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» Synthesizing Stochasticity in Biochemical Systems
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ICCMS
2009
118views more  ICCMS 2009»
13 years 5 months ago
Optimized Parallel Implementation of Gillespie's First Reaction Method on Graphics Processing Units
The simulation of chemical reacting systems is one of the most challenging topics in Systems Biology, due to their complexity and inherent randomness. The Gillespie's Stochas...
Cristian Dittamo, Davide Cangelosi
ENTCS
2010
119views more  ENTCS 2010»
13 years 7 months ago
Bio-PEPA for Epidemiological Models
Many models have been defined in order to describe the evolution of a disease in a population. The modelling of diseases is helpful to understand the mechanisms for their spread a...
Federica Ciocchetta, Jane Hillston
ENTCS
2010
103views more  ENTCS 2010»
13 years 4 months ago
A Model and Analysis of the AKAP Scaffold
We study the biochemical processes involved in scaffold-mediated crosstalk between the cAMP and the Raf-1/MEK/ERK pathways. We model the system by a continuous time Markov chain w...
Oana Andrei, Muffy Calder
SAC
2009
ACM
14 years 2 months ago
Modular implementation of adaptive decisions in stochastic simulations
We present a modular approach to implement adaptive decisions with existing scientific codes. Using a sophisticated system software tool based on the function call interception t...
Pilsung Kang 0002, Yang Cao, Naren Ramakrishnan, C...
CMSB
2009
Springer
14 years 2 months ago
Modelling Biological Clocks with Bio-PEPA: Stochasticity and Robustness for the Neurospora crassa Circadian Network
Circadian clocks are biochemical networks, present in nearly all living organisms, whose function is to regulate the expression of specific mRNAs and proteins to synchronise rhyth...
Ozgur E. Akman, Federica Ciocchetta, Andrea Degasp...