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: http://www3.enusa.es/webMathematica/Public/biokmod.html. 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 programs 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 their solutions 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 other codes. 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 likelihood. 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 Guillermo Sanchez