MoonFit, a minimal interface for fitting ODE dynamical models, bridging simulation by experimentalists and customization by C++ programmers
(2018) In bioRxiv- 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.
Here, 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... (More) - 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.
Here, 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. (Less)
Please use this url to cite or link to this publication:
https://lup.lub.lu.se/record/18771432-0c7f-4775-b871-e8e2d65cb7c5
- author
- Robert, Philippe A. ; Jönsson, Henrik LU and Meyer-Hermann, Michael
- organization
- publishing date
- 2018
- type
- Other contribution
- publication status
- published
- subject
- keywords
- ODE, parameter estimation, Graphical interface, C++
- in
- bioRxiv
- publisher
- bioRxiv
- DOI
- 10.1101/281188
- language
- English
- LU publication?
- yes
- id
- 18771432-0c7f-4775-b871-e8e2d65cb7c5
- date added to LUP
- 2019-07-31 15:38:32
- date last changed
- 2021-12-03 14:02:19
@misc{18771432-0c7f-4775-b871-e8e2d65cb7c5,
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.<br/><br/>Here, 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.}},
author = {{Robert, Philippe A. and Jönsson, Henrik and Meyer-Hermann, Michael}},
keywords = {{ODE; parameter estimation; Graphical interface; C++}},
language = {{eng}},
publisher = {{bioRxiv}},
series = {{bioRxiv}},
title = {{MoonFit, a minimal interface for fitting ODE dynamical models, bridging simulation by experimentalists and customization by C++ programmers}},
url = {{http://dx.doi.org/10.1101/281188}},
doi = {{10.1101/281188}},
year = {{2018}},
}