The first model consists of chains, which are infinite, by virtue of the periodic repeat of the simulation cell along the chain axis.
The fluorescence fitting procedure is repeated a number of times for each repeat of the simulation (32 times for the first stage of the fitting, and 120 times for the second stage), and the mean of the obtained values of L is used as the score of the run.
One day, he wanted to repeat one of the simulations for a longer time, but instead of repeating the whole simulation, he started the second run in the middle, typing in numbers from the first run for the initial conditions.
Throughout the module, students are asked to make predictions, record data and observations from repeated runs of the simulations, draw inferences from their observations and data, and construct explanations to explain why their predictions were or were not supported.
A repeat of the third saccade simulation with a greater number of trials demonstrates, unsurprisingly, improved parameter identifiability (Fig. A1 – right panel).
Third, DiNuP was used to identify the region of differential nucleosome positioning between the simulated region and the original region, repeating every degree of the simulation 1000 times.
To generate repeats of the pulling simulations, starting conformations were taken from different points of the 100 ps equilibration: the 100, the 90, 80, 70 and 60 ps conformations.
This analysis consists of a sequence of operations for deriving probability distributions for a selected set of model parameters and repeating the simulation of each realisations of the parameter set (Swaney and Hong 2009b).
In accordance with the ABC methodology, we repeat 100,000 times the simulation of a given scenario, each time with input parameters drawn from prior distributions (see Additional file 1: Supplemental Table S2).
The whole process is continuously repeated until the end of the simulation time.
This process was repeated at every frame of the simulation trajectory and the result temporally averaged.
