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IPPS
2006
IEEE
13 years 11 months ago
Performance analysis of stochastic process algebra models using stochastic simulation
We present a translation of a generic stochastic process algebra model into a form suitable for stochastic simulation. By systematically generating rate equations from a process d...
Jeremy T. Bradley, Stephen T. Gilmore, Nigel Thoma...
BMCBI
2004
323views more  BMCBI 2004»
13 years 5 months ago
Biochemical Network Stochastic Simulator (BioNetS): software for stochastic modeling of biochemical networks
Background: Intrinsic fluctuations due to the stochastic nature of biochemical reactions can have large effects on the response of biochemical networks. This is particularly true ...
David Adalsteinsson, David McMillen, Timothy C. El...
ICCMS
2009
118views more  ICCMS 2009»
13 years 3 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
BMCBI
2008
119views more  BMCBI 2008»
13 years 5 months ago
On deducing causality in metabolic networks
Background: Metabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to s...
Chiara Bodei, Andrea Bracciali, Davide Chiarugi
FPGA
2004
ACM
174views FPGA» more  FPGA 2004»
13 years 11 months ago
A compiled accelerator for biological cell signaling simulations
The simulation of large systems of biochemical reactions is a key part of research into molecular signaling and information processing in biological cells. However, it can be impr...
John F. Keane, Christopher Bradley, Carl Ebeling