Software

GRID (Genuine Rate IDentification)

GRID yields the dissociation rate spectrum of single molecule fluorescence survival time distributions by inverse Laplace transformation and enables correcting for photobleaching by global consideration of all time-lapse conditions. The GRID toolbox also includes a parameter prediction algorithm for nearest neighbour tracking. Parameters predicted by the algorithm ensure homogeneous tracking losses in all time-lapse conditions and thus enable GRID to perform a consistent global fit of all time-lapse conditions.
https://www.nature.com/articles/s41598-020-58634-y
https://gitlab.com/GebhardtLab/GRID

SPLIT (Speedy Partition of Legs In Tracks)

SPLIT is an automatized heuristic to separate different modes of motion (e.g. directed and diffusive motion) within a single track. As a criterion, SPLIT uses spatial information on each position in the track encoded within a recurrence plot. This plot reveals how many detections are in close proximity to each other within a track. Furthermore, SPLIT uses jump angles for classification of directed motion and offers averaging techniques dealing with localization errors in track coordinates.
https://doi.org/10.1101/2020.04.03.023614
https://gitlab.com/GebhardtLab/SPLIT

BIRD (Bursting Inference from mRNA Distributions)

BIRD is an inference algorithm for rate constants involved in bursts of mRNA expression. BIRD uses half analytical solutions for a fast and robust calculation of mRNA distributions from the underlying system of differential equations. To infer rate constants, measured mRNA histograms are fitted with these solutions using gradient-based methods.
https://doi.org/10.1101/2020.11.26.400069
https://gitlab.com/GebhardtLab/BIRD

CaiNet (Computer Aided Interactive gene NETwork simulation tool)

CaiNet is a fast computer aided interactive network simulation environment to set up and simulate arbitrary gene regulatory networks. CaiNet comes with a graphical user interface that automatically compiles a network into a hybrid stochastic-deterministic simulation framework. For a better understanding of the effects of noise within the network, noise arising from stochastic rates in gene expression can be turned on and off.
https://doi.org/10.1101/872374
https://gitlab.com/GebhardtLab/CaiNet

TrackIt

TrackIt is a tracking and analysis software which allows analyzing and comparing multiple single molecule fluorescence data sets.
A user-friendly GUI offers convenient tracking visualization, multiple state-of-the-art analysis procedures, display of results, and data im- and export at different levels to utilize external software tools. Furthermore, we developed an algorithm, which accounts for both tracking losses and suggests optimized tracking parameters when evaluating reaction rates.
For further details see here. The latest version of TrackIt can be downloaded from https://gitlab.com/GebhardtLab/TrackIt.

Nano-Positioning System Software

We developed a new method termed Nano-Positioning System (NPS) which allows the localisation of flexible domains in macromolecules by using probabilistic data analysis and combining single-molecule measurements with X-ray crystallography data. With this approach, single-pair fluorescence resonance energy transfer measurements can now be used as a quantitative tool for investigating the position and dynamics of flexible domains within macromolecular complexes. For further details see here.

Energy based step-finder algorithm

Analyzing the physical and chemical properties of single DNA based molecular machines often necessitates tracking motion on the length scale of base pairs. Although high resolution instruments have been developed that are capable to reach that limit, individual steps are often times hidden by a significant amount of noise which complicates data processing. We developed an effective algorithm termed Energy based step-finder (EBS) which detects steps in a high bandwidth signal by minimizing energy functionals. For further details see here.