Controlling Complexity of Cerebral Cortex Simulations-I: CxSystem, a Flexible Cortical Simulation Framework

Neural Computation
Vafa AndalibiSimo Vanni

Abstract

Simulation of the cerebral cortex requires a combination of extensive domain-specific knowledge and efficient software. However, when the complexity of the biological system is combined with that of the software, the likelihood of coding errors increases, which slows model adjustments. Moreover, few life scientists are familiar with software engineering and would benefit from simplicity in form of a high-level abstraction of the biological model. Our primary aim was to build a scalable cortical simulation framework for personal computers. We isolated an adjustable part of the domain-specific knowledge from the software. Next, we designed a framework that reads the model parameters from comma-separated value files and creates the necessary code for Brian2 model simulation. This separation allows rapid exploration of complex cortical circuits while decreasing the likelihood of coding errors and automatically using efficient hardware devices. Next, we tested the system on a simplified version of the neocortical microcircuit proposed by Markram and colleagues ( 2015 ). Our results indicate that the framework can efficiently perform simulations using Python, C <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:m...Continue Reading

References

Aug 15, 1997·Neural Computation·M L Hines, N T Carnevale
Jun 6, 1998·Proceedings of the National Academy of Sciences of the United States of America·H MarkramM Tsodyks
Feb 5, 2002·Annual Review of Physiology·Robert S Zucker, Wade G Regehr
Mar 2, 1962·Annals of the New York Academy of Sciences·W RALL
Jun 3, 2004·The Lancet Infectious Diseases·John McConnell
Nov 18, 2005·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Tim P Vogels, L F Abbott
Sep 6, 2006·EMBO Reports·Kyriaki SidiropoulouPanayiota Poirazi
Apr 20, 2007·Neuron·Padraig GleesonR Angus Silver
Jul 17, 2007·Journal of Computational Neuroscience·Romain BretteAlain Destexhe
Apr 9, 2008·Physiological Reviews·P Jesper SjöströmMichael Häusser
Aug 8, 2008·Neural Networks : the Official Journal of the International Neural Network Society·Brad AisaRandy O'Reilly
Aug 12, 2008·Proceedings of the National Academy of Sciences of the United States of America·Suzana Herculano-HouzelRoberto Lent
Sep 5, 2008·PLoS Computational Biology·Gustavo DecoKarl Friston
Apr 30, 2009·Annual Review of Neuroscience·Daniel E Feldman
Dec 17, 2009·Frontiers in Neuroscience·Dan F M Goodman, Romain Brette
Jan 19, 2010·Research in Gerontological Nursing·Victoria T GrandoVicki S Conn
Nov 4, 2010·Cerebral Cortex·N T MarkovK Knoblauch
Jan 1, 2009·Therapeutic Advances in Gastroenterology·Gideon M HirschfieldE Jenny Heathcote
Nov 5, 2011·Cerebral Cortex·David C Van EssenJohn Harwell
Oct 9, 2012·Science·Wulfram GerstnerGustavo Deco
Apr 17, 2013·Physiological Reviews·Björn Rasch, Jan Born
Oct 10, 2013·Frontiers in Neuroinformatics·Roger V HoangFrederick C Harris
Nov 2, 2013·Science·Nikola T MarkovHenry Kennedy
Jan 17, 2014·Frontiers in Neuroinformatics·Trevor BekolayChris Eliasmith
Sep 23, 2014·Eye·M Gemenetzi, A J Lotery
Oct 10, 2015·Cell·Henry MarkramFelix Schürmann
Jan 8, 2016·Scientific Reports·Esin YavuzThomas Nowotny
Nov 3, 2016·Journal of Neurophysiology·Mara Almog, Alon Korngreen
Aug 20, 2016·Neural Networks : the Official Journal of the International Neural Network Society·Zachary Tosi, Jeffrey Yoshimi
Aug 5, 2017·Frontiers in Neuroinformatics·Ruben A Tikidji-HamburyanTarek A El-Ghazawi
Apr 14, 2019·Neural Computation·Henri HokkanenSimo Vanni

❮ Previous
Next ❯

Citations

Apr 14, 2019·Neural Computation·Henri HokkanenSimo Vanni

❮ Previous
Next ❯

Software Mentioned

SLURM
Python
Brian2genn
PyNN
NeuroML
CxSystem
Windows
CxSystem Constructor
CUDA
NEST

Related Concepts

Related Feeds

Anxiety Disorders

Discover the latest research on anxiety disorders including agoraphobia, panic disorder, obsessive-compulsive disorder, and post-traumatic stress disorder here.