MoonFit, a minimal interface for fitting ODE dynamical models, bridging simulation by experimentalists and customization by C++ programmers

Abstract

The modelling of biological systems often consists into differential equation models that need to be fitted to experimental data. During this complex process, the practical experience of the biologist and the theoretical abstraction of the modeller require back-and-forth refinements of the model, design of new experiments and inclusion of more data-points into the fitting procedure. Available optimization interfaces rarely simultaneously allow customizations by the programmer and the capacity for the biologist to perform simulations or optimizations with a simple interface.\n\nHere, we provide the C++ code of a graphical user interface based on a user defined minimal C++ ODE model class. The graphical interface allows to perform simulations and optimizations without any knowledge in programming. The code was designed minimal and modular to be easily modified, with maximal freedom to link customized optimization libraries, solver or hand-made scripts. Moonfit is powerful enough to fit and compare models with high dimensionality, multiple datasets, to automatize optimizations, and to perform iterative fittings using data interpolation. We believe this will ease the interaction between modellers and experimental partners.\n\nAvailability: Moonfit is freely available via c++ source code and accompanying scripts from gitlab.com/Moonfit/MoonLight.