From jprocter at compbio.dundee.ac.uk  Tue Feb  1 10:51:17 2011
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Tue, 01 Feb 2011 15:51:17 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
Message-ID: <4D482BF5.70107@compbio.dundee.ac.uk>


Hi all (but Gregg in particular!)

I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
in the Genomancer project (http://code.google.com/p/genomancer/) is
stable enough to use. We'd like to set up an in house DAS1->2 proxy and
it looks like there's a moderate amount of commit activity in the
project at the moment, making me a little nervous about attempting to
use the code in a production(ish) setting.

many thanks in advance,
Jim.

-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.


From gregghelt at gmail.com  Fri Feb  4 10:19:08 2011
From: gregghelt at gmail.com (Gregg Helt)
Date: Fri, 4 Feb 2011 07:19:08 -0800
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <4D482BF5.70107@compbio.dundee.ac.uk>
References: <4D482BF5.70107@compbio.dundee.ac.uk>
Message-ID: <AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>

The core genomancer code is pretty stable, most of the recent work is
in plugins (and some work in the core to allow more extensive
plugins).

You should be able to get a working DAS1-->DAS2 proxy running from
the current head of the Trellis SVN repository -- you would just need
to add a web.xml config file with servlet parameters to get it going in a
servlet container like Tomcat, or alternatively run the built-in Jetty server
(ExampleJettyDas2Server) and edit servlet parameters directly in code.

But if the intent is to load DAS 1.x data into IGB, I don't think you
need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
already supports DAS 1.5 access.  In the "Data Access" tab, under
"Choose Data Sources and Data Sets" section click the "Configure"
button.  This brings up a window with a "Data Sources" tab, and in
that tab you can click the "Add" button to bring up a dialog that lets
you select "DAS" for the data source type, and enter the URL for a DAS
server.  This worked fine for loading data from the UCSC DAS 1.5
server -- I haven't tried accessing data from any other DAS servers
recently.

I'm forwarding to the genoviz-devel list for IGB developments and
discussion, to see if anyone currently working on IGB can add any more
info.

On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
>
> Hi all (but Gregg in particular!)
>
> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> in the Genomancer project (http://code.google.com/p/genomancer/) is
> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> it looks like there's a moderate amount of commit activity in the
> project at the moment, making me a little nervous about attempting to
> use the code in a production(ish) setting.
>
> many thanks in advance,
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter ?(JALVIEW/ENFIN) ?Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764 ?http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>


From andy.jenkinson at ebi.ac.uk  Fri Feb  4 11:08:51 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 4 Feb 2011 16:08:51 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
References: <4D482BF5.70107@compbio.dundee.ac.uk>
	<AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
Message-ID: <23C1AA47-31C1-4A57-B0DC-F410B7233501@ebi.ac.uk>

What does das1->das2 mean by the way, Jim? a client component to make das1 sources look like das2, server component to do same, or vice versa?

On 4 Feb 2011, at 15:19, Gregg Helt wrote:

> The core genomancer code is pretty stable, most of the recent work is
> in plugins (and some work in the core to allow more extensive
> plugins).
> 
> You should be able to get a working DAS1-->DAS2 proxy running from
> the current head of the Trellis SVN repository -- you would just need
> to add a web.xml config file with servlet parameters to get it going in a
> servlet container like Tomcat, or alternatively run the built-in Jetty server
> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
> 
> But if the intent is to load DAS 1.x data into IGB, I don't think you
> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> already supports DAS 1.5 access.  In the "Data Access" tab, under
> "Choose Data Sources and Data Sets" section click the "Configure"
> button.  This brings up a window with a "Data Sources" tab, and in
> that tab you can click the "Add" button to bring up a dialog that lets
> you select "DAS" for the data source type, and enter the URL for a DAS
> server.  This worked fine for loading data from the UCSC DAS 1.5
> server -- I haven't tried accessing data from any other DAS servers
> recently.
> 
> I'm forwarding to the genoviz-devel list for IGB developments and
> discussion, to see if anyone currently working on IGB can add any more
> info.
> 
> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> <jprocter at compbio.dundee.ac.uk> wrote:
>> 
>> Hi all (but Gregg in particular!)
>> 
>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>> it looks like there's a moderate amount of commit activity in the
>> project at the moment, making me a little nervous about attempting to
>> use the code in a production(ish) setting.
>> 
>> many thanks in advance,
>> Jim.
>> 
>> --
>> -------------------------------------------------------------------
>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>> 
>> _______________________________________________
>> 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



From jprocter at compbio.dundee.ac.uk  Fri Feb  4 11:13:34 2011
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Fri, 04 Feb 2011 16:13:34 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <23C1AA47-31C1-4A57-B0DC-F410B7233501@ebi.ac.uk>
References: <4D482BF5.70107@compbio.dundee.ac.uk>
	<AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
	<23C1AA47-31C1-4A57-B0DC-F410B7233501@ebi.ac.uk>
Message-ID: <4D4C25AE.8030900@compbio.dundee.ac.uk>

On 04/02/2011 16:08, Andy Jenkinson wrote:
> What does das1->das2 mean by the way, Jim? a client component to
> make das1 sources look like das2, server component to do same, or
> vice versa?
Something to allow a Das1 source to be read by a Das 2 client.
Previous versions of IGB did not support this, which kind of hampers
progress in a predominantly DAS1 environment :)

Jim.

-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.


From David.Nix at hci.utah.edu  Fri Feb  4 14:13:08 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Fri, 4 Feb 2011 12:13:08 -0700
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
Message-ID: <C9719DD4.7CF6%david.nix@hci.utah.edu>

Hello Jim,

If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455

GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.

IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.

-cheers, David

P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.


On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:

The core genomancer code is pretty stable, most of the recent work is
in plugins (and some work in the core to allow more extensive
plugins).

You should be able to get a working DAS1-->DAS2 proxy running from
the current head of the Trellis SVN repository -- you would just need
to add a web.xml config file with servlet parameters to get it going in a
servlet container like Tomcat, or alternatively run the built-in Jetty server
(ExampleJettyDas2Server) and edit servlet parameters directly in code.

But if the intent is to load DAS 1.x data into IGB, I don't think you
need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
already supports DAS 1.5 access.  In the "Data Access" tab, under
"Choose Data Sources and Data Sets" section click the "Configure"
button.  This brings up a window with a "Data Sources" tab, and in
that tab you can click the "Add" button to bring up a dialog that lets
you select "DAS" for the data source type, and enter the URL for a DAS
server.  This worked fine for loading data from the UCSC DAS 1.5
server -- I haven't tried accessing data from any other DAS servers
recently.

I'm forwarding to the genoviz-devel list for IGB developments and
discussion, to see if anyone currently working on IGB can add any more
info.

On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
>
> Hi all (but Gregg in particular!)
>
> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> in the Genomancer project (http://code.google.com/p/genomancer/) is
> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> it looks like there's a moderate amount of commit activity in the
> project at the moment, making me a little nervous about attempting to
> use the code in a production(ish) setting.
>
> many thanks in advance,
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
> _______________________________________________
> 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



From andy.jenkinson at ebi.ac.uk  Fri Feb  4 15:57:23 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 4 Feb 2011 20:57:23 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <C9719DD4.7CF6%david.nix@hci.utah.edu>
References: <C9719DD4.7CF6%david.nix@hci.utah.edu>
Message-ID: <1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>

Hi David,

I guess one of the big reasons to want a proxy is it allows you to use DAS sources you don't control, which is obviously potentially a really big benefit with so many DAS/1 sources around. I don't know if this is what Jim is trying to achieve though. In truth this has always been the difficulty with the das/das2 tech divide really, with such a huge existing implementation base there's a very high "activation energy" in switching!

What was the issue with the ensembl servers?

Jon and I have talked a few times about organising a DAS workshop in North America, we just need someone to host (and to an extent fund) it. Do you have any suggestions? Almost all of the attendees for our workshops are from Europe, in fact lots are from Hinxton. So what sort of demand do you think there would be stateside for such an event? Enough for a standalone workshop, or more conducive to an add-on to or collaboration with another event?

Maybe we can look into webcasting the talks? No idea how to go about this though!

On 4 Feb 2011, at 19:13, David Nix wrote:

> Hello Jim,
> 
> If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455
> 
> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.
> 
> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.
> 
> -cheers, David
> 
> P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.
> 
> 
> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
> 
> The core genomancer code is pretty stable, most of the recent work is
> in plugins (and some work in the core to allow more extensive
> plugins).
> 
> You should be able to get a working DAS1-->DAS2 proxy running from
> the current head of the Trellis SVN repository -- you would just need
> to add a web.xml config file with servlet parameters to get it going in a
> servlet container like Tomcat, or alternatively run the built-in Jetty server
> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
> 
> But if the intent is to load DAS 1.x data into IGB, I don't think you
> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> already supports DAS 1.5 access.  In the "Data Access" tab, under
> "Choose Data Sources and Data Sets" section click the "Configure"
> button.  This brings up a window with a "Data Sources" tab, and in
> that tab you can click the "Add" button to bring up a dialog that lets
> you select "DAS" for the data source type, and enter the URL for a DAS
> server.  This worked fine for loading data from the UCSC DAS 1.5
> server -- I haven't tried accessing data from any other DAS servers
> recently.
> 
> I'm forwarding to the genoviz-devel list for IGB developments and
> discussion, to see if anyone currently working on IGB can add any more
> info.
> 
> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> <jprocter at compbio.dundee.ac.uk> wrote:
>> 
>> Hi all (but Gregg in particular!)
>> 
>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>> it looks like there's a moderate amount of commit activity in the
>> project at the moment, making me a little nervous about attempting to
>> use the code in a production(ish) setting.
>> 
>> many thanks in advance,
>> Jim.
>> 
>> --
>> -------------------------------------------------------------------
>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>> 
>> _______________________________________________
>> 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
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das



From suzi at berkeleybop.org  Fri Feb  4 16:29:29 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Fri, 4 Feb 2011 13:29:29 -0800
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
References: <C9719DD4.7CF6%david.nix@hci.utah.edu>
	<1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
Message-ID: <2C831871-AF64-4587-85B8-5A6BC9EDED30@berkeleybop.org>

Gregg? Maybe you and I should talk about this. And perhaps you could get an idea when you are in Hinxton of what it takes to organize one of these.

Not a promise, but it might be possible for us to host this in Berkeley/Bay Area. We'll explore feasibility a bit more first. Be good to how many people might be interested.

-S

On Feb 4, 2011, at 12:57 PM, Andy Jenkinson wrote:

> Hi David,
> 
> I guess one of the big reasons to want a proxy is it allows you to use DAS sources you don't control, which is obviously potentially a really big benefit with so many DAS/1 sources around. I don't know if this is what Jim is trying to achieve though. In truth this has always been the difficulty with the das/das2 tech divide really, with such a huge existing implementation base there's a very high "activation energy" in switching!
> 
> What was the issue with the ensembl servers?
> 
> Jon and I have talked a few times about organising a DAS workshop in North America, we just need someone to host (and to an extent fund) it. Do you have any suggestions? Almost all of the attendees for our workshops are from Europe, in fact lots are from Hinxton. So what sort of demand do you think there would be stateside for such an event? Enough for a standalone workshop, or more conducive to an add-on to or collaboration with another event?
> 
> Maybe we can look into webcasting the talks? No idea how to go about this though!
> 
> On 4 Feb 2011, at 19:13, David Nix wrote:
> 
>> Hello Jim,
>> 
>> If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455
>> 
>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.
>> 
>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.
>> 
>> -cheers, David
>> 
>> P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.
>> 
>> 
>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>> 
>> The core genomancer code is pretty stable, most of the recent work is
>> in plugins (and some work in the core to allow more extensive
>> plugins).
>> 
>> You should be able to get a working DAS1-->DAS2 proxy running from
>> the current head of the Trellis SVN repository -- you would just need
>> to add a web.xml config file with servlet parameters to get it going in a
>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>> 
>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>> "Choose Data Sources and Data Sets" section click the "Configure"
>> button.  This brings up a window with a "Data Sources" tab, and in
>> that tab you can click the "Add" button to bring up a dialog that lets
>> you select "DAS" for the data source type, and enter the URL for a DAS
>> server.  This worked fine for loading data from the UCSC DAS 1.5
>> server -- I haven't tried accessing data from any other DAS servers
>> recently.
>> 
>> I'm forwarding to the genoviz-devel list for IGB developments and
>> discussion, to see if anyone currently working on IGB can add any more
>> info.
>> 
>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>> <jprocter at compbio.dundee.ac.uk> wrote:
>>> 
>>> Hi all (but Gregg in particular!)
>>> 
>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>> it looks like there's a moderate amount of commit activity in the
>>> project at the moment, making me a little nervous about attempting to
>>> use the code in a production(ish) setting.
>>> 
>>> many thanks in advance,
>>> Jim.
>>> 
>>> --
>>> -------------------------------------------------------------------
>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>> 
>>> _______________________________________________
>>> 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
>> 
>> 
>> _______________________________________________
>> 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



From sac at bioperl.org  Fri Feb  4 17:14:35 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Fri, 4 Feb 2011 14:14:35 -0800
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <2C831871-AF64-4587-85B8-5A6BC9EDED30@berkeleybop.org>
References: <C9719DD4.7CF6%david.nix@hci.utah.edu>
	<1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
	<2C831871-AF64-4587-85B8-5A6BC9EDED30@berkeleybop.org>
Message-ID: <AANLkTikQt2S8xRTq2u=ahtPhV918iWh_8ALGGt7ELtL7@mail.gmail.com>

On Fri, Feb 4, 2011 at 1:29 PM, Suzanna Lewis <suzi at berkeleybop.org> wrote:

> Gregg? Maybe you and I should talk about this. And perhaps you could get an
> idea when you are in Hinxton of what it takes to organize one of these.
>
> Not a promise, but it might be possible for us to host this in Berkeley/Bay
> Area. We'll explore feasibility a bit more first. Be good to how many people
> might be interested.
>

Count me in!

Steve


> -S
>
> On Feb 4, 2011, at 12:57 PM, Andy Jenkinson wrote:
>
> > Hi David,
> >
> > I guess one of the big reasons to want a proxy is it allows you to use
> DAS sources you don't control, which is obviously potentially a really big
> benefit with so many DAS/1 sources around. I don't know if this is what Jim
> is trying to achieve though. In truth this has always been the difficulty
> with the das/das2 tech divide really, with such a huge existing
> implementation base there's a very high "activation energy" in switching!
> >
> > What was the issue with the ensembl servers?
> >
> > Jon and I have talked a few times about organising a DAS workshop in
> North America, we just need someone to host (and to an extent fund) it. Do
> you have any suggestions? Almost all of the attendees for our workshops are
> from Europe, in fact lots are from Hinxton. So what sort of demand do you
> think there would be stateside for such an event? Enough for a standalone
> workshop, or more conducive to an add-on to or collaboration with another
> event?
> >
> > Maybe we can look into webcasting the talks? No idea how to go about this
> though!
> >
> > On 4 Feb 2011, at 19:13, David Nix wrote:
> >
> >> Hello Jim,
> >>
> >> If I make a suggestion.  If you're looking to visualize genomic data in
> IGB, it would be best to use a DAS/2 server such as the Classic (command
> line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2
> is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph,
> wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're
> continuing to develop the GenoPub DAS/2 server with 5 year grant support
> from NHLBI so expect continuing improvements (bulk uploading and file
> conversion, annotation via ontologies, super group visibility settings,
> additional file formats, etc.). See
> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our
> paper http://www.biomedcentral.com/1471-2105/11/455
> >>
> >> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz
> DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server
> to DAS/2 wouldn't require any data reformatting.  Although for large
> datasets, it's best to use one of the compressed binary data formats such as
> bar, bam, or useq.
> >>
> >> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
> works well for accessing their small annotation datasets (gene models:
> refseq, knowngenes), but the graph distribution wasn't functional the last I
> checked.  The problem appeared to be from the server side.
> >>
> >> -cheers, David
> >>
> >> P.S. I wish I could attend the DAS workshop this year and show you what
> we've been up to.  Any chance of getting a Skype conference call with posted
> presentations?  Would be great if someone hosted a DAS Workshop in the US.
> >>
> >>
> >> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
> >>
> >> The core genomancer code is pretty stable, most of the recent work is
> >> in plugins (and some work in the core to allow more extensive
> >> plugins).
> >>
> >> You should be able to get a working DAS1-->DAS2 proxy running from
> >> the current head of the Trellis SVN repository -- you would just need
> >> to add a web.xml config file with servlet parameters to get it going in
> a
> >> servlet container like Tomcat, or alternatively run the built-in Jetty
> server
> >> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
> >>
> >> But if the intent is to load DAS 1.x data into IGB, I don't think you
> >> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> >> already supports DAS 1.5 access.  In the "Data Access" tab, under
> >> "Choose Data Sources and Data Sets" section click the "Configure"
> >> button.  This brings up a window with a "Data Sources" tab, and in
> >> that tab you can click the "Add" button to bring up a dialog that lets
> >> you select "DAS" for the data source type, and enter the URL for a DAS
> >> server.  This worked fine for loading data from the UCSC DAS 1.5
> >> server -- I haven't tried accessing data from any other DAS servers
> >> recently.
> >>
> >> I'm forwarding to the genoviz-devel list for IGB developments and
> >> discussion, to see if anyone currently working on IGB can add any more
> >> info.
> >>
> >> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> >> <jprocter at compbio.dundee.ac.uk> wrote:
> >>>
> >>> Hi all (but Gregg in particular!)
> >>>
> >>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> >>> in the Genomancer project (http://code.google.com/p/genomancer/) is
> >>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> >>> it looks like there's a moderate amount of commit activity in the
> >>> project at the moment, making me a little nervous about attempting to
> >>> use the code in a production(ish) setting.
> >>>
> >>> many thanks in advance,
> >>> Jim.
> >>>
> >>> --
> >>> -------------------------------------------------------------------
> >>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> >>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> >>> The University of Dundee is a Scottish Registered Charity, No.
> SC015096.
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>

From chris at compbio.dundee.ac.uk  Mon Feb  7 05:34:36 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Mon, 07 Feb 2011 10:34:36 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
Message-ID: <4D4FCABC.7080103@compbio.dundee.ac.uk>

Hi,

I have a functioning ProServer install that works fine with Ensembl, but 
I'd like to get it working with IGB as well. However, it fails to load 
as it has a 'Missing MAPMASTER element'. I see I need to specify a URI 
to a known MAPMASTER source, but I've no idea how.

The server is for Arabidopsis data and I've found the Ensembl DAS 
sources for plants, but which can I use as a mapmaster?
http://plants.ensembl.org/das/dsn
Or am I barking up the wrong tree?

Any pointers much appreciated.
Cheers,

Chris



From andy.jenkinson at ebi.ac.uk  Mon Feb  7 06:40:11 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Mon, 7 Feb 2011 11:40:11 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <4D4FCABC.7080103@compbio.dundee.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
Message-ID: <0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>

Hi Chris,

The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100

So, barring any particular nuance of IGB, the correct mapmaster URL would be:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference

(assuming thaliana)

The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.

Cheers,
Andy

On 7 Feb 2011, at 10:34, Chris Cole wrote:

> Hi,
> 
> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
> 
> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
> http://plants.ensembl.org/das/dsn
> Or am I barking up the wrong tree?
> 
> Any pointers much appreciated.
> Cheers,
> 
> Chris
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das



From chris at compbio.dundee.ac.uk  Mon Feb  7 09:48:03 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Mon, 07 Feb 2011 14:48:03 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
Message-ID: <4D500623.4050803@compbio.dundee.ac.uk>

Hi Andy,

Thanks for the help. Looks like I was close...

I now get an error regarding the 'types' command. I haven't implemented 
it so that's not a surprise. However, I'm struggling to find 
documentation on the build_types() function and what data it should 
return. My source data only has one type: 'expression_tag' so how should 
I return that?
Cheers,

Chris

On 07/02/11 11:40, Andy Jenkinson wrote:
> Hi Chris,
>
> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>
> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>
> (assuming thaliana)
>
> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>
> Cheers,
> Andy
>
> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>
>> Hi,
>>
>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>
>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>> http://plants.ensembl.org/das/dsn
>> Or am I barking up the wrong tree?
>>
>> Any pointers much appreciated.
>> Cheers,
>>
>> Chris
>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096

From andy.jenkinson at ebi.ac.uk  Mon Feb  7 09:56:45 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Mon, 7 Feb 2011 14:56:45 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <4D500623.4050803@compbio.dundee.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
Message-ID: <48355836-341A-4DCC-976F-801308CBEF06@ebi.ac.uk>

The SourceAdaptor POD documents the build_types method. Just return an array containing a hash per type. For example:
return ( { 'type' => 'expression_tag', 'category' => 'experimental' } );

A more complete implementation would also include an ontology term and the 'count' for each type (i.e. the number of features of each type). Note that the build_types command takes segment parameters like the build_features method, except the segment is optional for build_types:
/das/yoursource/types
/das/yoursource/types?segment=X:1,100

Just make sure the content matches the types and categories used by the features command.

See the spec for more details:
http://www.biodas.org/documents/spec-1.6.html#types

On 7 Feb 2011, at 14:48, Chris Cole wrote:

> Hi Andy,
> 
> Thanks for the help. Looks like I was close...
> 
> I now get an error regarding the 'types' command. I haven't implemented it so that's not a surprise. However, I'm struggling to find documentation on the build_types() function and what data it should return. My source data only has one type: 'expression_tag' so how should I return that?
> Cheers,
> 
> Chris
> 
> On 07/02/11 11:40, Andy Jenkinson wrote:
>> Hi Chris,
>> 
>> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>> 
>> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>> 
>> (assuming thaliana)
>> 
>> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>> 
>> Cheers,
>> Andy
>> 
>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>> 
>>> Hi,
>>> 
>>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>> 
>>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>>> http://plants.ensembl.org/das/dsn
>>> Or am I barking up the wrong tree?
>>> 
>>> Any pointers much appreciated.
>>> Cheers,
>>> 
>>> Chris
>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
> 
> 
> -- 
> Dr Chris Cole
> Senior Bioinformatics Research Officer
> College of Life Sciences
> University of Dundee
> Dow Street
> Dundee
> DD1 5EH
> Scotland, UK
> 
> url: http://network.nature.com/profile/drchriscole
> e-mail: chris at compbio.dundee.ac.uk
> Tel: +44 (0)1382 388 721
> 
> The University of Dundee is a registered Scottish charity, No: SC015096



From jw12 at sanger.ac.uk  Mon Feb  7 09:59:07 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 7 Feb 2011 14:59:07 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <4D500623.4050803@compbio.dundee.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
Message-ID: <895C8BD6-42CC-4E26-93A3-E5BFC2478B20@sanger.ac.uk>

I've put a Andys previous answer to this question (when I asked it)   
here: http://biodasman.wordpress.com/2010/12/06/implementing-types-in-proserver/


On 7 Feb 2011, at 14:48, Chris Cole wrote:

> Hi Andy,
>
> Thanks for the help. Looks like I was close...
>
> I now get an error regarding the 'types' command. I haven't  
> implemented it so that's not a surprise. However, I'm struggling to  
> find documentation on the build_types() function and what data it  
> should return. My source data only has one type: 'expression_tag' so  
> how should I return that?
> Cheers,
>
> Chris
>
> On 07/02/11 11:40, Andy Jenkinson wrote:
>> Hi Chris,
>>
>> The 'reference' Ensembl sources are suitable for use as mapmasters,  
>> as they provide sequence information:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>>
>> So, barring any particular nuance of IGB, the correct mapmaster URL  
>> would be:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>>
>> (assuming thaliana)
>>
>> The reason for all this is I guess that IGB does not support the  
>> DAS 1.53E/1.6 sources command, which provides species and  
>> coordinate information directly.
>>
>> Cheers,
>> Andy
>>
>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>>
>>> Hi,
>>>
>>> I have a functioning ProServer install that works fine with  
>>> Ensembl, but I'd like to get it working with IGB as well. However,  
>>> it fails to load as it has a 'Missing MAPMASTER element'. I see I  
>>> need to specify a URI to a known MAPMASTER source, but I've no  
>>> idea how.
>>>
>>> The server is for Arabidopsis data and I've found the Ensembl DAS  
>>> sources for plants, but which can I use as a mapmaster?
>>> http://plants.ensembl.org/das/dsn
>>> Or am I barking up the wrong tree?
>>>
>>> Any pointers much appreciated.
>>> Cheers,
>>>
>>> Chris
>>>
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>
>
>
> -- 
> Dr Chris Cole
> Senior Bioinformatics Research Officer
> College of Life Sciences
> University of Dundee
> Dow Street
> Dundee
> DD1 5EH
> Scotland, UK
>
> url: http://network.nature.com/profile/drchriscole
> e-mail: chris at compbio.dundee.ac.uk
> Tel: +44 (0)1382 388 721
>
> The University of Dundee is a registered Scottish charity, No:  
> SC015096
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From David.Nix at hci.utah.edu  Mon Feb  7 10:58:49 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Mon, 7 Feb 2011 08:58:49 -0700
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
Message-ID: <C97564C9.7D28%david.nix@hci.utah.edu>

Ah, that makes sense.

As for a US meeting, there are 3 or 4 folks here at the U of Utah that would attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).  It might be best to make this part of a larger genomics/ proteomics meeting to start.  This would draw more folks who are interested in distributing their own data and working DAS access into their own applications.  Are their any appropriate upcoming meetings?

-cheers, D


On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:

Hi David,

I guess one of the big reasons to want a proxy is it allows you to use DAS sources you don't control, which is obviously potentially a really big benefit with so many DAS/1 sources around. I don't know if this is what Jim is trying to achieve though. In truth this has always been the difficulty with the das/das2 tech divide really, with such a huge existing implementation base there's a very high "activation energy" in switching!

