RaTrav: a tool for calculating mean first-passage times on biochemical networks.

ABSTRACT:

Background

The concept of mean first-passage times (MFPTs) occupies an important place in the theory of stochastic processes, with the methods of their calculation being equally important in theoretical physics, chemistry and biology. We present here a software tool designed to support computational biology studies where Markovian dynamics takes place and MFPTs between initial and single or multiple final states in network-like systems are used. Two methods are made available for which their efficiency is strongly dependent on the topology of the defined network: the combinatorial Hill technique and the Monte Carlo simulation method.

Results

After a brief introduction to RaTrav, we highlight the utility of MFPT calculations by providing two examples (accompanied by Additiona

SUBMITTER: Torchala M 

PROVIDER: S-EPMC4222613 | biostudies-literature | 2013 Nov

REPOSITORIES: biostudies-literature