Cardiff meeting feedback

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SAB: What people want

  • Proteomics: peptide hits on Gbrowse
  • Post translational modifications, especially phosphorylation, but every PTM we can get
  • On the Ortholog Data tab: add D. purpureum orthologs can can use Adamís list DONE (2011)
  • BLAST ALL genomes
  • Protein-protein interaction: low priority
  • Other species: BLAST would be enough + Gbrowse alignments
  • Rename DictyMart -> Advanced search



Other comments from users:

  • Community annotations need attributions to encourage people to contribute (comments following talk - Pascale)
    • Alan Kimmel:
      • put a link to dictyExpress on Front page (or one of the menus) DONE (2011)
      • put a link to the conference on the front page DONE (2011)
    • Dave Knecht: post new strains in DictyNews DONE (2011)
    • Paul Fisher has a tool to do statistical analyses of movement ñ we should like to

that in dictyBase

    • Pathostelium club meeting:

They would like to set up a group (I suggest Google groups? Since thatíd be independent of us and you can also create an email list)

      • Pascale Aug 9th: Contacted Pierre Cosson, Thierry Soldati, Adam Kuspa about setting up a google group
  • Data offered:
    • Gareth Bloomfield: could send at least AX4 improved data (check with Adam is

they are ok with that); he estimates several point mutations (which should be okay since they wonít change the gene models) and a small number of indels; problem is to identify the indels within coding regions as opposed to the larger number present in non-coding. Not sure how to address that (BLAST?)

    • Gareth suggests to also include AX2 and NC4 in dictyBaseÖ whenever weíre ready
    • Harry MacWilliams: (1) RNA seq of cell cycle data; (2) list of rblA-controled genes On it's way (2011)
    • Jonathan Chubb & Wolfgang Nellen: PTMs of histones (experimentally characterized)

'Fight for own interests' in the room: - adding at least one very close Dd relative: D. citrinum (Adam), favor even many more (Joan) - but don't have predictions. - databases (and even annotations) desired on Pp and Df ( Pauline; also should have at least one from each clade, and group 3 still missing) On it's way (Pp, Df 2011)




Other comments from users:

  • Everyone: Speed up Gene page loading! - we need to discuss how to accomplish - rethink some sort of caching? Or longterm, 'freezing' the front end and curating in the background with frequent releases?
  • Stock Center:
    • Annette: Stock Center makes contributions more 'anonymous'. Encourage citations to original paper when sending out orders. Sidd, can the reference of the ordered strain/plasmid be included in the email? ADDED REFS to email OK
  • Dave Knecht: post new strains/plasmids in DictyNews [moved up]
  • Many people: Charge for strains, suggested $10-20.-. people see that

the attitute is to order things one doesn't need. NOT FEASABLE

  • Formedium representative: Can the Stock Center become the american distributor for HL5? As such we get a 25% discount and thus could pay for shipping? But needs accounting, should be seen in conjunction with charging for strains and discussed with NH. NOT FEASABLE

Other comments:

  • Chris Sudgen: Asked how to create a 'clu' protein domain. Will work with him to get annotated in InterPro In Process (PFam slow)
  • Chris Hammann has annotations for ribosomal RNAs.

Not our responsibility, just seeing into the future with other species- Thomas Winckler wants to get P. violaceum sequenced, the only group 4ish Polysphondylium.

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