Neurofitter: a parameter tuning package for a wide range of electrophysiological neuron models
BMC Neuroscience volume 8, Article number: P5 (2007)
One of the major tasks of a neuroscientist who is developing a neuron model is to find suitable values for all the parameters of the model. This is, in general, a very complex job that can take a lot of time and that requires a lot of know-how when the parameter tuning is done by hand. We have developed a software tool called Neurofitter that can be used to automate the process of parameter searching for neuron models. The user has to provide time series data recorded during an experiment in the form of traces. Neurofitter will then run the computer model several times with different sets of values for the model parameters and will compare model output traces with the experimental data traces using the phase-plane trajectory method . This way Neurofitter maps every set of parameters values onto a fitness value that shows how well a model is able to reproduce the experimental data. This transforms the search for optimal parameters into a problem that can be solved with general optimization algorithms. The algorithms used by Neurofitter include Evolutionary Strategies, Particle Swarm Optimization and Mesh Adaptive Search. We will show some results obtained using the method to fit a single compartmental model, a simple network model and a complicated model of a Purkinje cell . The source code can be freely downloaded from Sourceforge http://neurofitter.sourceforge.net
Le Masson G, Maex R: Introduction to equation solving and parameter fitting. In: Computational neuroscience: realistic modeling for experimentalists. Edited by: De Schutter E. 2001, United Kingdom: CRC Press, 1-24. 1
Achard P, De Schutter E: Complex parameter landscape for a complex neuron model. PLoS Comput Biol. 2006, 2 (7): e94-10.1371/journal.pcbi.0020094.
Butera RJ, Rinzel J, Smith JC: Models of respiratory rhythm generation in the pre-Bötzinger complex. I. Bursting pacemaker neurons. J Neurophysiol. 1999, 82: 382-97.
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Van Geit, W., Achard, P. & De Schutter, E. Neurofitter: a parameter tuning package for a wide range of electrophysiological neuron models. BMC Neurosci 8 (Suppl 2), P5 (2007). https://doi.org/10.1186/1471-2202-8-S2-P5
- Particle Swarm Optimization
- Purkinje Cell
- Particle Swarm
- Time Series Data
- Parameter Tuning