RNA Sequence to NAscent Protein Simulation (rSNAPsim).

A) rSNAPsim is divided into four upper tabs and three lower tabs. Upper tabs allow the user to select and adjust sequences and then run simulations under varying conditions. Sequence selector allows the user to load a raw text file or GenBank file for their simulation needs. An option to pull from GenBank via accession number is available. All simulation parameters are also set on this tab. B) After a file is loaded, rSNAPsim allows the user to change the tRNA copy numbers and codon types under the Codon Adjustment tab. Post simulation, the lower tabs display simulation information such as average intensity over time of N simulations. C) Screen-shot of a kymograph. The kymograph tab allows the user to create their kymographs with varying display options. The Stochastic Simulation tab shows the time course data from the selected simulations. The Fluorescence Correlation Spectroscopy tab displays and compared simulated and experimental single-molecule translation dynamics, the auto-covariance function, and biophysical parameters, such as the elongation constant or ribosomal density. All functionality in the GUI is also available in a command-line module for Python included with rSNAPsim.