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» Biochemical Network Stochastic Simulator (BioNetS): software...
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BMCBI
2010
149views more  BMCBI 2010»
13 years 7 months ago
RuleMonkey: software for stochastic simulation of rule-based models
Background: The system-level dynamics of many molecular interactions, particularly protein-protein interactions, can be conveniently represented using reaction rules, which can be...
Joshua Colvin, Michael I. Monine, Ryan N. Gutenkun...
CMSB
2007
Springer
14 years 1 months ago
A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets
We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms. Each per...
David Gilbert, Monika Heiner, Sebastian Lehrack
JCB
2006
185views more  JCB 2006»
13 years 7 months ago
Bayesian Sequential Inference for Stochastic Kinetic Biochemical Network Models
As postgenomic biology becomes more predictive, the ability to infer rate parameters of genetic and biochemical networks will become increasingly important. In this paper, we expl...
Andrew Golightly, Darren J. Wilkinson
CDC
2008
IEEE
140views Control Systems» more  CDC 2008»
14 years 2 months ago
Model discrimination of polynomial systems via stochastic inputs
— Systems biologists are often faced with competing models for a given experimental system. Unfortunately, performing experiments can be time-consuming and expensive. Therefore, ...
Daniel Georgiev, Eric Klavins
FPGA
2004
ACM
174views FPGA» more  FPGA 2004»
14 years 27 days 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