Cell++--simulating biochemical pathways. Export

@article{citeulike:959123, abstract = {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. 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. 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 http://www.compsysbio.org/CellSim/.}, author = {Sanford, Chris and Yip, Matthew L. and White, Carl and Parkinson, John}, citeulike-article-id = {959123}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btl497}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/23/2918}, citeulike-linkout-2 = {http://www.ingentaconnect.com/content/oup/cabios/2006/00000022/00000023/art02918}, citeulike-linkout-3 = {http://view.ncbi.nlm.nih.gov/pubmed/17038347}, citeulike-linkout-4 = {http://www.hubmed.org/display.cgi?uids=17038347}, day = {1}, doi = {10.1093/bioinformatics/btl497}, issn = {1460-2059}, journal = {Bioinformatics (Oxford, England)}, keywords = {cell, modelling, simulation}, month = {December}, number = {23}, pages = {2918--2925}, posted-at = {2008-05-21 00:39:09}, priority = {0}, publisher = {Oxford University Press}, title = {Cell++--simulating biochemical pathways.}, url = {http://dx.doi.org/10.1093/bioinformatics/btl497}, volume = {22}, year = {2006} }

TY - JOUR ID - citeulike:959123 L3 - citeulike-article-id:959123 N2 - 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. 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. 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 http://www.compsysbio.org/CellSim/. IS - 23 JF - Bioinformatics (Oxford, England) SN - 1460-2059 EP - 2925 TI - Cell++--simulating biochemical pathways. PB - Oxford University Press VL - 22 SP - 2918 KW - cell KW - modelling KW - simulation AU - Sanford, Chris AU - Yip, Matthew AU - White, Carl AU - Parkinson, John PY - 2006/12/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btl497 ER -