Come see us at NeuroFly2016

NeuroFly 2016

Marta Costa will be talking tonight at 7pm with a poster at R-019.
Robert Court will be available at poster R-022.

We look forward to meeting everyone.

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Major new VFB release

We are proud to announce a major new VFB release. This sees some very significant enhancements to the data we serve: we have now mapped ~50% of the >16,000 single neurons from FlyCircuit to published neuron classes; we now host almost 18,000 images of VT lines along with curation of where they are expressed.

An example of the detailed image data available for neuron classes can be see by querying for neurons with synaptic terminals in the protocerebral bridge and sorting on available images. 111 of the 137 neuron classes returned are illustrated by one or more single neuron images:

Screen Shot 2016-08-10 at 11.40.18

This particular data comes from combining NBLAST clusters (described in a recent paper from VFB’s Marta Costa and Greg Jefferis) and detailed curation of the paper from Ann-Shyn Chiang’s group ‘A comprehensive wiring diagram of the protocerebral bridge for visual information processing in the Drosophila brain.’

Any of these neuron images can be used to search for predicted GAL4 driver lines using NBLAST on the fly (video tutorial).

We are working on integrating NBLAST queries directly into VFB, so soon you’ll be able obtain lists of predicted driver lines directly from neuron classes.

We now have ~18,000 images of VT expression patterns. Registered data kindly donated by Barry Dickson (Janelia/IMP), Katja Buhler (VRVis) and colleagues was bridged from the original T1 template space to the JFRC2 template used on the VFB site.

The VT lines are indexed to gross neuropils (data from BrainBase), e.g.

Screen Shot 2016-08-10 at 12.02.14

They are also indexed to individual neurons (curated from the literature):

Screen Shot 2016-08-10 at 12.00.54

This release also includes many more minor enhancements and extensions to data via curation by VFB and FlyBase of anatomy, expression and phenotypes.

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VFB 1.5 Launch – Monday 15th Feb

We are delighted to announce the official release of VFB 1.5. This
has already been available in beta for some time. It will become the
official version of VFB on Monday 15th Feb.

The new site features a new look and feel, a much improved image
browser and better integration of images into search results. Please
let us know what you think. Your feedback is essential to our
continued improvement.

The main focus of development is now our new 3D browser (watch this
space for demos) and improvements to our data architecture to speed
up the site, extend queries and support new visualisation tools.

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Finding similar neurons using NBLAST

You can now use NBLAST to find similar neurons, or GAL4 drivers that label a neuron of interest. The implementation is described here, and the how, with video demos here. You can start NBLASTing right away on the online app!

Neurons listed in the NBLAST results are linked to VFB, so you can see them on the viewer, together with any other image.

And see here how to find GAL4 drivers that label specific neurons.

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by | February 2, 2016 · 11:56 am

Flybase and Ontology Update

We have just updated to the latest release of the flybase database FB2015_05 and also have updated to the latest (2015-09-16) anatomy ontology.

Please follow the links for further details.

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Feeling adventurous?

Try out our new site which is currently undergoing beta testing:

bit.ly/vfbbeta

We would love to know what you think?

Simply leave a comment here, or use the report an issue or email us links on the site itself.

Expression_download

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by | October 2, 2015 · 11:27 am

Something we’re working on with geppetto.org for next year

geppettoengine:

Data from http://virtualflybrain.org

Something we’re working on with geppettoengine for next year.

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Flybase and Ontology Update

We have just updated to the latest release of the flybase database FB2015_03 and also have updated to the latest (2015-05-12) anatomy ontology.

Please follow the links for further details.

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Job opportunity at VFB

We’re looking for a web developer to help us build VFB 2.0. Please share with anyone you think may be interested. Details:

Are you interested in the challenge of designing web tools to provide accurate answers to biologically important questions couched in the language of biology? Are you interested in the challenges of communicating and interacting with 3D image data? Do you have an eye for web design?

Virtual Fly Brain are looking for a front end web developer to help redesign our site.

Virtual Fly Brain is a data integration hub for Drosophila neurobiology. We already integrate thousands of descriptions of neuroanatomy along with 10s of thousands of annotations of expression and 3D images of neuroanatomy. We have a clear semantic schema that provides the functionality our users need, and that runs from curation, through our OWL-based data models. Our new site must communicate these semantics clearly and elegantly whilst integrating an interactive 3D browser for images of neuroanatomy.

Details of the position, which is a combined post working with both VFB and The European Bank for induced pluripotent stem cells, are available on the EBI site.

Thanks!

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We are looking for a postdoctoral researcher

We are looking for a postdoctoral researcher, working part-time (0.5 FTE) to curate neuroanatomical expression data from the published literature. You will be based in the Virtual Fly Brain (VFB) group in the Department of Genetics, in central Cambridge, working as part of a team that is supervised by Dr Cahir O’Kane in the Department of Genetics, and colleagues in the MRC Laboratory of Molecular Biology in Cambridge, the European Bioinformatics Institute near Cambridge, and the University of Edinburgh.

The closing date is November 10, 2014.

http://www.jobs.cam.ac.uk/job/4538/

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