wiki:PomBasePlanningMeetingMinutes20120320

Issues Raised

  • AI EBI to contact Conrad
    • Arnaud has looked into this and we could potentially load these as a BAM file.
  • AI EBI Action subdomain
    • This is currently active
  • AI EBI to action selenium testing and check server is sufficiently powered
  • AI Change default browser link to "location" tab
    • Done
  • AI Mark/Dan? Check that all sequence features are available consistently on location and gene tabs See http://www.ebi.ac.uk/panda/jira/browse/PB-548
    • This is a web-data issue.
  • AI Mark/Dan? Blast against pombe genome giving no hits for short sequences http://www.ebi.ac.uk/panda/jira/browse/PB-556 (reported by user)
    • This is due to the threshold of the E-value being set to 10, currently working on being able to change the default for the PomBase? genome browser.
  • AI Mark/Dan? Difficult to link back to genomic regions with output provided
    • Will provide some examples for the next meeting
  • AI Mark Add a link from the protein section of the gene page to a PSI Blast (currently we link to NCBI from PomBase??, but any is OK)
    • This is a long term issue.
  • AI EBI provide a version of Ensembl help http://www.ebi.ac.uk/panda/jira/browse/PB-409
    • Midori has forwarded around the minutes from when this was discussed for having PomBase? Ver. x.y where x is the EG release and y is the Chado dump version number.
  • AI EBI Direct all Pombase Feedback to PomBase?? helpdesk "helpdesk@…" www.ebi.ac.uk/panda/jira/browse/PB-511
  • AI EBI Configure search so that PomBase?? is optional and EG site-wide is configureable http://www.ebi.ac.uk/panda/jira/browse/PB-513
  • AI EBI Change entry level text http://www.ebi.ac.uk/panda/jira/browse/PB-497
  • AI EBI Linking between browser and gene page http://www.ebi.ac.uk/panda/jira/browse/PB-435
    • provide a "button" to link to Ensembl from Gene pages and vice versa
    • reduce number of linked up/downstream genes
    • place link to Ensembl browser underneath the gene list
  • Speed of the PomBase? portal
    • Currently it is still being hosted via the Hinxton servers due to testing in London. Dan and Myself are currently in discussions with the ES team about using PomBase? as the test site for moving to London.
    • The reason for the push is that the only difference between my box and the servers at Hinxton is the version of PHP (mine: 5.3; Hx 5.2). Between the releases of 5.2 to 5.3 there have been major changes to the handling of garbage collection and memory management, so moving to the London servers that are using 5.3 might resolve this issue. This should solve the problem, but it is not guarantee.
  • AI Mark - EG Browser and the customisation to make it feel more friendly and to aid in the linking between the Drupal and ensembl services.

Currently PK is looking into the interaction between ES and and PomBase?.

FTP is ready to go, Val is generating a list of files (or tarring them up) ready for transfer.

Email aliases is a no go due to the awkward nature of enabling them with the current service provider. It is also noted that when users do have these replies start coming from both addresses, so for consistency our current email addresses shall remain.

JIRA Issues

  • Closure tables
    • Careful consideration needs to be made as to the logic behind the querying over closure tables.
    • Potentially can look into having 2 tables and having 2 numbers on the web site, but more thought needs to be placed into the implementation.
  • Sortable tables
    • For some this is already done
  • Loading of the VCF files
    • Potentially Chonkee could do this
  • Make the “Preview” image static to the top of the page.
  • GO term counting, when NOT, switch of the count
  • In a week update about the number of JIRA items and why the ones that remain are still unresolved.
Last modified 9 years ago Last modified on Mar 27, 2012, 2:17:11 PM