MAY 18 2009

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Contents

Genbank update

  • Status: GenBank will provide a new ID for the new contig.
  • Next thing is to fix the links with UniProt

Next Software update: Release 2-14

  • Done! (May 13) Excellent.
  • Synchronized with Dpur (May 18)

DDB_G search bug

  • Can this issue be addressed for the next release:

http://bugs.dictybase.org/issuetrackers/dictyBase%20Enhancements/0723 placed in next release

Searching the wiki pages

Would it be possible to search the wiki pages from the dictyBase main search tool?

see select * from cgm_chado.FEATUREPROP where value like 'Has Wiki Page'

Sidd will check if it's possible to tie a wiki search into the dictybase search. Easy: just make gene names of wiki pages searchable. More complicated (Sidd estimate 1-2 days), make whole wiki page searchable (and restrict to those linked to genes).

issue

Issues with GFF3 files

  • Some genes are missing:

http://bugs.dictybase.org/issuetrackers/dictyBase%20Enhancements/0779

    • ACTION ITEM: Sidd/Yulia: (1) provide a list of all genes missing from the GFF3 files (2) - less important - provide a list of all genes spanning contigs.
  • Gareth would like a version of the file with only primary features:

http://bugs.dictybase.org/issuetrackers/dictyBase%20Enhancements/0788

    • Ask Eric why our GFF files have both gene predictions and curated models? Why not only primary features?

Will be solved as a part of user request

Downloads

Yulia was to merge some files ?

  • dictyBase ID, gene names, synonyms, and gene products
  • DDB_G curation status
  • -> leave it like this for now
  • Adding geneID predition FASTA under Dictyostelium Sequences and Annotations? NO - make separate page with requested files and send this link to users if required.

Making a 'Protein' page and/or adding tabs or collapsible sections

  • Yulia will try to make the tabs more visible/ done, but she will make one more change, increase size of active tab about 20%.
  • Splice variants discussion. One tab for each, sequences and proteins, with the ability to toggle between the variants.
  • We'll send the prototype to a few usrs for feedback: Bill Loomis, Robert Insall, Thierry Soldati, Jeff Williams, Chris Thompson, Robin Williams, Gareth Bloomfield, Silvia Jimenez
  • Need to draft letter to these users. Letter sent to Yulia
  • Make new design of front page, fitting new gene page - Yulia + Petra - collect all links and try to re-organize

Ideas for Dicty09 meeting presentations

  • "New in dictyBase": new design, converter tool, what else?
  • modware

Back to Monday_meetings

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