cirsiumNeuron is a neuronal circuit simulator that can directly and
efficiently compute characterizations of stochastic behavior, i.e.,
noise, for multi-neuron circuits. It is still in its early stages of
development, so beware of bugs!
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:
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
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.
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.
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
accepted for publication by the Journal of Computational Neuroscience
Manuscript ID JCNS-D-17-00083R2
For questions please contact Deniz Kilinc: firstname.lastname@example.org
Copyright 2018 by Koc University and Deniz Kilinc, A. Gokcen Mahmutoglu, Alper Demir
All Rights Reserved