Blogs

[NEWS] Associated RNAi experiments listed for each Tripal Feature

Hi,

We have added a neat new function: On each chado feature (gene, transcript) we list the RNAi experiments that have been perfomed using this gene or transcript as a target. Here is an example: https://licebase.org/?q=feature/Lepeophtheirus/salmonis/mRNA/EMLSAT00000...

The experiments listed here follow standard access permissions, so make sure you are logged in to see all experiments listed.

 

 

 

Here is an example:

 

[Update] Scheduled service window 7. - 8. of May.

Update: The scheduled upgrades to the database have been finished with only minor service interruptions (downtime <10 min).

Dear LiceBase users,

There will be a scheduled downtime of LiceBase (all services incl. Blast,
GBrowse) due to an
migration of the database to a new server.

The database upgrade is scheduled 7th of May at 12.00

The service window is as follows:
Monday 7th of may from 12.00
Tuesday 8th of may to 12.00

RNAi form gallery image upload

There is also a slight change in the RNAi upload section. The field Gallery image now also supports direct upload of TIFF images which will be re-scaled and converted to jpeg for display.
This does not substitute uploading the original tiff as separate files because the resolution of gallery images is reduced automatically.

Updated LiceBase Hardware Stack

We have recently updated the LiceBase Hardware and Software stack. Both front-end and database back-end have been moved to
new and more powerful hardware running up-to-date operating systems and software. LiceBase should now be much more performant now.
In the meantime we have also adjusted the branding of GBrowse, so it looks more like LiceBase.
Enjoy!

Karl, Wei, and Michael

Update: Tigriopus kingsejongensis Genome

Update as of 9.5.2018:
We are still working on improving the user experience with the Tigriopus genome. We have now fixed the links and presentation of the gene models in GBrowse. When clicking on a gene model, the links back to LiceBase should work correctly. We have also added Blast results against the L. salmonis predicted proteins and SwissProt to all predicted T. kingsejongensis genes.
When searching in Blast results, now it is possible to restrict the search to one organism. In addition, the maximal number of hits per query can be selected.

[Update] Blast searches under Feature - Homology

We have recently extended and update the pre-computed Blast analyses for all the gene features. From now on, we will run these analyses in a regular interval.

The following Blast analyses are available: 

To see the blast results, navigate to a gene feature (they are not available for transcripts or proteins at the moment, you have to go to the corresponding gene),

and click on the 'Homology' link to the left to open the Homology pane:

Homology

The following BLAST results are available for this feature:

Moving to Let'sEncrypt Certificates

We have decided to move our SSL certificates to the free and open certification authority Let's Encrypt, for securing your connection to LiceBase. This will happen on the June 24., when or old certificate expires. We don't expect any notable glitches from the change, but please contact us if you have any problems.

The genome of the Atlantic salmon published in Nature

The genome sequence of the Atlantic salmon (the host fish of the Atlantic salmon louse) has been published in Nature:

Lien S., et al., Nature (2016)

The Atlantic salmon genome provides insights into rediploidization

Congrats (and thanks for 100 million years of co-evolution and hosting;)!

 

Ensembl Metazoa release 31 - With Lepeophtheirus salmonis genome is public

Ensembl Metazoa release 31 - March 2016 has been published, and it contains the genome of the Atlantic salmon louse as a new species. All genes, transcripts and proteins in LiceBase will now be linked against their  Ensembl counterparts. The links appear under Cross references in each gene page.

Pages

Subscribe to RSS - blogs