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Administrator's picture

[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:

Michael Dondrup's picture

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.

Michael Dondrup's picture

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;)!

 

Administrator's picture

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.

Administrator's picture

RNAi form problems with IE [Fixed]

We have disabled the Overlay module for the the administrative interface because it was interfering with the RNAi edit interface.

The form validation did not work correctly, the tabs did not open automatically on error. This happened even with the latest version of Internet Explorer.

While we do not recommend IE for use by Administrators and Annotators, it should work for most of you now.

Michael Dondrup's picture

Core Update Completed

Dear LiceBase users,

after a long update process, LiceBase is finally back up. You may now log in again, and you will find that no data was lost in the update process. Please report any problem you are experiencing to us. The differences between the new and previous versions with respect to the user interface will be appear as mostly minor.

The largest differences are:

Michael Dondrup's picture

Problems after Feide migration? (Read this)

LiceBase.org is now officially a Feide registered service provider. Users from the academic partners UiB and NMBU are able to log in using their organizatioal accounts.

So far, we haven't heard of any problems after the Feide migration, and are seeing that people seem to be happily using the migrated user profiles. So overall this was a big success :D

Administrator's picture

Maintenance downtime Monday, January 11 2016

There will be a scheduled maintenance downtime on Monday starting from 8 a.m. until approximately 3 p.m to perform necessary changes LiceBase and to finally migrate all user accounts to FEIDE.

During the downtime period, all LiceBase services including the genome browser and Blast will be unavailable or unstable. Please remember to log out from LiceBase by 6 am on January 11. We will send out a notification to all users once the the downtime is finshed, as always, this might take less time, but please don't rely on it.

Administrator's picture

Maintenance downtime Thursday, December 10 2015

There will be a scheduled maintenance downtime Thursday, December 10 2015 starting from 9 a.m. until approximately 3 p.m to install necessary updates for several components of LiceBase and to pave the way to migrating user accounts to FEIDE.

Michael Dondrup's picture

New Control Sequences CPY185 CTH210 CMi2471

CPY185 is the common negative control sequence for RNAi experiments. I have uploaded the sequence for use in the RNAi experiment annotation: https://licebase.org/CPY185%20%28negative%20control%29

Two more control candidates have been added:

Both are PCR products from transcribed mRNA in the Atlantic Cod.

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