{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,12]],"date-time":"2026-04-12T00:46:56Z","timestamp":1775954816913,"version":"3.50.1"},"reference-count":32,"publisher":"Oxford University Press (OUP)","issue":"23","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: With the generation of a wealth of information, detailing cellular components, their functions and interactions, there is a growing need for the development of new computational tools capable of interpreting these data within spatial and dynamic contexts. Here, we introduce Cell++, a novel stochastic simulation environment with the capacity to study a wide variety of biochemical processes within a spatial context.<\/jats:p>\n               <jats:p>Results: Focusing on three case studies, we highlight the potential impact of spatial organization in the evolution and engineering of signaling and metabolic pathways. In addition to altering signaling and metabolic efficiency, simulations also demonstrated features consistent with the phenomenon of metabolic channeling.<\/jats:p>\n               <jats:p>Availability: Cell++ is licensed under the GNU general public license (GPL) and has been successfully implemented under Linux and IRIX operating systems. Source code together with a simple tutorial is available at .<\/jats:p>\n               <jats:p>Contact: \u00a0jparkin@sickkids.ca<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data for this paper are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl497","type":"journal-article","created":{"date-parts":[[2006,10,13]],"date-time":"2006-10-13T07:47:15Z","timestamp":1160725635000},"page":"2918-2925","source":"Crossref","is-referenced-by-count":29,"title":["Cell++\u2014simulating biochemical pathways"],"prefix":"10.1093","volume":"22","author":[{"given":"Chris","family":"Sanford","sequence":"first","affiliation":[{"name":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"},{"name":"Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Matthew L.K.","family":"Yip","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Carl","family":"White","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"},{"name":"Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Parkinson","sequence":"additional","affiliation":[{"name":"Hospital for Sick Children, 555 University Avenue 1 \u00a0 1 \u00a0 \u00a0 Toronto, ON, M5G 1X8, Canada"},{"name":"Department of Molecular and Medical Genetics, University of Toronto 2 \u00a0 2 \u00a0 \u00a0 Toronto, ON, Canada"},{"name":"Department of Biochemistry, University of Toronto 3 \u00a0 3 \u00a0 \u00a0 ON, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,10,11]]},"reference":[{"key":"2023012409221277000_b1","doi-asserted-by":"crossref","first-page":"1001","DOI":"10.1016\/j.jmb.2005.09.024","article-title":"Distinct spatial and temporal distribution of ZAP70 and Lck following stimulation of interferon and T-cell receptors","volume":"353","author":"Ahmed","year":"2005","journal-title":"J. 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