From gregghelt at gmail.com  Wed Dec  3 16:54:06 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Wed, 3 Dec 2008 13:54:06 -0800
Subject: [DAS] Conference Call tomorrow
Message-ID: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>

Just a reminder to everyone that there's a DAS teleconference tomorrow,
Thursday December 4rth, at 9AM PST (5 PM GMT).

Please post topics you'd like covered for the agenda.

      thanks,
      Gregg

From gregghelt at gmail.com  Thu Dec  4 10:11:28 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Thu, 4 Dec 2008 07:11:28 -0800
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
Message-ID: <50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>

Actually, any objections to rescheduling for next week instead?  I'm sick
and not up for leading a discussion (was hoping it would go away before now
but no such luck).  And I haven't gotten any feedback on topics for an
agenda.

       Gregg

On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:

> Just a reminder to everyone that there's a DAS teleconference tomorrow,
> Thursday December 4rth, at 9AM PST (5 PM GMT).
>
> Please post topics you'd like covered for the agenda.
>
>       thanks,
>       Gregg
>

From aloraine at gmail.com  Thu Dec  4 10:22:28 2008
From: aloraine at gmail.com (Ann Loraine)
Date: Thu, 4 Dec 2008 10:22:28 -0500
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
	<50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
Message-ID: <83722dde0812040722x4daf6532j68593e210a752a1a@mail.gmail.com>

Fine with me. I'm out sick, as well.

On Thu, Dec 4, 2008 at 10:11 AM, Gregg Helt <gregghelt at gmail.com> wrote:
> Actually, any objections to rescheduling for next week instead?  I'm sick
> and not up for leading a discussion (was hoping it would go away before now
> but no such luck).  And I haven't gotten any feedback on topics for an
> agenda.
>
>       Gregg
>
> On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
>
>> Just a reminder to everyone that there's a DAS teleconference tomorrow,
>> Thursday December 4rth, at 9AM PST (5 PM GMT).
>>
>> Please post topics you'd like covered for the agenda.
>>
>>       thanks,
>>       Gregg
>>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>

From lincoln.stein at gmail.com  Thu Dec  4 10:30:46 2008
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Thu, 4 Dec 2008 10:30:46 -0500
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <83722dde0812040722x4daf6532j68593e210a752a1a@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
	<50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
	<83722dde0812040722x4daf6532j68593e210a752a1a@mail.gmail.com>
Message-ID: <6dce9a0b0812040730q5cc732f6j862a904248e7c926@mail.gmail.com>

I'm not sick, but I'm feeling better knowing that I will have an extra hour
to catch up with writing today.

Lincoln

On Thu, Dec 4, 2008 at 10:22 AM, Ann Loraine <aloraine at gmail.com> wrote:

> Fine with me. I'm out sick, as well.
>
> On Thu, Dec 4, 2008 at 10:11 AM, Gregg Helt <gregghelt at gmail.com> wrote:
> > Actually, any objections to rescheduling for next week instead?  I'm sick
> > and not up for leading a discussion (was hoping it would go away before
> now
> > but no such luck).  And I haven't gotten any feedback on topics for an
> > agenda.
> >
> >       Gregg
> >
> > On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
> >
> >> Just a reminder to everyone that there's a DAS teleconference tomorrow,
> >> Thursday December 4rth, at 9AM PST (5 PM GMT).
> >>
> >> Please post topics you'd like covered for the agenda.
> >>
> >>       thanks,
> >>       Gregg
> >>
> > _______________________________________________
> > DAS mailing list
> > DAS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das
> >
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>



-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>

From Steve_Chervitz at affymetrix.com  Thu Dec  4 12:40:13 2008
From: Steve_Chervitz at affymetrix.com (Chervitz, Steve)
Date: Thu, 4 Dec 2008 09:40:13 -0800
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <6dce9a0b0812040730q5cc732f6j862a904248e7c926@mail.gmail.com>
Message-ID: <C55D55FD.33A0D%Steve_Chervitz@affymetrix.com>

Here's a quick update on my action items:

[A-081030] SC: Merge DAS2 subscribers to DAS list. Redirect DAS2 posts to DAS list.
 ---> Done as of 12/3 (except for the redirecting stuff, which may be unnecessary).

