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» Interaction Models for Biochemical Reactions
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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
GG
2004
Springer
14 years 1 months ago
Analysis of Metabolic Pathways by Graph Transformation
Biochemical pathways, such as metabolic, regulatory, and signal transduction pathways, constitute complex networks of functional and physical interactions between molecular species...
Francesc Rosselló, Gabriel Valiente
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
BMCBI
2006
102views more  BMCBI 2006»
13 years 7 months ago
SNA - a toolbox for the stoichiometric analysis of metabolic networks
Background: Despite recent algorithmic and conceptual progress, the stoichiometric network analysis of large metabolic models remains a computationally challenging problem. Result...
Robert Urbanczik
AUTOMATICA
2006
118views more  AUTOMATICA 2006»
13 years 7 months ago
Diagonal stability of a class of cyclic systems and its connection with the secant criterion
We consider a class of systems with a cyclic interconnection structure that arises, among other examples, in dynamic models for certain biochemical reactions. We first show that a...
Murat Arcak, Eduardo D. Sontag