[ANN] Software for biochemical kinetics and equilibria

Petr Kuzmic pkuzmic at biokin.com
Sat Jan 13 14:22:49 EST 2001


I have put the DynaFit scripting manual online:
http://www.biokin.com/dynafit/scripting/

For potential new users, DynaFit [P. Kuzmic (1996) Anal. Biochem. 237,
260-273] is a program for the simulation and statistical analysis of
biochemical data.  The data can be either:

  (1) reaction progress over time; or
  (2) initial reaction velocities vs. initial concentrations; or
  (3) equilibrium composition vs. total concentrations.

For all three types of experimental data, the fitting model is specified
symbolically (see below under [mechanism]) and the entire program is
driven by a script or scenario in a plain text format.

EXAMPLE
------------- 8< ----------- 8< ------------
[task]
   data      = progress
   task      = fit
[mechanism]   
   E + S --> ES      :     k
   ES --> E + P      :     kr
[constants]
   k = 0.01 ?, kr = 1 ?
[concentrations]
   E  = 0.05 
   S  = 31      ; 31 microM...100%
[responses]
   P = 3.226 ?  ;  1 microM...3.226%                           
[progress]
   offset auto ?
   file ./examples/reductase/data/i0.txt
[settings]
   <Filter>    | Scale = minutes
   <Marquardt> | Interrupt = 100
   <Plot>      | DependentVar = conversion (%)
[output]
   directory ./examples/reductase/output/substrate/simple
[end]
------------- >8 ----------- >8 ------------

The online manual, also available in the PDF format (135 pages,
including Index), explains the syntax these script files.

The entire http://www.biokin.com/dynafit/scripting/ subsite was
generated automatically from LaTeX sources, so there are liable to be
some glitches.  If you find one please drop a me line (just click on
'webaster at biokin.com' at the bottom of each page).  Thank you.

        - Petr

_____________________________________________________________________
P e t r   K u z m i c,  Ph.D.               mailto:pkuzmic at biokin.com
BioKin Ltd. * Software and Consulting           http://www.biokin.com






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