      As of last night, everyone on the DAS/2 discussion list that was
      not already subscribed to the DAS list has been subscribed to it.
      There is now no need to cross-post between these lists!

[A-081030] SC: Consider making DAS list auto reject posts from non-subsribers.
 ---> Done as of 12/3.

      Actually, the list was already set to reject posts, meaning they
      were held for moderation. Now posts from non-subscribers
      will be automatically *discarded*. This will reduce the
      moderation load as there was still quite a bit of spam coming
      through leading to a long list of posts requiring moderation.

[A-081030] SC: Add Andy J and Jonathan W as admins to the DAS mailing list.
 ---> Done as of 12/3.

[A-081113] SC: Wikify the das/2.0 writeback HTML document in das/2.1 wiki.
 --->  Done as of 12/3.
       Writeback and Locking pages added to the 2.1 spec on biodas.org.

[A-081113] SC: Add AJ and JW as biodas.org sysops (so they can edit sidebar)
 ---> Not done, but I edited the sidebar to add link for DAS1.6 spec.
      I'm not an admin for this wiki. Will need to request it.

Steve

Lincoln Stein wrote on 4 Dec 2008 at 07:30:46 -0800:

> I'm not sick, but I'm feeling better knowing that I will have an extra hour
> to catch up with writing today.
>
> Lincoln
>
> On Thu, Dec 4, 2008 at 10:22 AM, Ann Loraine <aloraine at gmail.com> wrote:
>
> > Fine with me. I'm out sick, as well.
> >
> > On Thu, Dec 4, 2008 at 10:11 AM, Gregg Helt <gregghelt at gmail.com> wrote:
> > > Actually, any objections to rescheduling for next week instead?  I'm sick
> > > and not up for leading a discussion (was hoping it would go away before
> > now
> > > but no such luck).  And I haven't gotten any feedback on topics for an
> > > agenda.
> > >
> > >       Gregg
> > >
> > > On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
> > >
> > >> Just a reminder to everyone that there's a DAS teleconference tomorrow,
> > >> Thursday December 4rth, at 9AM PST (5 PM GMT).
> > >>
> > >> Please post topics you'd like covered for the agenda.
> > >>
> > >>       thanks,
> > >>       Gregg
>


-----------------------------------------


From suzi.lewis at gmail.com  Thu Dec  4 15:41:53 2008
From: suzi.lewis at gmail.com (Suzanna Lewis)
Date: Thu, 4 Dec 2008 21:41:53 +0100
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
	<50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
Message-ID: <ffc2dcdc0812041241l7efd2324jf4e76b0bf22bd40d@mail.gmail.com>

That would be great for me as I'm at at meeting in Edinburgh tomorrow, but
will be back in Berkeley next week (Tuesday) and there is much to discuss.

On Thu, Dec 4, 2008 at 4:11 PM, Gregg Helt <gregghelt at gmail.com> wrote:

> Actually, any objections to rescheduling for next week instead?  I'm sick
> and not up for leading a discussion (was hoping it would go away before now
> but no such luck).  And I haven't gotten any feedback on topics for an
> agenda.
>
>       Gregg
>
> On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
>
> > Just a reminder to everyone that there's a DAS teleconference tomorrow,
> > Thursday December 4rth, at 9AM PST (5 PM GMT).
> >
> > Please post topics you'd like covered for the agenda.
> >
> >       thanks,
> >       Gregg
> >
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>

From gregghelt at gmail.com  Wed Dec 10 15:56:49 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Wed, 10 Dec 2008 12:56:49 -0800
Subject: [DAS] DAS Teleconference Thursday December 11th, 9 AM PST
Message-ID: <50158cb00812101256n7fe814b6y7a936a4ed7ca893b@mail.gmail.com>

Just a reminder to everyone that there's a DAS teleconference tomorrow,
Thursday December 11th, at 9AM PST (5 PM GMT).

