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The key to sustainable sea lice control is in the genome.

Core Update Completed

Michael Dondrup's picture

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:

  • The New RNAi - Edit RNAi dialog now consists of vertical tabs, that can all be opened at the same time if desired, instead of horizontal ones, but the fields are exactly the same. This looks much cleaner to me than the old layout. Also, missing mandatory fields will open their tab automatically when we press Save.
  • Editing and creating new content will now happen in overlay.
  • The layout of genes and other feature pages is also more clean, with the resource links (Blast results, sequence, etc. moved to the left).
  • There is a new feature: a bulk sequence exporter. We are still testing it.
  • There is a new field Publication in RNAi experiments to link them to a publication entry. The entry must be already imported into LiceBase, use the Autocomplete function to find publications by their title. External links to e.g. PubMed won't work.
  • Annotators can see the access permissions for content pages.
  • The main RNAi view now has fields to search by both, Primary Target ID and Gene symbol, the separate view called Browse RNAi by target has been removed.
  • The RNAi gallery now has a more regular 4X4 layout. It will show the RNAi galery images grouped by phenotype. There is also a filter box, that allows to the filter the phentypes included in the gallery view.

There are few outstanding issues left, which we will try to resolve as soon as possible, the most important ones:

  •  Error in New RNAi: you cannot add New RNAi experiments yet, unless you fill out each and every numeric field, including non-mandatory ones. We are working on this issue with high priority. You can edit existing RNAi experiments without problems. 
    Edit: This has been fixed, you can now create new RNAi experiments as normal. The problem was caused by an unfixed issue with the update path ( see https://www.drupal.org/node/2679491 )
  • Links from Genes to external resources (Show in Ensembl, Blast this sequence, Show in GBrowse) have been removed, we are trying to bring them back soon. Fixed
  • The GO browser feature is gone for good, it was little used and has not been ported to Tripal 2 by the Tripal developers yet.
  • There is no Clone functionality for content yet. Fixed: There is now an option
    • Clone this <data type> at the top of a clonable page. Only Administrators and Annotators are able to clone pages.
  • The site search doesn’t find gene pages yet. You can use the Feature search instead.

 

 

Best regards,

Wei and Michael