Scientific software

Analysis of finite-length trajectories, discrete and continous

(Download paid version of the Software RDF, NOW)
RDF – Our software for analyzing, noisy, finite length, two-state trajectories finds a unique mechanism of Reduced Dimensions (RD form) from the actual noisy data, and translates it to a set of possible kinetic schemes. The general analysis buttons in the basic version can work on continous trajectories and higher order discrete trajectories, to supply model free information on the data.

Our complete toolbox for solving two-state trajectories takes the data, creates the noisy trajectory from it, filters noise, and analyzes the trajectory. The output includes: all the mechanism-free information contained in the data, the reduced dimensions form that best fits the data, and a set of possible kinetic schemes that are built from the RD form. The basic version also can find simple model to continous trajectories, where the general analysis buttons can work on continous trajectories and higher order discrete trajectories, to supply model free information on the data. Read more.

The software value apeparing in the following areas of research:
(1) Dynamics of DNA and RNA on the single molecule level
(2) Dynamics of proteins on the single molecule level
(3) Enzymatic activity
(4) Ion channel recordings
(5) Single molecule force measurements
(6) Quantum dots
(7) Diffusion of individual objects (bio-molecules, beads, etc.)

 

    • In addition, we release commands that are part of the software, yet are useful independently.
    • Each command comes in an interface. 
  • Exponential fit
  • Rank estimation of a 2D WT-PDF
  • 2D WT-PDFs

      Future projects

      Still, there are (at least) two other software that we intend      to develop. These are in the areas of expertise of O.  Flomenbom;

      (*) Dynamics – software for the simulations and the analysis of Fokker-Planck and Langevin equations with many arguments.
      (*) Proteins – software for simulations and analysis of the dynamics of proteins.