US Teleconference #: 866-692-3582
Conference #: 4977624

For UK callins, one of these, not sure which is most appropriate for
Hinxton:
   BIRMINGHAM:  0808-238-6019
   GLASGOW: 0808-238-6019
   LEEDS: 0808-238-6019
   LONDON: 0808-238-6019
   MANCHESTER: 0808-238-6019

Items I'd like to cover:
     Status of action items from previous teleconferences
     Writeback
     Overview of the UCSC-based DAS2 server I've been working on

If you would like to add to the agenda, please do.

      Gregg

From gregghelt at gmail.com  Thu Dec 11 10:47:03 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Thu, 11 Dec 2008 07:47:03 -0800
Subject: [DAS] Poka: alpha test of UCSC-based DAS2 server
Message-ID: <50158cb00812110747x65c658b4qeeb0e5da58ebf15d@mail.gmail.com>

I just deployed an alpha test of Poka, my UCSC-based DAS2 server onto the
Amazon Web Services EC2 cloud.  You can try it out at:
     http://www.genomancer.org:9095/das2/ucsc/genome/sources

Some sample queries in addition to the sources query above:

Segments (latest human genome):
http://www.genomancer.org:9095/das2/ucsc/genome/hg18/segments

Types (latest human genome):
http://www.genomancer.org:9095/das2/ucsc/genome/hg18/types

Features (latest human genome, genscan predictions around GABPA & ATP5J
region):
http://www.genomancer.org:9095/das2/ucsc/genome/hg18/features?segment=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fchr21;overlaps=26022853%3A26067933;type=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fgenscan

Features (latest human genome, mRNA alignments around GABPA & ATP5J region):

http://www.genomancer.org:9095/das2/ucsc/genome/hg18/features?segment=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fchr21;overlaps=26022853%3A26067933;type=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fmrna

If you want to try this out with a DAS2 client, you can use IGB and add the
following line to your igb_prefs.xml file:
<das2_server name="genomancer UCSC poka" url="
http://www.genomancer.org:9095/das2/ucsc/genome/sources" />
IGB has a bug that leads to duplicating each pairwise alignment annotation
(like the mRNA alignment example above).  This has been fixed in the source
code repository, but until there's a new IGB release it will show up if
you're using the standard IGB WebStart distribution.

This alpha test supports annotation types that are represented in the UCSC
genome database as BED, GENEPRED, or PSL style tables.  This covers roughly
half of all the annotation tracks available in the UCSC genome database.
I'm working on support for the other half...

Also, this version doesn't use alternative content formats or a number of
other optimizations, so response time is a bit slow.

And for this test phase, since it's using UCSC's shared public MySQL server,
I've restricted the server to only return features if there are < 1000
"top-level" features (for the mRNA example above, this averages out to
~10,000 total features including exons).  Otherwise it returns a
REQUEST_ENTITY_TOO_LARGE error as per the DAS2 spec.  Keep this in mind if
you're trying Poka out in IGB -- other than a diagnostic message in the
output console, IGB will silently ignore the error but no annotations will
show up.

Poka is implemented as a plugin to the Trellis DAS2 server framework.  Hence
the name Poka -- my favorite trellis climber is the passion flower vine, and
banana poka is a species of passion flower that has a tenuous UCSC
connection via sharing part of its name with the official UCSC mascot (the
banana slug).

If you get a chance to try it out, please let me know what you think.

       Gregg

From gregghelt at gmail.com  Wed Dec  3 21:54:06 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Wed, 3 Dec 2008 13:54:06 -0800
Subject: [DAS] Conference Call tomorrow
Message-ID: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>

Just a reminder to everyone that there's a DAS teleconference tomorrow,
Thursday December 4rth, at 9AM PST (5 PM GMT).

