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Physio - Pedersen Lab

Houston, Texas

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Pedersen Lab
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Kinetic Modeling Software

We have developed software to model kinetics of biochemical reactions using a simple graphic user interface. The interface gives the user easy and direct control over the number of states (up to 100), binding of ligands (up to six), rate constants, and starting conditions. The user can choose up to six distinct ligands and have one ligand vary over a user-defined range. It includes a check for thermodynamic consistency for cyclic models.

Screen shot of the model-creation interface

(click image to see the larger version of the figure)

The program will plot the kinetic progress of up to 100 distinct protein states. It can also plot the kinetic rates or their amplitudes against ligand concentration. The user can control which states are plotted or choose a linear combination of states. To help relate individual progress curves to the species, the results can be color coded from the user interface. The graph can be printed directly from the program. Rate constants and amplitudes can be output in ascii format for import into other software.

Screen shot of a plot of kinetic time traces

(click imfage to see the larger version of the figure)

Comparison of data with the model: The program will allow import of external kinetic data in ascii format. The data can be plotted for comparison with the output of the model. The data can also be fitted to multi-exponential functions and fitted to the model for optimization of rate constants.

How it works:

This software takes the rate constants from the GUI and fomulates the problem as a set of linear differential equations that are then solved by the eigenvalue method. The results are then simply plotted as a function of time. Alternatively, for reactions that are not first order, the kinetics can be computed by numerical integration.

Disclaimer: This software is “as is”. No claims or guarantees are made as to the validity of the calculations or the appropriateness of the software for a particular problem.

Note: The operating system requirement for this software: WIn NT, Win 2000 or Win XP.

Please contact Steen Pedersen for a copy of the program: pedersen@bcm.edu

Instructions for installing the program:

  1. Obtain the zipped folder;
  2. Unzip the folder;
  3. Run the set up file to install the program. You can specify the directory, or the default is "c:\Program Files\Project..." ;
  4. After installation, an item will appear in the start up "all programs" menu.

Download and install the help and tutorial files separately:

  1. Download the zipped help and tutorial files.
  2. Unzip the folder and save it under the directory where the software (viskin.exe) is located.

For quick start, refer to tutorial.

View the detailed help files online.

The software is free of use to all students and for any academic or research use. It is available on a free trial basis to all others.

For commercial use, please contact the PI: Steen E. Pedersen: pedersen@bcm.edu