Changes between Version 1 and Version 2 of PombasePlanningMeetingMinutes20130703


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Timestamp:
Jul 4, 2013, 12:15:30 AM (8 years ago)
Author:
antonialock
Comment:

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  • PombasePlanningMeetingMinutes20130703

    v1 v2  
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    44  Cambridge - Meeting Room B, Sanger Building
    5 Present: Steve, Paul, Dan, Mark, Midori, Val, Antonia [[BR]]
     5Present: Steve, Paul, Dan, Mark, Midori, Val, Antonia  
    66Remote: Kim
    77
     
    99= General =
    1010
    11 ==Update cycle and automated update pipeline ==
     11== Update cycle and automated update pipeline ==
    1212Dan explained the difference between the various tests they run to make sure that pages on the website behave and look as they should. These are:
    1313 * Standard health checks – these are run by Mark on a continuous basis where he just goes to different pages and looks at them manually.
     
    1919A Ftp directory has been created to support incoming large scale datasets. Dan can provide the single username and password required for uploading to ftp-private.ebi.ac.uk . We need to document how to submit data to this (acceptable data-types for each file format etc..).  Midori reckons that the instructions already online don’t need much changing, however we might want to make the link more prominent. Val thinks we should reword the link to something including “HTP..”
    2020
    21 [[BR]]
    2221Paul said that he is reluctant to ask for data until they have some form of “validation software” in place. This software would check that the files contain data that is compatible with what we can accept and display properly. This can be very simple to begin with. Val is keen to get going with collecting data and points out that if we need to go and find it ourselves then it would be a full-time job to locate data. If we get input from the community of where to find the stuff and what format it is in + the reference it will already make our job a lot easier.
    2322
    24 [[BR]]
    2523Users should be able to upload and visualize their data privately.
    2624
    27 [[BR]]
    28 
    2925Researchers doing transcriptome experiments should submit read-data (embl/genbank) ENA or Array express, once this is done we can display it using the accessions. The problem is that they often don’t supply the alignment, but we could produce these ourselves (Dan points out that we haven’t done this for pombe as of yet).
    3026
    31 [[BR]]
    3227So for each thing people submit we need an accession number (RNA seq data) or a file. The accession number can be from ENA , GEO or array express. Acceptable file formats include GFF3, BAM, or VCF.  We also require the genome assembly date + PMID. If there is an accession number the file should already have been validated.
    33 [[BR]]
     28
    3429Question: Paul/Val: Should we allow users to visualize RNA seq files or perhaps we should ‘force’ users to submit their RNA seq to elsewhere to get an accession number?
    3530
    36 
    37 [[BR]]
    3831 * AI: Document how to submit data to ftp directory (what file format for what data-types.  Using accession numbers or uploading data files, genome assembly date, PMID) (curators?)
    3932  * sub-AI: FAQ item to document what GFF3 is (curators)
    4033  * sub-AI: Short term solution = Change form from ‘submit data’ to something that lets people point us to the data + describes the data types at the source (genome version…). Make this in more of an ‘advert’ style format. Rename the link. (Midori)
    41 * AI: Need to document how users can visualize their data privately (who?)
    42 * AI: Search SRA for pombe (related to mapping of short reads?) (jira ticket created) (DAN)
    43 
    44 * future AI: Need to document how users can visualize their data privately (who?)
    45 * future AI: Make a validation system that lets people submit data in a format already made usable to us (Paul?)
     34 * AI: Need to document how users can visualize their data privately (who?)
     35 * AI: Search SRA for pombe (related to mapping of short reads?) (jira ticket created) (DAN)
     36
     37 * future AI: Need to document how users can visualize their data privately (who?)
     38 * future AI: Make a validation system that lets people submit data in a format already made usable to us (Paul?)
    4639
    4740 == Feedback pombe 2013 ==
     
    201194
    202195== Postponed Action Items ==
    203 * Demo of curation tool (postponed)
    204 * Mark to liaise with Giulietta to help with making a Pombe community curation video (postponed until curators have script)
     196 * Demo of curation tool (postponed)
     197 * Mark to liaise with Giulietta to help with making a Pombe community curation video (postponed until curators have script)
    205198 * Make a validation system that lets people submit data in a format already made usable to us (Paul?)
    206199 * Dan and Mark to see what files downloadable from !PomBase have previously been generated by ensembl. These should be easy to create automatic updates for (In progress?)
     
    211204 * Paul to see to that the restriction enzyme mappings get calculated (if REBASE doesn’t work out) and/or get included as a track.
    212205 * Antonia to follow up on co-curation once Sara is back from holiday (Antonia)
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