What was the issue with the ensembl servers?

Jon and I have talked a few times about organising a DAS workshop in North America, we just need someone to host (and to an extent fund) it. Do you have any suggestions? Almost all of the attendees for our workshops are from Europe, in fact lots are from Hinxton. So what sort of demand do you think there would be stateside for such an event? Enough for a standalone workshop, or more conducive to an add-on to or collaboration with another event?

Maybe we can look into webcasting the talks? No idea how to go about this though!

On 4 Feb 2011, at 19:13, David Nix wrote:

> Hello Jim,
>
> If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455
>
> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.
>
> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.
>
> -cheers, David
>
> P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.
>
>
> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>
> The core genomancer code is pretty stable, most of the recent work is
> in plugins (and some work in the core to allow more extensive
> plugins).
>
> You should be able to get a working DAS1-->DAS2 proxy running from
> the current head of the Trellis SVN repository -- you would just need
> to add a web.xml config file with servlet parameters to get it going in a
> servlet container like Tomcat, or alternatively run the built-in Jetty server
> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>
> But if the intent is to load DAS 1.x data into IGB, I don't think you
> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> already supports DAS 1.5 access.  In the "Data Access" tab, under
> "Choose Data Sources and Data Sets" section click the "Configure"
> button.  This brings up a window with a "Data Sources" tab, and in
> that tab you can click the "Add" button to bring up a dialog that lets
> you select "DAS" for the data source type, and enter the URL for a DAS
> server.  This worked fine for loading data from the UCSC DAS 1.5
> server -- I haven't tried accessing data from any other DAS servers
> recently.
>
> I'm forwarding to the genoviz-devel list for IGB developments and
> discussion, to see if anyone currently working on IGB can add any more
> info.
>
> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> <jprocter at compbio.dundee.ac.uk> wrote:
>>
>> Hi all (but Gregg in particular!)
>>
>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>> it looks like there's a moderate amount of commit activity in the
>> project at the moment, making me a little nervous about attempting to
>> use the code in a production(ish) setting.
>>
>> many thanks in advance,
>> Jim.
>>
>> --
>> -------------------------------------------------------------------
>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das




From David.Nix at hci.utah.edu  Mon Feb  7 11:58:17 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Mon, 7 Feb 2011 09:58:17 -0700
Subject: [DAS] US DAS workshop
In-Reply-To: <C9758737.6C26%aloraine@uncc.edu>
Message-ID: <C97572B9.7D42%david.nix@hci.utah.edu>

Hmm...

There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and the organizers might already have a set program.  There is a "Databases, Data Mining, Visualization and Curation" session by Alex Bateman and Ting Wang though.

-cheers, D




On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:

Hi,

Same for us here at UNC Charlotte.

Meetings I'm attending next include two major plant science meetings
(Arabidopsis and ASPB) and possibly ISMB in Vienna.

David are there any other meetings you and your group are planning to
attend?

The ideal setting would be a meeting where we can do outreach and hold
workshop event(s) for users, but also have a developers meeting where we
discuss future directions for the software, DAS spec, etc.

Are there other meetings that would be a good fit?

Best,

Ann

On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:

> Ah, that makes sense.
>
> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
> It might be best to make this part of a larger genomics/ proteomics meeting to
> start.  This would draw more folks who are interested in distributing their
> own data and working DAS access into their own applications.  Are their any
> appropriate upcoming meetings?
>
> -cheers, D
>
>
> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>
> Hi David,
>
> I guess one of the big reasons to want a proxy is it allows you to use DAS
> sources you don't control, which is obviously potentially a really big benefit
> with so many DAS/1 sources around. I don't know if this is what Jim is trying
> to achieve though. In truth this has always been the difficulty with the
> das/das2 tech divide really, with such a huge existing implementation base
> there's a very high "activation energy" in switching!
>
> What was the issue with the ensembl servers?
>
> Jon and I have talked a few times about organising a DAS workshop in North
> America, we just need someone to host (and to an extent fund) it. Do you have
> any suggestions? Almost all of the attendees for our workshops are from
> Europe, in fact lots are from Hinxton. So what sort of demand do you think
> there would be stateside for such an event? Enough for a standalone workshop,
> or more conducive to an add-on to or collaboration with another event?
>
> Maybe we can look into webcasting the talks? No idea how to go about this
> though!
>
> On 4 Feb 2011, at 19:13, David Nix wrote:
>
>> Hello Jim,
>>
>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>> it would be best to use a DAS/2 server such as the Classic (command line) or
>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>> expect continuing improvements (bulk uploading and file conversion,
>> annotation via ontologies, super group visibility settings, additional file
>> formats, etc.). See
>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>> http://www.biomedcentral.com/1471-2105/11/455
>>
>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>> server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2
>> wouldn't require any data reformatting.  Although for large datasets, it's
>> best to use one of the compressed binary data formats such as bar, bam, or
>> useq.
>>
>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works
>> well for accessing their small annotation datasets (gene models: refseq,
>> knowngenes), but the graph distribution wasn't functional the last I checked.
>> The problem appeared to be from the server side.
>>
>> -cheers, David
>>
>> P.S. I wish I could attend the DAS workshop this year and show you what we've
>> been up to.  Any chance of getting a Skype conference call with posted
>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>
>>
>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>
>> The core genomancer code is pretty stable, most of the recent work is
>> in plugins (and some work in the core to allow more extensive
>> plugins).
>>
>> You should be able to get a working DAS1-->DAS2 proxy running from
>> the current head of the Trellis SVN repository -- you would just need
>> to add a web.xml config file with servlet parameters to get it going in a
>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>
>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>> "Choose Data Sources and Data Sets" section click the "Configure"
>> button.  This brings up a window with a "Data Sources" tab, and in
>> that tab you can click the "Add" button to bring up a dialog that lets
>> you select "DAS" for the data source type, and enter the URL for a DAS
>> server.  This worked fine for loading data from the UCSC DAS 1.5
>> server -- I haven't tried accessing data from any other DAS servers
>> recently.
>>
>> I'm forwarding to the genoviz-devel list for IGB developments and
>> discussion, to see if anyone currently working on IGB can add any more
>> info.
>>
>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>
>>> Hi all (but Gregg in particular!)
>>>
>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>> it looks like there's a moderate amount of commit activity in the
>>> project at the moment, making me a little nervous about attempting to
>>> use the code in a production(ish) setting.
>>>
>>> many thanks in advance,
>>> Jim.
>>>
>>> --
>>> -------------------------------------------------------------------
>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
>
>
> ------------------------------------------------------------------------------
> The modern datacenter depends on network connectivity to access resources
> and provide services. The best practices for maximizing a physical server's
> connectivity to a physical network are well understood - see how these
> rules translate into the virtual world?
> http://p.sf.net/sfu/oracle-sfdevnlfb
> _______________________________________________
> Genoviz-devel mailing list
> Genoviz-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/genoviz-devel

--
Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
www.transvar.org





From jw12 at sanger.ac.uk  Mon Feb  7 12:42:55 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 7 Feb 2011 17:42:55 +0000
Subject: [DAS] example DAS sources working in GBrowse?
Message-ID: <21F8F18F-CBC1-4D7B-B91A-E89285DC15DB@sanger.ac.uk>

Hi

We have a das source here that we would like to show up in GBrowse but  
the people concerned are not able to view their data.
Has anyone got a working GBrowse config that we could see that  
attaches a DAS source?
The source we would like to attach is here http://das.sanger.ac.uk/das/pjazz_berghei/features?segment=berg01:1000,200000 
  and seems to be working fine.


Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From jw12 at sanger.ac.uk  Mon Feb  7 12:47:17 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 7 Feb 2011 17:47:17 +0000
Subject: [DAS] DAS examples
Message-ID: <780E2881-A99A-4244-9C8E-40719B78B681@sanger.ac.uk>

Hi

I'm putting together some example requests for the registry and normal  
DAS sources. We hope to use this for the DAS workshop this year as a  
quick reference.

If anyone has some example requests they would like added or has any  
suggestions to make this resource better please drop me or the list a  
line?

current draft is here: http://biodasman.wordpress.com/2011/01/19/das-glossary-first-draft/


Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From andy.jenkinson at ebi.ac.uk  Mon Feb  7 12:57:12 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Mon, 7 Feb 2011 17:57:12 +0000
Subject: [DAS] US DAS workshop
In-Reply-To: <C97572B9.7D42%david.nix@hci.utah.edu>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
Message-ID: <DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>

Might we add on to the end/beginning of GI instead of running concurrently (assuming CSHL can oblige)? Perhaps we can consider running a workshop at ISMB next year (California?) should interest be sufficient for an event at GI or the like this year?

I just noticed GI is actually in November though, by the way.

On 7 Feb 2011, at 16:58, David Nix wrote:

> Hmm...
> 
> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and the organizers might already have a set program.  There is a "Databases, Data Mining, Visualization and Curation" session by Alex Bateman and Ting Wang though.
> 
> -cheers, D
> 
> 
> 
> 
> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
> 
> Hi,
> 
> Same for us here at UNC Charlotte.
> 
> Meetings I'm attending next include two major plant science meetings
> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
> 
> David are there any other meetings you and your group are planning to
> attend?
> 
> The ideal setting would be a meeting where we can do outreach and hold
> workshop event(s) for users, but also have a developers meeting where we
> discuss future directions for the software, DAS spec, etc.
> 
> Are there other meetings that would be a good fit?
> 
> Best,
> 
> Ann
> 
> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
> 
>> Ah, that makes sense.
>> 
>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>> It might be best to make this part of a larger genomics/ proteomics meeting to
>> start.  This would draw more folks who are interested in distributing their
>> own data and working DAS access into their own applications.  Are their any
>> appropriate upcoming meetings?
>> 
>> -cheers, D
>> 
>> 
>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>> 
>> Hi David,
>> 
>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>> sources you don't control, which is obviously potentially a really big benefit
>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>> to achieve though. In truth this has always been the difficulty with the
>> das/das2 tech divide really, with such a huge existing implementation base
>> there's a very high "activation energy" in switching!
>> 
>> What was the issue with the ensembl servers?
>> 
>> Jon and I have talked a few times about organising a DAS workshop in North
>> America, we just need someone to host (and to an extent fund) it. Do you have
>> any suggestions? Almost all of the attendees for our workshops are from
>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>> there would be stateside for such an event? Enough for a standalone workshop,
>> or more conducive to an add-on to or collaboration with another event?
>> 
>> Maybe we can look into webcasting the talks? No idea how to go about this
>> though!
>> 
>> On 4 Feb 2011, at 19:13, David Nix wrote:
>> 
>>> Hello Jim,
>>> 
>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>> expect continuing improvements (bulk uploading and file conversion,
>>> annotation via ontologies, super group visibility settings, additional file
>>> formats, etc.). See
>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>> http://www.biomedcentral.com/1471-2105/11/455
>>> 
>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>> server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2
>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>> best to use one of the compressed binary data formats such as bar, bam, or
>>> useq.
>>> 
>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works
>>> well for accessing their small annotation datasets (gene models: refseq,
>>> knowngenes), but the graph distribution wasn't functional the last I checked.
>>> The problem appeared to be from the server side.
>>> 
>>> -cheers, David
>>> 
>>> P.S. I wish I could attend the DAS workshop this year and show you what we've
>>> been up to.  Any chance of getting a Skype conference call with posted
>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>> 
>>> 
>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>> 
>>> The core genomancer code is pretty stable, most of the recent work is
>>> in plugins (and some work in the core to allow more extensive
>>> plugins).
>>> 
>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>> the current head of the Trellis SVN repository -- you would just need
>>> to add a web.xml config file with servlet parameters to get it going in a
>>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>> 
>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>> button.  This brings up a window with a "Data Sources" tab, and in
>>> that tab you can click the "Add" button to bring up a dialog that lets
>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>> server -- I haven't tried accessing data from any other DAS servers
>>> recently.
>>> 
>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>> discussion, to see if anyone currently working on IGB can add any more
>>> info.
>>> 
>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>> 
>>>> Hi all (but Gregg in particular!)
>>>> 
>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>> it looks like there's a moderate amount of commit activity in the
>>>> project at the moment, making me a little nervous about attempting to
>>>> use the code in a production(ish) setting.
>>>> 
>>>> many thanks in advance,
>>>> Jim.
>>>> 
>>>> --
>>>> -------------------------------------------------------------------
>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>> 
>>>> _______________________________________________
>>>> 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
>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> The modern datacenter depends on network connectivity to access resources
>> and provide services. The best practices for maximizing a physical server's
>> connectivity to a physical network are well understood - see how these
>> rules translate into the virtual world?
>> http://p.sf.net/sfu/oracle-sfdevnlfb
>> _______________________________________________
>> Genoviz-devel mailing list
>> Genoviz-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
> 
> --
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 
> 
> 



From suzi at berkeleybop.org  Mon Feb  7 13:00:56 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Mon, 7 Feb 2011 10:00:56 -0800
Subject: [DAS] US DAS workshop
In-Reply-To: <DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
Message-ID: <2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>


On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:

> Might we add on to the end/beginning of GI instead of running concurrently (assuming CSHL can oblige)?

David Stewart is pretty open to this kind of thing given enough forewarning.

> Perhaps we can consider running a workshop at ISMB next year (California?) should interest be sufficient for an event at GI or the like this year?

ISMB is in California next year? Didn't know that. 2012 is far away though.


> 
> I just noticed GI is actually in November though, by the way.

There is also biology of genomes in May.

> 
> On 7 Feb 2011, at 16:58, David Nix wrote:
> 
>> Hmm...
>> 
>> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and the organizers might already have a set program.  There is a "Databases, Data Mining, Visualization and Curation" session by Alex Bateman and Ting Wang though.
>> 
>> -cheers, D
>> 
>> 
>> 
>> 
>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>> 
>> Hi,
>> 
>> Same for us here at UNC Charlotte.
>> 
>> Meetings I'm attending next include two major plant science meetings
>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>> 
>> David are there any other meetings you and your group are planning to
>> attend?
>> 
>> The ideal setting would be a meeting where we can do outreach and hold
>> workshop event(s) for users, but also have a developers meeting where we
>> discuss future directions for the software, DAS spec, etc.
>> 
>> Are there other meetings that would be a good fit?
>> 
>> Best,
>> 
>> Ann
>> 
>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>> 
>>> Ah, that makes sense.
>>> 
>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>>> It might be best to make this part of a larger genomics/ proteomics meeting to
>>> start.  This would draw more folks who are interested in distributing their
>>> own data and working DAS access into their own applications.  Are their any
>>> appropriate upcoming meetings?
>>> 
>>> -cheers, D
>>> 
>>> 
>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>> 
>>> Hi David,
>>> 
>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>> sources you don't control, which is obviously potentially a really big benefit
>>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>>> to achieve though. In truth this has always been the difficulty with the
>>> das/das2 tech divide really, with such a huge existing implementation base
>>> there's a very high "activation energy" in switching!
>>> 
>>> What was the issue with the ensembl servers?
>>> 
>>> Jon and I have talked a few times about organising a DAS workshop in North
>>> America, we just need someone to host (and to an extent fund) it. Do you have
>>> any suggestions? Almost all of the attendees for our workshops are from
>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>> there would be stateside for such an event? Enough for a standalone workshop,
>>> or more conducive to an add-on to or collaboration with another event?
>>> 
>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>> though!
>>> 
>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>> 
>>>> Hello Jim,
>>>> 
>>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>> expect continuing improvements (bulk uploading and file conversion,
>>>> annotation via ontologies, super group visibility settings, additional file
>>>> formats, etc.). See
>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>> 
>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2
>>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>>> best to use one of the compressed binary data formats such as bar, bam, or
>>>> useq.
>>>> 
>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works
>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>> knowngenes), but the graph distribution wasn't functional the last I checked.
>>>> The problem appeared to be from the server side.
>>>> 
>>>> -cheers, David
>>>> 
>>>> P.S. I wish I could attend the DAS workshop this year and show you what we've
>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>> 
>>>> 
>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>> 
>>>> The core genomancer code is pretty stable, most of the recent work is
>>>> in plugins (and some work in the core to allow more extensive
>>>> plugins).
>>>> 
>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>> the current head of the Trellis SVN repository -- you would just need
>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>> 
>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>> server -- I haven't tried accessing data from any other DAS servers
>>>> recently.
>>>> 
>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>> discussion, to see if anyone currently working on IGB can add any more
>>>> info.
>>>> 
>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>> 
>>>>> Hi all (but Gregg in particular!)
>>>>> 
>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>> it looks like there's a moderate amount of commit activity in the
>>>>> project at the moment, making me a little nervous about attempting to
>>>>> use the code in a production(ish) setting.
>>>>> 
>>>>> many thanks in advance,
>>>>> Jim.
>>>>> 
>>>>> --
>>>>> -------------------------------------------------------------------
>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> The modern datacenter depends on network connectivity to access resources
>>> and provide services. The best practices for maximizing a physical server's
>>> connectivity to a physical network are well understood - see how these
>>> rules translate into the virtual world?
>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>> _______________________________________________
>>> Genoviz-devel mailing list
>>> Genoviz-devel at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>> 
>> --
>> Ann Loraine
>> Associate Professor
>> Dept. of Bioinformatics and Genomics, UNCC
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> www.transvar.org
>> 
>> 
>> 
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das



From David.Nix at hci.utah.edu  Tue Feb  8 14:44:03 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Tue, 8 Feb 2011 12:44:03 -0700
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <C9759DCA.6C43%aloraine@uncc.edu>
Message-ID: <C976EB13.7DAA%david.nix@hci.utah.edu>

There are several of us here who are planning on attending with probably 2 talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 vs DAS/2, future directions, etc.) even if the DAS workshop doesn't materialize.

Would someone who knows Tim or Alex be willing to approach them and inquire about the feasibility of a DAS workshop?

Suzi any more thoughts on a Bay Area session?

-cheers, D


On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:

Hi,

Ting Wang is senior author on a Nature Methods review article (March 2010)
discussing visualization software for genomics.

The dates:

GENOME INFORMATICS
November 2 - 5, 2011
Abstract Deadline: August 12, 2011

I have a break from teaching in the fall so I will definitely try to attend.

The session on alternative splicing also looks very interesting.

Who in the developer's list is interested in attending, contributing to an
abstract, giving a talk?

Best wishes,

Ann







On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:

> Hmm...
>
> There's the Genome Informatics meeting in August at CSHL (
> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
> the organizers might already have a set program.  There is a "Databases, Data
> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
> though.
>
> -cheers, D
>
>
>
>
> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>
> Hi,
>
> Same for us here at UNC Charlotte.
>
> Meetings I'm attending next include two major plant science meetings
> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>
> David are there any other meetings you and your group are planning to
> attend?
>
> The ideal setting would be a meeting where we can do outreach and hold
> workshop event(s) for users, but also have a developers meeting where we
> discuss future directions for the software, DAS spec, etc.
>
> Are there other meetings that would be a good fit?
>
> Best,
>
> Ann
>
> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>
>> Ah, that makes sense.
>>
>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>> It might be best to make this part of a larger genomics/ proteomics meeting
>> to
>> start.  This would draw more folks who are interested in distributing their
>> own data and working DAS access into their own applications.  Are their any
>> appropriate upcoming meetings?
>>
>> -cheers, D
>>
>>
>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>
>> Hi David,
>>
>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>> sources you don't control, which is obviously potentially a really big
>> benefit
>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>> to achieve though. In truth this has always been the difficulty with the
>> das/das2 tech divide really, with such a huge existing implementation base
>> there's a very high "activation energy" in switching!
>>
>> What was the issue with the ensembl servers?
>>
>> Jon and I have talked a few times about organising a DAS workshop in North
>> America, we just need someone to host (and to an extent fund) it. Do you have
>> any suggestions? Almost all of the attendees for our workshops are from
>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>> there would be stateside for such an event? Enough for a standalone workshop,
>> or more conducive to an add-on to or collaboration with another event?
>>
>> Maybe we can look into webcasting the talks? No idea how to go about this
>> though!
>>
>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>
>>> Hello Jim,
>>>
>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>> expect continuing improvements (bulk uploading and file conversion,
>>> annotation via ontologies, super group visibility settings, additional file
>>> formats, etc.). See
>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>> http://www.biomedcentral.com/1471-2105/11/455
>>>
>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>> DAS/2
>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>> best to use one of the compressed binary data formats such as bar, bam, or
>>> useq.
>>>
>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>> works
>>> well for accessing their small annotation datasets (gene models: refseq,
>>> knowngenes), but the graph distribution wasn't functional the last I
>>> checked.
>>> The problem appeared to be from the server side.
>>>
>>> -cheers, David
>>>
>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>> we've
>>> been up to.  Any chance of getting a Skype conference call with posted
>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>
>>>
>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>
>>> The core genomancer code is pretty stable, most of the recent work is
>>> in plugins (and some work in the core to allow more extensive
>>> plugins).
>>>
>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>> the current head of the Trellis SVN repository -- you would just need
>>> to add a web.xml config file with servlet parameters to get it going in a
>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>> server
>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>
>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>> button.  This brings up a window with a "Data Sources" tab, and in
>>> that tab you can click the "Add" button to bring up a dialog that lets
>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>> server -- I haven't tried accessing data from any other DAS servers
>>> recently.
>>>
>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>> discussion, to see if anyone currently working on IGB can add any more
>>> info.
>>>
>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>
>>>> Hi all (but Gregg in particular!)
>>>>
>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>> it looks like there's a moderate amount of commit activity in the
>>>> project at the moment, making me a little nervous about attempting to
>>>> use the code in a production(ish) setting.
>>>>
>>>> many thanks in advance,
>>>> Jim.
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>
>>
>>
>>
----------------------------------------------------------------------------->>
-
>> The modern datacenter depends on network connectivity to access resources
>> and provide services. The best practices for maximizing a physical server's
>> connectivity to a physical network are well understood - see how these
>> rules translate into the virtual world?
>> http://p.sf.net/sfu/oracle-sfdevnlfb
>> _______________________________________________
>> Genoviz-devel mailing list
>> Genoviz-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>
> --
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
>
>
>

--
Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
www.transvar.org



------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world?
http://p.sf.net/sfu/oracle-sfdevnlfb
_______________________________________________
Genoviz-devel mailing list
Genoviz-devel at lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/genoviz-devel



From suzi at berkeleybop.org  Tue Feb  8 16:49:20 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Tue, 8 Feb 2011 16:49:20 -0500
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <C976EB13.7DAA%david.nix@hci.utah.edu>
References: <C976EB13.7DAA%david.nix@hci.utah.edu>
Message-ID: <5E1C5932-D100-45FC-AC99-A68EFE2CA89E@berkeleybop.org>


On Feb 8, 2011, at 2:44 PM, David Nix wrote:

> There are several of us here who are planning on attending with probably 2 talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 vs DAS/2, future directions, etc.) even if the DAS workshop doesn't materialize.
> 
> Would someone who knows Tim or Alex be willing to approach them and inquire about the feasibility of a DAS workshop?
who? I probably should know who you're talking about, but they aren't part of the GI meeting or part of CSHL so ...

> 
> Suzi any more thoughts on a Bay Area session?

Given enough lead time there is a good room I can reserve for holding the meeting. So I suppose all that needs to be done at this point is for me to check availability of this room and given that, set up a doodle poll.

I'm assuming no more than 40 people. 

