MesoRD
The MesoRD is a simulation tool used to simulate stochastic reaction-diffusion systems as modeled by the reaction diffusion master equation. The simulated systems are defined in the Systems Biology Markup Language with additions to define compartment geometries (Hattne et al. Bioinformatics, 2005, Fange et al. PNAS 2010). MesoRD has for instance been used to understand the noise induced phenotypes of the E. coli Min system (Fange and Elf PLoS CB, 2006; Fange Bioinformatics 2012).
vbSPT
vbSPT is an analytical tool that uses the information from thousands of short single-molecule trajectories to identify the number of underlying diffusive states as well as the state transition rates (Persson et al. Nat. Meth. 2013). The method is based on a variational Bayesian treatment of hidden Markov models. While other HMMs for diffusing particles use a fixed number of states (most often two or three) and individual long trajectories, the vbSPT method is capable of learning model parameters such as transition rates, as well as the number of diffusive states, from the experimental data. Furthermore, the method is able to extract useful information even from data sets with only a few points per trajectory.
SMeagol
SMeagol will help you optimize your experimental set-ups and make sure that there is no bias in your data analysis (Lindén et al. Bioinformatics 2016). The software creates realistic synthetic microscopy images by combining reaction diffusion simulations with simulations of the fluorophore photophysics and the photophysics of the optical system.
