Changes between Initial Version and Version 1 of PomBasePlanningMeetingMinutes20120711


Ignore:
Timestamp:
Jul 12, 2012, 5:11:36 PM (9 years ago)
Author:
gomidori
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • PomBasePlanningMeetingMinutes20120711

    v1 v1  
     1= Planning Meeting Tuesday 11 July 2012 - Minutes =
     2----
     3[wiki:PombasePlanningMeetingAgenda20120711 Agenda for this meeting]
     4----
     5Tuesday 11 July, 16:00, UCL
     6
     7Present: Val, Midori, Jürg, Antonia, Mark, Dan, Paul, Sam (part of meeting) [[BR]]
     8Remote: Kim [[BR]]
     9Apologies: Steve [[BR]]
     10Chair: Val [[BR]]
     11Minutes: Midori
     12
     13= Previous Action Items =
     14 * Henning/using OLS
     15  * PK has had a chat; HH receptive but they don't have resources to allocate so !PomBase would have to fund
     16  * will keep on back burner and revisit
     17 * Replication origins/Conrad
     18  * in progress; browser discussion (below) relevant
     19 * Selenium testing; server
     20  * London move & PHP upgrade have sorted speed issue
     21 * Link back to genomic regions; Mark to provide examples
     22  * What is this? BLAST output? linking to specific regions with description difficult ...
     23  * all BLAST issues on Jira, so no need for extensive discussion
     24 * Linking between browser and gene page
     25  * All in Jira, and all done
     26 * Interaction between EBI External Services and and !PomBase
     27  * Plan is still the same: Eugene's team will take over managing git repository; we (i.e. Mark) can submit to repository and restart server in London
     28  * estimated to happen around end of September
     29 * Explain differences in GO totals (later)
     30  * documentation task for curators; in progress
     31
     32 = General =
     33 == Usage stats ==
     34 * http://tinyurl.com/7qs2zap
     35 * Val explains motif search functionality
     36 * Lucene doesn't have adequate regexp support
     37 * Mark/Dan can probably deploy the script from GeneDB or equivalent
     38
     39 == Hosting data on tracks ==
     40 * Data must be on DAS server or incorp by ensembl to be available to public
     41  * i.e. no other way to show privately held data to everyone
     42 * BAM files - if user submits a BAM file to ENA, PomBase can serve the data
     43  * Dan et al will help people with bam sub one-on-one if necessary
     44 * ENA will also archive KCF
     45 * WIG and BIGWIG
     46  * WIG suitable only for small datasets
     47  * ENA has not yet committed to archiving BIGWIG files, but PK imagines it should be fine with them
     48
     49 == Future role of dev site ==
     50 * Mark and curators do all edits and updates on dev, then sync with/copy to www (i.e. no more having to make changes in parallel on both)
     51 * Envision these db/web instances
     52  * Mark's own box, for initial development; not visible anywhere else
     53  * proto-production ("staging" instance), which is then mirrored
     54  * split staging and live later if need arises
     55  * can make demo URLs available on ad hoc basis, e.g. for soliciting community feedback on new data or features
     56
     57 == Curating strain data ==
     58 * plan so far: offer option -- not mandatory -- to provide background strain details, e.g. marker alleles
     59 * brief summary of strain/genotype-allele/gene/etc. relations
     60 * AL: curating strain details can add a lot of time to curation (depending on paper)
     61 * great utility generally acknowledged, but any more comprehensive approach would require us to seek funding for new aspect of project
     62 * curation interface complicated, challenging, and still under discussion
     63  * current thinking is to collect strain details in early step of curation
     64 * Sam's strong opinion: worthwhile only to show complete genotypes; partial genotypes much less useful
     65  * specifically, need marker alleles included
     66 * have not yet determined what we'll do with strain background details once collected
     67 * further discussion of issues
     68 * brief demo of allele curation interface, with discussion
     69 * see whether we can get a dump of data (IDs, genotypes, etc.) from strain collection in Japan
     70 * tangent: it would be useful to display alleles, e.g. on protein feature map; could also provide alignment of different alleles of a gene
     71
     72 == Idle small talk, e.g. the recent misery of the weather ==
     73 * NZ winter is apparently cooler, but otherwise nicer, than UK summer
     74
     75 = Curation update =
     76 * Emailed
     77 * Brief discussion
     78
     79 = Web site status and next priorities =
     80 * Top priority: fix things that stopped working upon copy to www/preview removal
     81  * example: recent problem syncing between London servers
     82 * further discussion of syncing etc., with aim to avoid problem recurrence
     83 * curators will double-check current behaviour
     84
     85 == Update cycle process ==
     86 * pipeline tests have worked properly
     87 * still need to try live - can use Chado version with curation tool annotations
     88 * Mark having issues with API update, so live test will happen after he's back from wedding holiday
     89 * GeneDB decommissioning tasks and quick fixes; other quick fixes
     90  * on Jira
     91 * Handle annotation extensions
     92  * Needs a bit more work
     93 * Host a couple of HTP datasets
     94  * will become high priority once GeneDB decommissioned
     95 * PK keen to get other Schizo genomes & comparative analyses in soon
     96  * Fine with all as long as it doesn't delay GeneDB decommissioning tasks
     97  * bit of discussion of what's in those datasets
     98
     99 == Genome browser usability issues ==
     100 * Browser feedback from the EMBO course and any pending browser overhaul
     101  * See Feedback from Nick Rhind and Paco Antequera
     102   1. Ease of configuration and uploading datasets
     103   2. The display 
     104   3. zooming and browsing are not controllable
     105   4. resolution of tracks/data
     106   5. saving configurations
     107 * PK acknowledges cryptic error message upon upload of "bad" file format; also unintuitive configuration interface
     108 * PK: vertebrate genome users haven't requested extensive changes
     109 * Mark could make interface changes for !PomBase browser
     110 * Val: is this a good use of Mark's effort, when changes would be generally beneficial?
     111 * getting this feedback from pombe community because of extensive heterochromatin work
     112 * Jürg: aware of many communities that just don't use ensembl browser; they use Gbrowse or similar
     113 * Val, Midori - similar impressions from pombe and other communities: ensembl web browser simply not used
     114 * PK: suggests functional genomics viewer for chromatin-related data types; can demo at next meeting
     115  * additional description & discussion
     116 * Jürg: main issue isn't missing functionality; it's that the interface is too complicated
     117  * further discussion, with examples from Val
     118 * PK: EBI wants to "keep number of services manageable"; its role in PomBase is to provide ensembl deployment to meet community need
     119  * but feedback to date is that genome browsing needs are not being met
     120 * Val: ensembl interface requests should go to ensembl core team (even if they get assigned to Mark)
     121  * further discussion of ticket fate & communication
     122  * Jürg: improvements will serve ensembl well
     123
     124 = New action items =
     125 * Action: Curators look into acquiring data from strain collection in Japan
     126 * Action: Curators to monitor web site for problems (ongoing)
     127 * Action: Functional genomics views demo at next meeting (EBI)
     128 * Action: Val to circulate non-redundant list of genome browser requests & feedback from community
     129 * Action: PK et al. to create Jira tracker for Ensembl genome browser issues; PK to triage tickets
     130
     131 = AOB =
     132 * Next meeting
     133  * Will be in August; doodle poll for specific date
     134  * Invite Bert (EBI) for FG db demo
     135  * Meet at EBI if more convenient for Bert/demo; otherwise could do at Cambridge