> 
> -cheers, D
> 
> 
> On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
> 
> Hi,
> 
> Ting Wang is senior author on a Nature Methods review article (March 2010)
> discussing visualization software for genomics.
> 
> The dates:
> 
> GENOME INFORMATICS
> November 2 - 5, 2011
> Abstract Deadline: August 12, 2011
> 
> I have a break from teaching in the fall so I will definitely try to attend.
> 
> The session on alternative splicing also looks very interesting.
> 
> Who in the developer's list is interested in attending, contributing to an
> abstract, giving a talk?
> 
> Best wishes,
> 
> Ann
> 
> 
> 
> 
> 
> 
> 
> On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
> 
>> Hmm...
>> 
>> There's the Genome Informatics meeting in August at CSHL (
>> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
>> the organizers might already have a set program.  There is a "Databases, Data
>> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
>> though.
>> 
>> -cheers, D
>> 
>> 
>> 
>> 
>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>> 
>> Hi,
>> 
>> Same for us here at UNC Charlotte.
>> 
>> Meetings I'm attending next include two major plant science meetings
>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>> 
>> David are there any other meetings you and your group are planning to
>> attend?
>> 
>> The ideal setting would be a meeting where we can do outreach and hold
>> workshop event(s) for users, but also have a developers meeting where we
>> discuss future directions for the software, DAS spec, etc.
>> 
>> Are there other meetings that would be a good fit?
>> 
>> Best,
>> 
>> Ann
>> 
>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>> 
>>> Ah, that makes sense.
>>> 
>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>>> It might be best to make this part of a larger genomics/ proteomics meeting
>>> to
>>> start.  This would draw more folks who are interested in distributing their
>>> own data and working DAS access into their own applications.  Are their any
>>> appropriate upcoming meetings?
>>> 
>>> -cheers, D
>>> 
>>> 
>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>> 
>>> Hi David,
>>> 
>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>> sources you don't control, which is obviously potentially a really big
>>> benefit
>>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>>> to achieve though. In truth this has always been the difficulty with the
>>> das/das2 tech divide really, with such a huge existing implementation base
>>> there's a very high "activation energy" in switching!
>>> 
>>> What was the issue with the ensembl servers?
>>> 
>>> Jon and I have talked a few times about organising a DAS workshop in North
>>> America, we just need someone to host (and to an extent fund) it. Do you have
>>> any suggestions? Almost all of the attendees for our workshops are from
>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>> there would be stateside for such an event? Enough for a standalone workshop,
>>> or more conducive to an add-on to or collaboration with another event?
>>> 
>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>> though!
>>> 
>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>> 
>>>> Hello Jim,
>>>> 
>>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>> expect continuing improvements (bulk uploading and file conversion,
>>>> annotation via ontologies, super group visibility settings, additional file
>>>> formats, etc.). See
>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>> 
>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>>> DAS/2
>>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>>> best to use one of the compressed binary data formats such as bar, bam, or
>>>> useq.
>>>> 
>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>>> works
>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>> knowngenes), but the graph distribution wasn't functional the last I
>>>> checked.
>>>> The problem appeared to be from the server side.
>>>> 
>>>> -cheers, David
>>>> 
>>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>>> we've
>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>> 
>>>> 
>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>> 
>>>> The core genomancer code is pretty stable, most of the recent work is
>>>> in plugins (and some work in the core to allow more extensive
>>>> plugins).
>>>> 
>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>> the current head of the Trellis SVN repository -- you would just need
>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>>> server
>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>> 
>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>> server -- I haven't tried accessing data from any other DAS servers
>>>> recently.
>>>> 
>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>> discussion, to see if anyone currently working on IGB can add any more
>>>> info.
>>>> 
>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>> 
>>>>> Hi all (but Gregg in particular!)
>>>>> 
>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>> it looks like there's a moderate amount of commit activity in the
>>>>> project at the moment, making me a little nervous about attempting to
>>>>> use the code in a production(ish) setting.
>>>>> 
>>>>> many thanks in advance,
>>>>> Jim.
>>>>> 
>>>>> --
>>>>> -------------------------------------------------------------------
>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>>> 
>>> 
>>> 
> ----------------------------------------------------------------------------->>
> -
>>> The modern datacenter depends on network connectivity to access resources
>>> and provide services. The best practices for maximizing a physical server's
>>> connectivity to a physical network are well understood - see how these
>>> rules translate into the virtual world?
>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>> _______________________________________________
>>> Genoviz-devel mailing list
>>> Genoviz-devel at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>> 
>> --
>> Ann Loraine
>> Associate Professor
>> Dept. of Bioinformatics and Genomics, UNCC
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> www.transvar.org
>> 
>> 
>> 
> 
> --
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 
> 
> 
> ------------------------------------------------------------------------------
> The modern datacenter depends on network connectivity to access resources
> and provide services. The best practices for maximizing a physical server's
> connectivity to a physical network are well understood - see how these
> rules translate into the virtual world?
> http://p.sf.net/sfu/oracle-sfdevnlfb
> _______________________________________________
> Genoviz-devel mailing list
> Genoviz-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das



From andy.jenkinson at ebi.ac.uk  Wed Feb  9 12:19:12 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Wed, 9 Feb 2011 17:19:12 +0000
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <5E1C5932-D100-45FC-AC99-A68EFE2CA89E@berkeleybop.org>
References: <C976EB13.7DAA%david.nix@hci.utah.edu>
	<5E1C5932-D100-45FC-AC99-A68EFE2CA89E@berkeleybop.org>
Message-ID: <2E193A2E-9045-4122-BA98-39F0D28B7859@ebi.ac.uk>

Hi guys,

Just to mention, Mark Diekhans has kindly offered to help us arrange something at UCSC if we want, so we can consider that a solid offer. I shall defer to the Wisdom Of The List as to preference for location (no doubt Suzi would prefer Berkeley!). I'm not sure if the aim is to attract participation or just get together. Also, what sort of dates are people thinking of?

Cheers,
Andy

On 8 Feb 2011, at 21:49, Suzanna Lewis wrote:

> 
> On Feb 8, 2011, at 2:44 PM, David Nix wrote:
> 
>> There are several of us here who are planning on attending with probably 2 talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 vs DAS/2, future directions, etc.) even if the DAS workshop doesn't materialize.
>> 
>> Would someone who knows Tim or Alex be willing to approach them and inquire about the feasibility of a DAS workshop?
> who? I probably should know who you're talking about, but they aren't part of the GI meeting or part of CSHL so ...
> 
>> 
>> Suzi any more thoughts on a Bay Area session?
> 
> Given enough lead time there is a good room I can reserve for holding the meeting. So I suppose all that needs to be done at this point is for me to check availability of this room and given that, set up a doodle poll.
> 
> I'm assuming no more than 40 people. 
> 
>> 
>> -cheers, D
>> 
>> 
>> On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>> 
>> Hi,
>> 
>> Ting Wang is senior author on a Nature Methods review article (March 2010)
>> discussing visualization software for genomics.
>> 
>> The dates:
>> 
>> GENOME INFORMATICS
>> November 2 - 5, 2011
>> Abstract Deadline: August 12, 2011
>> 
>> I have a break from teaching in the fall so I will definitely try to attend.
>> 
>> The session on alternative splicing also looks very interesting.
>> 
>> Who in the developer's list is interested in attending, contributing to an
>> abstract, giving a talk?
>> 
>> Best wishes,
>> 
>> Ann
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>> 
>>> Hmm...
>>> 
>>> There's the Genome Informatics meeting in August at CSHL (
>>> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
>>> the organizers might already have a set program.  There is a "Databases, Data
>>> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
>>> though.
>>> 
>>> -cheers, D
>>> 
>>> 
>>> 
>>> 
>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>> 
>>> Hi,
>>> 
>>> Same for us here at UNC Charlotte.
>>> 
>>> Meetings I'm attending next include two major plant science meetings
>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>> 
>>> David are there any other meetings you and your group are planning to
>>> attend?
>>> 
>>> The ideal setting would be a meeting where we can do outreach and hold
>>> workshop event(s) for users, but also have a developers meeting where we
>>> discuss future directions for the software, DAS spec, etc.
>>> 
>>> Are there other meetings that would be a good fit?
>>> 
>>> Best,
>>> 
>>> Ann
>>> 
>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>> 
>>>> Ah, that makes sense.
>>>> 
>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>>>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>>>> It might be best to make this part of a larger genomics/ proteomics meeting
>>>> to
>>>> start.  This would draw more folks who are interested in distributing their
>>>> own data and working DAS access into their own applications.  Are their any
>>>> appropriate upcoming meetings?
>>>> 
>>>> -cheers, D
>>>> 
>>>> 
>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>>> 
>>>> Hi David,
>>>> 
>>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>>> sources you don't control, which is obviously potentially a really big
>>>> benefit
>>>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>>>> to achieve though. In truth this has always been the difficulty with the
>>>> das/das2 tech divide really, with such a huge existing implementation base
>>>> there's a very high "activation energy" in switching!
>>>> 
>>>> What was the issue with the ensembl servers?
>>>> 
>>>> Jon and I have talked a few times about organising a DAS workshop in North
>>>> America, we just need someone to host (and to an extent fund) it. Do you have
>>>> any suggestions? Almost all of the attendees for our workshops are from
>>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>>> there would be stateside for such an event? Enough for a standalone workshop,
>>>> or more conducive to an add-on to or collaboration with another event?
>>>> 
>>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>>> though!
>>>> 
>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>> 
>>>>> Hello Jim,
>>>>> 
>>>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>>> expect continuing improvements (bulk uploading and file conversion,
>>>>> annotation via ontologies, super group visibility settings, additional file
>>>>> formats, etc.). See
>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>> 
>>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>>>> DAS/2
>>>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>>>> best to use one of the compressed binary data formats such as bar, bam, or
>>>>> useq.
>>>>> 
>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>>>> works
>>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>>> knowngenes), but the graph distribution wasn't functional the last I
>>>>> checked.
>>>>> The problem appeared to be from the server side.
>>>>> 
>>>>> -cheers, David
>>>>> 
>>>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>>>> we've
>>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>>> 
>>>>> 
>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>> 
>>>>> The core genomancer code is pretty stable, most of the recent work is
>>>>> in plugins (and some work in the core to allow more extensive
>>>>> plugins).
>>>>> 
>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>> the current head of the Trellis SVN repository -- you would just need
>>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>>>> server
>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>>> 
>>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>> server -- I haven't tried accessing data from any other DAS servers
>>>>> recently.
>>>>> 
>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>> discussion, to see if anyone currently working on IGB can add any more
>>>>> info.
>>>>> 
>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>> 
>>>>>> Hi all (but Gregg in particular!)
>>>>>> 
>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>> project at the moment, making me a little nervous about attempting to
>>>>>> use the code in a production(ish) setting.
>>>>>> 
>>>>>> many thanks in advance,
>>>>>> Jim.
>>>>>> 
>>>>>> --
>>>>>> -------------------------------------------------------------------
>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>> 
>>>> 
>>>> 
>>>> 
>> ----------------------------------------------------------------------------->>
>> -
>>>> The modern datacenter depends on network connectivity to access resources
>>>> and provide services. The best practices for maximizing a physical server's
>>>> connectivity to a physical network are well understood - see how these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>> 
>>> --
>>> Ann Loraine
>>> Associate Professor
>>> Dept. of Bioinformatics and Genomics, UNCC
>>> North Carolina Research Campus
>>> 600 Laureate Way
>>> Kannapolis, NC 28081
>>> 704-250-5750
>>> www.transvar.org
>>> 
>>> 
>>> 
>> 
>> --
>> Ann Loraine
>> Associate Professor
>> Dept. of Bioinformatics and Genomics, UNCC
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> www.transvar.org
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> The modern datacenter depends on network connectivity to access resources
>> and provide services. The best practices for maximizing a physical server's
>> connectivity to a physical network are well understood - see how these
>> rules translate into the virtual world?
>> http://p.sf.net/sfu/oracle-sfdevnlfb
>> _______________________________________________
>> Genoviz-devel mailing list
>> Genoviz-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>> 
>> 
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
> 



From chris at compbio.dundee.ac.uk  Thu Feb 10 03:53:03 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Thu, 10 Feb 2011 08:53:03 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <48355836-341A-4DCC-976F-801308CBEF06@ebi.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
	<48355836-341A-4DCC-976F-801308CBEF06@ebi.ac.uk>
Message-ID: <4D53A76F.7040609@compbio.dundee.ac.uk>

Yup that did it. Thanks!

I'm using an older version which doesn't quite as a full a description 
of the build_types() method.

Sorry for not replying earlier - been having webserver and database 
issues that needed fixing first.
Cheers,

Chris

On 07/02/11 14:56, Andy Jenkinson wrote:
> The SourceAdaptor POD documents the build_types method. Just return an array containing a hash per type. For example:
> return ( { 'type' =>  'expression_tag', 'category' =>  'experimental' } );
>
> A more complete implementation would also include an ontology term and the 'count' for each type (i.e. the number of features of each type). Note that the build_types command takes segment parameters like the build_features method, except the segment is optional for build_types:
> /das/yoursource/types
> /das/yoursource/types?segment=X:1,100
>
> Just make sure the content matches the types and categories used by the features command.
>
> See the spec for more details:
> http://www.biodas.org/documents/spec-1.6.html#types
>
> On 7 Feb 2011, at 14:48, Chris Cole wrote:
>
>> Hi Andy,
>>
>> Thanks for the help. Looks like I was close...
>>
>> I now get an error regarding the 'types' command. I haven't implemented it so that's not a surprise. However, I'm struggling to find documentation on the build_types() function and what data it should return. My source data only has one type: 'expression_tag' so how should I return that?
>> Cheers,
>>
>> Chris
>>
>> On 07/02/11 11:40, Andy Jenkinson wrote:
>>> Hi Chris,
>>>
>>> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>>>
>>> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>>>
>>> (assuming thaliana)
>>>
>>> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>>>
>>> Cheers,
>>> Andy
>>>
>>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>>>
>>>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>>>> http://plants.ensembl.org/das/dsn
>>>> Or am I barking up the wrong tree?
>>>>
>>>> Any pointers much appreciated.
>>>> Cheers,
>>>>
>>>> Chris
>>>>
>>>>
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>
>>
>> --
>> Dr Chris Cole
>> Senior Bioinformatics Research Officer
>> College of Life Sciences
>> University of Dundee
>> Dow Street
>> Dundee
>> DD1 5EH
>> Scotland, UK
>>
>> url: http://network.nature.com/profile/drchriscole
>> e-mail: chris at compbio.dundee.ac.uk
>> Tel: +44 (0)1382 388 721
>>
>> The University of Dundee is a registered Scottish charity, No: SC015096
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096

From chris at compbio.dundee.ac.uk  Thu Feb 10 03:53:45 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Thu, 10 Feb 2011 08:53:45 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <895C8BD6-42CC-4E26-93A3-E5BFC2478B20@sanger.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
	<895C8BD6-42CC-4E26-93A3-E5BFC2478B20@sanger.ac.uk>
Message-ID: <4D53A799.1020507@compbio.dundee.ac.uk>

Useful to know. Thanks.

On 07/02/11 14:59, Jonathan Warren wrote:
> I've put a Andys previous answer to this question (when I asked it)
> here:
> http://biodasman.wordpress.com/2010/12/06/implementing-types-in-proserver/
>
>
> On 7 Feb 2011, at 14:48, Chris Cole wrote:
>
>> Hi Andy,
>>
>> Thanks for the help. Looks like I was close...
>>
>> I now get an error regarding the 'types' command. I haven't
>> implemented it so that's not a surprise. However, I'm struggling to
>> find documentation on the build_types() function and what data it
>> should return. My source data only has one type: 'expression_tag' so
>> how should I return that?
>> Cheers,
>>
>> Chris
>>
>> On 07/02/11 11:40, Andy Jenkinson wrote:
>>> Hi Chris,
>>>
>>> The 'reference' Ensembl sources are suitable for use as mapmasters,
>>> as they provide sequence information:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>>>
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>>>
>>>
>>> So, barring any particular nuance of IGB, the correct mapmaster URL
>>> would be:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>>>
>>> (assuming thaliana)
>>>
>>> The reason for all this is I guess that IGB does not support the DAS
>>> 1.53E/1.6 sources command, which provides species and coordinate
>>> information directly.
>>>
>>> Cheers,
>>> Andy
>>>
>>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a functioning ProServer install that works fine with Ensembl,
>>>> but I'd like to get it working with IGB as well. However, it fails
>>>> to load as it has a 'Missing MAPMASTER element'. I see I need to
>>>> specify a URI to a known MAPMASTER source, but I've no idea how.
>>>>
>>>> The server is for Arabidopsis data and I've found the Ensembl DAS
>>>> sources for plants, but which can I use as a mapmaster?
>>>> http://plants.ensembl.org/das/dsn
>>>> Or am I barking up the wrong tree?
>>>>
>>>> Any pointers much appreciated.
>>>> Cheers,
>>>>
>>>> Chris
>>>>
>>>>
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>
>>
>> --
>> Dr Chris Cole
>> Senior Bioinformatics Research Officer
>> College of Life Sciences
>> University of Dundee
>> Dow Street
>> Dundee
>> DD1 5EH
>> Scotland, UK
>>
>> url: http://network.nature.com/profile/drchriscole
>> e-mail: chris at compbio.dundee.ac.uk
>> Tel: +44 (0)1382 388 721
>>
>> The University of Dundee is a registered Scottish charity, No: SC015096
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> blog: http://biodasman.wordpress.com/
> jw12 at sanger.ac.uk
> Ext: 2314
> Telephone: 01223 492314
>
>
>
>
>
>
>
>
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096

From suzi at berkeleybop.org  Sun Feb 13 05:42:33 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Sun, 13 Feb 2011 11:42:33 +0100
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <C97A83FD.6DB2%aloraine@uncc.edu>
References: <C97A83FD.6DB2%aloraine@uncc.edu>
Message-ID: <2A209F00-FC2B-4E31-A0F0-CED1A8243DBA@berkeleybop.org>

UCSC is fine with me, and I don't even need to fly to get there. 

I'm also extremely happy if they and/or Mark Diekhans will take this on. Much easier for me to simply attend - I just wanted to be sure that the meeting happens.

In my head I was thinking of this largely as a developer's meeting/workshop for coordinating efforts.

-S


On Feb 11, 2011, at 3:13 PM, Ann Loraine wrote:

> I think it would be very helpful to have a meeting at UCSC.
> 
> UCSC is such an important data provider that it would be good for all of us
> to have more interactions with the team there.
> 
> Very best wishes,
> 
> Ann
> 
> 
> On 2/9/11 9:19 AM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
> 
>> Hi guys,
>> 
>> Just to mention, Mark Diekhans has kindly offered to help us arrange something
>> at UCSC if we want, so we can consider that a solid offer. I shall defer to
>> the Wisdom Of The List as to preference for location (no doubt Suzi would
>> prefer Berkeley!). I'm not sure if the aim is to attract participation or just
>> get together. Also, what sort of dates are people thinking of?
>> 
>> Cheers,
>> Andy
>> 
>> On 8 Feb 2011, at 21:49, Suzanna Lewis wrote:
>> 
>>> 
>>> On Feb 8, 2011, at 2:44 PM, David Nix wrote:
>>> 
>>>> There are several of us here who are planning on attending with probably 2
>>>> talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk
>>>> on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1
>>>> vs DAS/2, future directions, etc.) even if the DAS workshop doesn't
>>>> materialize.
>>>> 
>>>> Would someone who knows Tim or Alex be willing to approach them and inquire
>>>> about the feasibility of a DAS workshop?
>>> who? I probably should know who you're talking about, but they aren't part of
>>> the GI meeting or part of CSHL so ...
>>> 
>>>> 
>>>> Suzi any more thoughts on a Bay Area session?
>>> 
>>> Given enough lead time there is a good room I can reserve for holding the
>>> meeting. So I suppose all that needs to be done at this point is for me to
>>> check availability of this room and given that, set up a doodle poll.
>>> 
>>> I'm assuming no more than 40 people.
>>> 
>>>> 
>>>> -cheers, D
>>>> 
>>>> 
>>>> On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> Ting Wang is senior author on a Nature Methods review article (March 2010)
>>>> discussing visualization software for genomics.
>>>> 
>>>> The dates:
>>>> 
>>>> GENOME INFORMATICS
>>>> November 2 - 5, 2011
>>>> Abstract Deadline: August 12, 2011
>>>> 
>>>> I have a break from teaching in the fall so I will definitely try to attend.
>>>> 
>>>> The session on alternative splicing also looks very interesting.
>>>> 
>>>> Who in the developer's list is interested in attending, contributing to an
>>>> abstract, giving a talk?
>>>> 
>>>> Best wishes,
>>>> 
>>>> Ann
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>> 
>>>>> Hmm...
>>>>> 
>>>>> There's the Genome Informatics meeting in August at CSHL (
>>>>> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
>>>>> the organizers might already have a set program.  There is a "Databases,
>>>>> Data
>>>>> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
>>>>> though.
>>>>> 
>>>>> -cheers, D
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Same for us here at UNC Charlotte.
>>>>> 
>>>>> Meetings I'm attending next include two major plant science meetings
>>>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>>> 
>>>>> David are there any other meetings you and your group are planning to
>>>>> attend?
>>>>> 
>>>>> The ideal setting would be a meeting where we can do outreach and hold
>>>>> workshop event(s) for users, but also have a developers meeting where we
>>>>> discuss future directions for the software, DAS spec, etc.
>>>>> 
>>>>> Are there other meetings that would be a good fit?
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Ann
>>>>> 
>>>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>>> 
>>>>>> Ah, that makes sense.
>>>>>> 
>>>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that
>>>>>> would
>>>>>> attend an out of state meeting.  The bay area would be ideal (thanks
>>>>>> Suzi!).
>>>>>> It might be best to make this part of a larger genomics/ proteomics
>>>>>> meeting
>>>>>> to
>>>>>> start.  This would draw more folks who are interested in distributing
>>>>>> their
>>>>>> own data and working DAS access into their own applications.  Are their
>>>>>> any
>>>>>> appropriate upcoming meetings?
>>>>>> 
>>>>>> -cheers, D
>>>>>> 
>>>>>> 
>>>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>>>>> 
>>>>>> Hi David,
>>>>>> 
>>>>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>>>>> sources you don't control, which is obviously potentially a really big
>>>>>> benefit
>>>>>> with so many DAS/1 sources around. I don't know if this is what Jim is
>>>>>> trying
>>>>>> to achieve though. In truth this has always been the difficulty with the
>>>>>> das/das2 tech divide really, with such a huge existing implementation base
>>>>>> there's a very high "activation energy" in switching!
>>>>>> 
>>>>>> What was the issue with the ensembl servers?
>>>>>> 
>>>>>> Jon and I have talked a few times about organising a DAS workshop in North
>>>>>> America, we just need someone to host (and to an extent fund) it. Do you
>>>>>> have
>>>>>> any suggestions? Almost all of the attendees for our workshops are from
>>>>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>>>>> there would be stateside for such an event? Enough for a standalone
>>>>>> workshop,
>>>>>> or more conducive to an add-on to or collaboration with another event?
>>>>>> 
>>>>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>>>>> though!
>>>>>> 
>>>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>>> 
>>>>>>> Hello Jim,
>>>>>>> 
>>>>>>> If I make a suggestion.  If you're looking to visualize genomic data in
>>>>>>> IGB,
>>>>>>> it would be best to use a DAS/2 server such as the Classic (command line)
>>>>>>> or
>>>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is
>>>>>>> well
>>>>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig,
>>>>>>> bar,
>>>>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>>>>> expect continuing improvements (bulk uploading and file conversion,
>>>>>>> annotation via ontologies, super group visibility settings, additional
>>>>>>> file
>>>>>>> formats, etc.). See
>>>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our
>>>>>>> paper
>>>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>>> 
>>>>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz
>>>>>>> DAS/2
>>>>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>>>>>> DAS/2
>>>>>>> wouldn't require any data reformatting.  Although for large datasets,
>>>>>>> it's
>>>>>>> best to use one of the compressed binary data formats such as bar, bam,
>>>>>>> or
>>>>>>> useq.
>>>>>>> 
>>>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>>>>>> works
>>>>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>>>>> knowngenes), but the graph distribution wasn't functional the last I
>>>>>>> checked.
>>>>>>> The problem appeared to be from the server side.
>>>>>>> 
>>>>>>> -cheers, David
>>>>>>> 
>>>>>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>>>>>> we've
>>>>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>>>>> presentations?  Would be great if someone hosted a DAS Workshop in the
>>>>>>> US.
>>>>>>> 
>>>>>>> 
>>>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>>> 
>>>>>>> The core genomancer code is pretty stable, most of the recent work is
>>>>>>> in plugins (and some work in the core to allow more extensive
>>>>>>> plugins).
>>>>>>> 
>>>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>>>> the current head of the Trellis SVN repository -- you would just need
>>>>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>>>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>>>>>> server
>>>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>>>>> 
>>>>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>>>> server -- I haven't tried accessing data from any other DAS servers
>>>>>>> recently.
>>>>>>> 
>>>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>>>> discussion, to see if anyone currently working on IGB can add any more
>>>>>>> info.
>>>>>>> 
>>>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>>> 
>>>>>>>> Hi all (but Gregg in particular!)
>>>>>>>> 
>>>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>>>> project at the moment, making me a little nervous about attempting to
>>>>>>>> use the code in a production(ish) setting.
>>>>>>>> 
>>>>>>>> many thanks in advance,
>>>>>>>> Jim.
>>>>>>>> 
>>>>>>>> --
>>>>>>>> -------------------------------------------------------------------
>>>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> DAS mailing list
>>>>>>> DAS at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>> ----------------------------------------------------------------------------
>>>> ->>
>>>> -
>>>>>> The modern datacenter depends on network connectivity to access resources
>>>>>> and provide services. The best practices for maximizing a physical
>>>>>> server's
>>>>>> connectivity to a physical network are well understood - see how these
>>>>>> rules translate into the virtual world?
>>>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>>>> _______________________________________________
>>>>>> Genoviz-devel mailing list
>>>>>> Genoviz-devel at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>>> 
>>>>> --
>>>>> Ann Loraine
>>>>> Associate Professor
>>>>> Dept. of Bioinformatics and Genomics, UNCC
>>>>> North Carolina Research Campus
>>>>> 600 Laureate Way
>>>>> Kannapolis, NC 28081
>>>>> 704-250-5750
>>>>> www.transvar.org
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> --
>>>> Ann Loraine
>>>> Associate Professor
>>>> Dept. of Bioinformatics and Genomics, UNCC
>>>> North Carolina Research Campus
>>>> 600 Laureate Way
>>>> Kannapolis, NC 28081
>>>> 704-250-5750
>>>> www.transvar.org
>>>> 
>>>> 
>>>> 
>>>> ----------------------------------------------------------------------------
>>>> --
>>>> The modern datacenter depends on network connectivity to access resources
>>>> and provide services. The best practices for maximizing a physical server's
>>>> connectivity to a physical network are well understood - see how these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>> 
> 
> -- 
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 
> 



From jw12 at sanger.ac.uk  Thu Feb 17 07:36:22 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Feb 2011 12:36:22 +0000
Subject: [DAS] DAS Workshop Registration Closing Soon
Message-ID: <B3363C0E-BB13-4D30-8E4C-9CBCFB48FCF1@sanger.ac.uk>

Registration closes for the DAS workshop at 5pm this Friday GMT.  
Limited places still available.
Please note that for the tutorials day (Day 1) it is advisable to know  
at least one of PERL, Java or Javascript.
Further information and registration from here: http://www.ebi.ac.uk/training/onsite/110302DAS.html

There are still a few places for short talks on the second day if you  
have anything to talk about of interest to the DAS community.



Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From jw12 at sanger.ac.uk  Mon Feb 21 07:13:04 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 21 Feb 2011 12:13:04 +0000
Subject: [DAS] US DAS workshop
In-Reply-To: <2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
Message-ID: <3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>

So the current situation as far as I can see is that we have at least  
two offers of venues to host a possible DAS workshop in the US. One  
east coast and one west coast? Which is great.
However, at the moment we have no funding and we are not sure what  
format the workshop should be.

