Making use of very detailed neurophysiological, anatomical, and behavioral data to build biologically-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalability, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multi-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions or ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further development of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effectively collaborate using a modern neural simulation platform. 3
IntroductionAdvances in functional, anatomical, and behavioral neuroscience techniques have led to an increase in the data available for modeling complex dynamics of biologically inspired neural networks at many levels of abstraction, from in-depth descriptions and analyses of individual membrane channels to large-scale investigations of whole brain activity. This wealth of data is essential for creating realistic neural models and increases our understanding of animal and human behavior. Furthermore, it has pushed the modeling community towards the design of increasingly complex models, incorporating unprecedented amount of biophysical and anatomical constraints. These large-scale neural models are often non-linear dynamical systems which can be analytically intractable and require numerical simulation to gain insight into their behavior. Emergent properties of large-scale neural networks often remain unnoticed until the whole system is simulated and components are allowed to interact (Cannon et al., 2002).An additional level of complexity is finding a neural simulator and simulation environment that would enable the large variety of researchers from neurophysiology, psychology and computational modeling to share data and work collaboratively (an excellent review can be found in Brette et al., 2007). Most available software packages are specialized in different applications.