cirsiumNeuron is a neuronal circuit simulator that can directly and efficiently compute characterizations of stochastic behavior, i.e., noise, for multi-neuron circuits.
cirsiumNeuron requires the SUNDIALS suite and the MATLAB interface of SUNDIALS called sundialsTB. In order to install SUNDIALS and sundialsTB, please download SUNDIALS (version 2.6.0), which is available at http://computation.llnl.gov/casc/sundials/main.html, and follow the installation instructions given at the above link. In order to install sundialsTB, within MATLAB, navigate to the sundialsTB subdirectory and run the script called "install_STB.m". You will need a C compiler that is recognized by MATLAB in order to generate .mex files. The installed sundialsTB and the source code for cirsiumNeuron should be added to the MATLAB path before attempting to use cirsiumNeuron.
Please type "help circuit" in MATLAB for a brief tutorial on how to construct a simple circuit with cirsiumNeuron.
Please see the papers below for the details of the formulations and techniques implemented in cirsiumNeuron:
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Kilinc D, Demir A (2017) Noise in neuronal and electronic circuits: A general modeling framework and non-Monte Carlo simulation techniques. IEEE Transactions on Biomedical Circuits and Systems 11(4):958–974. http://ieeexplore.ieee.org/abstract/document/7938326/
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Kilinc D, Demir A (2015) Simulation of noise in neurons and neuronal circuits. In Proceedings of the IEEE/ACM International Conference on Computer-Aided Design (ICCAD), IEEE, pp. 589–596. http://ieeexplore.ieee.org/abstract/document/7372623/
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Mahmutoglu A. G., Demir A. (2013). CIRSIUM: A circuit simulator in MATLAB with object oriented design. In 2013 9th Conference on Ph. D. Research in Microelectronics and Electronics (PRIME), IEEE, pp. 173-176. http://ieeexplore.ieee.org/abstract/document/6603134/
The directory "run_scripts" contains the scripts that were used to generate the results reported in the manuscript below
Title: Spike Timing Precision of Neuronal Circuits Authors: Deniz Kilinc, Alper Demir Journal of computational neuroscience, 44, 341-362. https://link.springer.com/article/10.1007/s10827-018-0682-z
For questions please contact Deniz Kilinc: [email protected]
Copyright 2018 by Koc University and Deniz Kilinc, A. Gokcen Mahmutoglu, Alper Demir. All Rights Reserved