Abstract
The Parallel Circuit SIMulator (PCSIM) is a software package for simulation of neural circuits. It is primarily designed for distributed simulation of large scale networks of spiking point neurons. Although its computational core is written in C++, PCSIM's primary interface is implemented in the Python programming language, which is a powerful programming environment and allows the user to easily integrate the neural circuit simulator with data analysis and visualization tools to manage the full neural modeling life cycle. The main focus of this paper is to describe PCSIM's full integration into Python and the benefits thereof. In particular we will investigate how the automatically generated bidirectional interface and PCSIM's object-oriented modular framework enable the user to adopt a hybrid modeling approach: using and extending PCSIM's functionality either employing pure Python or C++ and thus combining the advantages of both worlds. Furthermore, we describe several supplementary PCSIM packages written in pure Python and tailored towards setting up and analyzing neural simulations.
Highlights
Given the complex nonlinear nature of the dynamics of biological neural systems, many of their properties can be investigated only through computer simulations
While these examples concentrate on the Python aspect of the hybrid modeling, we show in the Section “Extending
The application programming interface of PCSIM is an objectoriented framework composed of many classes interacting together to achieve the desired operation
Summary
Given the complex nonlinear nature of the dynamics of biological neural systems, many of their properties can be investigated only through computer simulations. It has been brought to attention that it is of importance to use large neural networks with biologically realistic connectivity (on the order of 104 synapses per neuron) as simulation models of mammalian cortical networks (Morrison et al, 2005). In the Section “Custom Network Elements” we demonstrate another advantage of the hybrid modeling approach: we show how PCSIM’s concept of a general network element can be used as an interface to another simulation tool. While these examples concentrate on the Python aspect of the hybrid modeling, we show in the Section “Extending. Www.frontiersin.org multi-threaded simulation to match the scaling achieved with an equivalent distributed simulation
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