FEB 12 2010

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Contents

Update on Software Release

d_pur_search_output

Update on automated gene products in dictyBase

in_paranoid_automated_gp_example

Rob Insall requests

  • making the blast search default to discoideum only when the window comes up (or both, if you prefer, but I think discoideum is more what people want)
Suggestion
add 'select organism' dropdown with options 'all', 'D. discoideum', 'D. purpureum', etc.
enable saving selected organism in cookies
databases restricted to selected organism
Image:Blast organism dropdown 1.jpg
Image:Blast_organism_dropdown_2.png
  • refreshing the MacOS widget so it goes direct to the right site and includes purpureum?


Setting up JBrowse demo

next meeting : Sidd

Priorities

Software release (Feb 1) 2.16

  • last meeting we decided on this:
  1. [2 days] Reports to help prioritizing curation targets :Dec 20 2009 :Sidd
  2. [4 weeks] Make a public D. purpureum site (Includes roll out of new gene page) :Early January :Sidd + Yulia (Feb 5) Done

Next software release (Feb 26th) 2.17

  1. Reengineer menus [ 2 weeks]  :End of January :Yulia
  2. Remove GeneDB ids. Matt Barriman and Rob Kay agreed; however maybe we can have another look and decide if any information is valuable. The major issue is that IDs are out of date. Do not display
  3. Updating existing inparanoid links [ 2 days] :Yulia Feb 5th
    1. Will get valid ids by parsing inparanoid data files Done
    2. Do we remove previous Inparanoid links data from database or just remove those from display? (Now they are stored as 'Inparanoid V. 5.1'), should we keep them and add v. 7.0? Do not display, add new version, display Inparanoid links with version (Inparanoid v.7.0)
    3. What do we link, gene or gene model? do we link by DDB_G or DDB id DDB_GXXXXXX
  4. Updating automated gene products
  1. [3 weeks] Implement a database table for Stock Center orders  :Sidd

Next next release 2.18 (April 16?)

  • Sidd, Eric and Yulia will discuss a plan on Feb 24th, will then have a better idea of timing.
  1. [3 months] Migrating reference tables to Chado : Sidd
  2. [6 months] Migrate GO tables to Chado for writing OBO2 and GAF files into dictybase. This will allow us to (1) borrow a curation tool, either from the EBI, or maybe implement PAINT; and (2) upload ISS annotations generated with PAINT.
  3. Other genomes: pallidum, fasciculatum [ 4 weeks - to be re-evaluated after purpureum is finished ] : Sidd
    • automated gene products (based on Dicty) [ 2 weeks ]: Sidd
    • write paper about dictyBase handling of multi-species data
  4. Storing and displaying ortholog data (Inparanoid, panther): [4 weeks] Yulia
How do we display data and what data do we store
Add new Orthologs (Homologs) tab
List of organisms
Data to display

Image:otrhologs_layout.png

More

  1. purureum:
    • InterPro domains from JGI [ 2 weeks ]: Yulia
    • Update BLAST alignments between Dd & Dp [ 3 weeks? ] : Sidd
Adding combo blast databases.
  1. GenBank update: including the pombe sequence deletion? [ 2 weeks ]: Sidd
  2. Reorganize static pages and sites [ 8 weeks ] Yulia
  3. [4 weeks] Update InterPro2GO annotations; make this a regular process (should be done after every GenBank update and/or InterPro update) (depends on go?)
  4. [many weeks?] Improving search tool (?)
  5. integrate RNA-seq data (transcript coverage)
  6. UniProt synchronization

Software maintenance/OS maintenance/Bug fixes [1 day/week/1 developer]

  1. Gene page
  2. Managing GenBank update
  3. Core software packaging/installation
  4. Genome Browse handling
  5. Database patching
  6. Improvement of software testing
  7. Improvement of software architecture
  8. Error handling
  9. ID mapping

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