The Fruit Fly Brain Observatory: From Structure to Function

Nh, Ukani; C, Yeh; Tomkins, Adam; Zhou, Yiyin; Florescu, Dorian; Ortiz, CL; Huang, Yu-Chi; Wang, C; Mk, Turkcan; T, Liu; Richmond, Paul; Lo, Chung‐Mau; Coca, Daniel; Chiang, Ann‐Shyn; Aa, Lazar

doi:10.1101/580290

Cited by 10 publications

(14 citation statements)

References 64 publications

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“…The CX web application is built upon several key software components that collectively constitute the Fruit Fly Brain Observatory , an open-source platform for the emulation and biological validation of fruit fly brain models in health and disease (Ukani et al, 2016b ) (Figure 2 ):…”

Section: Software Architecturementioning

confidence: 99%

Generating Executable Models of the Drosophila Central Complex

Givon

Lazar

Yeh

2017

Front. Behav. Neurosci.

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The central complex (CX) is a set of neuropils in the center of the fly brain that have been implicated as playing an important role in vision-mediated behavior and integration of spatial information with locomotor control. In contrast to currently available data regarding the neural circuitry of neuropils in the fly's vision and olfactory systems, comparable data for the CX neuropils is relatively incomplete; many categories of neurons remain only partly characterized, and the synaptic connectivity between CX neurons has yet to be fully determined. Successful modeling of the information processing functions of the CX neuropils therefore requires a means of easily constructing and testing a range of hypotheses regarding both the high-level structure of their neural circuitry and the properties of their constituent neurons and synapses. To this end, we have created a web application that enables simultaneous graphical querying and construction of executable models of the CX neural circuitry based upon currently available information regarding the geometry and polarity of the arborizations of identified local and projection neurons in the CX. The application's novel functionality is made possible by the Fruit Fly Brain Observatory, a platform for collaborative study and development of fruit fly brain models.

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Section: Software Architecturementioning

confidence: 99%

Generating Executable Models of the Drosophila Central Complex

Givon

Lazar

Yeh

2017

Front. Behav. Neurosci.

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“…Preview of the animation demonstrating the AMP LPU in response to a staircase concentration waveform. The animation was rendered by NeuroGFX (Ukani et al, 2019). Each of the OSN groups consists of 25 fruit fly OTP/BSG cascades.…”

Section: Evaluating the Temporal Response Of The Amp Lpumentioning

confidence: 99%

“…We visualize the 50 PSTHs and provide the preview and the link to the animation in Figure 9. The animation is rendered by NeuroGFX, a key component of FFBO (Ukani et al, 2019) (both NeuroGFX and FFBO are briefly presented in the Methods and Materials section). As shown, the top plot in the animation (and in Figure 9) shows the staircase odorant waveform, and the bottom plot shows the 3D view of the 50 PSTHs.…”

Section: Evaluating the Temporal Response Of The Amp Lpumentioning

confidence: 99%

“…The Fruit Fly Brain Observatory (FFBO) (Ukani et al, 2019) is an open-source platform for the emulation and biological validation of fruit fly brain models in health and disease. It provides users highly intuitive tools to execute neural circuit models on modern commodity hardware (Givon and Lazar, 2016).…”

Section: Simulation Setup In the Fruit Fly Brain Observatory Platformmentioning

confidence: 99%

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A Molecular Odorant Transduction Model and the Complexity of Combinatorial Encoding in the Drosophila Antenna

Lazar¹,

Yeh²

2017

Preprint

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In the past two decades, substantial amount of work characterized the odorant receptors, neuroanatomy and odorant response properties of the early olfactory system of Drosophila melanogaster. Yet many odorant receptors remain only partly characterized, the odorant transduction process and the axon hillock spiking mechanism have yet to be fully determined.The essential functionality of olfactory sensory neurons (OSNs) is to jointly encode both odorant identity and odorant concentration. We model identity and concentration by an odorant-receptor binding rate tensor modulated by the odorant concentration profile and an odorant-receptor dissociation rate tensor, and quantitatively describe the ligand binding/dissociation process.To validate our modeling approach, we first propose an algorithm for estimating the affinity and the dissociation rate of an odorant-receptor pair. We then apply the algorithm to estimate the affinity and dissociation rate for (acetone, Or59b) using two different datasets of electrophysiology recordings. Second, we evaluate the temporal response of the Or59b OSN model to acetone with a multitude of stimuli, including step, ramp and parabolic odorant waveforms. We further interrogate the model with staircase and noisy waveforms.. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under aThe copyright holder for this preprint (which was not . http://dx.doi.org/10.1101/237669 doi: bioRxiv preprint first posted online Dec. 21, 2017; 2 Lastly, we evaluate the affinity and the dissociation rate for different odorantreceptor pairs including (methyl butyrate, Or59b) and (butyraldehyde, Or7a).We demonstrate how to evaluate the odorant transduction process and biological spike generator cascade underlying the fruit fly OSN model at the circuit level of the antennae and maxillary palps under two scenarios. First, we empirically estimate the odorant-receptor affinity of the active receptor model in response to constant concentration odorants using the spike count records in the DoOR database. Second, we evaluate and graphically visualize the temporal response of the antennae and maxillary palps using a staircase odorant concentration waveform. Finally, we describe how to construct, execute and explore various instantiations of the antennae and maxillary palps as a parallel information preprocessor in the open-source Fruit Fly Brain Observatory platform.

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“…First, the 3D GUI, called the NeuroNLP window (see Figure 2b , top middle-left), supports the visual exploration of fly brain data, including neuron morphology, synaptome, and connectome from all available data sources, stored in the NeuroArch Database ( Givon et al, 2015 ). With plain English queries (see Figure 2b , top middle-left), a layperson can perform sophisticated database queries with only knowledge of fly brain neuroanatomy ( Ukani et al, 2019 ).…”

Section: Introductionmentioning

confidence: 99%

Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era

Lazar

Liu

Türkcan

et al. 2021

eLife

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In recent years, a wealth of Drosophila neuroscience data have become available including cell type, connectome/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 have developed FlyBrainLab, a unique open-source computing platform that integrates 3D exploration and visualization of diverse datasets with interactive exploration of the functional logic of modeled executable brain circuits. FlyBrainLab's User Interface, Utilities Libraries and Circuit Libraries bring together neuroanatomical, neurogenetic and electrophysiological datasets with computational models of different researchers for validation and comparison within the same platform. Seeking to transcend the limitations of the connectome/synaptome, FlyBrainLab also provides libraries for molecular transduction arising in sensory coding in vision/olfaction. Together with sensory neuron activity data, these libraries serve as entry points for the exploration, analysis, comparison and evaluation of circuit functions of the fruit fly brain.

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The Fruit Fly Brain Observatory: From Structure to Function

Cited by 10 publications

References 64 publications

Generating Executable Models of the Drosophila Central Complex

Generating Executable Models of the Drosophila Central Complex

A Molecular Odorant Transduction Model and the Complexity of Combinatorial Encoding in the Drosophila Antenna

Accelerating with FlyBrainLab the discovery of the functional logic of the Drosophila brain in the connectomic and synaptomic era

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