WBConfCall 2011.11.17-Agenda and Minutes

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 Dear All,
Here are minutes from the conference call yesterday.
Thank you to Matt for checking over the notes I made about the
incorporation of (many) other genomes.

Please send corrections to me.


Mary Ann

Minutes from the conference call Nov 17th 2011

* 1) Infrastructure changes.
* WormBook mirror: will move from wormbase.sanger.ac.uk to
* wormbook.ensemblgenomes.org
* => the link on the main WormBook site needs to be changed to the new URL
* WormBase mirror: will go offline next week Friday
* => the link should be removed from the respective WormBase master and
* mirror sites
* I announced that already a few weeks/month back, but as the deadline
* is approaching, I think it is worth bringing that topic up again.

Michael P: These changes happen on 25th Nov.

Discussion about Sanger FTP site.

Kev: We are still using Sanger FTP. Code will not be ported to EBI until 2012.

Todd: There should be a single FTP site - ftp.wormbase.org
This mirrors the Sanger site, but there is a delay in data being availabe
on Sanger FTP and ftp.wormbase

Raymond: Would be good if there were two dynamic links which were updated as
data became available (for current and dev release).
Q. Is there a plan to have this on ftp.wormbase
A. Yes. There will be automatically updated symbolic links pointing to
appropriate releases (Todd)

Q. Is the link to the dev release created when it is staged to
A. Yes (Todd)

There is a delay of 1 month between release being made available at Sanger
and ftp.wormbase.
Todd: It does not take that long but it allows for any problems to be resolved.

Todd: Release is not staged on ftp.wormbase but in(by?) a staging machine:
1) data mirrored from Sanger
2) convolutions
3) push to ftp site and create sym. link.

Raymond: it's useful to have new release (dev) ASAP. Would like to continue to
get latest release by cron. job to Sanger.

Resolution: Todd will push development release to a Caltech server
after it has been synched from Hinxton to OICR

* Models
* 1) From Michael Paulini
* I would like to clean up some tags in the Homology_group and Accession_number
* In Homology_group i would like to change
* DB_info Database ?Database ?Database_field ?Accession_number XREF
* to
* DB_info Database ?Database ?Database_field ?Accession_number
* and in Accession_number remove following then unused tags:
* Web_location
* 3d_data
* Homology_group

This model need further consideration. Other classes should also be reviewed.

* 2) Extending WormBase beyond nematodes.
* Another thing for the agenda would be, if there has been a decision on
* extending outside of nematodes (based on the flatworm thing last
* week).

Useful information:
SchistoDB http://schistodb.net/schistodb20/ (is this the one?) Uses GUS.
Schistosoma japonicum available at GeneDB
http://www.genedb.org/Homepage/Sjaponicum also being loaded into
a GUS database (a collaboration involving J.Kissinger and a group from Shaghai).

Are we able to accommodate flatworms in WormBase?
SchistoDB (Brazil)
- has the infrastructure to handle incoming data.
- The PI (Guilherme Oliveira) is writing a Brazilian application to
establish flatwormDB using existing GUS

- 50 genomes project - including flatworms (10-20%)
- picking high profile genomes across the phylum
- generating preliminary draft genomes for each one. This way, many
groups in the community get a little
information, rather than a few groups getting a lot of information.
- a new MRC funded position is available for informatician working on
gene finding. Assemblies will be done
within Berriman group
- from an overall list of ~100 genomes, the ~50 most tractable will be
- from list of 100 genomes, effort will be put into first 50.
- at the time of writing, 30 are in progress, 3 are assembled.
- Example: Onchocerca volvulus (roundworm causing river blindness) has
1/2 of genome ~250 pieces.
- data will be available by the end of Dec 2011.

The pipeline:
@ get sequences (fasta)
@ submit to INSDC - can we skip this step? (Matt)
@ analysis - homolgies, repeats
@ to Todd
@ make GBrowse and BlastDB

Exploring doing more than GBrowse and Blasts:
Gary W created a 100 genomes acedb. It worked, but was slow.
It certainly simplies certain processes if all genomes are in acedb,
but with clunky
availability, it it necessary?

Todd: We could use ace for data integration and then create a separate
database for driving the website.

It's hard work getting data in and out of acedb. Would be easier with
a relational database e.g. Oracle, though
this is not an option we would seriously consider at the moment.

Take-home message: acedb doesn't scale well for speed, but it can cope.

Q. How deep do we want integration of all these new genomes to be?

- initially, the ability to browse and blast will be fine.
- the species have been chosen because groups are working on them i.e.
there is community interest.
- we therefore do need scope to go deeper in the future and as groups
do further work.
- the initial findings will lead to publications which will the create
the need for further integration,
and this should be addressed in the grant renewal.

Currently Blasts are not available for all species (in WormBase). This
is because they are hard coded.
The new website will look at what's available and then create Blasts
accordingly - Xiaoqi is working on this.

Ascaris - if there are no orthlogs, certainly need Blast.
Trichinella - available on gbrowse, but no Blasts
S.ratti - there is a problem - should be resolved with new site.

Michael P: Heterorhabditis bacteriophora will be WS229.

Trichinella should have been in WS226.
Todd: it's 1/2 way in place.

Michael P:
Orthologies to elegans genes are in GFF file, along with
approved-style gene names.

Tier I and II genes have orthologies to tier III proteins. This info.
is in the acedb database (not flatfiles)
and appears under Other_orthologs in the Gene summary page.

Q. Website displays - what do we need?
- browsable way to hilight clade specfic genes
- host information e.g.  Mark Blaxter has decorative icons in his Nat.
Gen. nematoda phylogeny paper
or e.g. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2432500/figure/pntd-0000258-g001/
- all 50 genomes are parastites, but not all human.
- In orthoMCL you can click and select what you want to see when
defining a group e.g. IN clade I & II BUT NOT
V. (see http://orthomcl.org/cgi-bin/OrthoMclWeb.cgi?rm=groupQueryForm&type=ppform

- Interactive phylogeny browser - would be good.

Raymond: acedb has benefits. Could it be used to store all data other
than sequence data.
Kevin: The website would need a way to link from non-seq to seq data

50 genomes - RNA seq data.
- no
- will sequence RNA if provided but but in most cases is not practical
given the time-frame.
- although there will be a mixture of analysis method, mostly it will
be highly automated gene finding.
- if someone is doing RNAi, will be relatively trivial to do
additional RNA sequencing, resulting in better gene models.

Raymond: Is it possible to include genomic and RNA seq when assembling?
Matt: It could be done, but currently the pipeline does not allow it.
It will be done later though.