fitting with dynafit?

Pedro Mendes mendes at
Fri Aug 10 10:13:27 EST 2001

At the risk of making some publicity to my own work:

Least squares problems, especially with many data points and many 
variables, have many local minima in the error surface. This makes
solving these problems with Levenberg-Marquardt (or other gradient
descent methods) a challange. You need to be really close to the
solution for these methods to converge. With the program GEPASI
(which I am the author of), you can do the fitting with many different
algorithms, including Levenberg-Marquardt . Importantly Gepasi contains
Genetic Algoriths, Evolutionary programming and Multistart (with L-M) 
which all have a much bigger chance of solving your fitting problem.
The only drawback to these methods is that they will take longer time
to run.

Gepasi is available for free at
There is also a paper in the journal Bioinformatics discussing these issues 
(and optimisation in general):

Mendes & Kell (1998) "Non-linear optimization of biochemical pathways: 
applications to metabolic engineering and parameter estimation." 
Bioinformatics, 4(10):869-83

Abstract in PubMed:

Disclaimer: I am the author of both the software and the paper that I 
mentioned above, so my opinion is definitly biased...

Pedro Mendes
Assistant Research Professor
Virginia Bioinformatics Institute
Virginia Tech

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