Introduction to CircuitML: Modeling Local Processing Units in the drosophila brain
The brain of the fruit fly Drosophila Melanogaster is an attractive system for studying the logic underlying neural circuits because it implements a rich behavior repertoire with a number of neural components that is five orders of magnitude smaller than that of vertebrates. Analysis of the fly's connectome using a powerful toolkit of well-developed genetic techniques and advanced electrophysiological recording tools enables the fly's neural circuitry to be experimentally mapped into functional units, called Local Processing Units (LPU). Many tools are already available to enable neuroscientists to create an accurate model of the entire fly brain, but none of them provides a method to specify those circuits in a way that both biologists and engineers can work together. Also, the development of plausible LPU models requires the ability to specify and instantiate subcircuits without explicit reference to their constituent neurons and internal connections. To this end, we present a neural circuit specification language called CircuitML for construction of LPUs. CircuitML has been designed as an extension to NeuroML; it provides constructs for defining subcircuits that comprise neural primitives supported by NeuroML. Subcircuits are endowed with interface ports that enable connections to other subcircuits via neural connectivity patterns. We have used CircuitML to specify an LPU-based model of the fly olfactory system.