I think Andy and myself are keen for this to happen in some way. Maybe  
(after this workshop in the UK next week) we can come up with a short  
5-10 question doodle poll that can be sent around to relevant email  
lists in the US to get an idea of the likely attendance numbers, best  
location, format and likely background of attendees etc.

This email discussion on the list hasn't convinced me that there is a  
massive demand for a general workshop - however I would hope that at  
the least Andy and myself would be able to come over and have a  
developers meeting with the current active DAS developers..... So it  
would be good to see what might come back from this doodle poll?

As a related topic: We are hoping to video many of the presentations  
at the workshop next week to be made available shortly after over the  
web. As always the tutorials and presentations will be available  
online from the biodas wiki:
http://www.biodas.org/wiki/DASWorkshop2011

Hope to see some of you soon.

Thanks

Jonathan.


On 7 Feb 2011, at 18:00, Suzanna Lewis wrote:

>
> On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:
>
>> Might we add on to the end/beginning of GI instead of running  
>> concurrently (assuming CSHL can oblige)?
>
> David Stewart is pretty open to this kind of thing given enough  
> forewarning.
>
>> Perhaps we can consider running a workshop at ISMB next year  
>> (California?) should interest be sufficient for an event at GI or  
>> the like this year?
>
> ISMB is in California next year? Didn't know that. 2012 is far away  
> though.
>
>
>>
>> I just noticed GI is actually in November though, by the way.
>
> There is also biology of genomes in May.
>
>>
>> On 7 Feb 2011, at 16:58, David Nix wrote:
>>
>>> Hmm...
>>>
>>> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml) 
>>> .  It's not the bay area and the organizers might already have a  
>>> set program.  There is a "Databases, Data Mining, Visualization  
>>> and Curation" session by Alex Bateman and Ting Wang though.
>>>
>>> -cheers, D
>>>
>>>
>>>
>>>
>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>
>>> Hi,
>>>
>>> Same for us here at UNC Charlotte.
>>>
>>> Meetings I'm attending next include two major plant science meetings
>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>
>>> David are there any other meetings you and your group are planning  
>>> to
>>> attend?
>>>
>>> The ideal setting would be a meeting where we can do outreach and  
>>> hold
>>> workshop event(s) for users, but also have a developers meeting  
>>> where we
>>> discuss future directions for the software, DAS spec, etc.
>>>
>>> Are there other meetings that would be a good fit?
>>>
>>> Best,
>>>
>>> Ann
>>>
>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>
>>>> Ah, that makes sense.
>>>>
>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah  
>>>> that would
>>>> attend an out of state meeting.  The bay area would be ideal  
>>>> (thanks Suzi!).
>>>> It might be best to make this part of a larger genomics/  
>>>> proteomics meeting to
>>>> start.  This would draw more folks who are interested in  
>>>> distributing their
>>>> own data and working DAS access into their own applications.  Are  
>>>> their any
>>>> appropriate upcoming meetings?
>>>>
>>>> -cheers, D
>>>>
>>>>
>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>  
>>>> wrote:
>>>>
>>>> Hi David,
>>>>
>>>> I guess one of the big reasons to want a proxy is it allows you  
>>>> to use DAS
>>>> sources you don't control, which is obviously potentially a  
>>>> really big benefit
>>>> with so many DAS/1 sources around. I don't know if this is what  
>>>> Jim is trying
>>>> to achieve though. In truth this has always been the difficulty  
>>>> with the
>>>> das/das2 tech divide really, with such a huge existing  
>>>> implementation base
>>>> there's a very high "activation energy" in switching!
>>>>
>>>> What was the issue with the ensembl servers?
>>>>
>>>> Jon and I have talked a few times about organising a DAS workshop  
>>>> in North
>>>> America, we just need someone to host (and to an extent fund) it.  
>>>> Do you have
>>>> any suggestions? Almost all of the attendees for our workshops  
>>>> are from
>>>> Europe, in fact lots are from Hinxton. So what sort of demand do  
>>>> you think
>>>> there would be stateside for such an event? Enough for a  
>>>> standalone workshop,
>>>> or more conducive to an add-on to or collaboration with another  
>>>> event?
>>>>
>>>> Maybe we can look into webcasting the talks? No idea how to go  
>>>> about this
>>>> though!
>>>>
>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>
>>>>> Hello Jim,
>>>>>
>>>>> If I make a suggestion.  If you're looking to visualize genomic  
>>>>> data in IGB,
>>>>> it would be best to use a DAS/2 server such as the Classic  
>>>>> (command line) or
>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.   
>>>>> DAS/2 is well
>>>>> suited to moving large amounts of sliced graph (gr, sgr,  
>>>>> bedgraph, wig, bar,
>>>>> useq...) and alignment data (ie BAM) to client apps.  We're  
>>>>> continuing to
>>>>> develop the GenoPub DAS/2 server with 5 year grant support from  
>>>>> NHLBI so
>>>>> expect continuing improvements (bulk uploading and file  
>>>>> conversion,
>>>>> annotation via ontologies, super group visibility settings,  
>>>>> additional file
>>>>> formats, etc.). See
>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2   
>>>>> and our paper
>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>
>>>>> GenoViz folks, correct me if I'm wrong here but I believe the  
>>>>> GenoViz DAS/2
>>>>> server supports  DAS xml datasets so moving data from a DAS/1  
>>>>> server to DAS/2
>>>>> wouldn't require any data reformatting.  Although for large  
>>>>> datasets, it's
>>>>> best to use one of the compressed binary data formats such as  
>>>>> bar, bam, or
>>>>> useq.
>>>>>
>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1  
>>>>> servers.  This works
>>>>> well for accessing their small annotation datasets (gene models:  
>>>>> refseq,
>>>>> knowngenes), but the graph distribution wasn't functional the  
>>>>> last I checked.
>>>>> The problem appeared to be from the server side.
>>>>>
>>>>> -cheers, David
>>>>>
>>>>> P.S. I wish I could attend the DAS workshop this year and show  
>>>>> you what we've
>>>>> been up to.  Any chance of getting a Skype conference call with  
>>>>> posted
>>>>> presentations?  Would be great if someone hosted a DAS Workshop  
>>>>> in the US.
>>>>>
>>>>>
>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>
>>>>> The core genomancer code is pretty stable, most of the recent  
>>>>> work is
>>>>> in plugins (and some work in the core to allow more extensive
>>>>> plugins).
>>>>>
>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>> the current head of the Trellis SVN repository -- you would just  
>>>>> need
>>>>> to add a web.xml config file with servlet parameters to get it  
>>>>> going in a
>>>>> servlet container like Tomcat, or alternatively run the built-in  
>>>>> Jetty server
>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in  
>>>>> code.
>>>>>
>>>>> But if the intent is to load DAS 1.x data into IGB, I don't  
>>>>> think you
>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>> that tab you can click the "Add" button to bring up a dialog  
>>>>> that lets
>>>>> you select "DAS" for the data source type, and enter the URL for  
>>>>> a DAS
>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>> server -- I haven't tried accessing data from any other DAS  
>>>>> servers
>>>>> recently.
>>>>>
>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>> discussion, to see if anyone currently working on IGB can add  
>>>>> any more
>>>>> info.
>>>>>
>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>
>>>>>> Hi all (but Gregg in particular!)
>>>>>>
>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of  
>>>>>> Trellis/Ivy
>>>>>> in the Genomancer project (http://code.google.com/p/ 
>>>>>> genomancer/) is
>>>>>> stable enough to use. We'd like to set up an in house DAS1->2  
>>>>>> proxy and
>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>> project at the moment, making me a little nervous about  
>>>>>> attempting to
>>>>>> use the code in a production(ish) setting.
>>>>>>
>>>>>> many thanks in advance,
>>>>>> Jim.
>>>>>>
>>>>>> --
>>>>>> -------------------------------------------------------------------
>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research  
>>>>>> Group
>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>> The University of Dundee is a Scottish Registered Charity, No.  
>>>>>> SC015096.
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The modern datacenter depends on network connectivity to access  
>>>> resources
>>>> and provide services. The best practices for maximizing a  
>>>> physical server's
>>>> connectivity to a physical network are well understood - see how  
>>>> these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>
>>> --
>>> Ann Loraine
>>> Associate Professor
>>> Dept. of Bioinformatics and Genomics, UNCC
>>> North Carolina Research Campus
>>> 600 Laureate Way
>>> Kannapolis, NC 28081
>>> 704-250-5750
>>> www.transvar.org
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> 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

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From ljgarcia at ebi.ac.uk  Mon Feb 21 08:27:05 2011
From: ljgarcia at ebi.ac.uk (Leyla Garcia)
Date: Mon, 21 Feb 2011 13:27:05 +0000
Subject: [DAS] DAS client libraries
In-Reply-To: <3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
	<3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
Message-ID: <4D626829.3060302@ebi.ac.uk>

Hi All,

I need to know what DAS client libraries are available. So far I am 
aware of JsDAS and Bio::DAS::Lite but still do not know more about them.
If you have a DAS client library, could you please send me this information?

Client Library Name
Web page
Language
Platform
Clients built upon it
Main advantages
Known restrictions/disadvantages
Currently supported (yes/no, who)
Current version
DAS spec supported

Thanks,

Leyla

From thomas.a.down at gmail.com  Mon Feb 21 08:44:55 2011
From: thomas.a.down at gmail.com (Thomas Down)
Date: Mon, 21 Feb 2011 13:44:55 +0000
Subject: [DAS] DAS client libraries
In-Reply-To: <4D626829.3060302@ebi.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
	<3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
	<4D626829.3060302@ebi.ac.uk>
Message-ID: <AANLkTikFPOVe4evUYXHWLJfFPj7TEQPhc5Y3nkCGmMdZ@mail.gmail.com>

On Mon, Feb 21, 2011 at 1:27 PM, Leyla Garcia <ljgarcia at ebi.ac.uk> wrote:

> Hi All,
>
> I need to know what DAS client libraries are available. So far I am aware
> of JsDAS and Bio::DAS::Lite but still do not know more about them.
> If you have a DAS client library, could you please send me this
> information?
>

Well, it hasn't really been "sold" as a library, but it is open source (BSD
license) and would be fairly easy to separate out if another client wanted
to use it, so:


> Client Library Name
>

das.js


> Web page
>

http://github.com/dasmoth/dalliance


> Language
>

Javascript


> Platform
>

Modern web browsers, plus IE8+.


> Clients built upon it
>

Dalliance


> Main advantages


Very lightweight.
No external dependencies
Designed for asynchronous operation.
Can do cross-origin fetching (including credentialed CORS) on most browsers.
Empirical testing suggests it's pretty tolerant of any DAS XML "in the wild"
at the moment.


> Known restrictions/disadvantages
>

Missing support for a few things we don't currently use in Dalliance (e.g.
DSN requests, structure extension, etc.).
Currently not easy to cancel in-flight requests (although that's something
we're working on).


> Currently supported (yes/no, who)
>

Yes, file a ticket in Github or e-mail me.


> Current version
>

Linked to Dalliance releases, current version is 0.5.7 (0.6 should be out in
the next few days, but doesn't have any major changes to the DAS backend).


> DAS spec supported
>

1.5, 1.6

           Thomas.

From jw12 at sanger.ac.uk  Mon Feb 21 09:45:14 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 21 Feb 2011 14:45:14 +0000
Subject: [DAS] DAS client libraries
In-Reply-To: <4D626829.3060302@ebi.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
	<3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
	<4D626829.3060302@ebi.ac.uk>
Message-ID: <0847ADF7-D140-46D8-B223-8A98FEB45688@sanger.ac.uk>


On 21 Feb 2011, at 13:27, Leyla Garcia wrote:

> Hi All,
>
> I need to know what DAS client libraries are available. So far I am  
> aware of JsDAS and Bio::DAS::Lite but still do not know more about  
> them.
> If you have a DAS client library, could you please send me this  
> information?
>
> Client Library Name

Dasobert
> Web page

http://www.spice-3d.org/dasobert/
> Language
Java
> Platform
> Clients built upon it

Spice, DAS Registry, Jalview.....

> Main advantages
Java ? :)


> Known restrictions/disadvantages

Have to read code or find in docs how to access xml attributes and  
elements as hash based not method/object.
Probably needs more documentation and support for asynchronous requests.

> Currently supported (yes/no, who)

yes - though development has been allied to the DAS Registry over the  
last 3 years and mostly validation so not all that useful for "normal  
clients". Jonathan Warren
Hence reason for discussion about Dasobert on day 3 of this years  
workshop- do we want to go with JAXB generated classes? What do we do  
with Dasobert now?
> Current version

http://www.derkholm.net/svn/repos/dasobert/trunk/ has some 1.6 support  
and has moved to using Lists rather than arrays[ ] for old version  
with arrays use oldTrunk under branches.

> DAS spec supported
1.53/1.6
>
> Thanks,
>
> Leyla
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From David.Nix at hci.utah.edu  Tue Feb 22 11:05:54 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Tue, 22 Feb 2011 09:05:54 -0700
Subject: [DAS] US DAS workshop
In-Reply-To: <3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
Message-ID: <C9892CF2.8047%david.nix@hci.utah.edu>

Sounds good Jonathan,

Thanks for pursuing this.  I would agree, there isn't a huge demand for a general workshop (just yet) in the US.  Most bioinformatics folks I know just haven't heard about DAS.  And even when I explain it to them the don't understand it nor appreciate what a common language for data distribution can do.  That will hopefully change....

Folks might not have heard but the SRA has been cut.  http://www.ncbi.nlm.nih.gov/sra for the official announcement and http://seqanswers.com/forums/showthread.php?t=9431 for a thread on SeqAnswers.  This is the primary data repository for all things related to next generation sequencing in the US. It's not clear where folks are going to put their fastq and bam files.  It's kind of ridiculous how fragmented the data repository problem has become. Here are the recommendations for where folks should bury, I mean send their data in the US:

[cid:3381210354_50664721]

Ouch!  Each of these repositories has their own methods of encoding meta data and distributing primary data and analysis. The data distribution problem is becoming intractable.

I think we (DAS folks) should speak up loud and clear and make sure that DAS is considered as a technology to link these disparate island of information.

-cheers, D




On 2/21/11 5:13 AM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:

So the current situation as far as I can see is that we have at least
two offers of venues to host a possible DAS workshop in the US. One
east coast and one west coast? Which is great.
However, at the moment we have no funding and we are not sure what
format the workshop should be.

I think Andy and myself are keen for this to happen in some way. Maybe
(after this workshop in the UK next week) we can come up with a short
5-10 question doodle poll that can be sent around to relevant email
lists in the US to get an idea of the likely attendance numbers, best
location, format and likely background of attendees etc.

This email discussion on the list hasn't convinced me that there is a
massive demand for a general workshop - however I would hope that at
the least Andy and myself would be able to come over and have a
developers meeting with the current active DAS developers..... So it
would be good to see what might come back from this doodle poll?

As a related topic: We are hoping to video many of the presentations
at the workshop next week to be made available shortly after over the
web. As always the tutorials and presentations will be available
online from the biodas wiki:
http://www.biodas.org/wiki/DASWorkshop2011

Hope to see some of you soon.

Thanks

Jonathan.


On 7 Feb 2011, at 18:00, Suzanna Lewis wrote:

>
> On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:
>
>> Might we add on to the end/beginning of GI instead of running
>> concurrently (assuming CSHL can oblige)?
>
> David Stewart is pretty open to this kind of thing given enough
> forewarning.
>
>> Perhaps we can consider running a workshop at ISMB next year
>> (California?) should interest be sufficient for an event at GI or
>> the like this year?
>
> ISMB is in California next year? Didn't know that. 2012 is far away
> though.
>
>
>>
>> I just noticed GI is actually in November though, by the way.
>
> There is also biology of genomes in May.
>
>>
>> On 7 Feb 2011, at 16:58, David Nix wrote:
>>
>>> Hmm...
>>>
>>> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml)
>>> .  It's not the bay area and the organizers might already have a
>>> set program.  There is a "Databases, Data Mining, Visualization
>>> and Curation" session by Alex Bateman and Ting Wang though.
>>>
>>> -cheers, D
>>>
>>>
>>>
>>>
>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>
>>> Hi,
>>>
>>> Same for us here at UNC Charlotte.
>>>
>>> Meetings I'm attending next include two major plant science meetings
>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>
>>> David are there any other meetings you and your group are planning
>>> to
>>> attend?
>>>
>>> The ideal setting would be a meeting where we can do outreach and
>>> hold
>>> workshop event(s) for users, but also have a developers meeting
>>> where we
>>> discuss future directions for the software, DAS spec, etc.
>>>
>>> Are there other meetings that would be a good fit?
>>>
>>> Best,
>>>
>>> Ann
>>>
>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>
>>>> Ah, that makes sense.
>>>>
>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah
>>>> that would
>>>> attend an out of state meeting.  The bay area would be ideal
>>>> (thanks Suzi!).
>>>> It might be best to make this part of a larger genomics/
>>>> proteomics meeting to
>>>> start.  This would draw more folks who are interested in
>>>> distributing their
>>>> own data and working DAS access into their own applications.  Are
>>>> their any
>>>> appropriate upcoming meetings?
>>>>
>>>> -cheers, D
>>>>
>>>>
>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>
>>>> wrote:
>>>>
>>>> Hi David,
>>>>
>>>> I guess one of the big reasons to want a proxy is it allows you
>>>> to use DAS
>>>> sources you don't control, which is obviously potentially a
>>>> really big benefit
>>>> with so many DAS/1 sources around. I don't know if this is what
>>>> Jim is trying
>>>> to achieve though. In truth this has always been the difficulty
>>>> with the
>>>> das/das2 tech divide really, with such a huge existing
>>>> implementation base
>>>> there's a very high "activation energy" in switching!
>>>>
>>>> What was the issue with the ensembl servers?
>>>>
>>>> Jon and I have talked a few times about organising a DAS workshop
>>>> in North
>>>> America, we just need someone to host (and to an extent fund) it.
>>>> Do you have
>>>> any suggestions? Almost all of the attendees for our workshops
>>>> are from
>>>> Europe, in fact lots are from Hinxton. So what sort of demand do
>>>> you think
>>>> there would be stateside for such an event? Enough for a
>>>> standalone workshop,
>>>> or more conducive to an add-on to or collaboration with another
>>>> event?
>>>>
>>>> Maybe we can look into webcasting the talks? No idea how to go
>>>> about this
>>>> though!
>>>>
>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>
>>>>> Hello Jim,
>>>>>
>>>>> If I make a suggestion.  If you're looking to visualize genomic
>>>>> data in IGB,
>>>>> it would be best to use a DAS/2 server such as the Classic
>>>>> (command line) or
>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.
>>>>> DAS/2 is well
>>>>> suited to moving large amounts of sliced graph (gr, sgr,
>>>>> bedgraph, wig, bar,
>>>>> useq...) and alignment data (ie BAM) to client apps.  We're
>>>>> continuing to
>>>>> develop the GenoPub DAS/2 server with 5 year grant support from
>>>>> NHLBI so
>>>>> expect continuing improvements (bulk uploading and file
>>>>> conversion,
>>>>> annotation via ontologies, super group visibility settings,
>>>>> additional file
>>>>> formats, etc.). See
>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2
>>>>> and our paper
>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>
>>>>> GenoViz folks, correct me if I'm wrong here but I believe the
>>>>> GenoViz DAS/2
>>>>> server supports  DAS xml datasets so moving data from a DAS/1
>>>>> server to DAS/2
>>>>> wouldn't require any data reformatting.  Although for large
>>>>> datasets, it's
>>>>> best to use one of the compressed binary data formats such as
>>>>> bar, bam, or
>>>>> useq.
>>>>>
>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1
>>>>> servers.  This works
>>>>> well for accessing their small annotation datasets (gene models:
>>>>> refseq,
>>>>> knowngenes), but the graph distribution wasn't functional the
>>>>> last I checked.
>>>>> The problem appeared to be from the server side.
>>>>>
>>>>> -cheers, David
>>>>>
>>>>> P.S. I wish I could attend the DAS workshop this year and show
>>>>> you what we've
>>>>> been up to.  Any chance of getting a Skype conference call with
>>>>> posted
>>>>> presentations?  Would be great if someone hosted a DAS Workshop
>>>>> in the US.
>>>>>
>>>>>
>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>
>>>>> The core genomancer code is pretty stable, most of the recent
>>>>> work is
>>>>> in plugins (and some work in the core to allow more extensive
>>>>> plugins).
>>>>>
>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>> the current head of the Trellis SVN repository -- you would just
>>>>> need
>>>>> to add a web.xml config file with servlet parameters to get it
>>>>> going in a
>>>>> servlet container like Tomcat, or alternatively run the built-in
>>>>> Jetty server
>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in
>>>>> code.
>>>>>
>>>>> But if the intent is to load DAS 1.x data into IGB, I don't
>>>>> think you
>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>> that tab you can click the "Add" button to bring up a dialog
>>>>> that lets
>>>>> you select "DAS" for the data source type, and enter the URL for
>>>>> a DAS
>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>> server -- I haven't tried accessing data from any other DAS
>>>>> servers
>>>>> recently.
>>>>>
>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>> discussion, to see if anyone currently working on IGB can add
>>>>> any more
>>>>> info.
>>>>>
>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>
>>>>>> Hi all (but Gregg in particular!)
>>>>>>
>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of
>>>>>> Trellis/Ivy
>>>>>> in the Genomancer project (http://code.google.com/p/
>>>>>> genomancer/) is
>>>>>> stable enough to use. We'd like to set up an in house DAS1->2
>>>>>> proxy and
>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>> project at the moment, making me a little nervous about
>>>>>> attempting to
>>>>>> use the code in a production(ish) setting.
>>>>>>
>>>>>> many thanks in advance,
>>>>>> Jim.
>>>>>>
>>>>>> --
>>>>>> -------------------------------------------------------------------
>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research
>>>>>> Group
>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>> The University of Dundee is a Scottish Registered Charity, No.
>>>>>> SC015096.
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The modern datacenter depends on network connectivity to access
>>>> resources
>>>> and provide services. The best practices for maximizing a
>>>> physical server's
>>>> connectivity to a physical network are well understood - see how
>>>> these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>
>>> --
>>> Ann Loraine
>>> Associate Professor
>>> Dept. of Bioinformatics and Genomics, UNCC
>>> North Carolina Research Campus
>>> 600 Laureate Way
>>> Kannapolis, NC 28081
>>> 704-250-5750
>>> www.transvar.org
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> 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

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.
_______________________________________________
DAS mailing list
DAS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/das

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From andy.jenkinson at ebi.ac.uk  Tue Feb 22 13:10:11 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Tue, 22 Feb 2011 18:10:11 +0000
Subject: [DAS] US DAS workshop
In-Reply-To: <C9894D75.70F4%aloraine@uncc.edu>
References: <C9894D75.70F4%aloraine@uncc.edu>
Message-ID: <CFF23102-D83E-4D1E-9799-58744A8C13ED@ebi.ac.uk>

Just to add, the EBI will continue to support its SRA:
http://www.ebi.ac.uk/ena/SRA_announcement_Feb_2011.pdf

I have not heard of any DDBJ (also part of INSDC) plans to stop accepting submissions either. Is the availability of bandwidth workable for submissions at either of these? They should continue to sync as normal. I hear the east-west coast bandwidth isn't too great anyway, and the transatlantic link is OK.

