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The Art and Science of Model Translation

Robert Nachbar
Organization: Merck Research Laboratories

Wolfram Technology Conference 2013
Conference location

Champaign, Illinois, USA

Sharing information is one of the foundation stones of collaborative research. The exchange of mathematical and computational models between different software packages with perfect fidelity is required. Often times this task is difficult due to differences in the languages and the function libraries available to each, and at best it is tedious. Moreover, one does not necessarily need a full translation of an input file, as is done, for example, by the Unix command f2c for FORTRAN to C conversion. To meet these needs in our day-to-day modeling work, we have developed a set of practices and computational tools that facilitate the conversion of models from packages such as NONMEM, ACSL, Berkeley Madonna, Jacobian, and MATLAB to Mathematica, and to a lesser extent from Mathematica to some of the others. Our methods make use of the symbolic computing capabilities of Mathematica, and demonstrate that code can, indeed, be treated as data. An additional benefit is that they permit one to rigorously prove that models independently implemented in different languages are identical, or not. The methods are based largely on string and expression replacement rules. We will show examples of the techniques applied to models for pharmacokinetics, disease progression, and ecology.

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