FlyBrainLab: Accelerating the Discovery of the Functional Logic of theDrosophilaBrain in the Connectomic/Synaptomic Era

Abstract

In recent years, a wealth of Drosophila neuroscience data have become available. These include cell type, connectome and synaptome datasets for both the larva and adult fly. To facilitate integration across data modalities and to accelerate the understanding of the functional logic of the fly brain, we developed an interactive computing environment called FlyBrainLab.FlyBrainLab is uniquely positioned towards accelerating the discovery of the functional logic of the Drosophila brain. Its interactive open source architecture seamlessly integrates and brings together computational models with neuroanatomical, neurogenetic and electrophysiological data, changing the organization of neuroscientific fly brain data from a group of unconnected databases, arrays and tables, to a well structured data and executable circuit repository. The FlyBrainLab User Interface supports a highly intuitive and automated workflow that streamlines the 3D exploration and visualization of fly brain circuits, and the interactive exploration of the functional logic of executable circuits created directly from the explored and visualized fly brain data.FlyBrainLab methodologically supports the efficient comparison of fly brain circuit models, across model instances developed by different researchers, across different developmental stages of the fruit fly and across different datasets. The FlyBrainLab Utility and Circuit Libraries accelerate the creation of models of executable circuits. The Utility Libraries help untangle the graph structure of neural circuits from raw connectome and synaptome data. The Circuit Libraries facilitate the exploration of neural circuits of the neuropils of the central complex and, the development and implementation of models of the adult and larva fruit fly early olfactory systems.To elevate its executable circuit construction capability beyond the connectome, FlyBrainLab provides additional libraries for molecular transduction arising in sensory coding in vision and olfaction. Together with sensory neuron activity data, these libraries serve as entry points for discovering circuit function in the sensory systems of the fruit fly brain. They also enable the biological validation of developed executable circuits within the same platform.

The Functional Logic of Odor Information Processing in the Drosophila Antennal Lobe

“…The evaluation of a large number of circuits is only possible via massively parallel simulation on Graphical Processing Units (GPUs) [26, 27]. Furthermore, for each circuit configuration, we computed empirical distributions of identity recovery across randomly sampled parameters, providing insights into the computational capabilities of model structures, rather than specific parameterizations of said models.…”

A Programmable Ontology Encompassing the Functional Logic of the Drosophila Brain

“…In this paper, we presented a programmable ontology that expands the scope of the current ontology of Drosophila brain anatomy [15, 16] to encompass the functional logic of the fly brain. The programmable ontology provides a language not only for defining functional circuit motifs but also for programmatically exploring their functional logic.…”

“…Using these calculations, we create a second graph in which ports, such as LNs ( → )OSNs and LNs ( ← )OSNs (see also Figure 6), are distinct nodes rather than the nodes for OSNs and PNs themselves. We then use Graphviz to compile this graph into a file in Scalable Vector Graph format; we use a custom Javascript script to make the diagram interactive in the NeuroGFX window of the FlyBrainLab user interface [16], and allow button presses on the diagram to interact with the 3D visualization of the morphology of neurons, and highlight the connections they are a part of in the visualized diagram.…”

“…First, the FeedbackCircuits Library provides tools for interactively visualizing and exploring the connectivity patterns in the AL circuit operational on the FlyBrainLab computing platform [16]. Figure 9A shows a typical FlyBrainLab user interface in which a diagram of the DM4 glomerulus circuit was automatically generated and displayed (see also Materials and Methods).…”

“…Traditionally, ontologies formally define the classification of the anatomical structure of the Drosophila nervous system and the relationships among anatomical entities [15, 16]. Characterizing the functional logic of sensory circuits calls for modeling the environment the fruit flies live in.…”