Please post topics you'd like covered for the agenda.

      thanks,
      Gregg


From gregghelt at gmail.com  Thu Dec  4 15:11:28 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Thu, 4 Dec 2008 07:11:28 -0800
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
Message-ID: <50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>

Actually, any objections to rescheduling for next week instead?  I'm sick
and not up for leading a discussion (was hoping it would go away before now
but no such luck).  And I haven't gotten any feedback on topics for an
agenda.

       Gregg

On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:

> Just a reminder to everyone that there's a DAS teleconference tomorrow,
> Thursday December 4rth, at 9AM PST (5 PM GMT).
>
> Please post topics you'd like covered for the agenda.
>
>       thanks,
>       Gregg
>


From aloraine at gmail.com  Thu Dec  4 15:22:28 2008
From: aloraine at gmail.com (Ann Loraine)
Date: Thu, 4 Dec 2008 10:22:28 -0500
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
	<50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
Message-ID: <83722dde0812040722x4daf6532j68593e210a752a1a@mail.gmail.com>

Fine with me. I'm out sick, as well.

On Thu, Dec 4, 2008 at 10:11 AM, Gregg Helt <gregghelt at gmail.com> wrote:
> Actually, any objections to rescheduling for next week instead?  I'm sick
> and not up for leading a discussion (was hoping it would go away before now
> but no such luck).  And I haven't gotten any feedback on topics for an
> agenda.
>
>       Gregg
>
> On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
>
>> Just a reminder to everyone that there's a DAS teleconference tomorrow,
>> Thursday December 4rth, at 9AM PST (5 PM GMT).
>>
>> Please post topics you'd like covered for the agenda.
>>
>>       thanks,
>>       Gregg
>>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>


From lincoln.stein at gmail.com  Thu Dec  4 15:30:46 2008
From: lincoln.stein at gmail.com (Lincoln Stein)
Date: Thu, 4 Dec 2008 10:30:46 -0500
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <83722dde0812040722x4daf6532j68593e210a752a1a@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
	<50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
	<83722dde0812040722x4daf6532j68593e210a752a1a@mail.gmail.com>
Message-ID: <6dce9a0b0812040730q5cc732f6j862a904248e7c926@mail.gmail.com>

I'm not sick, but I'm feeling better knowing that I will have an extra hour
to catch up with writing today.

Lincoln

On Thu, Dec 4, 2008 at 10:22 AM, Ann Loraine <aloraine at gmail.com> wrote:

> Fine with me. I'm out sick, as well.
>
> On Thu, Dec 4, 2008 at 10:11 AM, Gregg Helt <gregghelt at gmail.com> wrote:
> > Actually, any objections to rescheduling for next week instead?  I'm sick
> > and not up for leading a discussion (was hoping it would go away before
> now
> > but no such luck).  And I haven't gotten any feedback on topics for an
> > agenda.
> >
> >       Gregg
> >
> > On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
> >
> >> Just a reminder to everyone that there's a DAS teleconference tomorrow,
> >> Thursday December 4rth, at 9AM PST (5 PM GMT).
> >>
> >> Please post topics you'd like covered for the agenda.
> >>
> >>       thanks,
> >>       Gregg
> >>
> > _______________________________________________
> > DAS mailing list
> > DAS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das
> >
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>



-- 
Lincoln D. Stein

Ontario Institute for Cancer Research
101 College St., Suite 800
Toronto, ON, Canada M5G0A3
416 673-8514
Assistant: Stacey Quinn <Stacey.Quinn at oicr.on.ca>

Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724 USA
(516) 367-8380
Assistant: Sandra Michelsen <michelse at cshl.edu>


From Steve_Chervitz at affymetrix.com  Thu Dec  4 17:40:13 2008
From: Steve_Chervitz at affymetrix.com (Chervitz, Steve)
Date: Thu, 4 Dec 2008 09:40:13 -0800
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <6dce9a0b0812040730q5cc732f6j862a904248e7c926@mail.gmail.com>
Message-ID: <C55D55FD.33A0D%Steve_Chervitz@affymetrix.com>

Here's a quick update on my action items:

[A-081030] SC: Merge DAS2 subscribers to DAS list. Redirect DAS2 posts to DAS list.
 ---> Done as of 12/3 (except for the redirecting stuff, which may be unnecessary).