On 22 Feb 2011, at 16:24, Ann Loraine wrote:

> The announcement says we can deposit RNA-Seq and epigenomic data to GEO and
> transcript assemblies to GenBank/TSA.
> 
> Will GEO capture and make available the FASTQ files? (Or some other format
> for reads?)
> 
> I like how easy GEO makes it to do a bulk download of CEL files.
> 
> Will it provide the same easy method for accessing FASTQ?
> 
> Tools in common use (e.g., bowtie, tophat) are changing at a lightning pace
> and it's important to have access to the "raw" sequence data well into the
> future. 
> 
> 
> On 2/22/11 11:05 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
> 
>> Sounds good Jonathan,
>> 
>> Thanks for pursuing this.  I would agree, there isn't a huge demand for a
>> general workshop (just yet) in the US.  Most bioinformatics folks I know just
>> haven't heard about DAS.  And even when I explain it to them the don't
>> understand it nor appreciate what a common language for data distribution can
>> do.  That will hopefully change....
>> 
>> Folks might not have heard but the SRA has been cut.
>> http://www.ncbi.nlm.nih.gov/sra for the official announcement and
>> http://seqanswers.com/forums/showthread.php?t=9431 for a thread on SeqAnswers.
>> This is the primary data repository for all things related to next generation
>> sequencing in the US. It's not clear where folks are going to put their fastq
>> and bam files.  It's kind of ridiculous how fragmented the data repository
>> problem has become. Here are the recommendations for where folks should bury,
>> I mean send their data in the US:
>> 
>> [cid:3381210354_50664721]
>> 
>> Ouch!  Each of these repositories has their own methods of encoding meta data
>> and distributing primary data and analysis. The data distribution problem is
>> becoming intractable.
>> 
>> I think we (DAS folks) should speak up loud and clear and make sure that DAS
>> is considered as a technology to link these disparate island of information.
>> 
>> -cheers, D
>> 
>> 
>> 
>> 
>> On 2/21/11 5:13 AM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:
>> 
>> So the current situation as far as I can see is that we have at least
>> two offers of venues to host a possible DAS workshop in the US. One
>> east coast and one west coast? Which is great.
>> However, at the moment we have no funding and we are not sure what
>> format the workshop should be.
>> 
>> I think Andy and myself are keen for this to happen in some way. Maybe
>> (after this workshop in the UK next week) we can come up with a short
>> 5-10 question doodle poll that can be sent around to relevant email
>> lists in the US to get an idea of the likely attendance numbers, best
>> location, format and likely background of attendees etc.
>> 
>> This email discussion on the list hasn't convinced me that there is a
>> massive demand for a general workshop - however I would hope that at
>> the least Andy and myself would be able to come over and have a
>> developers meeting with the current active DAS developers..... So it
>> would be good to see what might come back from this doodle poll?
>> 
>> As a related topic: We are hoping to video many of the presentations
>> at the workshop next week to be made available shortly after over the
>> web. As always the tutorials and presentations will be available
>> online from the biodas wiki:
>> http://www.biodas.org/wiki/DASWorkshop2011
>> 
>> Hope to see some of you soon.
>> 
>> Thanks
>> 
>> Jonathan.
>> 
>> 
>> On 7 Feb 2011, at 18:00, Suzanna Lewis wrote:
>> 
>>> 
>>> On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:
>>> 
>>>> Might we add on to the end/beginning of GI instead of running
>>>> concurrently (assuming CSHL can oblige)?
>>> 
>>> David Stewart is pretty open to this kind of thing given enough
>>> forewarning.
>>> 
>>>> Perhaps we can consider running a workshop at ISMB next year
>>>> (California?) should interest be sufficient for an event at GI or
>>>> the like this year?
>>> 
>>> ISMB is in California next year? Didn't know that. 2012 is far away
>>> though.
>>> 
>>> 
>>>> 
>>>> I just noticed GI is actually in November though, by the way.
>>> 
>>> There is also biology of genomes in May.
>>> 
>>>> 
>>>> On 7 Feb 2011, at 16:58, David Nix wrote:
>>>> 
>>>>> Hmm...
>>>>> 
>>>>> There's the Genome Informatics meeting in August at CSHL (
>>>>> http://meetings.cshl.edu/meetings/info11.shtml)
>>>>> .  It's not the bay area and the organizers might already have a
>>>>> set program.  There is a "Databases, Data Mining, Visualization
>>>>> and Curation" session by Alex Bateman and Ting Wang though.
>>>>> 
>>>>> -cheers, D
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Same for us here at UNC Charlotte.
>>>>> 
>>>>> Meetings I'm attending next include two major plant science meetings
>>>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>>> 
>>>>> David are there any other meetings you and your group are planning
>>>>> to
>>>>> attend?
>>>>> 
>>>>> The ideal setting would be a meeting where we can do outreach and
>>>>> hold
>>>>> workshop event(s) for users, but also have a developers meeting
>>>>> where we
>>>>> discuss future directions for the software, DAS spec, etc.
>>>>> 
>>>>> Are there other meetings that would be a good fit?
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Ann
>>>>> 
>>>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>>> 
>>>>>> Ah, that makes sense.
>>>>>> 
>>>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah
>>>>>> that would
>>>>>> attend an out of state meeting.  The bay area would be ideal
>>>>>> (thanks Suzi!).
>>>>>> It might be best to make this part of a larger genomics/
>>>>>> proteomics meeting to
>>>>>> start.  This would draw more folks who are interested in
>>>>>> distributing their
>>>>>> own data and working DAS access into their own applications.  Are
>>>>>> their any
>>>>>> appropriate upcoming meetings?
>>>>>> 
>>>>>> -cheers, D
>>>>>> 
>>>>>> 
>>>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>
>>>>>> wrote:
>>>>>> 
>>>>>> Hi David,
>>>>>> 
>>>>>> I guess one of the big reasons to want a proxy is it allows you
>>>>>> to use DAS
>>>>>> sources you don't control, which is obviously potentially a
>>>>>> really big benefit
>>>>>> with so many DAS/1 sources around. I don't know if this is what
>>>>>> Jim is trying
>>>>>> to achieve though. In truth this has always been the difficulty
>>>>>> with the
>>>>>> das/das2 tech divide really, with such a huge existing
>>>>>> implementation base
>>>>>> there's a very high "activation energy" in switching!
>>>>>> 
>>>>>> What was the issue with the ensembl servers?
>>>>>> 
>>>>>> Jon and I have talked a few times about organising a DAS workshop
>>>>>> in North
>>>>>> America, we just need someone to host (and to an extent fund) it.
>>>>>> Do you have
>>>>>> any suggestions? Almost all of the attendees for our workshops
>>>>>> are from
>>>>>> Europe, in fact lots are from Hinxton. So what sort of demand do
>>>>>> you think
>>>>>> there would be stateside for such an event? Enough for a
>>>>>> standalone workshop,
>>>>>> or more conducive to an add-on to or collaboration with another
>>>>>> event?
>>>>>> 
>>>>>> Maybe we can look into webcasting the talks? No idea how to go
>>>>>> about this
>>>>>> though!
>>>>>> 
>>>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>>> 
>>>>>>> Hello Jim,
>>>>>>> 
>>>>>>> If I make a suggestion.  If you're looking to visualize genomic
>>>>>>> data in IGB,
>>>>>>> it would be best to use a DAS/2 server such as the Classic
>>>>>>> (command line) or
>>>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.
>>>>>>> DAS/2 is well
>>>>>>> suited to moving large amounts of sliced graph (gr, sgr,
>>>>>>> bedgraph, wig, bar,
>>>>>>> useq...) and alignment data (ie BAM) to client apps.  We're
>>>>>>> continuing to
>>>>>>> develop the GenoPub DAS/2 server with 5 year grant support from
>>>>>>> NHLBI so
>>>>>>> expect continuing improvements (bulk uploading and file
>>>>>>> conversion,
>>>>>>> annotation via ontologies, super group visibility settings,
>>>>>>> additional file
>>>>>>> formats, etc.). See
>>>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2
>>>>>>> and our paper
>>>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>>> 
>>>>>>> GenoViz folks, correct me if I'm wrong here but I believe the
>>>>>>> GenoViz DAS/2
>>>>>>> server supports  DAS xml datasets so moving data from a DAS/1
>>>>>>> server to DAS/2
>>>>>>> wouldn't require any data reformatting.  Although for large
>>>>>>> datasets, it's
>>>>>>> best to use one of the compressed binary data formats such as
>>>>>>> bar, bam, or
>>>>>>> useq.
>>>>>>> 
>>>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1
>>>>>>> servers.  This works
>>>>>>> well for accessing their small annotation datasets (gene models:
>>>>>>> refseq,
>>>>>>> knowngenes), but the graph distribution wasn't functional the
>>>>>>> last I checked.
>>>>>>> The problem appeared to be from the server side.
>>>>>>> 
>>>>>>> -cheers, David
>>>>>>> 
>>>>>>> P.S. I wish I could attend the DAS workshop this year and show
>>>>>>> you what we've
>>>>>>> been up to.  Any chance of getting a Skype conference call with
>>>>>>> posted
>>>>>>> presentations?  Would be great if someone hosted a DAS Workshop
>>>>>>> in the US.
>>>>>>> 
>>>>>>> 
>>>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>>> 
>>>>>>> The core genomancer code is pretty stable, most of the recent
>>>>>>> work is
>>>>>>> in plugins (and some work in the core to allow more extensive
>>>>>>> plugins).
>>>>>>> 
>>>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>>>> the current head of the Trellis SVN repository -- you would just
>>>>>>> need
>>>>>>> to add a web.xml config file with servlet parameters to get it
>>>>>>> going in a
>>>>>>> servlet container like Tomcat, or alternatively run the built-in
>>>>>>> Jetty server
>>>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in
>>>>>>> code.
>>>>>>> 
>>>>>>> But if the intent is to load DAS 1.x data into IGB, I don't
>>>>>>> think you
>>>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>>>> that tab you can click the "Add" button to bring up a dialog
>>>>>>> that lets
>>>>>>> you select "DAS" for the data source type, and enter the URL for
>>>>>>> a DAS
>>>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>>>> server -- I haven't tried accessing data from any other DAS
>>>>>>> servers
>>>>>>> recently.
>>>>>>> 
>>>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>>>> discussion, to see if anyone currently working on IGB can add
>>>>>>> any more
>>>>>>> info.
>>>>>>> 
>>>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>>> 
>>>>>>>> Hi all (but Gregg in particular!)
>>>>>>>> 
>>>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of
>>>>>>>> Trellis/Ivy
>>>>>>>> in the Genomancer project (http://code.google.com/p/
>>>>>>>> genomancer/) is
>>>>>>>> stable enough to use. We'd like to set up an in house DAS1->2
>>>>>>>> proxy and
>>>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>>>> project at the moment, making me a little nervous about
>>>>>>>> attempting to
>>>>>>>> use the code in a production(ish) setting.
>>>>>>>> 
>>>>>>>> many thanks in advance,
>>>>>>>> Jim.
>>>>>>>> 
>>>>>>>> --
>>>>>>>> -------------------------------------------------------------------
>>>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research
>>>>>>>> Group
>>>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>>>> The University of Dundee is a Scottish Registered Charity, No.
>>>>>>>> SC015096.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> DAS mailing list
>>>>>>> DAS at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> --------------------------------------------------------------------------
>>>>>> ----
>>>>>> The modern datacenter depends on network connectivity to access
>>>>>> resources
>>>>>> and provide services. The best practices for maximizing a
>>>>>> physical server's
>>>>>> connectivity to a physical network are well understood - see how
>>>>>> these
>>>>>> rules translate into the virtual world?
>>>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>>>> _______________________________________________
>>>>>> Genoviz-devel mailing list
>>>>>> Genoviz-devel at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>>> 
>>>>> --
>>>>> Ann Loraine
>>>>> Associate Professor
>>>>> Dept. of Bioinformatics and Genomics, UNCC
>>>>> North Carolina Research Campus
>>>>> 600 Laureate Way
>>>>> Kannapolis, NC 28081
>>>>> 704-250-5750
>>>>> www.transvar.org
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> Jonathan Warren
>> Senior Developer and DAS coordinator
>> blog: http://biodasman.wordpress.com/
>> jw12 at sanger.ac.uk
>> Ext: 2314
>> Telephone: 01223 492314
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>> 
> 
> -- 
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 



From jzhang at ximpleware.com  Fri Feb 25 20:25:55 2011
From: jzhang at ximpleware.com (jimmy Zhang)
Date: Fri, 25 Feb 2011 17:25:55 -0800
Subject: [DAS] [ANN]VTD-XML 2.10
In-Reply-To: <E0CA4C49-6C87-4222-B82E-F71CECD51916@sanger.ac.uk>
References: <E0CA4C49-6C87-4222-B82E-F71CECD51916@sanger.ac.uk>
Message-ID: <241E9E98F7494B2CB7492D06DC172C2D@JimmyZhangPC>

VTD-XML 2.10 is now released. It can be downloaded at
https://sourceforge.net/projects/vtd-xml/files/vtd-xml/ximpleware_2.10/.
This release includes a number of new features and enhancement.

* The core API of VTD-XML has been expanded. Users can now perform
cut/paste/insert on an empty element.
* This release also adds the support of deeper location cache support for
parsing and indexing. This feature is useful for application performance
tuning for
processing various XML documents.
* The java version also added support for processing zip and gzip files.
Direct processing of httpURL based XML is enhanced.
* Extended Java version now support Iso-8859-10~16 encoding.
* A full featured C++ port is released.
* C version of VTD-XML now make use of thread local storage to achieve
thread safety for multi-threaded application.
* There are also a number of bugs fixed. Special thanks to Jozef Aerts, John
Sillers, Chris Tornau and a number of other users for input and suggestions


From aroberts at broadinstitute.org  Mon Feb 28 13:34:10 2011
From: aroberts at broadinstitute.org (Andrew Roberts)
Date: Mon, 28 Feb 2011 13:34:10 -0500
Subject: [DAS] RELAX NG schema for "sequence" command
Message-ID: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>

Hello,

	I'm working on some validations, and I think I may have found an  
error in sequence.rng (www.dasregistry.org/validation1.6/ 
sequence.rng).  It appears that this schema makes no provision for the  
actual text data that belongs to the sequence element (i.e. the bases  
themselves).  Is this a known issue?

	If not, I think the solution is to add a <text/> element inside the  
sequence element.  Line 10 should read,

                 <attribute name="start"><data type="integer"></data></ 
attribute><attribute name="stop"><data type="integer"></data></ 
attribute><optional><attribute name="version"><text></text></ 
attribute></optional><optional><attribute name="label"><text></text></ 
attribute></optional><text/></element>

Cheers,

Andrew

From jw12 at sanger.ac.uk  Mon Feb 28 13:52:00 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 28 Feb 2011 18:52:00 +0000
Subject: [DAS] RELAX NG schema for "sequence" command
In-Reply-To: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>
References: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>
Message-ID: <51BE8FEB-E4B6-4931-BFD6-79BE35A6F171@sanger.ac.uk>

Hi
Welcome to the DAS list :)
I'm guessing that when I made an edit on Friday I inadvertently  
deleted or moved the text element to the wrong place!
Ill check it.

Thanks for the info!


On 28 Feb 2011, at 18:34, Andrew Roberts wrote:

> Hello,
>
> 	I'm working on some validations, and I think I may have found an  
> error in sequence.rng (www.dasregistry.org/validation1.6/ 
> sequence.rng).  It appears that this schema makes no provision for  
> the actual text data that belongs to the sequence element (i.e. the  
> bases themselves).  Is this a known issue?
>
> 	If not, I think the solution is to add a <text/> element inside the  
> sequence element.  Line 10 should read,
>
>                <attribute name="start"><data type="integer"></data></ 
> attribute><attribute name="stop"><data type="integer"></data></ 
> attribute><optional><attribute name="version"><text></text></ 
> attribute></optional><optional><attribute name="label"><text></ 
> text></attribute></optional><text/></element>
>
> Cheers,
>
> Andrew
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 

From ljgarcia at ebi.ac.uk  Mon Feb 28 14:38:43 2011
From: ljgarcia at ebi.ac.uk (ljgarcia at ebi.ac.uk)
Date: Mon, 28 Feb 2011 19:38:43 -0000 (UTC)
Subject: [DAS] RELAX NG schema for "sequence" command
In-Reply-To: <51BE8FEB-E4B6-4931-BFD6-79BE35A6F171@sanger.ac.uk>
References: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>
	<51BE8FEB-E4B6-4931-BFD6-79BE35A6F171@sanger.ac.uk>
Message-ID: <58547.86.9.203.124.1298921923.squirrel@webmail.ebi.ac.uk>

Hi,

Rafael and I also noted it this afternoon. We used trang in order to
transform sequence.rng into sequence.xsd, then we used Jaxb and we got
nothing about the content. However, a while ago we did the same procedure
and it worked. We were wondering what could it be.

Jonathan, please let us know when you update the rng schema.

Thanks,

Leyla

> Hi
> Welcome to the DAS list :)
> I'm guessing that when I made an edit on Friday I inadvertently
> deleted or moved the text element to the wrong place!
> Ill check it.
>
> Thanks for the info!
>
>
> On 28 Feb 2011, at 18:34, Andrew Roberts wrote:
>
>> Hello,
>>
>> 	I'm working on some validations, and I think I may have found an
>> error in sequence.rng (www.dasregistry.org/validation1.6/
>> sequence.rng).  It appears that this schema makes no provision for
>> the actual text data that belongs to the sequence element (i.e. the
>> bases themselves).  Is this a known issue?
>>
>> 	If not, I think the solution is to add a <text/> element inside the
>> sequence element.  Line 10 should read,
>>
>>                <attribute name="start"><data type="integer"></data></
>> attribute><attribute name="stop"><data type="integer"></data></
>> attribute><optional><attribute name="version"><text></text></
>> attribute></optional><optional><attribute name="label"><text></
>> text></attribute></optional><text/></element>
>>
>> Cheers,
>>
>> Andrew
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> blog: http://biodasman.wordpress.com/
> jw12 at sanger.ac.uk
> Ext: 2314
> Telephone: 01223 492314
>
>
>
>
>
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>



From thomas.a.down at gmail.com  Mon Feb 28 16:17:43 2011
From: thomas.a.down at gmail.com (Thomas Down)
Date: Mon, 28 Feb 2011 21:17:43 +0000
Subject: [DAS] Announcing Dalliance 0.6
Message-ID: <AANLkTikrz0F+RcTSMX8YJOnPfMPER2ffXu-Dn2NJrFC-@mail.gmail.com>

I'm very pleased to announce the latest release of Dalliance, an interactive
genome viewer and DAS client for the web.  You can try the latest release in
any modern web browser here:

            http://www.biodalliance.org/

Major improvements since version 0.5 include:

         - Better DAS/1.6 support, including complex features defined using
the PART/PARENT system.
         - Keyboard navigation improvements (in particular, tap space to
toggle instantly between two zoom levels).
         - Direct export of the current display in SVG or PDF format.
         - Binary data support: you can now directly add bigwig or bigbed
data to the browser (see http://www.biodalliance.org/bin.html).

As always, comments and suggestions welcome!

                   Thomas Down.

From jprocter at compbio.dundee.ac.uk  Tue Feb  1 15:51:17 2011
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Tue, 01 Feb 2011 15:51:17 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
Message-ID: <4D482BF5.70107@compbio.dundee.ac.uk>


Hi all (but Gregg in particular!)

I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
in the Genomancer project (http://code.google.com/p/genomancer/) is
stable enough to use. We'd like to set up an in house DAS1->2 proxy and
it looks like there's a moderate amount of commit activity in the
project at the moment, making me a little nervous about attempting to
use the code in a production(ish) setting.

many thanks in advance,
Jim.

-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.



From gregghelt at gmail.com  Fri Feb  4 15:19:08 2011
From: gregghelt at gmail.com (Gregg Helt)
Date: Fri, 4 Feb 2011 07:19:08 -0800
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <4D482BF5.70107@compbio.dundee.ac.uk>
References: <4D482BF5.70107@compbio.dundee.ac.uk>
Message-ID: <AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>

The core genomancer code is pretty stable, most of the recent work is
in plugins (and some work in the core to allow more extensive
plugins).

You should be able to get a working DAS1-->DAS2 proxy running from
the current head of the Trellis SVN repository -- you would just need
to add a web.xml config file with servlet parameters to get it going in a
servlet container like Tomcat, or alternatively run the built-in Jetty server
(ExampleJettyDas2Server) and edit servlet parameters directly in code.

But if the intent is to load DAS 1.x data into IGB, I don't think you
need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
already supports DAS 1.5 access.  In the "Data Access" tab, under
"Choose Data Sources and Data Sets" section click the "Configure"
button.  This brings up a window with a "Data Sources" tab, and in
that tab you can click the "Add" button to bring up a dialog that lets
you select "DAS" for the data source type, and enter the URL for a DAS
server.  This worked fine for loading data from the UCSC DAS 1.5
server -- I haven't tried accessing data from any other DAS servers
recently.

I'm forwarding to the genoviz-devel list for IGB developments and
discussion, to see if anyone currently working on IGB can add any more
info.

On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
>
> Hi all (but Gregg in particular!)
>
> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> in the Genomancer project (http://code.google.com/p/genomancer/) is
> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> it looks like there's a moderate amount of commit activity in the
> project at the moment, making me a little nervous about attempting to
> use the code in a production(ish) setting.
>
> many thanks in advance,
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter ?(JALVIEW/ENFIN) ?Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764 ?http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>



From andy.jenkinson at ebi.ac.uk  Fri Feb  4 16:08:51 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 4 Feb 2011 16:08:51 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
References: <4D482BF5.70107@compbio.dundee.ac.uk>
	<AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
Message-ID: <23C1AA47-31C1-4A57-B0DC-F410B7233501@ebi.ac.uk>

What does das1->das2 mean by the way, Jim? a client component to make das1 sources look like das2, server component to do same, or vice versa?

On 4 Feb 2011, at 15:19, Gregg Helt wrote:

> The core genomancer code is pretty stable, most of the recent work is
> in plugins (and some work in the core to allow more extensive
> plugins).
> 
> You should be able to get a working DAS1-->DAS2 proxy running from
> the current head of the Trellis SVN repository -- you would just need
> to add a web.xml config file with servlet parameters to get it going in a
> servlet container like Tomcat, or alternatively run the built-in Jetty server
> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
> 
> But if the intent is to load DAS 1.x data into IGB, I don't think you
> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> already supports DAS 1.5 access.  In the "Data Access" tab, under
> "Choose Data Sources and Data Sets" section click the "Configure"
> button.  This brings up a window with a "Data Sources" tab, and in
> that tab you can click the "Add" button to bring up a dialog that lets
> you select "DAS" for the data source type, and enter the URL for a DAS
> server.  This worked fine for loading data from the UCSC DAS 1.5
> server -- I haven't tried accessing data from any other DAS servers
> recently.
> 
> I'm forwarding to the genoviz-devel list for IGB developments and
> discussion, to see if anyone currently working on IGB can add any more
> info.
> 
> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> <jprocter at compbio.dundee.ac.uk> wrote:
>> 
>> Hi all (but Gregg in particular!)
>> 
>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>> it looks like there's a moderate amount of commit activity in the
>> project at the moment, making me a little nervous about attempting to
>> use the code in a production(ish) setting.
>> 
>> many thanks in advance,
>> Jim.
>> 
>> --
>> -------------------------------------------------------------------
>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>> 
>> _______________________________________________
>> 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




From jprocter at compbio.dundee.ac.uk  Fri Feb  4 16:13:34 2011
From: jprocter at compbio.dundee.ac.uk (Jim Procter)
Date: Fri, 04 Feb 2011 16:13:34 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <23C1AA47-31C1-4A57-B0DC-F410B7233501@ebi.ac.uk>
References: <4D482BF5.70107@compbio.dundee.ac.uk>
	<AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
	<23C1AA47-31C1-4A57-B0DC-F410B7233501@ebi.ac.uk>
Message-ID: <4D4C25AE.8030900@compbio.dundee.ac.uk>

On 04/02/2011 16:08, Andy Jenkinson wrote:
> What does das1->das2 mean by the way, Jim? a client component to
> make das1 sources look like das2, server component to do same, or
> vice versa?
Something to allow a Das1 source to be read by a Das 2 client.
Previous versions of IGB did not support this, which kind of hampers
progress in a predominantly DAS1 environment :)

Jim.

-- 
-------------------------------------------------------------------
J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
The University of Dundee is a Scottish Registered Charity, No. SC015096.



From David.Nix at hci.utah.edu  Fri Feb  4 19:13:08 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Fri, 4 Feb 2011 12:13:08 -0700
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <AANLkTimU+2KUz410u8y7U1oc7EMxqTxyLqM6ZAEzhGAD@mail.gmail.com>
Message-ID: <C9719DD4.7CF6%david.nix@hci.utah.edu>

Hello Jim,

If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455

GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.

IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.

-cheers, David

P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.


On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:

The core genomancer code is pretty stable, most of the recent work is
in plugins (and some work in the core to allow more extensive
plugins).

You should be able to get a working DAS1-->DAS2 proxy running from
the current head of the Trellis SVN repository -- you would just need
to add a web.xml config file with servlet parameters to get it going in a
servlet container like Tomcat, or alternatively run the built-in Jetty server
(ExampleJettyDas2Server) and edit servlet parameters directly in code.

But if the intent is to load DAS 1.x data into IGB, I don't think you
need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
already supports DAS 1.5 access.  In the "Data Access" tab, under
"Choose Data Sources and Data Sets" section click the "Configure"
button.  This brings up a window with a "Data Sources" tab, and in
that tab you can click the "Add" button to bring up a dialog that lets
you select "DAS" for the data source type, and enter the URL for a DAS
server.  This worked fine for loading data from the UCSC DAS 1.5
server -- I haven't tried accessing data from any other DAS servers
recently.

I'm forwarding to the genoviz-devel list for IGB developments and
discussion, to see if anyone currently working on IGB can add any more
info.

On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk> wrote:
>
> Hi all (but Gregg in particular!)
>
> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> in the Genomancer project (http://code.google.com/p/genomancer/) is
> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> it looks like there's a moderate amount of commit activity in the
> project at the moment, making me a little nervous about attempting to
> use the code in a production(ish) setting.
>
> many thanks in advance,
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
> _______________________________________________
> 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




From andy.jenkinson at ebi.ac.uk  Fri Feb  4 20:57:23 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Fri, 4 Feb 2011 20:57:23 +0000
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <C9719DD4.7CF6%david.nix@hci.utah.edu>
References: <C9719DD4.7CF6%david.nix@hci.utah.edu>
Message-ID: <1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>

Hi David,

I guess one of the big reasons to want a proxy is it allows you to use DAS sources you don't control, which is obviously potentially a really big benefit with so many DAS/1 sources around. I don't know if this is what Jim is trying to achieve though. In truth this has always been the difficulty with the das/das2 tech divide really, with such a huge existing implementation base there's a very high "activation energy" in switching!

What was the issue with the ensembl servers?

Jon and I have talked a few times about organising a DAS workshop in North America, we just need someone to host (and to an extent fund) it. Do you have any suggestions? Almost all of the attendees for our workshops are from Europe, in fact lots are from Hinxton. So what sort of demand do you think there would be stateside for such an event? Enough for a standalone workshop, or more conducive to an add-on to or collaboration with another event?

Maybe we can look into webcasting the talks? No idea how to go about this though!

