New version 4.1 of BIOKMOD for MATHEMATICA 6 is available
- To: mathgroup at smc.vnet.net
- Subject: [mg86295] New version 4.1 of BIOKMOD for MATHEMATICA 6 is available
- From: Guillermo Sanchez <guillermo.sanchez at hotmail.com>
- Date: Fri, 7 Mar 2008 02:33:44 -0500 (EST)
BIOKMOD is a Mathematica tool for biokinetic modeling and fitting.
New version 4.1 of BIOKMOD is available at http://web.usal.es/guillermo/biokmod.htm
This version requires Mathematica 6. The program help has been
enhanced. The are included some notebooks where they are described
details (computations) of papers published by the author
To run BIOKMOD with all capability it is necessary Mathematica however
BIOKMODWEB, a webMathematica application, has some of the most usual
features of BIOKMOD. BIOKMODWEB can be run directly at:
The version 4 includes (i) a package to solve system of ordinary
linear differential equations (SOLDE) with special application to
compartmental and physiological models; (ii) A package for fitting
data, it can be applied to fit the transfer rates using experimental
data; iii) A specific package for optimal design; iv) Some packages
for solving the currents ICRP Models, they have special applications
to calculate internal dose and bioassay data evaluations.
Some tutorials are included about: i) Compartmental and physiological
modeling (linear and non linear), ii) Random intakes in occupational
exposures and their implication in the bioassays, iii) Analytical
methods to evaluate the uncertainties associated with the biokinetic
model parameters, iv) Non linear regression techniques to the
bioassay data fitting, v) Optimal design applied to perform bioassay
BIOKMOD has the following features to our knowledge are not included
in any other.
a) The user himself can build compartmental models in a very easy way
generating automatically the system of differential equations and
b) It gives analytical and numerical solutions (other codes only give
the numerical). Even the solutions can be given as function of some
parameters. The accumulated disintegrations in a compartment or region
can be computed exactly by analytical integration, what is more
precise than the method of the mean resident time often applied for
c) Apart from acute, chronic and multi-inputs, it can practically be
used for any kind of continuous inputs (exponentials, periodic, etc.),
even for random inputs.
d) The intakes can be estimated fitting bioassay data where not only
the intake quantities but also other parameters (AMAD, f1, etc.) can
be also assumed unknown. For non linear fitting are applied the
optimization algorithm included in Mathematica such as
DifferentialEvolution (a genetic algorithm) , NelderMead (Nelder-Mead
simplex algorithm), RandomSearch, and SimulatedAnnealing (a biased
random-walk search method) and specific method as the maximum
e) Analytical expressions instead of simulation can be used for
sensitivity and uncertainty analysis.
f) Optimal design tools.
g) The full version included practically all Currents ICRP Models.
The help includes many examples.
There are some publications where BIOKMOD has been used (some
available at the author website: http://web.usal.es/guillermo)
Comments are wellcome
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