OCT 1 2008

From DictyWiki

Contents 1 Agenda 1.1 From Dicty meeting: 1.2 Advisory Committee comments: 1.3 Other topics 1.4 Developmental tasks for next release (Added by Siddhartha)

Agenda

From Dicty meeting:

• GFF3/FASTA problem reported

• New D. discoideum sequences (Rob Kay/Gareth Bloomfield)

Advisory Committee comments:

• slide 20: Bill - make clear that floatigs can mean unrelated concatemers (scaffolds)

• slide 28: nomenclature: they were fine with our new nomenclature guidelines, Bill doesn't like 'long' names.

• slide 30: Yes, delete dubious genes! Maybe even put on front page the new gene count from time to time (Rob?, Bill?)

• slide 33: Unique gene model: was approved as a good idea by everyone. Dave K wants to have more help, as it's not clear what's on Gbrowse. Wants small protocols for typical tasks.

• slide 33: Need to have a quick access/visual clue about the kind of gene

model directly from Gbrowse or gene page. (Pascale: we may consider using grey instead of paler shades of blue and red?)

• slide 35: Standard Strain. Jeff: don't call it standard, but 'recommended'. The point was also made that new people should be advised not to use DH1 or such tricky strains -> we need a strategy for guidance what to pick.

• slide 54: Integrate other genomes: Dave remarked that in the mock-up it needs to be made clearer what's D. discoideum, and needs to set more apart, and made clear that the other genomes are blast hits. Everyone also asked for comparative genomics. We said that for now we just have blastP hits, many to many, and that comparative genomics is further away as it requires more thinking how to do and to represent.

Other topics

• Textpresso: paper (pdf) downloads of researchers. Want to send email to Listserv (Petra).
  • Need to have page for upload to a specific folder
  • Upload Verification by ListServ subscriber email
  • What is the cutoff date? Call for papers of year 2004 and before?? Duplicates should not be a problem.

• When can we release D. purpureum? Adam needs to be contacted. Rex?

• Francisco R. contacted me and mentioned curation of Dp genome (JGI) and he wants to do an alignment of actin genes between Dd, Dp, and Df.

• Integrate PANTHER domains?

• Conference pictures: Kei Inoue uploaded all the japanese taken pictures on their website. He told me I should get those I want for our site. But is it necessary? We could host those that other people send, and could link to their site?

http://cosmos.bot.kyoto-u.ac.jp/cgi-bin/dicty2008/ig.cgi?root=dicty2008&sort=top

Developmental tasks for next release (Added by Siddhartha)

• Protein domain
  • Search by domain name/keyword.
  • Store and retrieve domain data from local database(Replace DAS resource).

• Upgrade biomart to version 0.7
  • Uniprot id output
  • Customized fasta header
  • Activate webservice

• Setup draft version of PhysarumBase
  • Gbrowse
  • EST/cDNA alignment

• Dpur update
  • Available datasets
  • Protein domain ?
  • Comparison of Gene model.

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