPR 466624"]}],"id":[{"id":"10.13039\/501100001321","id-type":"DOI","asserted-by":"publisher"}]},{"name":"South African Medical Research"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2023,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Motivation<\/jats:title>\n                  <jats:p>Target discovery and drug evaluation for diseases with complex mechanisms call for a streamlined chemical systems analysis platform. Currently available tools lack the emphasis on reaction kinetics, access to relevant databases, and algorithms to visualize perturbations on a chemical scale providing quantitative details as well streamlined visual data analytics functionality.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>CytoCopasi, a Maven-based application for Cytoscape that combines the chemical systems analysis features of COPASI with the visualization and database access tools of Cytoscape and its plugin applications has been developed. The diverse functionality of CytoCopasi through ab initio model construction, model construction via pathway and parameter databases KEGG and BRENDA is presented. The comparative systems biology visualization analysis toolset is illustrated through a drug competence study on the cancerous RAF\/MEK\/ERK pathway.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>The COPASI files, simulation data, native libraries, and the manual are available on https:\/\/github.com\/scientificomputing\/CytoCopasi.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btad745","type":"journal-article","created":{"date-parts":[[2023,12,9]],"date-time":"2023-12-09T18:36:28Z","timestamp":1702146988000},"source":"Crossref","is-referenced-by-count":4,"title":["CytoCopasi: a chemical systems biology target and drug discovery visual data analytics platform"],"prefix":"10.1093","volume":"39","author":[{"given":"Hikmet Emre","family":"Kaya","sequence":"first","affiliation":[{"name":"Department of Chemistry, Scientific Computing Research Unit, PD Hahn Building, University of Cape Town , Rondebosch 7701, South Africa"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9898-3708","authenticated-orcid":false,"given":"Kevin J","family":"Naidoo","sequence":"additional","affiliation":[{"name":"Department of Chemistry, Scientific Computing Research Unit, PD Hahn Building, University of Cape Town , Rondebosch 7701, South Africa"}]}],"member":"286","published-online":{"date-parts":[[2023,12,9]]},"reference":[{"key":"2023122005554437700_btad745-B1","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/nrg3643","article-title":"Constraint-based models predict metabolic and associated cellular functions","volume":"15","author":"Bordbar","year":"2014","journal-title":"Nat Rev Genet"},{"author":"Box","key":"2023122005554437700_btad745-B10"},{"key":"2023122005554437700_btad745-B2","doi-asserted-by":"crossref","first-page":"5811","DOI":"10.1038\/ncomms6811","article-title":"Constitutive and ligand-induced EGFR signalling triggers 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