Monthly Archives: June 2013

Improvements in speed of display

Third-party registered  image stacks, such as the FlyCircuit neurons and lineage clones  now load much quicker on our Viewer. We hope these improvements enable users to look at the registered images, even when using a slower internet connection.

In 2 to 3 weeks, we will be adding even more image stacks to the site, so stay tuned!

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The changes are over

We are pleased to announce that all planned work on releasing 3D third party stack data for this release is now finished.

The FlyCircuit neurons and Tzumin Lee’s clones are now fully operational on the new, faster and more reliable server.

We are now back to business as usual and have more exciting stuff in the pipeline, including lots more 3D third party stacks for next month’s release.

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Planned server migration

We plan to migrate our site to a new server within the following two days. We need to do so to improve site speed and stability.

From the user point of view, nothing will change – the site will be available at its current address and all the functionality will remain the same.

We expect short periods of intermittent site availability problems while the DNS (domain name service) is being propagated – depending on your location and ISP type.

Shall you notice something unusual with the site over the coming two days please try to refresh the page(s) or try again later.

We will try to keep disruption to a minimum. Should everything go smooth our users are unlikely to even notice anything in most cases.



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New clusters and display of image stacks

We are pleased to announce a new release of VFB (2013/06/11) including the addition of important new features and content.

New content:

We have integrated lineage clone data from Tzumin Lee’s lab (HHMI-JFRC) (95 clones) [1] and added two new queries: one retrieves lineage clones that overlap a neuropil domain, and the other returns all neurons that are part of a specific lineage. In addition, we have released an improved version of the FlyCircuit neuron clusters obtained by nblast, these clusters now include less outlier neurons than previously. Searches on the site only return results from the current version. If you have done extensive work with the previous clusters, please see our previous post here regarding access to the old version. We also now display the shorter FlyCircuit neuron name (eg. fru-M-000134 instead of  FruMARCM-M001976_seg001) for neurons on the site and for neurons in cluster pages. This is to match the names shown on the FlyCircuit website. We will soon be providing a file with mappings between the long names and short names.

We have also updated the FlyBase Chado and anatomy ontology to the lastest versions, which means more expression results and anatomy information.

New features:

You can now view registered, third party, 3D image data directly on our stack browser in combination with painted neuropil domains. This is true for all registered anatomical dataset currently integrated by VFB: FlyCircuit single neurons (16132 stacks) and the lineage clone data from Tzumin Lee. To display a stack in the viewer, look for the “See in Viewer” link from the term info window or result lists.

We are currently working on being able to display more than one image stack at the same time, and making more image data available in the stack browser including GAL4 lines from Janelia Farm and lineage clones from Kei Ito’s lab (Tokyo University) [2], so keep an eye out for more news.

[1] Yu et al., 2013
[2] Ito et al., 2013


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Server functionality issues and planned downtime

We are carrying out work on releasing clone data. This requires updates to crucial components of the server. As a result, the server is running limited functionality at the moment and we expect short periods of downtime over the following day or two.

Full server functionality will be restored shortly, and we will follow that with an announcement with details of all our new features. Watch this space.


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