      As of last night, everyone on the DAS/2 discussion list that was
      not already subscribed to the DAS list has been subscribed to it.
      There is now no need to cross-post between these lists!

[A-081030] SC: Consider making DAS list auto reject posts from non-subsribers.
 ---> Done as of 12/3.

      Actually, the list was already set to reject posts, meaning they
      were held for moderation. Now posts from non-subscribers
      will be automatically *discarded*. This will reduce the
      moderation load as there was still quite a bit of spam coming
      through leading to a long list of posts requiring moderation.

[A-081030] SC: Add Andy J and Jonathan W as admins to the DAS mailing list.
 ---> Done as of 12/3.

[A-081113] SC: Wikify the das/2.0 writeback HTML document in das/2.1 wiki.
 --->  Done as of 12/3.
       Writeback and Locking pages added to the 2.1 spec on biodas.org.

[A-081113] SC: Add AJ and JW as biodas.org sysops (so they can edit sidebar)
 ---> Not done, but I edited the sidebar to add link for DAS1.6 spec.
      I'm not an admin for this wiki. Will need to request it.

Steve

Lincoln Stein wrote on 4 Dec 2008 at 07:30:46 -0800:

> I'm not sick, but I'm feeling better knowing that I will have an extra hour
> to catch up with writing today.
>
> Lincoln
>
> On Thu, Dec 4, 2008 at 10:22 AM, Ann Loraine <aloraine at gmail.com> wrote:
>
> > Fine with me. I'm out sick, as well.
> >
> > On Thu, Dec 4, 2008 at 10:11 AM, Gregg Helt <gregghelt at gmail.com> wrote:
> > > Actually, any objections to rescheduling for next week instead?  I'm sick
> > > and not up for leading a discussion (was hoping it would go away before
> > now
> > > but no such luck).  And I haven't gotten any feedback on topics for an
> > > agenda.
> > >
> > >       Gregg
> > >
> > > On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
> > >
> > >> Just a reminder to everyone that there's a DAS teleconference tomorrow,
> > >> Thursday December 4rth, at 9AM PST (5 PM GMT).
> > >>
> > >> Please post topics you'd like covered for the agenda.
> > >>
> > >>       thanks,
> > >>       Gregg
>


-----------------------------------------



From suzi.lewis at gmail.com  Thu Dec  4 20:41:53 2008
From: suzi.lewis at gmail.com (Suzanna Lewis)
Date: Thu, 4 Dec 2008 21:41:53 +0100
Subject: [DAS] Conference Call tomorrow
In-Reply-To: <50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
References: <50158cb00812031354l61558548nb5e495a76c7e005b@mail.gmail.com>
	<50158cb00812040711k19ecf059qa5bb0df6abc4270c@mail.gmail.com>
Message-ID: <ffc2dcdc0812041241l7efd2324jf4e76b0bf22bd40d@mail.gmail.com>

That would be great for me as I'm at at meeting in Edinburgh tomorrow, but
will be back in Berkeley next week (Tuesday) and there is much to discuss.

On Thu, Dec 4, 2008 at 4:11 PM, Gregg Helt <gregghelt at gmail.com> wrote:

> Actually, any objections to rescheduling for next week instead?  I'm sick
> and not up for leading a discussion (was hoping it would go away before now
> but no such luck).  And I haven't gotten any feedback on topics for an
> agenda.
>
>       Gregg
>
> On Wed, Dec 3, 2008 at 1:54 PM, Gregg Helt <gregghelt at gmail.com> wrote:
>
> > Just a reminder to everyone that there's a DAS teleconference tomorrow,
> > Thursday December 4rth, at 9AM PST (5 PM GMT).
> >
> > Please post topics you'd like covered for the agenda.
> >
> >       thanks,
> >       Gregg
> >
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>


From gregghelt at gmail.com  Wed Dec 10 20:56:49 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Wed, 10 Dec 2008 12:56:49 -0800
Subject: [DAS] DAS Teleconference Thursday December 11th, 9 AM PST
Message-ID: <50158cb00812101256n7fe814b6y7a936a4ed7ca893b@mail.gmail.com>

Just a reminder to everyone that there's a DAS teleconference tomorrow,
Thursday December 11th, at 9AM PST (5 PM GMT).

