seeing the unseeable the science of ce库llular simulation - human 看了看不见的细胞模拟人类的科学.pptVIP

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seeing the unseeable the science of ce库llular simulation - human 看了看不见的细胞模拟人类的科学.ppt

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SimCell: A Novel Computational Approach to Cellular Simulation David Wishart University of Alberta Toronto, Dec. 6, 2004 Why Simulate a Cell? Physicists Chemists Biologists What’s it good for? Basic Science/”Understanding Life” Predicting Phenotype from Genotype Understanding/Predicting Metabolism Understanding Cellular Networks Understanding Cell-Cell Communication Understanding Pathogenicity/Toxicity “Raising the Bar” for Biologists Are We Ready To Simulate A Cell? 100’s of completed genomes 1000’s of known reactions 10,000’s of known 3D structures 100,000’s of protein-ligand interactions 1,000,000’s of known proteins enzymes Decades of biological/chemical know-how Computational Mathematical resources Metabolism (KEGG/MetaCyc) Interactions (BIND, DIP) Pathways (Transpath/Biocarta) How to do it? Genomics Genometrics Proteomics Proteometrics Metabolomics Metabometrics Phenomics Phenometrics Bioinformatics Biosimulation Quantify, quantify, quantify How to Do it?Three Types of Simulation How To Do it? (Computationally) How To Do it? (Computationally) Who’s Doing It? E-cell Project (Keio University, Japan) BioSpice Project (Arkin, Berkeley) Metabolic Engineering Working Group (Palsson Church, UCSD, Harvard) Silicon Cell Project (Netherlands) Virtual Cell Project (UConn) Gene Network Sciences Inc. (Cornell) Project CyberCell (Edmonton/Calgary) Adam Arkin B. Palsson-Genetic Circuits Gene Network Sciences Nationalism in Simulation Petri Nets – Germany, Japan Flux-Balance Analysis – USA Pi Calculus – France ODE’s and PDE’s – Japan, UK Agent-Based methods (CA) - Canada Some Problems… Almost all simulation systems are ultimately based on solving either ordinary differential equations (ODEs), partial differential equations (PDEs) or stochastic differential equations (SDEs) Differential equations are “hard” to work with when simulating spatial phenomena, when dealing with discrete events (binding, switching), non continuous variables (low copy number) or when key