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
Douglas Armstrong (current project PI)
Former devs: Nestor Milyaev (2009-2012)
Ontology editing, FlyBase support and data annotation:
Department of Genetics, University of Cambridge
Alex Holmes
Cahir O'Kane (current project PI)
Former contributors: Michael Ashburner (original PI and grant holder), Simon Reeve (2009 - 2011), Nicole Staudt (2015-2016)
Department of Physiology, Development and Neuroscience
Gillian Millburn
Aoife Larkin
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)
Helen Parkinson (current project PI)

Funding

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 content:

  • 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.

VFB supp