US Teleconference #: 866-692-3582
Conference #: 4977624

For UK callins, one of these, not sure which is most appropriate for
Hinxton:
   BIRMINGHAM:  0808-238-6019
   GLASGOW: 0808-238-6019
   LEEDS: 0808-238-6019
   LONDON: 0808-238-6019
   MANCHESTER: 0808-238-6019

Items I'd like to cover:
     Status of action items from previous teleconferences
     Writeback
     Overview of the UCSC-based DAS2 server I've been working on

If you would like to add to the agenda, please do.

      Gregg


From gregghelt at gmail.com  Thu Dec 11 15:47:03 2008
From: gregghelt at gmail.com (Gregg Helt)
Date: Thu, 11 Dec 2008 07:47:03 -0800
Subject: [DAS] Poka: alpha test of UCSC-based DAS2 server
Message-ID: <50158cb00812110747x65c658b4qeeb0e5da58ebf15d@mail.gmail.com>

I just deployed an alpha test of Poka, my UCSC-based DAS2 server onto the
Amazon Web Services EC2 cloud.  You can try it out at:
     http://www.genomancer.org:9095/das2/ucsc/genome/sources

Some sample queries in addition to the sources query above:

Segments (latest human genome):
http://www.genomancer.org:9095/das2/ucsc/genome/hg18/segments

Types (latest human genome):
http://www.genomancer.org:9095/das2/ucsc/genome/hg18/types

Features (latest human genome, genscan predictions around GABPA & ATP5J
region):
http://www.genomancer.org:9095/das2/ucsc/genome/hg18/features?segment=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fchr21;overlaps=26022853%3A26067933;type=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fgenscan

Features (latest human genome, mRNA alignments around GABPA & ATP5J region):

http://www.genomancer.org:9095/das2/ucsc/genome/hg18/features?segment=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fchr21;overlaps=26022853%3A26067933;type=http%3A%2F%2Fwww.genomancer.org%3A9095%2Fdas2%2Fucsc%2Fgenome%2Fhg18%2Fmrna

If you want to try this out with a DAS2 client, you can use IGB and add the
following line to your igb_prefs.xml file:
<das2_server name="genomancer UCSC poka" url="
http://www.genomancer.org:9095/das2/ucsc/genome/sources" />
IGB has a bug that leads to duplicating each pairwise alignment annotation
(like the mRNA alignment example above).  This has been fixed in the source
code repository, but until there's a new IGB release it will show up if
you're using the standard IGB WebStart distribution.

This alpha test supports annotation types that are represented in the UCSC
genome database as BED, GENEPRED, or PSL style tables.  This covers roughly
half of all the annotation tracks available in the UCSC genome database.
I'm working on support for the other half...

Also, this version doesn't use alternative content formats or a number of
other optimizations, so response time is a bit slow.

And for this test phase, since it's using UCSC's shared public MySQL server,
I've restricted the server to only return features if there are < 1000
"top-level" features (for the mRNA example above, this averages out to
~10,000 total features including exons).  Otherwise it returns a
REQUEST_ENTITY_TOO_LARGE error as per the DAS2 spec.  Keep this in mind if
you're trying Poka out in IGB -- other than a diagnostic message in the
output console, IGB will silently ignore the error but no annotations will
show up.

Poka is implemented as a plugin to the Trellis DAS2 server framework.  Hence
the name Poka -- my favorite trellis climber is the passion flower vine, and
banana poka is a species of passion flower that has a tenuous UCSC
connection via sharing part of its name with the official UCSC mascot (the
banana slug).

If you get a chance to try it out, please let me know what you think.

       Gregg