Thanks to over 20 participants of the LiceBase workshops held in Bergen and Oslo for being enthusiastic about using LiceBase and the Genome. In addition to giving an overview of the basic functions of Tripal, Blast, and GBrowse I have also received a lot of valuable positive feedback and constructive criticism how to make LiceBase and upcoming courses better. The course slides are available for every user under Documentation -> Courses -> Introductory course materials. The course excercises are on the last slide of Part 4 of the course slides.

As a side note, for a course that mainly consists of clicking through a web-site or program it is good to have the users see the mouse pointer. I used Omni-Dazzle for Mac in Oslo and found it good to present and scribble on the screen; in Bergen, it was sometime hard to follow the mouse clicks.

Feedback

I had the impression that the participants where highly motivated to find and annotate their genes of interest. In its current state the database is already sufficiently complex and feature-rich. It will need some restructuring to improve user friendliness and accessibility to new users. In addition, it become obvious that each course needs to include sections on sequence analysis, bioinformatics, and genomics. In general the schedule was quite tense, but in the end everyone should have been enabled to find their genes of interest. 

There are several specific topics where we need to do some follow-up, these are mainly related to naming conventions. In particular we found:

• We need naming conventions for the titles and other fields in RNAi experiments.
• We need naming conventions for novel or unknown genes and sequences which are added to the database.
• We need to agree on naming conventions for gene names, gene descriptions and synonyms.
• We need to discuss with Ensembl how we should report back on updated annotations. 

With respect to LiceBase functions, there is some need to improve the following points:

• Links in the Blast results need to be configurable. They are often not linking to the correct database, because they cannot be configured per BLAST database.
• It is a bit odd that Protein sequences have a link to view them in GBrowse, but there is no information for proteins in GBrowse at the moment.
• Protein sequences (EMLSAP IDs) are not linked to the generating transcripts, while cryptic polypetide-auto sequences are. therefore, users have to search for gene and protein by their numeric ID which is the same for trnscripts and proteins - for now only!
• It is a bit cumbersome to having to use AmiGO and KEGG to search the GO or BRITE hierarchy and then come back to LiceBase to open the exact path found there. Instead it would be better if the KEGG and GO pages and Tripal had a search functionality on their own. 

I hope some of this is going to get solved in Tripal 2. We will not be able to attempt to solve it before a migration to Tripal 2.