Controlling complexity of cerebral cortex simulations. I: CxSystem, a flexible cortical simulation framework. (English) Zbl 1470.92018

Andalibi, Vafa; Hokkanen, Henri; Vanni, Simo

Neural Comput. 31, No. 6, 1048-1065 (2019).

Summary: 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++, and GPU devices. The most efficient device varied with computer hardware and the duration and scale of the simulated system. The speed of Brian2 was retained despite an overlying layer of software. However, the Python and C++ devices inherited the single core limitation of Brian2.
The CxSystem framework supports exploration of complex models on personal computers and thus has the potential to facilitate research on cortical networks and systems.
For Part II, see [the authors, ibid. 31, No. 6, 1066–1084 (2019; Zbl 1470.92024)].

MSC:

92B20	Neural networks for/in biological studies, artificial life and related topics
92-08	Computational methods for problems pertaining to biology

Keywords:

cerebral cortex computer simulation; neocortical microcircuit; Brian2 model simulation

Citations:

Zbl 1470.92024

Software:

NEURON; Python; NeuroML; CxSystem; Nengo; PyNEST; GeNN; NEST; Pynn; Brian; SpineML; NineML; neuroConstruct; Simbrain

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