earlier data simulator

The outdated matlab script used to simulate synthetic smFRET trajectories before July 2019, can be found here.

Please, find the current version of the simulator here.

The focus of the simulation is on empirically reproducing typical smFRET data. Each state trajectory is simulated in continuous time according to the supplied transition rate matrix . If needed, degenerate states are introduced. In the end, the traces are discretised using a typical sampling rate of a camera-based smFRET setup: the intensity is obtained by integration over each state that is occupied during a given frame. The following parameters are used to simulate real-world experiments:

• the Gaussian* distribution of the fluorescence intensity of each state (leading to not necessarily Gaussian FRET distributions)
• the distribution of a possible per-trace offset,
• the bleach rate and a fixed minimal trace length.

* Although strictly speaking Poissonian, the photon counts observed in typical camera-based smFRET experiments (N>10) are very well modeled by Gaussian distributions.