Changes between Initial Version and Version 1 of PomBasePlanningMeetingMinutes20120320


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Timestamp:
Mar 27, 2012, 2:17:11 PM (10 years ago)
Author:
markmcdowall
Comment:

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  • PomBasePlanningMeetingMinutes20120320

    v1 v1  
     1=== Issues Raised ===
     2
     3  * AI EBI to contact Conrad
     4    * Arnaud has looked into this and we could potentially load these as a BAM file.
     5  * AI EBI Action subdomain
     6    * This is currently active
     7  * AI EBI to action selenium testing and check server is sufficiently powered
     8  * AI Change default browser link to "location" tab
     9    * Done
     10  * 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
     11    * This is a web-data issue.
     12  * 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)
     13    * 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.
     14  * AI Mark/Dan Difficult to link back to genomic regions with output provided
     15    * Will provide some examples for the next meeting
     16  * 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)
     17    * This is a long term issue.
     18  * AI EBI provide a version of Ensembl help http://www.ebi.ac.uk/panda/jira/browse/PB-409
     19    * 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.
     20
     21  * AI EBI Direct all Pombase Feedback to PomBase? helpdesk "helpdesk@…" www.ebi.ac.uk/panda/jira/browse/PB-511
     22  * 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
     23  * AI EBI Change entry level text http://www.ebi.ac.uk/panda/jira/browse/PB-497
     24  * AI EBI Linking between browser and gene page http://www.ebi.ac.uk/panda/jira/browse/PB-435
     25    * provide a "button" to link to Ensembl from Gene pages and vice versa
     26    * reduce number of linked up/downstream genes
     27    * place link to Ensembl browser underneath the gene list
     28  * Speed of the PomBase portal
     29    * 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.
     30    * 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.
     31  * 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.
     32
     33
     34Currently PK is looking into the interaction between ES and and PomBase.
     35
     36FTP is ready to go, Val is generating a list of files (or tarring them up) ready for transfer.
     37
     38Email 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.
     39
     40=== JIRA Issues ===
     41  * Closure tables
     42    * Careful consideration needs to be made as to the logic behind the querying over closure tables.
     43    * 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.
     44  * Sortable tables
     45    * For some this is already done
     46  * Loading of the VCF files
     47    * Potentially Chonkee could do this
     48  * Make the “Preview” image static to the top of the page.
     49  * GO term counting, when NOT, switch of the count
     50  * In a week update about the number of JIRA items and why the ones that remain are still unresolved.
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     52