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News about Virtual Fly Brain (VFB)

1 - New Split-GAL4 report pages on FlyBase

FlyBase now has ‘Split System Combination’ pages displaying curated information for Split-GAL4 lines.

FlyBase has added report pages for split driver lines, where two (or more) hemidrivers are combined to restrict functional driver expression to the intersection of the hemidriver expression patterns. These are predominantly ‘split GAL4’ system combinations using a DBD and AD line currently, but more complex combinations may be included in the future.

example_hemi_combo

These new ‘split system combinations’ pages (e.g. GAL4DBD.R72B05∩Hsap\RELAAD.ple), include information specific to that combination. Currently these include the FlyBase identifier (FBco), synonyms, the transgenic hemidriver alleles that make up the combination, expression pattern data and links to stocks corresponding to the combination.

example_FBco_report

The combination pages have been added to hitlists, so if you search for a regulatory region that drives expression of one of the hemidrivers in a combination (e.g. R72B05, VT064569, ple) you will see the relevant combination(s) in the hitlist. Searching for combination names is also supported (e.g. MB195B). These new report pages will get improvements during the coming months, including images of expression patterns when available.

example_FBco_hitlist

2 - Transcriptomics data available for cell types on VFB

Transcriptomics data is now available on VFB! Find scRNAseq clusters from the Term Info pane for a cell type of interest.

We now incorporate scRNAseq data from multiple studies, including the Fly Cell Atlas project and other datasets that identify nervous system cell types. These datasets can be found by searching for ‘scRNAseq’ and filtering to ‘Dataset’.

Clusters can be found for particular cell types via the ‘Single cell transcriptomics data for..’ query on the cell type Term Info pane.

transcriptomics_query

Genes for a particular cluster can be filtered by function and sorted by expression level and extent (proportion of cells in cluster expressing the gene). As with other VFB search results, these can be exported as a csv. Note that we currently only include genes that have extent > 0.2 in a cluster.

cluster_genes

Data can also be retrieved using VFB_connect.

We pull scRNAseq data from FlyBase, which takes it from the Single Cell Expression Atlas.

3 - Larval split-GAL4 line raw images release

Raw images from the 1020 Larval split-GAL4 lines and 350 Generation 1 LexA lines included in Meissner et al., 2024 are now available on VFB.

The raw image data for the larval split-GAL4 and Gen 1 LexA lines from Meissner, G. W., et al. “A split-GAL4 driver line resource for Drosophila CNS cell types.” bioRxiv (2024)._ DOI: 10.1101/2024.01.09.574419 is available on VFB here: https://raw.larval.flylight.virtualflybrain.org/

Example_larval_split_image

For each image, the confocal stack in TIFF format can be downloaded by selecting an image or all TIFF stacks and z-projections for a line can be downloaded by selecting a line name. Line and image names can be searched at the top right.

We are working on fully integrating these images into VFB. This raw data site does not include full genotypes but these will be included in the curated release on the main VFB site in a later release.

The larval split-GAL4 line release was annotated and provided via the Zlatic lab

4 - Fix for problems with current Safari release

Virtual Fly Brain 3D browser won’t load on Safari Version 15.3 (17612.4.9.1.8) with an experimental feature enabled. Please follow these instructions to disable it until Apple fixes the issue.

We are aware that VFB’s secure websocket connection is failing to connect on the latest version of Safari on MacOS meaning that no data can be pulled from our servers.

The issue is down to an ’experimental feature’ (NSURLSession WebSocket) being set to ON by default which seams to break most sites using secure websockets.

To turn resolve this issue turn this off:

In Safari on the desktop:

 Under 'Develop' expand 'Experimental Features' untick 'NSURLSession WebSocket'

If you don’t see the Develop menu in the menu bar, choose Safari > Preferences, click Advanced, then select “Show Develop menu in menu bar”. Restarting Safari may be necessary if the list of features under ‘Experimental Features’ are greyed out.

On IOS devices:

 Open the Settings app

 Scroll down and tap on “Safari”
 
 Scroll down to the bottom and tap on “Advanced”
 
 Tap on “Experimental Features” at the bottom
 
 Scroll down until you see “NSURLSession WebSocket"
 
 Disable “NSURLSession WebSocket”

5 - Google search results issue

VFB has been affected by an issue with google’s indexing which has affected our ranking in their search results. We applogise for any inconvenience but have been assured this is now fixed and should get back to normal soon.

Google Statement:

December 6-14
An internal issue caused an increase of redirect errors during indexing, and associated email notifications. 
This was not due to any website issues, but was due to an internal Google issue. 
Pages that were dropped from the index have been scheduled for recrawling.