The Fruit Fly Brain Observatory: from structure to function

Abstract

SummaryThe Fruit Fly Brain Observatory (FFBO) is a collaborative effort between experimentalists, theorists and computational neuroscientists at Columbia University, National Tsing Hua University and Sheffield University with the goal to (i) create an open platform for the emulation and biological validation of fruit fly brain models in health and disease, (ii) standardize tools and methods for graphical rendering, representation and manipulation of brain circuits, (iii) standardize tools for representation of fruit fly brain data and its abstractions and support for natural language queries, (iv) create a focus for the neuroscience community with interests in the fruit fly brain and encourage the sharing of fruit fly brain structural data and executable code worldwide. NeuroNLP and NeuroGFX, two key FFBO applications, aim to address two major challenges, respectively: i) seamlessly integrate structural and genetic data from multiple sources that can be intuitively queried, effectively visualized and extensively manipulated, ii) devise executable brain circuit models anchored in structural data for understanding and developing novel hypotheses about brain function. NeuroNLP enables researchers to use plain English (or other languages) to probe biological data that are integrated into a novel database system, called NeuroArch, that we developed for integrating biological and abstract data models of the fruit fly brain. With powerful 3D graphical visualization, NeuroNLP presents a highly accessible portal for the fruit fly brain data. NeuroGFX provides users highly intuitive tools to execute neural circuit models with Neurokernel, an open-source platform for emulating the fruit fly brain, with full data support from the NeuroArch database and visualization support from an interactive graphical interface. Brain circuits can be configured with high flexibility and investigated on multiple levels, e.g., whole brain, neuropil, and local circuit levels. The FFBO is publicly available and accessible at http://fruitflybrain.org from any modern web browsers, including those running on smartphones. *

A molecular odorant transduction model and the complexity of spatio-temporal encoding in the Drosophila antenna

“…We visualize the 50 PSTHs and provide the preview to the animation in Fig 9. The animation is rendered by NeuroGFX, a key component of FFBO [44] (both NeuroGFX and FFBO are briefly presented in the Methods and Materials section). As shown, the top plot in the animation (and in Fig 9) shows the staircase odorant waveform, and the bottom plot shows the 3D view of the 50 PSTHs.…”

“…The Fruit Fly Brain Observatory (FFBO) [44] 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 [52].…”

Generating Executable Models of the Drosophila Central Complex

“…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):…”

NeuroNLP: a natural language portal for aggregated fruit fly brain data

“…The architecture of the FFBO [1] is sketched in Figure 1. NeuroNLP utilizes two main modules in the architecture, namely, the natural language processing (NLP) module and the NeuroArch Database.…”