MAR 16 2009

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Genbank update

  • Fixed the unexpected gbrowse breakdown.
  • Run the genbank export without the 'gene' flag update.
    • Run from testdb first and if alright the run from test.
  • Get password from eric and upload
  • Inform karen.

[Action items]

  1. delete old C2 record from GenBank

D. purpureum

  • Needs to rerun the patches from start along with software testing.

ID mapping tool

  • Some bugs to fix
  • A few features requested by P&P :improve HTML, remove blank lines, allow conversion between different IDs to different IDs.

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

Next Software update

  • Tentative date: April 1
  • Contents
    • Adding 'Protein' page and Tabs
    • ID conversion tool
    • dictyExpress?

Topics carried over from previous meetings

Plan to re-open Stock Center

  • Marc starts March 16
  • Trying to get Jakob in next week: March 23
  • Need to reactivate ordering buttons
  • Need to announce that we reopen March 23 for order; we'll start collecting strains later
  • Barcoding should be implemented immediately: New strains and strains that are requested thawed and restored. Can buy cryovials with barcoding on. Need barcode reader that plugs into USB port. Need two fields in database, for internal barcode and second for barcode that is scanned in, plus read-out when match and non-match.

DDB_G - DDB-UniProt mapping file

  • Remove promoter elements DDB IDs
  • add links to DDB_G if can be found

Scripts for the Update Downloads page

Updating electronic InterPro2GO mappings

  • Current ones date from April 2007


No progress....

  • [ACTION ITEM]: Yulia to change links to external resources to include Identifier (for eg: EC:; UniProt: Q12345) -> Should we move this to the Issue Tracker and implement in the next software release?
  • Issues with dicty database import (updates)
  • BioMart: status: Sidd will work on that once he's done with purpureum
  • InterMine: having problems loading out GFF3 file
  • GO curation tool: Protein2GO
    • One consideration is that the old file format will be retired on 1st Aug 2009.
  • Physarum site: looking for related species: working on Gene Predictions and Blast server (Sidd and Yulia);

Nov 24-2008: [ON HOLD] problem with script for loading and testing being overlapping (???) Cannot afford to spend a lot of time on this until the next release.

  • Modware paper

  • Other Ensemblized Genomes: Rex to pursue with the EBI

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