On 4 Feb 2011, at 19:13, David Nix wrote:

> Hello Jim,
> 
> If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455
> 
> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.
> 
> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.
> 
> -cheers, David
> 
> P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.
> 
> 
> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
> 
> The core genomancer code is pretty stable, most of the recent work is
> in plugins (and some work in the core to allow more extensive
> plugins).
> 
> You should be able to get a working DAS1-->DAS2 proxy running from
> the current head of the Trellis SVN repository -- you would just need
> to add a web.xml config file with servlet parameters to get it going in a
> servlet container like Tomcat, or alternatively run the built-in Jetty server
> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
> 
> But if the intent is to load DAS 1.x data into IGB, I don't think you
> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> already supports DAS 1.5 access.  In the "Data Access" tab, under
> "Choose Data Sources and Data Sets" section click the "Configure"
> button.  This brings up a window with a "Data Sources" tab, and in
> that tab you can click the "Add" button to bring up a dialog that lets
> you select "DAS" for the data source type, and enter the URL for a DAS
> server.  This worked fine for loading data from the UCSC DAS 1.5
> server -- I haven't tried accessing data from any other DAS servers
> recently.
> 
> I'm forwarding to the genoviz-devel list for IGB developments and
> discussion, to see if anyone currently working on IGB can add any more
> info.
> 
> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> <jprocter at compbio.dundee.ac.uk> wrote:
>> 
>> Hi all (but Gregg in particular!)
>> 
>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>> it looks like there's a moderate amount of commit activity in the
>> project at the moment, making me a little nervous about attempting to
>> use the code in a production(ish) setting.
>> 
>> many thanks in advance,
>> Jim.
>> 
>> --
>> -------------------------------------------------------------------
>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>> 
>> _______________________________________________
>> 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
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das




From suzi at berkeleybop.org  Fri Feb  4 21:29:29 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Fri, 4 Feb 2011 13:29:29 -0800
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
References: <C9719DD4.7CF6%david.nix@hci.utah.edu>
	<1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
Message-ID: <2C831871-AF64-4587-85B8-5A6BC9EDED30@berkeleybop.org>

Gregg? Maybe you and I should talk about this. And perhaps you could get an idea when you are in Hinxton of what it takes to organize one of these.

Not a promise, but it might be possible for us to host this in Berkeley/Bay Area. We'll explore feasibility a bit more first. Be good to how many people might be interested.

-S

On Feb 4, 2011, at 12:57 PM, Andy Jenkinson wrote:

> Hi David,
> 
> I guess one of the big reasons to want a proxy is it allows you to use DAS sources you don't control, which is obviously potentially a really big benefit with so many DAS/1 sources around. I don't know if this is what Jim is trying to achieve though. In truth this has always been the difficulty with the das/das2 tech divide really, with such a huge existing implementation base there's a very high "activation energy" in switching!
> 
> What was the issue with the ensembl servers?
> 
> Jon and I have talked a few times about organising a DAS workshop in North America, we just need someone to host (and to an extent fund) it. Do you have any suggestions? Almost all of the attendees for our workshops are from Europe, in fact lots are from Hinxton. So what sort of demand do you think there would be stateside for such an event? Enough for a standalone workshop, or more conducive to an add-on to or collaboration with another event?
> 
> Maybe we can look into webcasting the talks? No idea how to go about this though!
> 
> On 4 Feb 2011, at 19:13, David Nix wrote:
> 
>> Hello Jim,
>> 
>> If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455
>> 
>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.
>> 
>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.
>> 
>> -cheers, David
>> 
>> P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.
>> 
>> 
>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>> 
>> The core genomancer code is pretty stable, most of the recent work is
>> in plugins (and some work in the core to allow more extensive
>> plugins).
>> 
>> You should be able to get a working DAS1-->DAS2 proxy running from
>> the current head of the Trellis SVN repository -- you would just need
>> to add a web.xml config file with servlet parameters to get it going in a
>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>> 
>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>> "Choose Data Sources and Data Sets" section click the "Configure"
>> button.  This brings up a window with a "Data Sources" tab, and in
>> that tab you can click the "Add" button to bring up a dialog that lets
>> you select "DAS" for the data source type, and enter the URL for a DAS
>> server.  This worked fine for loading data from the UCSC DAS 1.5
>> server -- I haven't tried accessing data from any other DAS servers
>> recently.
>> 
>> I'm forwarding to the genoviz-devel list for IGB developments and
>> discussion, to see if anyone currently working on IGB can add any more
>> info.
>> 
>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>> <jprocter at compbio.dundee.ac.uk> wrote:
>>> 
>>> Hi all (but Gregg in particular!)
>>> 
>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>> it looks like there's a moderate amount of commit activity in the
>>> project at the moment, making me a little nervous about attempting to
>>> use the code in a production(ish) setting.
>>> 
>>> many thanks in advance,
>>> Jim.
>>> 
>>> --
>>> -------------------------------------------------------------------
>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>> 
>>> _______________________________________________
>>> 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
>> 
>> 
>> _______________________________________________
>> 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




From sac at bioperl.org  Fri Feb  4 22:14:35 2011
From: sac at bioperl.org (Steve Chervitz)
Date: Fri, 4 Feb 2011 14:14:35 -0800
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <2C831871-AF64-4587-85B8-5A6BC9EDED30@berkeleybop.org>
References: <C9719DD4.7CF6%david.nix@hci.utah.edu>
	<1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
	<2C831871-AF64-4587-85B8-5A6BC9EDED30@berkeleybop.org>
Message-ID: <AANLkTikQt2S8xRTq2u=ahtPhV918iWh_8ALGGt7ELtL7@mail.gmail.com>

On Fri, Feb 4, 2011 at 1:29 PM, Suzanna Lewis <suzi at berkeleybop.org> wrote:

> Gregg? Maybe you and I should talk about this. And perhaps you could get an
> idea when you are in Hinxton of what it takes to organize one of these.
>
> Not a promise, but it might be possible for us to host this in Berkeley/Bay
> Area. We'll explore feasibility a bit more first. Be good to how many people
> might be interested.
>

Count me in!

Steve


> -S
>
> On Feb 4, 2011, at 12:57 PM, Andy Jenkinson wrote:
>
> > Hi David,
> >
> > I guess one of the big reasons to want a proxy is it allows you to use
> DAS sources you don't control, which is obviously potentially a really big
> benefit with so many DAS/1 sources around. I don't know if this is what Jim
> is trying to achieve though. In truth this has always been the difficulty
> with the das/das2 tech divide really, with such a huge existing
> implementation base there's a very high "activation energy" in switching!
> >
> > What was the issue with the ensembl servers?
> >
> > Jon and I have talked a few times about organising a DAS workshop in
> North America, we just need someone to host (and to an extent fund) it. Do
> you have any suggestions? Almost all of the attendees for our workshops are
> from Europe, in fact lots are from Hinxton. So what sort of demand do you
> think there would be stateside for such an event? Enough for a standalone
> workshop, or more conducive to an add-on to or collaboration with another
> event?
> >
> > Maybe we can look into webcasting the talks? No idea how to go about this
> though!
> >
> > On 4 Feb 2011, at 19:13, David Nix wrote:
> >
> >> Hello Jim,
> >>
> >> If I make a suggestion.  If you're looking to visualize genomic data in
> IGB, it would be best to use a DAS/2 server such as the Classic (command
> line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2
> is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph,
> wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're
> continuing to develop the GenoPub DAS/2 server with 5 year grant support
> from NHLBI so expect continuing improvements (bulk uploading and file
> conversion, annotation via ontologies, super group visibility settings,
> additional file formats, etc.). See
> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our
> paper http://www.biomedcentral.com/1471-2105/11/455
> >>
> >> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz
> DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server
> to DAS/2 wouldn't require any data reformatting.  Although for large
> datasets, it's best to use one of the compressed binary data formats such as
> bar, bam, or useq.
> >>
> >> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
> works well for accessing their small annotation datasets (gene models:
> refseq, knowngenes), but the graph distribution wasn't functional the last I
> checked.  The problem appeared to be from the server side.
> >>
> >> -cheers, David
> >>
> >> P.S. I wish I could attend the DAS workshop this year and show you what
> we've been up to.  Any chance of getting a Skype conference call with posted
> presentations?  Would be great if someone hosted a DAS Workshop in the US.
> >>
> >>
> >> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
> >>
> >> The core genomancer code is pretty stable, most of the recent work is
> >> in plugins (and some work in the core to allow more extensive
> >> plugins).
> >>
> >> You should be able to get a working DAS1-->DAS2 proxy running from
> >> the current head of the Trellis SVN repository -- you would just need
> >> to add a web.xml config file with servlet parameters to get it going in
> a
> >> servlet container like Tomcat, or alternatively run the built-in Jetty
> server
> >> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
> >>
> >> But if the intent is to load DAS 1.x data into IGB, I don't think you
> >> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> >> already supports DAS 1.5 access.  In the "Data Access" tab, under
> >> "Choose Data Sources and Data Sets" section click the "Configure"
> >> button.  This brings up a window with a "Data Sources" tab, and in
> >> that tab you can click the "Add" button to bring up a dialog that lets
> >> you select "DAS" for the data source type, and enter the URL for a DAS
> >> server.  This worked fine for loading data from the UCSC DAS 1.5
> >> server -- I haven't tried accessing data from any other DAS servers
> >> recently.
> >>
> >> I'm forwarding to the genoviz-devel list for IGB developments and
> >> discussion, to see if anyone currently working on IGB can add any more
> >> info.
> >>
> >> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> >> <jprocter at compbio.dundee.ac.uk> wrote:
> >>>
> >>> Hi all (but Gregg in particular!)
> >>>
> >>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
> >>> in the Genomancer project (http://code.google.com/p/genomancer/) is
> >>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
> >>> it looks like there's a moderate amount of commit activity in the
> >>> project at the moment, making me a little nervous about attempting to
> >>> use the code in a production(ish) setting.
> >>>
> >>> many thanks in advance,
> >>> Jim.
> >>>
> >>> --
> >>> -------------------------------------------------------------------
> >>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> >>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> >>> The University of Dundee is a Scottish Registered Charity, No.
> SC015096.
> >>>
> >>> _______________________________________________
> >>> 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
> >>
> >>
> >> _______________________________________________
> >> 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
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>


From chris at compbio.dundee.ac.uk  Mon Feb  7 10:34:36 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Mon, 07 Feb 2011 10:34:36 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
Message-ID: <4D4FCABC.7080103@compbio.dundee.ac.uk>

Hi,

I have a functioning ProServer install that works fine with Ensembl, but 
I'd like to get it working with IGB as well. However, it fails to load 
as it has a 'Missing MAPMASTER element'. I see I need to specify a URI 
to a known MAPMASTER source, but I've no idea how.

The server is for Arabidopsis data and I've found the Ensembl DAS 
sources for plants, but which can I use as a mapmaster?
http://plants.ensembl.org/das/dsn
Or am I barking up the wrong tree?

Any pointers much appreciated.
Cheers,

Chris




From andy.jenkinson at ebi.ac.uk  Mon Feb  7 11:40:11 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Mon, 7 Feb 2011 11:40:11 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <4D4FCABC.7080103@compbio.dundee.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
Message-ID: <0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>

Hi Chris,

The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100

So, barring any particular nuance of IGB, the correct mapmaster URL would be:
http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference

(assuming thaliana)

The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.

Cheers,
Andy

On 7 Feb 2011, at 10:34, Chris Cole wrote:

> Hi,
> 
> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
> 
> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
> http://plants.ensembl.org/das/dsn
> Or am I barking up the wrong tree?
> 
> Any pointers much appreciated.
> Cheers,
> 
> Chris
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das




From chris at compbio.dundee.ac.uk  Mon Feb  7 14:48:03 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Mon, 07 Feb 2011 14:48:03 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
Message-ID: <4D500623.4050803@compbio.dundee.ac.uk>

Hi Andy,

Thanks for the help. Looks like I was close...

I now get an error regarding the 'types' command. I haven't implemented 
it so that's not a surprise. However, I'm struggling to find 
documentation on the build_types() function and what data it should 
return. My source data only has one type: 'expression_tag' so how should 
I return that?
Cheers,

Chris

On 07/02/11 11:40, Andy Jenkinson wrote:
> Hi Chris,
>
> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>
> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>
> (assuming thaliana)
>
> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>
> Cheers,
> Andy
>
> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>
>> Hi,
>>
>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>
>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>> http://plants.ensembl.org/das/dsn
>> Or am I barking up the wrong tree?
>>
>> Any pointers much appreciated.
>> Cheers,
>>
>> Chris
>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096


From andy.jenkinson at ebi.ac.uk  Mon Feb  7 14:56:45 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Mon, 7 Feb 2011 14:56:45 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <4D500623.4050803@compbio.dundee.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
Message-ID: <48355836-341A-4DCC-976F-801308CBEF06@ebi.ac.uk>

The SourceAdaptor POD documents the build_types method. Just return an array containing a hash per type. For example:
return ( { 'type' => 'expression_tag', 'category' => 'experimental' } );

A more complete implementation would also include an ontology term and the 'count' for each type (i.e. the number of features of each type). Note that the build_types command takes segment parameters like the build_features method, except the segment is optional for build_types:
/das/yoursource/types
/das/yoursource/types?segment=X:1,100

Just make sure the content matches the types and categories used by the features command.

See the spec for more details:
http://www.biodas.org/documents/spec-1.6.html#types

On 7 Feb 2011, at 14:48, Chris Cole wrote:

> Hi Andy,
> 
> Thanks for the help. Looks like I was close...
> 
> I now get an error regarding the 'types' command. I haven't implemented it so that's not a surprise. However, I'm struggling to find documentation on the build_types() function and what data it should return. My source data only has one type: 'expression_tag' so how should I return that?
> Cheers,
> 
> Chris
> 
> On 07/02/11 11:40, Andy Jenkinson wrote:
>> Hi Chris,
>> 
>> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>> 
>> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>> 
>> (assuming thaliana)
>> 
>> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>> 
>> Cheers,
>> Andy
>> 
>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>> 
>>> Hi,
>>> 
>>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>> 
>>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>>> http://plants.ensembl.org/das/dsn
>>> Or am I barking up the wrong tree?
>>> 
>>> Any pointers much appreciated.
>>> Cheers,
>>> 
>>> Chris
>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
> 
> 
> -- 
> Dr Chris Cole
> Senior Bioinformatics Research Officer
> College of Life Sciences
> University of Dundee
> Dow Street
> Dundee
> DD1 5EH
> Scotland, UK
> 
> url: http://network.nature.com/profile/drchriscole
> e-mail: chris at compbio.dundee.ac.uk
> Tel: +44 (0)1382 388 721
> 
> The University of Dundee is a registered Scottish charity, No: SC015096




From jw12 at sanger.ac.uk  Mon Feb  7 14:59:07 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 7 Feb 2011 14:59:07 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <4D500623.4050803@compbio.dundee.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
Message-ID: <895C8BD6-42CC-4E26-93A3-E5BFC2478B20@sanger.ac.uk>

I've put a Andys previous answer to this question (when I asked it)   
here: http://biodasman.wordpress.com/2010/12/06/implementing-types-in-proserver/


On 7 Feb 2011, at 14:48, Chris Cole wrote:

> Hi Andy,
>
> Thanks for the help. Looks like I was close...
>
> I now get an error regarding the 'types' command. I haven't  
> implemented it so that's not a surprise. However, I'm struggling to  
> find documentation on the build_types() function and what data it  
> should return. My source data only has one type: 'expression_tag' so  
> how should I return that?
> Cheers,
>
> Chris
>
> On 07/02/11 11:40, Andy Jenkinson wrote:
>> Hi Chris,
>>
>> The 'reference' Ensembl sources are suitable for use as mapmasters,  
>> as they provide sequence information:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>>
>> So, barring any particular nuance of IGB, the correct mapmaster URL  
>> would be:
>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>>
>> (assuming thaliana)
>>
>> The reason for all this is I guess that IGB does not support the  
>> DAS 1.53E/1.6 sources command, which provides species and  
>> coordinate information directly.
>>
>> Cheers,
>> Andy
>>
>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>>
>>> Hi,
>>>
>>> I have a functioning ProServer install that works fine with  
>>> Ensembl, but I'd like to get it working with IGB as well. However,  
>>> it fails to load as it has a 'Missing MAPMASTER element'. I see I  
>>> need to specify a URI to a known MAPMASTER source, but I've no  
>>> idea how.
>>>
>>> The server is for Arabidopsis data and I've found the Ensembl DAS  
>>> sources for plants, but which can I use as a mapmaster?
>>> http://plants.ensembl.org/das/dsn
>>> Or am I barking up the wrong tree?
>>>
>>> Any pointers much appreciated.
>>> Cheers,
>>>
>>> Chris
>>>
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>
>
>
> -- 
> Dr Chris Cole
> Senior Bioinformatics Research Officer
> College of Life Sciences
> University of Dundee
> Dow Street
> Dundee
> DD1 5EH
> Scotland, UK
>
> url: http://network.nature.com/profile/drchriscole
> e-mail: chris at compbio.dundee.ac.uk
> Tel: +44 (0)1382 388 721
>
> The University of Dundee is a registered Scottish charity, No:  
> SC015096
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From David.Nix at hci.utah.edu  Mon Feb  7 15:58:49 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Mon, 7 Feb 2011 08:58:49 -0700
Subject: [DAS] Status of Trellis/Ivy and DAS1 to DAS2 proxying
In-Reply-To: <1C6F89FE-708B-4961-BAF4-9E5385952E6C@ebi.ac.uk>
Message-ID: <C97564C9.7D28%david.nix@hci.utah.edu>

Ah, that makes sense.

As for a US meeting, there are 3 or 4 folks here at the U of Utah that would attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).  It might be best to make this part of a larger genomics/ proteomics meeting to start.  This would draw more folks who are interested in distributing their own data and working DAS access into their own applications.  Are their any appropriate upcoming meetings?

-cheers, D


On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:

Hi David,

I guess one of the big reasons to want a proxy is it allows you to use DAS sources you don't control, which is obviously potentially a really big benefit with so many DAS/1 sources around. I don't know if this is what Jim is trying to achieve though. In truth this has always been the difficulty with the das/das2 tech divide really, with such a huge existing implementation base there's a very high "activation energy" in switching!

What was the issue with the ensembl servers?

Jon and I have talked a few times about organising a DAS workshop in North America, we just need someone to host (and to an extent fund) it. Do you have any suggestions? Almost all of the attendees for our workshops are from Europe, in fact lots are from Hinxton. So what sort of demand do you think there would be stateside for such an event? Enough for a standalone workshop, or more conducive to an add-on to or collaboration with another event?

Maybe we can look into webcasting the talks? No idea how to go about this though!

On 4 Feb 2011, at 19:13, David Nix wrote:

> Hello Jim,
>
> If I make a suggestion.  If you're looking to visualize genomic data in IGB, it would be best to use a DAS/2 server such as the Classic (command line) or GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar, useq...) and alignment data (ie BAM) to client apps.  We're continuing to develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so expect continuing improvements (bulk uploading and file conversion, annotation via ontologies, super group visibility settings, additional file formats, etc.). See http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper http://www.biomedcentral.com/1471-2105/11/455
>
> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2 server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2 wouldn't require any data reformatting.  Although for large datasets, it's best to use one of the compressed binary data formats such as bar, bam, or useq.
>
> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works well for accessing their small annotation datasets (gene models: refseq, knowngenes), but the graph distribution wasn't functional the last I checked.  The problem appeared to be from the server side.
>
> -cheers, David
>
> P.S. I wish I could attend the DAS workshop this year and show you what we've been up to.  Any chance of getting a Skype conference call with posted presentations?  Would be great if someone hosted a DAS Workshop in the US.
>
>
> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>
> The core genomancer code is pretty stable, most of the recent work is
> in plugins (and some work in the core to allow more extensive
> plugins).
>
> You should be able to get a working DAS1-->DAS2 proxy running from
> the current head of the Trellis SVN repository -- you would just need
> to add a web.xml config file with servlet parameters to get it going in a
> servlet container like Tomcat, or alternatively run the built-in Jetty server
> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>
> But if the intent is to load DAS 1.x data into IGB, I don't think you
> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
> already supports DAS 1.5 access.  In the "Data Access" tab, under
> "Choose Data Sources and Data Sets" section click the "Configure"
> button.  This brings up a window with a "Data Sources" tab, and in
> that tab you can click the "Add" button to bring up a dialog that lets
> you select "DAS" for the data source type, and enter the URL for a DAS
> server.  This worked fine for loading data from the UCSC DAS 1.5
> server -- I haven't tried accessing data from any other DAS servers
> recently.
>
> I'm forwarding to the genoviz-devel list for IGB developments and
> discussion, to see if anyone currently working on IGB can add any more
> info.
>
> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
> <jprocter at compbio.dundee.ac.uk> wrote:
>>
>> Hi all (but Gregg in particular!)
>>
>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>> it looks like there's a moderate amount of commit activity in the
>> project at the moment, making me a little nervous about attempting to
>> use the code in a production(ish) setting.
>>
>> many thanks in advance,
>> Jim.
>>
>> --
>> -------------------------------------------------------------------
>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>
>> _______________________________________________
>> 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
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das





From David.Nix at hci.utah.edu  Mon Feb  7 16:58:17 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Mon, 7 Feb 2011 09:58:17 -0700
Subject: [DAS] US DAS workshop
In-Reply-To: <C9758737.6C26%aloraine@uncc.edu>
Message-ID: <C97572B9.7D42%david.nix@hci.utah.edu>

Hmm...

There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and the organizers might already have a set program.  There is a "Databases, Data Mining, Visualization and Curation" session by Alex Bateman and Ting Wang though.

-cheers, D




On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:

Hi,

Same for us here at UNC Charlotte.

Meetings I'm attending next include two major plant science meetings
(Arabidopsis and ASPB) and possibly ISMB in Vienna.

David are there any other meetings you and your group are planning to
attend?

The ideal setting would be a meeting where we can do outreach and hold
workshop event(s) for users, but also have a developers meeting where we
discuss future directions for the software, DAS spec, etc.

Are there other meetings that would be a good fit?

Best,

Ann

On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:

> Ah, that makes sense.
>
> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
> It might be best to make this part of a larger genomics/ proteomics meeting to
> start.  This would draw more folks who are interested in distributing their
> own data and working DAS access into their own applications.  Are their any
> appropriate upcoming meetings?
>
> -cheers, D
>
>
> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>
> Hi David,
>
> I guess one of the big reasons to want a proxy is it allows you to use DAS
> sources you don't control, which is obviously potentially a really big benefit
> with so many DAS/1 sources around. I don't know if this is what Jim is trying
> to achieve though. In truth this has always been the difficulty with the
> das/das2 tech divide really, with such a huge existing implementation base
> there's a very high "activation energy" in switching!
>
> What was the issue with the ensembl servers?
>
> Jon and I have talked a few times about organising a DAS workshop in North
> America, we just need someone to host (and to an extent fund) it. Do you have
> any suggestions? Almost all of the attendees for our workshops are from
> Europe, in fact lots are from Hinxton. So what sort of demand do you think
> there would be stateside for such an event? Enough for a standalone workshop,
> or more conducive to an add-on to or collaboration with another event?
>
> Maybe we can look into webcasting the talks? No idea how to go about this
> though!
>
> On 4 Feb 2011, at 19:13, David Nix wrote:
>
>> Hello Jim,
>>
>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>> it would be best to use a DAS/2 server such as the Classic (command line) or
>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>> expect continuing improvements (bulk uploading and file conversion,
>> annotation via ontologies, super group visibility settings, additional file
>> formats, etc.). See
>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>> http://www.biomedcentral.com/1471-2105/11/455
>>
>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>> server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2
>> wouldn't require any data reformatting.  Although for large datasets, it's
>> best to use one of the compressed binary data formats such as bar, bam, or
>> useq.
>>
>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works
>> well for accessing their small annotation datasets (gene models: refseq,
>> knowngenes), but the graph distribution wasn't functional the last I checked.
>> The problem appeared to be from the server side.
>>
>> -cheers, David
>>
>> P.S. I wish I could attend the DAS workshop this year and show you what we've
>> been up to.  Any chance of getting a Skype conference call with posted
>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>
>>
>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>
>> The core genomancer code is pretty stable, most of the recent work is
>> in plugins (and some work in the core to allow more extensive
>> plugins).
>>
>> You should be able to get a working DAS1-->DAS2 proxy running from
>> the current head of the Trellis SVN repository -- you would just need
>> to add a web.xml config file with servlet parameters to get it going in a
>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>
>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>> "Choose Data Sources and Data Sets" section click the "Configure"
>> button.  This brings up a window with a "Data Sources" tab, and in
>> that tab you can click the "Add" button to bring up a dialog that lets
>> you select "DAS" for the data source type, and enter the URL for a DAS
>> server.  This worked fine for loading data from the UCSC DAS 1.5
>> server -- I haven't tried accessing data from any other DAS servers
>> recently.
>>
>> I'm forwarding to the genoviz-devel list for IGB developments and
>> discussion, to see if anyone currently working on IGB can add any more
>> info.
>>
>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>
>>> Hi all (but Gregg in particular!)
>>>
>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>> it looks like there's a moderate amount of commit activity in the
>>> project at the moment, making me a little nervous about attempting to
>>> use the code in a production(ish) setting.
>>>
>>> many thanks in advance,
>>> Jim.
>>>
>>> --
>>> -------------------------------------------------------------------
>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>
>>> _______________________________________________
>>> 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
>>
>>
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
>
>
> ------------------------------------------------------------------------------
> The modern datacenter depends on network connectivity to access resources
> and provide services. The best practices for maximizing a physical server's
> connectivity to a physical network are well understood - see how these
> rules translate into the virtual world?
> http://p.sf.net/sfu/oracle-sfdevnlfb
> _______________________________________________
> Genoviz-devel mailing list
> Genoviz-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/genoviz-devel

--
Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
www.transvar.org






From jw12 at sanger.ac.uk  Mon Feb  7 17:42:55 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 7 Feb 2011 17:42:55 +0000
Subject: [DAS] example DAS sources working in GBrowse?
Message-ID: <21F8F18F-CBC1-4D7B-B91A-E89285DC15DB@sanger.ac.uk>

Hi

We have a das source here that we would like to show up in GBrowse but  
the people concerned are not able to view their data.
Has anyone got a working GBrowse config that we could see that  
attaches a DAS source?
The source we would like to attach is here http://das.sanger.ac.uk/das/pjazz_berghei/features?segment=berg01:1000,200000 
  and seems to be working fine.


Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From jw12 at sanger.ac.uk  Mon Feb  7 17:47:17 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 7 Feb 2011 17:47:17 +0000
Subject: [DAS] DAS examples
Message-ID: <780E2881-A99A-4244-9C8E-40719B78B681@sanger.ac.uk>

Hi

I'm putting together some example requests for the registry and normal  
DAS sources. We hope to use this for the DAS workshop this year as a  
quick reference.

If anyone has some example requests they would like added or has any  
suggestions to make this resource better please drop me or the list a  
line?

current draft is here: http://biodasman.wordpress.com/2011/01/19/das-glossary-first-draft/


Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From andy.jenkinson at ebi.ac.uk  Mon Feb  7 17:57:12 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Mon, 7 Feb 2011 17:57:12 +0000
Subject: [DAS] US DAS workshop
In-Reply-To: <C97572B9.7D42%david.nix@hci.utah.edu>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
Message-ID: <DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>

Might we add on to the end/beginning of GI instead of running concurrently (assuming CSHL can oblige)? Perhaps we can consider running a workshop at ISMB next year (California?) should interest be sufficient for an event at GI or the like this year?

I just noticed GI is actually in November though, by the way.

On 7 Feb 2011, at 16:58, David Nix wrote:

> Hmm...
> 
> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and the organizers might already have a set program.  There is a "Databases, Data Mining, Visualization and Curation" session by Alex Bateman and Ting Wang though.
> 
> -cheers, D
> 
> 
> 
> 
> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
> 
> Hi,
> 
> Same for us here at UNC Charlotte.
> 
> Meetings I'm attending next include two major plant science meetings
> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
> 
> David are there any other meetings you and your group are planning to
> attend?
> 
> The ideal setting would be a meeting where we can do outreach and hold
> workshop event(s) for users, but also have a developers meeting where we
> discuss future directions for the software, DAS spec, etc.
> 
> Are there other meetings that would be a good fit?
> 
> Best,
> 
> Ann
> 
> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
> 
>> Ah, that makes sense.
>> 
>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>> It might be best to make this part of a larger genomics/ proteomics meeting to
>> start.  This would draw more folks who are interested in distributing their
>> own data and working DAS access into their own applications.  Are their any
>> appropriate upcoming meetings?
>> 
>> -cheers, D
>> 
>> 
>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>> 
>> Hi David,
>> 
>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>> sources you don't control, which is obviously potentially a really big benefit
>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>> to achieve though. In truth this has always been the difficulty with the
>> das/das2 tech divide really, with such a huge existing implementation base
>> there's a very high "activation energy" in switching!
>> 
>> What was the issue with the ensembl servers?
>> 
>> Jon and I have talked a few times about organising a DAS workshop in North
>> America, we just need someone to host (and to an extent fund) it. Do you have
>> any suggestions? Almost all of the attendees for our workshops are from
>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>> there would be stateside for such an event? Enough for a standalone workshop,
>> or more conducive to an add-on to or collaboration with another event?
>> 
>> Maybe we can look into webcasting the talks? No idea how to go about this
>> though!
>> 
>> On 4 Feb 2011, at 19:13, David Nix wrote:
>> 
>>> Hello Jim,
>>> 
>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>> expect continuing improvements (bulk uploading and file conversion,
>>> annotation via ontologies, super group visibility settings, additional file
>>> formats, etc.). See
>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>> http://www.biomedcentral.com/1471-2105/11/455
>>> 
>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>> server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2
>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>> best to use one of the compressed binary data formats such as bar, bam, or
>>> useq.
>>> 
>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works
>>> well for accessing their small annotation datasets (gene models: refseq,
>>> knowngenes), but the graph distribution wasn't functional the last I checked.
>>> The problem appeared to be from the server side.
>>> 
>>> -cheers, David
>>> 
>>> P.S. I wish I could attend the DAS workshop this year and show you what we've
>>> been up to.  Any chance of getting a Skype conference call with posted
>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>> 
>>> 
>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>> 
>>> The core genomancer code is pretty stable, most of the recent work is
>>> in plugins (and some work in the core to allow more extensive
>>> plugins).
>>> 
>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>> the current head of the Trellis SVN repository -- you would just need
>>> to add a web.xml config file with servlet parameters to get it going in a
>>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>> 
>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>> button.  This brings up a window with a "Data Sources" tab, and in
>>> that tab you can click the "Add" button to bring up a dialog that lets
>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>> server -- I haven't tried accessing data from any other DAS servers
>>> recently.
>>> 
>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>> discussion, to see if anyone currently working on IGB can add any more
>>> info.
>>> 
>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>> 
>>>> Hi all (but Gregg in particular!)
>>>> 
>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>> it looks like there's a moderate amount of commit activity in the
>>>> project at the moment, making me a little nervous about attempting to
>>>> use the code in a production(ish) setting.
>>>> 
>>>> many thanks in advance,
>>>> Jim.
>>>> 
>>>> --
>>>> -------------------------------------------------------------------
>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>> 
>>>> _______________________________________________
>>>> 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
>>> 
>>> 
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> The modern datacenter depends on network connectivity to access resources
>> and provide services. The best practices for maximizing a physical server's
>> connectivity to a physical network are well understood - see how these
>> rules translate into the virtual world?
>> http://p.sf.net/sfu/oracle-sfdevnlfb
>> _______________________________________________
>> Genoviz-devel mailing list
>> Genoviz-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
> 
> --
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 
> 
> 




From suzi at berkeleybop.org  Mon Feb  7 18:00:56 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Mon, 7 Feb 2011 10:00:56 -0800
Subject: [DAS] US DAS workshop
In-Reply-To: <DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
Message-ID: <2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>


On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:

> Might we add on to the end/beginning of GI instead of running concurrently (assuming CSHL can oblige)?

David Stewart is pretty open to this kind of thing given enough forewarning.

> Perhaps we can consider running a workshop at ISMB next year (California?) should interest be sufficient for an event at GI or the like this year?

ISMB is in California next year? Didn't know that. 2012 is far away though.


> 
> I just noticed GI is actually in November though, by the way.

There is also biology of genomes in May.

> 
> On 7 Feb 2011, at 16:58, David Nix wrote:
> 
>> Hmm...
>> 
>> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and the organizers might already have a set program.  There is a "Databases, Data Mining, Visualization and Curation" session by Alex Bateman and Ting Wang though.
>> 
>> -cheers, D
>> 
>> 
>> 
>> 
>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>> 
>> Hi,
>> 
>> Same for us here at UNC Charlotte.
>> 
>> Meetings I'm attending next include two major plant science meetings
>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>> 
>> David are there any other meetings you and your group are planning to
>> attend?
>> 
>> The ideal setting would be a meeting where we can do outreach and hold
>> workshop event(s) for users, but also have a developers meeting where we
>> discuss future directions for the software, DAS spec, etc.
>> 
>> Are there other meetings that would be a good fit?
>> 
>> Best,
>> 
>> Ann
>> 
>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>> 
>>> Ah, that makes sense.
>>> 
>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>>> It might be best to make this part of a larger genomics/ proteomics meeting to
>>> start.  This would draw more folks who are interested in distributing their
>>> own data and working DAS access into their own applications.  Are their any
>>> appropriate upcoming meetings?
>>> 
>>> -cheers, D
>>> 
>>> 
>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>> 
>>> Hi David,
>>> 
>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>> sources you don't control, which is obviously potentially a really big benefit
>>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>>> to achieve though. In truth this has always been the difficulty with the
>>> das/das2 tech divide really, with such a huge existing implementation base
>>> there's a very high "activation energy" in switching!
>>> 
>>> What was the issue with the ensembl servers?
>>> 
>>> Jon and I have talked a few times about organising a DAS workshop in North
>>> America, we just need someone to host (and to an extent fund) it. Do you have
>>> any suggestions? Almost all of the attendees for our workshops are from
>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>> there would be stateside for such an event? Enough for a standalone workshop,
>>> or more conducive to an add-on to or collaboration with another event?
>>> 
>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>> though!
>>> 
>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>> 
>>>> Hello Jim,
>>>> 
>>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>> expect continuing improvements (bulk uploading and file conversion,
>>>> annotation via ontologies, super group visibility settings, additional file
>>>> formats, etc.). See
>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>> 
>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to DAS/2
>>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>>> best to use one of the compressed binary data formats such as bar, bam, or
>>>> useq.
>>>> 
>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This works
>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>> knowngenes), but the graph distribution wasn't functional the last I checked.
>>>> The problem appeared to be from the server side.
>>>> 
>>>> -cheers, David
>>>> 
>>>> P.S. I wish I could attend the DAS workshop this year and show you what we've
>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>> 
>>>> 
>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>> 
>>>> The core genomancer code is pretty stable, most of the recent work is
>>>> in plugins (and some work in the core to allow more extensive
>>>> plugins).
>>>> 
>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>> the current head of the Trellis SVN repository -- you would just need
>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>> servlet container like Tomcat, or alternatively run the built-in Jetty server
>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>> 
>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>> server -- I haven't tried accessing data from any other DAS servers
>>>> recently.
>>>> 
>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>> discussion, to see if anyone currently working on IGB can add any more
>>>> info.
>>>> 
>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>> 
>>>>> Hi all (but Gregg in particular!)
>>>>> 
>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>> it looks like there's a moderate amount of commit activity in the
>>>>> project at the moment, making me a little nervous about attempting to
>>>>> use the code in a production(ish) setting.
>>>>> 
>>>>> many thanks in advance,
>>>>> Jim.
>>>>> 
>>>>> --
>>>>> -------------------------------------------------------------------
>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>>> 
>>> 
>>> ------------------------------------------------------------------------------
>>> The modern datacenter depends on network connectivity to access resources
>>> and provide services. The best practices for maximizing a physical server's
>>> connectivity to a physical network are well understood - see how these
>>> rules translate into the virtual world?
>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>> _______________________________________________
>>> Genoviz-devel mailing list
>>> Genoviz-devel at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>> 
>> --
>> Ann Loraine
>> Associate Professor
>> Dept. of Bioinformatics and Genomics, UNCC
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> www.transvar.org
>> 
>> 
>> 
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das




From David.Nix at hci.utah.edu  Tue Feb  8 19:44:03 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Tue, 8 Feb 2011 12:44:03 -0700
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <C9759DCA.6C43%aloraine@uncc.edu>
Message-ID: <C976EB13.7DAA%david.nix@hci.utah.edu>

There are several of us here who are planning on attending with probably 2 talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 vs DAS/2, future directions, etc.) even if the DAS workshop doesn't materialize.

Would someone who knows Tim or Alex be willing to approach them and inquire about the feasibility of a DAS workshop?

Suzi any more thoughts on a Bay Area session?

-cheers, D


On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:

Hi,

Ting Wang is senior author on a Nature Methods review article (March 2010)
discussing visualization software for genomics.

The dates:

GENOME INFORMATICS
November 2 - 5, 2011
Abstract Deadline: August 12, 2011

I have a break from teaching in the fall so I will definitely try to attend.

The session on alternative splicing also looks very interesting.

Who in the developer's list is interested in attending, contributing to an
abstract, giving a talk?

Best wishes,

Ann







On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:

> Hmm...
>
> There's the Genome Informatics meeting in August at CSHL (
> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
> the organizers might already have a set program.  There is a "Databases, Data
> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
> though.
>
> -cheers, D
>
>
>
>
> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>
> Hi,
>
> Same for us here at UNC Charlotte.
>
> Meetings I'm attending next include two major plant science meetings
> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>
> David are there any other meetings you and your group are planning to
> attend?
>
> The ideal setting would be a meeting where we can do outreach and hold
> workshop event(s) for users, but also have a developers meeting where we
> discuss future directions for the software, DAS spec, etc.
>
> Are there other meetings that would be a good fit?
>
> Best,
>
> Ann
>
> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>
>> Ah, that makes sense.
>>
>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>> It might be best to make this part of a larger genomics/ proteomics meeting
>> to
>> start.  This would draw more folks who are interested in distributing their
>> own data and working DAS access into their own applications.  Are their any
>> appropriate upcoming meetings?
>>
>> -cheers, D
>>
>>
>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>
>> Hi David,
>>
>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>> sources you don't control, which is obviously potentially a really big
>> benefit
>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>> to achieve though. In truth this has always been the difficulty with the
>> das/das2 tech divide really, with such a huge existing implementation base
>> there's a very high "activation energy" in switching!
>>
>> What was the issue with the ensembl servers?
>>
>> Jon and I have talked a few times about organising a DAS workshop in North
>> America, we just need someone to host (and to an extent fund) it. Do you have
>> any suggestions? Almost all of the attendees for our workshops are from
>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>> there would be stateside for such an event? Enough for a standalone workshop,
>> or more conducive to an add-on to or collaboration with another event?
>>
>> Maybe we can look into webcasting the talks? No idea how to go about this
>> though!
>>
>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>
>>> Hello Jim,
>>>
>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>> expect continuing improvements (bulk uploading and file conversion,
>>> annotation via ontologies, super group visibility settings, additional file
>>> formats, etc.). See
>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>> http://www.biomedcentral.com/1471-2105/11/455
>>>
>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>> DAS/2
>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>> best to use one of the compressed binary data formats such as bar, bam, or
>>> useq.
>>>
>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>> works
>>> well for accessing their small annotation datasets (gene models: refseq,
>>> knowngenes), but the graph distribution wasn't functional the last I
>>> checked.
>>> The problem appeared to be from the server side.
>>>
>>> -cheers, David
>>>
>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>> we've
>>> been up to.  Any chance of getting a Skype conference call with posted
>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>
>>>
>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>
>>> The core genomancer code is pretty stable, most of the recent work is
>>> in plugins (and some work in the core to allow more extensive
>>> plugins).
>>>
>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>> the current head of the Trellis SVN repository -- you would just need
>>> to add a web.xml config file with servlet parameters to get it going in a
>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>> server
>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>
>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>> button.  This brings up a window with a "Data Sources" tab, and in
>>> that tab you can click the "Add" button to bring up a dialog that lets
>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>> server -- I haven't tried accessing data from any other DAS servers
>>> recently.
>>>
>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>> discussion, to see if anyone currently working on IGB can add any more
>>> info.
>>>
>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>
>>>> Hi all (but Gregg in particular!)
>>>>
>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>> it looks like there's a moderate amount of commit activity in the
>>>> project at the moment, making me a little nervous about attempting to
>>>> use the code in a production(ish) setting.
>>>>
>>>> many thanks in advance,
>>>> Jim.
>>>>
>>>> --
>>>> -------------------------------------------------------------------
>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>
>>>> _______________________________________________
>>>> 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
>>>
>>>
>>> _______________________________________________
>>> DAS mailing list
>>> DAS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/das
>>
>>
>>
>>
----------------------------------------------------------------------------->>
-
>> The modern datacenter depends on network connectivity to access resources
>> and provide services. The best practices for maximizing a physical server's
>> connectivity to a physical network are well understood - see how these
>> rules translate into the virtual world?
>> http://p.sf.net/sfu/oracle-sfdevnlfb
>> _______________________________________________
>> Genoviz-devel mailing list
>> Genoviz-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>
> --
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
>
>
>

--
Ann Loraine
Associate Professor
Dept. of Bioinformatics and Genomics, UNCC
North Carolina Research Campus
600 Laureate Way
Kannapolis, NC 28081
704-250-5750
www.transvar.org



------------------------------------------------------------------------------
The modern datacenter depends on network connectivity to access resources
and provide services. The best practices for maximizing a physical server's
connectivity to a physical network are well understood - see how these
rules translate into the virtual world?
http://p.sf.net/sfu/oracle-sfdevnlfb
_______________________________________________
Genoviz-devel mailing list
Genoviz-devel at lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/genoviz-devel




From suzi at berkeleybop.org  Tue Feb  8 21:49:20 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Tue, 8 Feb 2011 16:49:20 -0500
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <C976EB13.7DAA%david.nix@hci.utah.edu>
References: <C976EB13.7DAA%david.nix@hci.utah.edu>
Message-ID: <5E1C5932-D100-45FC-AC99-A68EFE2CA89E@berkeleybop.org>


On Feb 8, 2011, at 2:44 PM, David Nix wrote:

> There are several of us here who are planning on attending with probably 2 talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 vs DAS/2, future directions, etc.) even if the DAS workshop doesn't materialize.
> 
> Would someone who knows Tim or Alex be willing to approach them and inquire about the feasibility of a DAS workshop?
who? I probably should know who you're talking about, but they aren't part of the GI meeting or part of CSHL so ...

> 
> Suzi any more thoughts on a Bay Area session?

Given enough lead time there is a good room I can reserve for holding the meeting. So I suppose all that needs to be done at this point is for me to check availability of this room and given that, set up a doodle poll.

I'm assuming no more than 40 people. 

> 
> -cheers, D
> 
> 
> On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
> 
> Hi,
> 
> Ting Wang is senior author on a Nature Methods review article (March 2010)
> discussing visualization software for genomics.
> 
> The dates:
> 
> GENOME INFORMATICS
> November 2 - 5, 2011
> Abstract Deadline: August 12, 2011
> 
> I have a break from teaching in the fall so I will definitely try to attend.
> 
> The session on alternative splicing also looks very interesting.
> 
> Who in the developer's list is interested in attending, contributing to an
> abstract, giving a talk?
> 
> Best wishes,
> 
> Ann
> 
> 
> 
> 
> 
> 
> 
> On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
> 
>> Hmm...
>> 
>> There's the Genome Informatics meeting in August at CSHL (
>> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
>> the organizers might already have a set program.  There is a "Databases, Data
>> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
>> though.
>> 
>> -cheers, D
>> 
>> 
>> 
>> 
>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>> 
>> Hi,
>> 
>> Same for us here at UNC Charlotte.
>> 
>> Meetings I'm attending next include two major plant science meetings
>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>> 
>> David are there any other meetings you and your group are planning to
>> attend?
>> 
>> The ideal setting would be a meeting where we can do outreach and hold
>> workshop event(s) for users, but also have a developers meeting where we
>> discuss future directions for the software, DAS spec, etc.
>> 
>> Are there other meetings that would be a good fit?
>> 
>> Best,
>> 
>> Ann
>> 
>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>> 
>>> Ah, that makes sense.
>>> 
>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>>> It might be best to make this part of a larger genomics/ proteomics meeting
>>> to
>>> start.  This would draw more folks who are interested in distributing their
>>> own data and working DAS access into their own applications.  Are their any
>>> appropriate upcoming meetings?
>>> 
>>> -cheers, D
>>> 
>>> 
>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>> 
>>> Hi David,
>>> 
>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>> sources you don't control, which is obviously potentially a really big
>>> benefit
>>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>>> to achieve though. In truth this has always been the difficulty with the
>>> das/das2 tech divide really, with such a huge existing implementation base
>>> there's a very high "activation energy" in switching!
>>> 
>>> What was the issue with the ensembl servers?
>>> 
>>> Jon and I have talked a few times about organising a DAS workshop in North
>>> America, we just need someone to host (and to an extent fund) it. Do you have
>>> any suggestions? Almost all of the attendees for our workshops are from
>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>> there would be stateside for such an event? Enough for a standalone workshop,
>>> or more conducive to an add-on to or collaboration with another event?
>>> 
>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>> though!
>>> 
>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>> 
>>>> Hello Jim,
>>>> 
>>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>> expect continuing improvements (bulk uploading and file conversion,
>>>> annotation via ontologies, super group visibility settings, additional file
>>>> formats, etc.). See
>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>> 
>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>>> DAS/2
>>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>>> best to use one of the compressed binary data formats such as bar, bam, or
>>>> useq.
>>>> 
>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>>> works
>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>> knowngenes), but the graph distribution wasn't functional the last I
>>>> checked.
>>>> The problem appeared to be from the server side.
>>>> 
>>>> -cheers, David
>>>> 
>>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>>> we've
>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>> 
>>>> 
>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>> 
>>>> The core genomancer code is pretty stable, most of the recent work is
>>>> in plugins (and some work in the core to allow more extensive
>>>> plugins).
>>>> 
>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>> the current head of the Trellis SVN repository -- you would just need
>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>>> server
>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>> 
>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>> server -- I haven't tried accessing data from any other DAS servers
>>>> recently.
>>>> 
>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>> discussion, to see if anyone currently working on IGB can add any more
>>>> info.
>>>> 
>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>> 
>>>>> Hi all (but Gregg in particular!)
>>>>> 
>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>> it looks like there's a moderate amount of commit activity in the
>>>>> project at the moment, making me a little nervous about attempting to
>>>>> use the code in a production(ish) setting.
>>>>> 
>>>>> many thanks in advance,
>>>>> Jim.
>>>>> 
>>>>> --
>>>>> -------------------------------------------------------------------
>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>> 
>>>>> _______________________________________________
>>>>> 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
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>>> 
>>> 
>>> 
> ----------------------------------------------------------------------------->>
> -
>>> The modern datacenter depends on network connectivity to access resources
>>> and provide services. The best practices for maximizing a physical server's
>>> connectivity to a physical network are well understood - see how these
>>> rules translate into the virtual world?
>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>> _______________________________________________
>>> Genoviz-devel mailing list
>>> Genoviz-devel at lists.sourceforge.net
>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>> 
>> --
>> Ann Loraine
>> Associate Professor
>> Dept. of Bioinformatics and Genomics, UNCC
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> www.transvar.org
>> 
>> 
>> 
> 
> --
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 
> 
> 
> ------------------------------------------------------------------------------
> The modern datacenter depends on network connectivity to access resources
> and provide services. The best practices for maximizing a physical server's
> connectivity to a physical network are well understood - see how these
> rules translate into the virtual world?
> http://p.sf.net/sfu/oracle-sfdevnlfb
> _______________________________________________
> Genoviz-devel mailing list
> Genoviz-devel at lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
> 
> 
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das




From andy.jenkinson at ebi.ac.uk  Wed Feb  9 17:19:12 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Wed, 9 Feb 2011 17:19:12 +0000
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <5E1C5932-D100-45FC-AC99-A68EFE2CA89E@berkeleybop.org>
References: <C976EB13.7DAA%david.nix@hci.utah.edu>
	<5E1C5932-D100-45FC-AC99-A68EFE2CA89E@berkeleybop.org>
Message-ID: <2E193A2E-9045-4122-BA98-39F0D28B7859@ebi.ac.uk>

Hi guys,

Just to mention, Mark Diekhans has kindly offered to help us arrange something at UCSC if we want, so we can consider that a solid offer. I shall defer to the Wisdom Of The List as to preference for location (no doubt Suzi would prefer Berkeley!). I'm not sure if the aim is to attract participation or just get together. Also, what sort of dates are people thinking of?

