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.)

Our complete toolbox for analyzing two-state trajectories takes two conjugated column vectors of random times (or any other kind of non-negative observations) and the associated time increment, and gives as an output all the mechanism-free information contained in the data, and the reduced dimensions form that best fits the data. The subroutine works in Matlab environment and uses the optimization toolbox.
Read more on the subroutine.
Now we develop an independent interface that analysis the time trajectory.


In addition, we release commands that are part of the software, yet are useful independently.
Each command comes in an interface. 
Exponential fit

Our routine takes as an input a vector of random times (or any other kind of non-negative observations) and the associated time increment,
and gives as an output the optimal exponential expansion of the probability density function that is constructed from the random times:
that is, the output is a set of L amplitudes and L conjugated rates.
The method is based on the Pade approximation method with Longman recursion relation, and a maximum likelihood technique. Read more.
Rank estimation of a 2D WT-PDF

Our subroutine takes two column vectors of random times (or any other kind of non-negative observations) and the associated time increment,
and gives as an output the rank of the two-dimensional waiting time probability density function (2D WT-PDF) built from these random times.
The subroutine is based on singular value decomposition of the second order cumulative WT-PDF,
and on noise-analysis of the ratios of successive singular values.
Read more.
• 2D WT-PDFs
Our subroutine takes two column vectors of random times
(or any other kind of non-negative observations) and the associated time increment,
and gives as an output the eigenvalues and the matrices of coefficients,
in the exponential expansions of all four two-dimensional WT-PDFs.
Read more.

      Future projects

      Still, there are (at least) two other software that we intend
      to develop. These are in the fields 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.

PRODUCTS 

  (*)      RDF website 
(docs & videos ; download paid version ; download free partial version; etc,)
  
  

  experimental two-state time trajectories.

Submit an experimental two-state trajectory to

bps@flomenbom.net, 

and get the results from our analysis within a week 

A-per-case estimation of the analysis-time is given upon submission. 

The cost of our analysis: 100$ per 108 data points, for the academia,

and 930$ per 108 data points, for those not affilated with the academia.

The payment is performed through a safe web-interface after the data and the affiliation of the clients are checked. 

The data should be submitted as text files. 

A brief description on the type of the experiments and the noise type is useful.

For the scheme of our analysis, click below

 

The full description of the output from our analysis is presented in Software description.

     (*) We are finalizing the first-version of the software RDF.

This software analyzes noisy, finite length, experimental two-state time trajectory.

The most important feature of the software finds the most accurate RD (reduced dimension)

form that can generate the data, and then translates this RD form to a set of kinetic schemes.  

A full description of the output from our analysis is given in Software description. 

I - reduced prices to researchers

    This learning-the-product option is restricted per computer & per email-address.

II - The software, plus a help-option, costs ~100$ to 350$ for a yearly license, to researchers,  
     and from 1240$ for useres others
III - An introductory price, for a year, to any first time user.
       The prices: 99$ for a user affilated with research and 1050$ for others.  

IV - For labs that need more than 1050$ in licenses' puchases, a special price is given for the 11th permit on.