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

Abstract
Data availability
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Abstract

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.

Data availability

Code Availability and InstallationStable and tested FlyBrainLab installation instructions for user-side components and utility libraries are available at https://github.com/FlyBrainLab/FlyBrainLab for Linux, MacOS and Windows. The installation and use of FlyBrainLab does not require a GPU, but a service-side backend must be running, for example, on a cloud service, that the user-side of FlyBrainLab can connect to. By default, the user-side-only installation will access the backend services hosted on our public servers. Note that users do not have write permission to the NeuroArch Database, nor will they be able to access a Neurokernel Server for execution. The server-side backend codebase is publicly available at https://github.com/fruitflybrain and https://github.com/neurokernel.A full installation of FlyBrainLab, including all backend and frontend components, is available as a Docker image at https://hub.docker.com/r/fruitflybrain/fbl. The image requires a Linux host with at least 1 CUDA-enabled GPU and the nvidia-docker package (https://github.com/NVIDIA/nvidia-docker) installed. For a custom installation of the complete FlyBrainLab platform, a shell script is available at https://github.com/FlyBrainLab/FlyBrainLab.To help users get started, a number of tutorials are available written as Jupyter notebooks at https://github.com/FlyBrainLab/Tutorials, including a reference to English queries at https://github.com/FlyBrainLab/Tutorials/blob/master/tutorials/getting_started/1b_nlp_queries.ipynb. An overview of the FlyBrainLab resources is available at https://github.com/FlyBrainLab/FlyBrainLab/wiki/FlyBrainLab-Resources.Data AvailabilityThe NeuroArch Database created from publicly available FlyCircuit, Hemibrain and Larva L1EM datasets can be downloaded from https://github.com/FlyBrainLab/dataset. The same repository provides Jupyter notebooks for loading publicly available datasets, such as the FlyCircuit dataset with inferred connectivity, the Hemibrain dataset and the Larva L1 EM dataset, into the NeuroArch Database.

The following previously published data sets were used

1. Ann-Shyn Chiang et al
(2011) FlyCircuit
FlyCircuit DB.

https://doi.org/10.1016/j.cub.2010.11.056; http://flycircuit.tw
1. Tomoko Ohyama et al
(2015) L1EM
CATMAID, L1EM.

https://doi.org/10.1038/nature14297
1. C. Shan Xu et al
(2020) Hemibrain
neuPrint, Hemibrain.

https://doi.org/10.1101/2020.01.21.911859; gs://hemibrain-release/neuprint/hemibrain_v1.0.1_neo4j_inputs.zip
1. Shin-ya Takemura et al
(2014) Medulla 7 Column Data
N/A.

https://doi.org/10.1073/pnas.1509820112; https://github.com/janelia-flyem/ConnectomeHackathon2015

Article and author information

Author details

Aurel A Lazar

Department of Electrical Engineering, Columbia University, New York, United States

For correspondence
aurel@ee.columbia.edu

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4261-8709
Tingkai Liu

Department of Electrical Engineering, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-3075-7648
Mehmet Kerem Turkcan

Department of Electrical Engineering, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-9273-7293
Yiyin Zhou

Department of Electrical Engineering, Columbia University, New York, United States

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0003-4618-4039

Funding

Air Force Office of Scientific Research (FA9550-16-1-0410)

Mehmet Kerem Turkcan

Defense Advanced Research Projects Agency (HR0011-19-9-0035)

Aurel A Lazar
Tingkai Liu
Mehmet Kerem Turkcan
Yiyin Zhou

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.