Neurofitter swMATH ID: 9289 Software Authors: Van Geit, W.; De Schutter, E.; Achard, P. Description: Automated neuron model optimization techniques: The increase in complexity of computational neuron models makes the hand tuning of model parameters more difficult than ever. Fortunately, the parallel increase in computer power allows scientists to automate this tuning. Optimization algorithms need two essential components. The first one is a function that measures the difference between the output of the model with a given set of parameters and the data. This error function or fitness function makes the ranking of different parameter sets possible. The second component is a search algorithm that explores the parameter space to find the best parameter set in a minimal amount of time. In this review we distinguish three types of error functions: feature-based ones, point-by-point comparison of voltage traces and multi-objective functions. We then detail several popular search algorithms, including brute-force methods, simulated annealing, genetic algorithms, evolution strategies, differential evolution and particle-swarm optimization. Last, we shortly describe Neurofitter, a free software package that combines a phase-plane trajectory density fitness function with several search algorithms. Homepage: http://neurofitter.sourceforge.net/ Keywords: Automated tuning; Error function; Fitness function Related Software: NEURON; Matlab; RKToolbox; DLMF; L-BFGS-B-C; GitHub; ADiGator; OPTI; LBFGS-B; L-BFGS; EnKF; L-BFGS-B; MOPSO; Gephi; BRENT Cited in: 14 Publications Further Publications: http://neurofitter.sourceforge.net/index.html?section=Publications all top 5 Cited by 47 Authors 2 Lin, Wei 1 Achard, P. 1 Bal, Thierry 1 Bărbulescu, Ruxandra 1 Bartlett, Edward L. 1 Buhry, Laure 1 Burghi, Thiago B. 1 Ching, Shinung 1 Čiegis, Raimondas 1 Ciuprina, Gabriela 1 Coventry, Brandon S. 1 De Schutter, Erik 1 Destexhe, Alain 1 Diekman, Casey O. 1 Doelman, Arjen 1 Fairhurst, David J. 1 Gerstner, Wulfram 1 Giremus, Audrey 1 Grassia, Filippo 1 Grivel, Eric 1 Ioan, Daniel 1 Jolivet, Renaud 1 Lai, Yingcheng 1 Li, Jr-Shin 1 Ma, Huanfei 1 Meilūnas, Mečislavas 1 Moye, Matthew J. 1 Narayanan, Vignesh 1 Nijmeijer, Henk 1 Parthasarathy, Aravindakshan 1 Piwkowska, Zuzanna 1 Pospischil, Martin 1 Renaud-Le Masson, Sylvie 1 Roth, Arnd 1 Saïghi, Sylvain 1 Schoukens, Maarten 1 Schürmann, Felix 1 Senn, Walter 1 Sepulchre, Rodolphe J. 1 Silveira, Luís Miguel 1 Sommer, Alexandra L. 1 Tumanova, Natalija 1 Tyukin, Ivan Yu. 1 van der Scheer, H. T. 1 Van Geit, W. 1 van Leeuwen, Cees 1 Zhou, Shijie all top 5 Cited in 9 Serials 4 Biological Cybernetics 3 Journal of Computational Neuroscience 1 Physics Letters. A 1 Automatica 1 Neural Computation 1 SIAM Journal on Applied Dynamical Systems 1 Central European Journal of Mathematics 1 Mathematical Modelling of Natural Phenomena 1 The Journal of Mathematical Neuroscience all top 5 Cited in 8 Fields 11 Biology and other natural sciences (92-XX) 4 Systems theory; control (93-XX) 3 Ordinary differential equations (34-XX) 2 Probability theory and stochastic processes (60-XX) 2 Numerical analysis (65-XX) 1 Statistics (62-XX) 1 Statistical mechanics, structure of matter (82-XX) 1 Operations research, mathematical programming (90-XX) Citations by Year