Berkeley Madonna Version 10–A simulation package for solving mathematical models
Frank V. Marcoline, John Furth, Smita Nayak, Michael Grabe, Robert I. Macey
Abstract
Berkeley Madonna is a software program that provides an easy and intuitive environment for graphically building and numerically solving mathematical equations. Our users range from college undergraduates with little or no mathematical experience to academic researchers and professionals building and simulating sophisticated mathematical models that represent complex systems in the biological, chemical, and engineering fields. Here we briefly describe our recent advances including a new Java-based user interface introduced in Version 9 and our transition from a 32- to 64-bit architecture with the release of Version 10. We take the reader through an example tutorial that illustrates how to construct a mathematical model in Berkeley Madonna while highlighting some of the recent changes to the software. Specifically, we construct a standard pharmacokinetic model of the antifungal medication amphotericin B taken from the literature and discuss aspects related to model building, key numerical considerations, data fitting, and graphical visualization. We end by discussing planned functionality and features intended for future releases.