Original Research Article
Neurofitter: A parameter tuning package for a wide range of electrophysiological neuron models
1 Theoretical Neurobiology, University of Antwerp, Belgium
2 Computational Neuroscience Unit, Okinawa Institute of Science and Technology, Japan
3 Volen Center for Complex System, Brandeis University, USA
The increase in available computational power and the higher quality of experimental recordings have turned the tuning of neuron model parameters into a problem that can be solved by automatic global optimization algorithms. Neurofitter is a software tool that interfaces existing neural simulation software and sophisticated optimization algorithms with a new way to compute the error measure. This error measure represents how well a given parameter set is able to reproduce the experimental data. It is based on the phase-plane trajectory density method, which is insensitive to small phase differences between model and data. Neurofitter enables the effortless combination of many different time-dependent data traces into the error measure, allowing the neuroscientist to focus on what are the seminal properties of the model.
We show results obtained by applying Neurofitter to a simple single compartmental model and a complex multi-compartmental Purkinje cell (PC) model. These examples show that the method is able to solve a variety of tuning problems and demonstrate details of its practical application.
Keywords: parameter tuning, neuron, model, simulator, automatic, optimization algorithms, software, electrophysiology
Copyright: © 2007 Van Geit, Achard and De Schutter. This is an open-access article subject to an exclusive license agreement between the authors and the Frontiers Research Foundation, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are credited.
*Correspondence: Erik De Schutter, Computational Neuroscience Unit, Okinawa Institute of Science and Technology, 7542 Onna, Onna-son, Kunigami, Okinawa 904-0411, Japan. e-mail: erik@oist.jp
Citation: Van Geit W , Achard P and De Schutter E (2007) Neurofitter: A parameter tuning package for a wide range of electrophysiological neuron models. Front. Neuroinform. 1:1. doi:10.3389/neuro.11.001.2007
Received: 30 August 2007; paper pending published: 10 September 2007; accepted: 24 September 2007; published online: 02 November 2007.
Edited by:
Jan G. Bjaalie, International Neuroinformatics Coordination Facility , Sweden; University of Oslo, Norway
Reviewed by:
Robert C. Cannon, Textensor Limited, UK
Michael Hines, Yale University, USA
Michael Hines, Yale University, USA
*Correspondence: Erik De Schutter, Computational Neuroscience Unit, Okinawa Institute of Science and Technology, 7542 Onna, Onna-son, Kunigami, Okinawa 904-0411, Japan. e-mail: erik@oist.jp
