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PubMed · 17038347

Cell++--simulating biochemical pathways.

Chris Sanford·Matthew L K Yip·Carl White·John Parkinson
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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/.

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BiochemistryCell Physiological PhenomenaComputer SimulationModels, BiologicalProgramming LanguagesProteomeSignal TransductionSoftwareUser-Computer InterfaceJournal ArticleResearch Support, Non-U.S. Gov't

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Chris Sanford, Matthew L K Yip, Carl White, John Parkinson. 2006-10-11. Cell++--simulating biochemical pathways.. https://doi.org/10.1093/bioinformatics%2Fbtl497

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