About Virtual Fly Brain

What is Virtual Fly Brain?

Welcome to Virtual Fly Brain (VFB) - an interactive tool for neurobiologists to explore the detailed neuroanatomy, neuron connectivity and gene expression of Drosophila melanogaster. Our goal is to make it easier for researchers to find relevant anatomical information and reagents.

We integrate the neuroanatomical and expression data from the published literature, as well as image datasets onto the same brain template, making it possible to run cross searches, find similar neurons and compare image data on our 3D Viewer.


Who we are

Virtual Fly Brain members and their contribution

3D Viewer, online tools, server and the website

Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh
Robert Court (Lead DevOps) Douglas Armstrong (current project PI) Former devs: Nestor Milyaev (2009-2012)

Ontology editing, FlyBase support and data annotation

Department of Genetics, University of Cambridge
Cahir O'Kane (current project PI) Former contributors: Michael Ashburner (original PI and grant holder), Simon Reeve (2009-2011), Nicole Staudt (2015-2016), Alex Holmes (2017-2019)
Department of Physiology, Development and Neuroscience
Clare Pilgrim (Ontology editor/Curator) Alex McLachlan (Curator/UX Tester) Aoife Larkin (Curator) Gillian Millburn (Senior Curator) Nick Brown current project PI)
Department of Zoology, University of Cambridge
Marta Costa (current project Co-I)

Image processing, registration and NBLAST neuron search

MRC Laboratory of Molecular Biology, Cambridge
Greg Jefferis (current project PI)

Schema development & Web development

European Bioinformatics Institute (EMBL-EBI), Cambridge
David Osumi-Sutherland (current project Co-I) Nico Matentzoglu (developer) Helen Parkinson (current project PI)

Software engineering, Geppetto customisation, graphics design

MetaCell Ltd., LLC, Oxford, UK - Boston, MA

Funding

Virtual Fly Brain is supported by a grant from the Wellcome Trust: Virtual Fly Brain (Grant ref: 208379/Z/17/Z) (October 2017 to September 2021) following Virtual Fly Brain: a global informatics hub for Drosophila neurobiology (WT105023MA) (October 2014 to September 2017).

This work was previously supported by a research award from the BBSRC to Douglas Armstrong and Michael Ashburner. Details of this grant at Cambridge and Edinburgh. A UK e-Science Theme award to Douglas Armstrong helped us establish the project.

Marta Costa was also supported by a Isaac Newton Trust grant (October 2012 to September 2013).

Collaborators

The IIP3D server, Woolz software and client-side tools* are developed by MRC Human Genetics Unit (MRC HGU): Richard Baldock, Nick Burton, Bill Hill, Zsolt Husz
(*) An on-going development of the client-side tools is done in collaboration between the MRC HGU and Edinburgh University Visit the EMAGE gene expression database to see other tools the MRC HGU have developed.

Expression data is collaboratively curated by VFB and FlyBase. Phenotype data is curated by FlyBase. Expression and phenotype data displayed on VFB is stored and maintained by FlyBase.

Acknowledgements

We would like to thank Arnim Jenett of HHMI Janelia Research Campus, and Kei Ito and Kazunori Shinomiya of Tokyo University for the painted adult brain stack that we use on the 3D Brain Viewer.

We thank the group of A.S. Chiang (Brain Research Center, National Tsing Hua University, Taiwan) for making their FlyCircuit raw data available. We also thank Kei Ito (Tokyo University) and Tzumin Lee (HHMI Janelia Research Campus) for providing us with their neuroblast clone data.

We also thank the following researchers for their hard work in reviewing elements of VFB categories:

  • Liria Masuda Nakagawa (Department of Genetics, University of Cambridge, Cambridge) for review of the larval olfactory system;
  • Orie Shafer (Molecular, Cellular and Developmental Biology, University of Michigan) for reviewing VFB pacemaker neuron terms and related content;
  • Jo Young (Institute for Adaptive and Neural Computation, University of Edinburgh) for review of the central complex;
  • Gregory Jefferis (MRC Laboratory of Molecular Biology, Cambridge) for review of the adult olfactory system.

Virtual Fly Brain uses open source software from a variety of sources:

  • the OWL-API underpins handling of all ontology metadata and queries on VFB with help from the OWLtools and brain libraries;
  • the super fast ontology queries that drive VFB would not be possible without the elk reasoner.

Publications

For more information on the technology behind the VFB website:

For details on the anatomy ontology:

How to cite us

Please use the format below:

Milyaev, N., Osumi-Sutherland, D., Reeve, S., Burton, N., Baldock, R. A. and Armstrong, J. D. (2012). The Virtual Fly Brain browser and query interface . Bioinformatics 28, 411-5.

@article{10.1093/bioinformatics/btr677,
                        author = {Milyaev, Nestor and Osumi-Sutherland, David and Reeve, Simon and Burton, Nicholas and Baldock, Richard A. and Armstrong, J. Douglas},
                        title = "{The Virtual Fly Brain browser and query interface}",
                        journal = {Bioinformatics},
                        volume = {28},
                        number = {3},
                        pages = {411-415},
                        year = {2011},
                        month = {12},
                        abstract = "{Motivation: Sources of neuroscience data in Drosophila are diverse and disparate making integrated search and retrieval difficult. A major obstacle to this is the lack of a comprehensive and logically structured anatomical framework and an intuitive interface.Results: We present an online resource that provides a convenient way to study and query fly brain anatomy, expression and genetic data. We extended the newly developed BrainName nomenclature for the adult fly brain into a logically structured ontology that relates a comprehensive set of published neuron classes to the brain regions they innervate. The Virtual Fly Brain interface allows users to explore the structure of the Drosophila brain by browsing 3D images of a brain with subregions displayed as coloured overlays. An integrated query mechanism allows complex searches of underlying anatomy, cells, expression and other data from community databases.Availability: Virtual Fly Brain is freely available online at www.virtualflybrain.orgContact:jda@inf.ed.ac.uk}",
                        issn = {1367-4803},
                        doi = {10.1093/bioinformatics/btr677},
                        url = {https://doi.org/10.1093/bioinformatics/btr677},
                        eprint = {https://academic.oup.com/bioinformatics/article-pdf/28/3/411/467487/btr677.pdf},
                    }
                    

VFB supports the efforts of the Research Resource Identification Initiative to enable unambiguous mentions of resources in the biomedical literature through the use of Research Resource Identifiers (RRIDs). To refer to VFB in your paper, please use RRID:SCR_004229, in addition to citing the paper.

Contact us

To report a bug on the site, use the Report an issue page. For help, comments or suggestions, please use support@virtualflybrain.org.

To be kept updated on new features and data sign up to our mailing list using the subscribe button on the right.

To tell us about new data that you generated that could be incorporated into VFB see here.

Using our software or registered image data

The VFB software can be embedded in any third-party website where it can provide the same functionality as on the VFB website. This is because it was developed as part of an open source project and freely distributed under a GNU GPL2 license.

If you use our registered image stacks in any publication, please cite the original authors and the VFB project.