NeuroGFX: a graphical functional explorer for fruit fly brain circuits

Abstract

Recently, multiple focused efforts have resulted in substantial increase in the availability of connectome data in the fruit fly brain. Elucidating neural circuit function from such structural data calls for a scalable computational modeling methodology. We propose such a methodology that includes i) a brain emulation engine, with an architecture that can tackle the complexity of whole brain modeling, ii) a database that supports tight integration of biological and modeling data along with support for domain specific queries and circuit transformations, and iii) a graphical interface that allows for total flexibility in configuring neural circuits and visualizing run-time results, both anchored on model abstractions closely reflecting biological structure. Towards the realization of such a methodology, we have developed NeuroGFX and integrated it into the architecture of the Fruit Fly Brain Observatory (http://fruitflybrain.org). The computational infrastructure in NeuroGFX is provided by Neurokernel, an open source platform for the emulation of the fruit fly brain, and NeuroArch, a database for querying and executing fruit fly brain circuits. The integration of the two enables the algorithmic construction/manipulation/revision of executable circuits on multiple levels of abstraction of the same model organism. The power of this computational infrastructure can be leveraged through an intuitive graphical interface that allows visualizing execution results in the context of biological structure. This provides an environment where computational researchers can present configurable, executable neural circuits, and experimental scientists can easily explore circuit structure and function ultimately leading to biological validation. With these capabilities, NeuroGFX enables the exploration of function from circuit structure at whole brain, neuropil, and local circuit level of abstraction. By allowing for independently developed models to be integrated at the architectural level, NeuroGFX provides an open plug and play, collaborative environment for whole brain computational modeling of the fruit fly. Additional Details NeuroGFX builds upon two major modules of the FFBO architecture [1], Neurokernel [2] and NeuroArch [3]. Both have been designed with the explicit aim of facilitating the generation of executable neural circuit models on GPUs. NeuroGFX conjoins the simultaneous operations of model exploration on NeuroArch and model execution on Neurokernel in a unified graphical web interface, presents queried connectomic data as a reconfigurable circuit diagram, and renders interactive simulation results. NeuroGFX facilitates construction and execution of neural circuitry at various brain levels of abstraction. We demonstrate below the capabilities of NeuroGFX on the whole brain, neuropil and local circuit level. *

The functional logic of odor information processing in the Drosophila antennal lobe

“…Note that LNs are connecting pre-/post-synaptically to the OSN-to-PN synapses in each glomerulus. While additional LN types both in terms of innervation patterns and neurotransmitter profile exist [12,31,32,34], we found that these three LN types, and the uni-glomerular PNs (henceforth referred to simply as PNs) alone, are sufficient for disentangling the syntactic and semantic information streams of the odorant stimuli. The functional significance of other LN/PN types remains an open question.…”

Generating Executable Models of the Drosophila Central Complex

“…NeuroGFX provides a reconfigurable graphical interface for navigation, manipulation, and execution of the CX neural circuit; a screenshot of this interface appears in Figure 3 . (Yeh et al, 2016 ). Regions of neuropils comprised by and accessory to the central complex may be rendered in 3D.…”

“…(Yeh et al, 2016). Regions of neuropils comprised by and accessory to the central complex may be rendered in 3D.…”