STOCHSIM: modelling of stochastic biomolecular processes
نویسندگان
چکیده
SUMMARY STOCHSIM is a stochastic simulator for chemical reactions. Molecules are represented as individual software objects that react according to probabilities derived from concentrations and rate constants. Version 1.2 of STOCHSIM provides a novel cross-platform graphical interface written in Perl/Tk. A simple two-dimensional spatial structure has also been implemented, in which nearest-neighbour interactions of molecules in a 2-D lattice can be simulated.
منابع مشابه
Detailed comparison between StochSim and SSA.
Morton-Firth and Bray's stochastic simulator (StochSim) and Gillespie's stochastic simulation algorithm (SSA) are two important methods for stochastic modelling and simulation of biochemical systems. They have been widely applied to different biological problems. A key question is discussed here: Are these two methods equivalent? These two methods are compared using fundamental probability anal...
متن کاملApplication of Stochastic Optimal Control, Game Theory and Information Fusion for Cyber Defense Modelling
The present paper addresses an effective cyber defense model by applying information fusion based game theoretical approaches. In the present paper, we are trying to improve previous models by applying stochastic optimal control and robust optimization techniques. Jump processes are applied to model different and complex situations in cyber games. Applying jump processes we propose some m...
متن کاملModelling the bacterial chemotaxis receptor complex.
The pathway controlling chemotaxis in Escherichia coli is the simplest and most well understood cell signalling system to date. However, quantitative models based on the available data still fail to reproduce important features of the pathway. Most notably, the observed sensitivity of cells to very small changes in stimulus concentrations cannot be reproduced by conventional models based on the...
متن کاملStochastic Simulation Methods for Solving Systems with Multi-State Species
(ABSTRACT) Gillespie's stochastic simulation algorithm (SSA) has been a conventional method for stochas-tic modeling and simulation of biochemical systems. However, its population-based scheme faces the challenge from multi-state situations in many biochemical models. To tackle this problem, Morton-Firth and Bray's stochastic simulator (StochSim) was proposed with a particle-based scheme. The t...
متن کاملFUZZY INFORMATION AND STOCHASTICS
In applications there occur different forms of uncertainty. The twomost important types are randomness (stochastic variability) and imprecision(fuzziness). In modelling, the dominating concept to describe uncertainty isusing stochastic models which are based on probability. However, fuzzinessis not stochastic in nature and therefore it is not considered in probabilisticmodels.Since many years t...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 17 6 شماره
صفحات -
تاریخ انتشار 2001