M Hucka, A Finney, BJ Bornstein, SM Keating… - Systems biology, 2004 - IET
Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The …
The tau-leaping method of simulating the stochastic time evolution of a well-stirred chemically reacting system uses a Poisson approximation to take time steps that leap over …
We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms …
Stochastic modeling techniques have emerged as a powerful tool to study the time evolution of processes in many research fields including (bio) chemical engineering and biology. One …
A highly desired part of the synthetic biology toolbox is an embedded chemical microcontroller, capable of autonomously following a logic program specified by a set of …
The explicit tau-leaping procedure attempts to speed up the stochastic simulation of a chemically reacting system by approximating the number of firings of each reaction channel …
T Tian, K Burrage - The Journal of chemical physics, 2004 - pubs.aip.org
This paper discusses efficient simulation methods for stochastic chemical kinetics. Based on the τ-leap and midpoint τ-leap methods of Gillespie [DT Gillespie, J. Chem. Phys. 115, 1716 …
Dynamic modeling and simulation of signal transduction pathways is an important topic in systems biology and is obtaining growing attention from researchers with experimental or …
T Székely Jr, K Burrage - Computational and structural biotechnology …, 2014 - Elsevier
Natural systems are, almost by definition, heterogeneous: this can be either a boon or an obstacle to be overcome, depending on the situation. Traditionally, when constructing …