As part of my research and teaching efforts I often write custom software for analysis and data simulation. Below is a sampling of some of these packages that might be useful to others (freely provided).
Model-free distance distributions using 2D-MEM Laplace Inversion
Distance distribution analysis of time-resolved FRET data using Laplace inversion via the maximum entropy method (MEM) (Note: this discussion focuses on the 2D version of my maximum entropy routine that is specific for time-resolved FRET data. A large part of the text below is from the Supplementary information in our paper from a few years back: Wu et al, PNAS 2008. If you need to perform maximum entropy on just a single decay trace you can use the 1D maximum entropy routine on my site.
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Savuka: A general purpose global analysis program
Savuka is a global analysis package that allows the user to graphically view, model, simulate, manipulate and globally fit data. The program is, for the most part, not geared toward any particular type of data and therefore should be suitable for most applications where the above features are needed. What can I do with Savuka? Here is a sampling of some of Savuka’s features:
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Forster Distance Calculator
Calculates the Forster distance from the absorption spectrum of the acceptor and the fluorescence spectrum of the donor (and knowledge of the donor fluorescence quantum yield and acceptor extinction coefficient). The program will automatically interpolate the data so the data can be collected with different pitches along the wavelength axis (i.e. 1nm increment for fluorescence and 0.5 nm increments for absorption). The user also needs to supply an estimate for kappa-squared (orientation factor) and the index of refraction between the donor and acceptor. Several
The chevron simulator will allow you to interactively simulate a chevron plot by adjusting the microscopic rates, m-values, optical properties and equilibrium population of each specie using sliders. The calculated observables (rates and amplitudes) can be overlaid on experimental data, which you can import into the program.
Molecular Biophysics Class Examples
Visualizing how changing a parameter affects a result can be useful for honing one’s intuition. Below are simple programs that plot an observable and allow the user to change the input parameters using GUI sliders. Executables (Mac OS X) for the helix-coil zipper model, the Shottky 2-state model and the Gibbs-Helmholz equation are provided and discussed below.
CF-TCSPC Data Processor
This program will allow the user to graphical select files to include in the processing of continuous-flow TCSPC data saved using Becker and Hickl SPC software. Once the user has tagged the files as either buffer blank, NATA, protein or for discarding, the program will sum and appropriately average the data and perform all baseline and buffer
Time-resolved SAXS data processor
The time-resolved SAXS experiments at BioCAT often contain a hundred or more images in a single scan of the channel or single-shot of a stopped-flow device. There are typically fifty or more scans in each experiment. To facilitate the processing of this type of data we have written software that will automatically apply I0/I1 correction and perform background correction. The software will also automatically calculate the radius of gyration and zero angle scattering
Time-resolved FRET simulator
To help with experiment design and testing of our various analysis routines we often simulate TCSPC data for donor and acceptor channels. In using this program the user specifies the properties of the donor and acceptor distance distributions and based on these parameters time-resolved decays of the donor and acceptor fluorescence are calculated. The outputs can be saved to a file for teaching/training/testing in data analysis.
MEM for Anisotropy
Labview based MEM routine for time-resolved anisotropy data. The idea behind this is that 2DMEM Laplace inversion can be applied to anisotropy data as well as to time-resolved FRET data. One of the dimensions is still the excited state relaxation rate distribution for the excited fluorophore. The second dimension