Cheers,
Andy

On 8 Feb 2011, at 21:49, Suzanna Lewis wrote:

> 
> On Feb 8, 2011, at 2:44 PM, David Nix wrote:
> 
>> There are several of us here who are planning on attending with probably 2 talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1 vs DAS/2, future directions, etc.) even if the DAS workshop doesn't materialize.
>> 
>> Would someone who knows Tim or Alex be willing to approach them and inquire about the feasibility of a DAS workshop?
> who? I probably should know who you're talking about, but they aren't part of the GI meeting or part of CSHL so ...
> 
>> 
>> Suzi any more thoughts on a Bay Area session?
> 
> Given enough lead time there is a good room I can reserve for holding the meeting. So I suppose all that needs to be done at this point is for me to check availability of this room and given that, set up a doodle poll.
> 
> I'm assuming no more than 40 people. 
> 
>> 
>> -cheers, D
>> 
>> 
>> On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>> 
>> Hi,
>> 
>> Ting Wang is senior author on a Nature Methods review article (March 2010)
>> discussing visualization software for genomics.
>> 
>> The dates:
>> 
>> GENOME INFORMATICS
>> November 2 - 5, 2011
>> Abstract Deadline: August 12, 2011
>> 
>> I have a break from teaching in the fall so I will definitely try to attend.
>> 
>> The session on alternative splicing also looks very interesting.
>> 
>> Who in the developer's list is interested in attending, contributing to an
>> abstract, giving a talk?
>> 
>> Best wishes,
>> 
>> Ann
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>> 
>>> Hmm...
>>> 
>>> There's the Genome Informatics meeting in August at CSHL (
>>> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
>>> the organizers might already have a set program.  There is a "Databases, Data
>>> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
>>> though.
>>> 
>>> -cheers, D
>>> 
>>> 
>>> 
>>> 
>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>> 
>>> Hi,
>>> 
>>> Same for us here at UNC Charlotte.
>>> 
>>> Meetings I'm attending next include two major plant science meetings
>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>> 
>>> David are there any other meetings you and your group are planning to
>>> attend?
>>> 
>>> The ideal setting would be a meeting where we can do outreach and hold
>>> workshop event(s) for users, but also have a developers meeting where we
>>> discuss future directions for the software, DAS spec, etc.
>>> 
>>> Are there other meetings that would be a good fit?
>>> 
>>> Best,
>>> 
>>> Ann
>>> 
>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>> 
>>>> Ah, that makes sense.
>>>> 
>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that would
>>>> attend an out of state meeting.  The bay area would be ideal (thanks Suzi!).
>>>> It might be best to make this part of a larger genomics/ proteomics meeting
>>>> to
>>>> start.  This would draw more folks who are interested in distributing their
>>>> own data and working DAS access into their own applications.  Are their any
>>>> appropriate upcoming meetings?
>>>> 
>>>> -cheers, D
>>>> 
>>>> 
>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>>> 
>>>> Hi David,
>>>> 
>>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>>> sources you don't control, which is obviously potentially a really big
>>>> benefit
>>>> with so many DAS/1 sources around. I don't know if this is what Jim is trying
>>>> to achieve though. In truth this has always been the difficulty with the
>>>> das/das2 tech divide really, with such a huge existing implementation base
>>>> there's a very high "activation energy" in switching!
>>>> 
>>>> What was the issue with the ensembl servers?
>>>> 
>>>> Jon and I have talked a few times about organising a DAS workshop in North
>>>> America, we just need someone to host (and to an extent fund) it. Do you have
>>>> any suggestions? Almost all of the attendees for our workshops are from
>>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>>> there would be stateside for such an event? Enough for a standalone workshop,
>>>> or more conducive to an add-on to or collaboration with another event?
>>>> 
>>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>>> though!
>>>> 
>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>> 
>>>>> Hello Jim,
>>>>> 
>>>>> If I make a suggestion.  If you're looking to visualize genomic data in IGB,
>>>>> it would be best to use a DAS/2 server such as the Classic (command line) or
>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is well
>>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig, bar,
>>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>>> expect continuing improvements (bulk uploading and file conversion,
>>>>> annotation via ontologies, super group visibility settings, additional file
>>>>> formats, etc.). See
>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our paper
>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>> 
>>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz DAS/2
>>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>>>> DAS/2
>>>>> wouldn't require any data reformatting.  Although for large datasets, it's
>>>>> best to use one of the compressed binary data formats such as bar, bam, or
>>>>> useq.
>>>>> 
>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>>>> works
>>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>>> knowngenes), but the graph distribution wasn't functional the last I
>>>>> checked.
>>>>> The problem appeared to be from the server side.
>>>>> 
>>>>> -cheers, David
>>>>> 
>>>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>>>> we've
>>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>>> presentations?  Would be great if someone hosted a DAS Workshop in the US.
>>>>> 
>>>>> 
>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>> 
>>>>> The core genomancer code is pretty stable, most of the recent work is
>>>>> in plugins (and some work in the core to allow more extensive
>>>>> plugins).
>>>>> 
>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>> the current head of the Trellis SVN repository -- you would just need
>>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>>>> server
>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>>> 
>>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>> server -- I haven't tried accessing data from any other DAS servers
>>>>> recently.
>>>>> 
>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>> discussion, to see if anyone currently working on IGB can add any more
>>>>> info.
>>>>> 
>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>> 
>>>>>> Hi all (but Gregg in particular!)
>>>>>> 
>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>> project at the moment, making me a little nervous about attempting to
>>>>>> use the code in a production(ish) setting.
>>>>>> 
>>>>>> many thanks in advance,
>>>>>> Jim.
>>>>>> 
>>>>>> --
>>>>>> -------------------------------------------------------------------
>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>>> 
>>>>>> _______________________________________________
>>>>>> 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
>>>>> 
>>>>> 
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>> 
>>>> 
>>>> 
>>>> 
>> ----------------------------------------------------------------------------->>
>> -
>>>> The modern datacenter depends on network connectivity to access resources
>>>> and provide services. The best practices for maximizing a physical server's
>>>> connectivity to a physical network are well understood - see how these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>> 
>>> --
>>> Ann Loraine
>>> Associate Professor
>>> Dept. of Bioinformatics and Genomics, UNCC
>>> North Carolina Research Campus
>>> 600 Laureate Way
>>> Kannapolis, NC 28081
>>> 704-250-5750
>>> www.transvar.org
>>> 
>>> 
>>> 
>> 
>> --
>> Ann Loraine
>> Associate Professor
>> Dept. of Bioinformatics and Genomics, UNCC
>> North Carolina Research Campus
>> 600 Laureate Way
>> Kannapolis, NC 28081
>> 704-250-5750
>> www.transvar.org
>> 
>> 
>> 
>> ------------------------------------------------------------------------------
>> The modern datacenter depends on network connectivity to access resources
>> and provide services. The best practices for maximizing a physical server's
>> connectivity to a physical network are well understood - see how these
>> rules translate into the virtual world?
>> http://p.sf.net/sfu/oracle-sfdevnlfb
>> _______________________________________________
>> Genoviz-devel mailing list
>> Genoviz-devel at lists.sourceforge.net
>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>> 
>> 
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
> 




From chris at compbio.dundee.ac.uk  Thu Feb 10 08:53:03 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Thu, 10 Feb 2011 08:53:03 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <48355836-341A-4DCC-976F-801308CBEF06@ebi.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
	<48355836-341A-4DCC-976F-801308CBEF06@ebi.ac.uk>
Message-ID: <4D53A76F.7040609@compbio.dundee.ac.uk>

Yup that did it. Thanks!

I'm using an older version which doesn't quite as a full a description 
of the build_types() method.

Sorry for not replying earlier - been having webserver and database 
issues that needed fixing first.
Cheers,

Chris

On 07/02/11 14:56, Andy Jenkinson wrote:
> The SourceAdaptor POD documents the build_types method. Just return an array containing a hash per type. For example:
> return ( { 'type' =>  'expression_tag', 'category' =>  'experimental' } );
>
> A more complete implementation would also include an ontology term and the 'count' for each type (i.e. the number of features of each type). Note that the build_types command takes segment parameters like the build_features method, except the segment is optional for build_types:
> /das/yoursource/types
> /das/yoursource/types?segment=X:1,100
>
> Just make sure the content matches the types and categories used by the features command.
>
> See the spec for more details:
> http://www.biodas.org/documents/spec-1.6.html#types
>
> On 7 Feb 2011, at 14:48, Chris Cole wrote:
>
>> Hi Andy,
>>
>> Thanks for the help. Looks like I was close...
>>
>> I now get an error regarding the 'types' command. I haven't implemented it so that's not a surprise. However, I'm struggling to find documentation on the build_types() function and what data it should return. My source data only has one type: 'expression_tag' so how should I return that?
>> Cheers,
>>
>> Chris
>>
>> On 07/02/11 11:40, Andy Jenkinson wrote:
>>> Hi Chris,
>>>
>>> The 'reference' Ensembl sources are suitable for use as mapmasters, as they provide sequence information:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>>>
>>> So, barring any particular nuance of IGB, the correct mapmaster URL would be:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>>>
>>> (assuming thaliana)
>>>
>>> The reason for all this is I guess that IGB does not support the DAS 1.53E/1.6 sources command, which provides species and coordinate information directly.
>>>
>>> Cheers,
>>> Andy
>>>
>>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a functioning ProServer install that works fine with Ensembl, but I'd like to get it working with IGB as well. However, it fails to load as it has a 'Missing MAPMASTER element'. I see I need to specify a URI to a known MAPMASTER source, but I've no idea how.
>>>>
>>>> The server is for Arabidopsis data and I've found the Ensembl DAS sources for plants, but which can I use as a mapmaster?
>>>> http://plants.ensembl.org/das/dsn
>>>> Or am I barking up the wrong tree?
>>>>
>>>> Any pointers much appreciated.
>>>> Cheers,
>>>>
>>>> Chris
>>>>
>>>>
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>
>>
>> --
>> Dr Chris Cole
>> Senior Bioinformatics Research Officer
>> College of Life Sciences
>> University of Dundee
>> Dow Street
>> Dundee
>> DD1 5EH
>> Scotland, UK
>>
>> url: http://network.nature.com/profile/drchriscole
>> e-mail: chris at compbio.dundee.ac.uk
>> Tel: +44 (0)1382 388 721
>>
>> The University of Dundee is a registered Scottish charity, No: SC015096
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096


From chris at compbio.dundee.ac.uk  Thu Feb 10 08:53:45 2011
From: chris at compbio.dundee.ac.uk (Chris Cole)
Date: Thu, 10 Feb 2011 08:53:45 +0000
Subject: [DAS] Configuring a valid MAPMASTER?
In-Reply-To: <895C8BD6-42CC-4E26-93A3-E5BFC2478B20@sanger.ac.uk>
References: <4D4FCABC.7080103@compbio.dundee.ac.uk>
	<0E258A8F-96F7-4501-8029-4C47C93E9E90@ebi.ac.uk>
	<4D500623.4050803@compbio.dundee.ac.uk>
	<895C8BD6-42CC-4E26-93A3-E5BFC2478B20@sanger.ac.uk>
Message-ID: <4D53A799.1020507@compbio.dundee.ac.uk>

Useful to know. Thanks.

On 07/02/11 14:59, Jonathan Warren wrote:
> I've put a Andys previous answer to this question (when I asked it)
> here:
> http://biodasman.wordpress.com/2010/12/06/implementing-types-in-proserver/
>
>
> On 7 Feb 2011, at 14:48, Chris Cole wrote:
>
>> Hi Andy,
>>
>> Thanks for the help. Looks like I was close...
>>
>> I now get an error regarding the 'types' command. I haven't
>> implemented it so that's not a surprise. However, I'm struggling to
>> find documentation on the build_types() function and what data it
>> should return. My source data only has one type: 'expression_tag' so
>> how should I return that?
>> Cheers,
>>
>> Chris
>>
>> On 07/02/11 11:40, Andy Jenkinson wrote:
>>> Hi Chris,
>>>
>>> The 'reference' Ensembl sources are suitable for use as mapmasters,
>>> as they provide sequence information:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/entry_points
>>>
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference/sequence?segment=1:1,100
>>>
>>>
>>> So, barring any particular nuance of IGB, the correct mapmaster URL
>>> would be:
>>> http://plants.ensembl.org/das/Arabidopsis_thaliana.TAIR10.reference
>>>
>>> (assuming thaliana)
>>>
>>> The reason for all this is I guess that IGB does not support the DAS
>>> 1.53E/1.6 sources command, which provides species and coordinate
>>> information directly.
>>>
>>> Cheers,
>>> Andy
>>>
>>> On 7 Feb 2011, at 10:34, Chris Cole wrote:
>>>
>>>> Hi,
>>>>
>>>> I have a functioning ProServer install that works fine with Ensembl,
>>>> but I'd like to get it working with IGB as well. However, it fails
>>>> to load as it has a 'Missing MAPMASTER element'. I see I need to
>>>> specify a URI to a known MAPMASTER source, but I've no idea how.
>>>>
>>>> The server is for Arabidopsis data and I've found the Ensembl DAS
>>>> sources for plants, but which can I use as a mapmaster?
>>>> http://plants.ensembl.org/das/dsn
>>>> Or am I barking up the wrong tree?
>>>>
>>>> Any pointers much appreciated.
>>>> Cheers,
>>>>
>>>> Chris
>>>>
>>>>
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>
>>
>>
>> --
>> Dr Chris Cole
>> Senior Bioinformatics Research Officer
>> College of Life Sciences
>> University of Dundee
>> Dow Street
>> Dundee
>> DD1 5EH
>> Scotland, UK
>>
>> url: http://network.nature.com/profile/drchriscole
>> e-mail: chris at compbio.dundee.ac.uk
>> Tel: +44 (0)1382 388 721
>>
>> The University of Dundee is a registered Scottish charity, No: SC015096
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> blog: http://biodasman.wordpress.com/
> jw12 at sanger.ac.uk
> Ext: 2314
> Telephone: 01223 492314
>
>
>
>
>
>
>
>
>


-- 
Dr Chris Cole
Senior Bioinformatics Research Officer
College of Life Sciences
University of Dundee
Dow Street
Dundee
DD1 5EH
Scotland, UK

url: http://network.nature.com/profile/drchriscole
e-mail: chris at compbio.dundee.ac.uk
Tel: +44 (0)1382 388 721

The University of Dundee is a registered Scottish charity, No: SC015096


From suzi at berkeleybop.org  Sun Feb 13 10:42:33 2011
From: suzi at berkeleybop.org (Suzanna Lewis)
Date: Sun, 13 Feb 2011 11:42:33 +0100
Subject: [DAS] [Genoviz-devel] US DAS workshop
In-Reply-To: <C97A83FD.6DB2%aloraine@uncc.edu>
References: <C97A83FD.6DB2%aloraine@uncc.edu>
Message-ID: <2A209F00-FC2B-4E31-A0F0-CED1A8243DBA@berkeleybop.org>

UCSC is fine with me, and I don't even need to fly to get there. 

I'm also extremely happy if they and/or Mark Diekhans will take this on. Much easier for me to simply attend - I just wanted to be sure that the meeting happens.

In my head I was thinking of this largely as a developer's meeting/workshop for coordinating efforts.

-S


On Feb 11, 2011, at 3:13 PM, Ann Loraine wrote:

> I think it would be very helpful to have a meeting at UCSC.
> 
> UCSC is such an important data provider that it would be good for all of us
> to have more interactions with the team there.
> 
> Very best wishes,
> 
> Ann
> 
> 
> On 2/9/11 9:19 AM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
> 
>> Hi guys,
>> 
>> Just to mention, Mark Diekhans has kindly offered to help us arrange something
>> at UCSC if we want, so we can consider that a solid offer. I shall defer to
>> the Wisdom Of The List as to preference for location (no doubt Suzi would
>> prefer Berkeley!). I'm not sure if the aim is to attract participation or just
>> get together. Also, what sort of dates are people thinking of?
>> 
>> Cheers,
>> Andy
>> 
>> On 8 Feb 2011, at 21:49, Suzanna Lewis wrote:
>> 
>>> 
>>> On Feb 8, 2011, at 2:44 PM, David Nix wrote:
>>> 
>>>> There are several of us here who are planning on attending with probably 2
>>>> talks and or posters (GenoPub, GNomEx and BST). Would be nice to have a talk
>>>> on just DAS (history, apps, data sources, advantages/ disadvantages, DAS/1
>>>> vs DAS/2, future directions, etc.) even if the DAS workshop doesn't
>>>> materialize.
>>>> 
>>>> Would someone who knows Tim or Alex be willing to approach them and inquire
>>>> about the feasibility of a DAS workshop?
>>> who? I probably should know who you're talking about, but they aren't part of
>>> the GI meeting or part of CSHL so ...
>>> 
>>>> 
>>>> Suzi any more thoughts on a Bay Area session?
>>> 
>>> Given enough lead time there is a good room I can reserve for holding the
>>> meeting. So I suppose all that needs to be done at this point is for me to
>>> check availability of this room and given that, set up a doodle poll.
>>> 
>>> I'm assuming no more than 40 people.
>>> 
>>>> 
>>>> -cheers, D
>>>> 
>>>> 
>>>> On 2/7/11 11:02 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>> 
>>>> Hi,
>>>> 
>>>> Ting Wang is senior author on a Nature Methods review article (March 2010)
>>>> discussing visualization software for genomics.
>>>> 
>>>> The dates:
>>>> 
>>>> GENOME INFORMATICS
>>>> November 2 - 5, 2011
>>>> Abstract Deadline: August 12, 2011
>>>> 
>>>> I have a break from teaching in the fall so I will definitely try to attend.
>>>> 
>>>> The session on alternative splicing also looks very interesting.
>>>> 
>>>> Who in the developer's list is interested in attending, contributing to an
>>>> abstract, giving a talk?
>>>> 
>>>> Best wishes,
>>>> 
>>>> Ann
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> 
>>>> On 2/7/11 11:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>> 
>>>>> Hmm...
>>>>> 
>>>>> There's the Genome Informatics meeting in August at CSHL (
>>>>> http://meetings.cshl.edu/meetings/info11.shtml).  It's not the bay area and
>>>>> the organizers might already have a set program.  There is a "Databases,
>>>>> Data
>>>>> Mining, Visualization and Curation" session by Alex Bateman and Ting Wang
>>>>> though.
>>>>> 
>>>>> -cheers, D
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Same for us here at UNC Charlotte.
>>>>> 
>>>>> Meetings I'm attending next include two major plant science meetings
>>>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>>> 
>>>>> David are there any other meetings you and your group are planning to
>>>>> attend?
>>>>> 
>>>>> The ideal setting would be a meeting where we can do outreach and hold
>>>>> workshop event(s) for users, but also have a developers meeting where we
>>>>> discuss future directions for the software, DAS spec, etc.
>>>>> 
>>>>> Are there other meetings that would be a good fit?
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Ann
>>>>> 
>>>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>>> 
>>>>>> Ah, that makes sense.
>>>>>> 
>>>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah that
>>>>>> would
>>>>>> attend an out of state meeting.  The bay area would be ideal (thanks
>>>>>> Suzi!).
>>>>>> It might be best to make this part of a larger genomics/ proteomics
>>>>>> meeting
>>>>>> to
>>>>>> start.  This would draw more folks who are interested in distributing
>>>>>> their
>>>>>> own data and working DAS access into their own applications.  Are their
>>>>>> any
>>>>>> appropriate upcoming meetings?
>>>>>> 
>>>>>> -cheers, D
>>>>>> 
>>>>>> 
>>>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>>>>>> 
>>>>>> Hi David,
>>>>>> 
>>>>>> I guess one of the big reasons to want a proxy is it allows you to use DAS
>>>>>> sources you don't control, which is obviously potentially a really big
>>>>>> benefit
>>>>>> with so many DAS/1 sources around. I don't know if this is what Jim is
>>>>>> trying
>>>>>> to achieve though. In truth this has always been the difficulty with the
>>>>>> das/das2 tech divide really, with such a huge existing implementation base
>>>>>> there's a very high "activation energy" in switching!
>>>>>> 
>>>>>> What was the issue with the ensembl servers?
>>>>>> 
>>>>>> Jon and I have talked a few times about organising a DAS workshop in North
>>>>>> America, we just need someone to host (and to an extent fund) it. Do you
>>>>>> have
>>>>>> any suggestions? Almost all of the attendees for our workshops are from
>>>>>> Europe, in fact lots are from Hinxton. So what sort of demand do you think
>>>>>> there would be stateside for such an event? Enough for a standalone
>>>>>> workshop,
>>>>>> or more conducive to an add-on to or collaboration with another event?
>>>>>> 
>>>>>> Maybe we can look into webcasting the talks? No idea how to go about this
>>>>>> though!
>>>>>> 
>>>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>>> 
>>>>>>> Hello Jim,
>>>>>>> 
>>>>>>> If I make a suggestion.  If you're looking to visualize genomic data in
>>>>>>> IGB,
>>>>>>> it would be best to use a DAS/2 server such as the Classic (command line)
>>>>>>> or
>>>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.  DAS/2 is
>>>>>>> well
>>>>>>> suited to moving large amounts of sliced graph (gr, sgr, bedgraph, wig,
>>>>>>> bar,
>>>>>>> useq...) and alignment data (ie BAM) to client apps.  We're continuing to
>>>>>>> develop the GenoPub DAS/2 server with 5 year grant support from NHLBI so
>>>>>>> expect continuing improvements (bulk uploading and file conversion,
>>>>>>> annotation via ontologies, super group visibility settings, additional
>>>>>>> file
>>>>>>> formats, etc.). See
>>>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2  and our
>>>>>>> paper
>>>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>>> 
>>>>>>> GenoViz folks, correct me if I'm wrong here but I believe the GenoViz
>>>>>>> DAS/2
>>>>>>> server supports  DAS xml datasets so moving data from a DAS/1 server to
>>>>>>> DAS/2
>>>>>>> wouldn't require any data reformatting.  Although for large datasets,
>>>>>>> it's
>>>>>>> best to use one of the compressed binary data formats such as bar, bam,
>>>>>>> or
>>>>>>> useq.
>>>>>>> 
>>>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1 servers.  This
>>>>>>> works
>>>>>>> well for accessing their small annotation datasets (gene models: refseq,
>>>>>>> knowngenes), but the graph distribution wasn't functional the last I
>>>>>>> checked.
>>>>>>> The problem appeared to be from the server side.
>>>>>>> 
>>>>>>> -cheers, David
>>>>>>> 
>>>>>>> P.S. I wish I could attend the DAS workshop this year and show you what
>>>>>>> we've
>>>>>>> been up to.  Any chance of getting a Skype conference call with posted
>>>>>>> presentations?  Would be great if someone hosted a DAS Workshop in the
>>>>>>> US.
>>>>>>> 
>>>>>>> 
>>>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>>> 
>>>>>>> The core genomancer code is pretty stable, most of the recent work is
>>>>>>> in plugins (and some work in the core to allow more extensive
>>>>>>> plugins).
>>>>>>> 
>>>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>>>> the current head of the Trellis SVN repository -- you would just need
>>>>>>> to add a web.xml config file with servlet parameters to get it going in a
>>>>>>> servlet container like Tomcat, or alternatively run the built-in Jetty
>>>>>>> server
>>>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in code.
>>>>>>> 
>>>>>>> But if the intent is to load DAS 1.x data into IGB, I don't think you
>>>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>>>> that tab you can click the "Add" button to bring up a dialog that lets
>>>>>>> you select "DAS" for the data source type, and enter the URL for a DAS
>>>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>>>> server -- I haven't tried accessing data from any other DAS servers
>>>>>>> recently.
>>>>>>> 
>>>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>>>> discussion, to see if anyone currently working on IGB can add any more
>>>>>>> info.
>>>>>>> 
>>>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>>> 
>>>>>>>> Hi all (but Gregg in particular!)
>>>>>>>> 
>>>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of Trellis/Ivy
>>>>>>>> in the Genomancer project (http://code.google.com/p/genomancer/) is
>>>>>>>> stable enough to use. We'd like to set up an in house DAS1->2 proxy and
>>>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>>>> project at the moment, making me a little nervous about attempting to
>>>>>>>> use the code in a production(ish) setting.
>>>>>>>> 
>>>>>>>> many thanks in advance,
>>>>>>>> Jim.
>>>>>>>> 
>>>>>>>> --
>>>>>>>> -------------------------------------------------------------------
>>>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
>>>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>>>> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> DAS mailing list
>>>>>>> DAS at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> 
>>>> ----------------------------------------------------------------------------
>>>> ->>
>>>> -
>>>>>> The modern datacenter depends on network connectivity to access resources
>>>>>> and provide services. The best practices for maximizing a physical
>>>>>> server's
>>>>>> connectivity to a physical network are well understood - see how these
>>>>>> rules translate into the virtual world?
>>>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>>>> _______________________________________________
>>>>>> Genoviz-devel mailing list
>>>>>> Genoviz-devel at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>>> 
>>>>> --
>>>>> Ann Loraine
>>>>> Associate Professor
>>>>> Dept. of Bioinformatics and Genomics, UNCC
>>>>> North Carolina Research Campus
>>>>> 600 Laureate Way
>>>>> Kannapolis, NC 28081
>>>>> 704-250-5750
>>>>> www.transvar.org
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> --
>>>> Ann Loraine
>>>> Associate Professor
>>>> Dept. of Bioinformatics and Genomics, UNCC
>>>> North Carolina Research Campus
>>>> 600 Laureate Way
>>>> Kannapolis, NC 28081
>>>> 704-250-5750
>>>> www.transvar.org
>>>> 
>>>> 
>>>> 
>>>> ----------------------------------------------------------------------------
>>>> --
>>>> The modern datacenter depends on network connectivity to access resources
>>>> and provide services. The best practices for maximizing a physical server's
>>>> connectivity to a physical network are well understood - see how these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>> 
>>>> 
>>>> _______________________________________________
>>>> DAS mailing list
>>>> DAS at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/das
>>> 
>> 
> 
> -- 
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 
> 




From jw12 at sanger.ac.uk  Thu Feb 17 12:36:22 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Thu, 17 Feb 2011 12:36:22 +0000
Subject: [DAS] DAS Workshop Registration Closing Soon
Message-ID: <B3363C0E-BB13-4D30-8E4C-9CBCFB48FCF1@sanger.ac.uk>

Registration closes for the DAS workshop at 5pm this Friday GMT.  
Limited places still available.
Please note that for the tutorials day (Day 1) it is advisable to know  
at least one of PERL, Java or Javascript.
Further information and registration from here: http://www.ebi.ac.uk/training/onsite/110302DAS.html

There are still a few places for short talks on the second day if you  
have anything to talk about of interest to the DAS community.



Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From jw12 at sanger.ac.uk  Mon Feb 21 12:13:04 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 21 Feb 2011 12:13:04 +0000
Subject: [DAS] US DAS workshop
In-Reply-To: <2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
Message-ID: <3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>

So the current situation as far as I can see is that we have at least  
two offers of venues to host a possible DAS workshop in the US. One  
east coast and one west coast? Which is great.
However, at the moment we have no funding and we are not sure what  
format the workshop should be.

I think Andy and myself are keen for this to happen in some way. Maybe  
(after this workshop in the UK next week) we can come up with a short  
5-10 question doodle poll that can be sent around to relevant email  
lists in the US to get an idea of the likely attendance numbers, best  
location, format and likely background of attendees etc.

This email discussion on the list hasn't convinced me that there is a  
massive demand for a general workshop - however I would hope that at  
the least Andy and myself would be able to come over and have a  
developers meeting with the current active DAS developers..... So it  
would be good to see what might come back from this doodle poll?

As a related topic: We are hoping to video many of the presentations  
at the workshop next week to be made available shortly after over the  
web. As always the tutorials and presentations will be available  
online from the biodas wiki:
http://www.biodas.org/wiki/DASWorkshop2011

Hope to see some of you soon.

Thanks

Jonathan.


On 7 Feb 2011, at 18:00, Suzanna Lewis wrote:

>
> On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:
>
>> Might we add on to the end/beginning of GI instead of running  
>> concurrently (assuming CSHL can oblige)?
>
> David Stewart is pretty open to this kind of thing given enough  
> forewarning.
>
>> Perhaps we can consider running a workshop at ISMB next year  
>> (California?) should interest be sufficient for an event at GI or  
>> the like this year?
>
> ISMB is in California next year? Didn't know that. 2012 is far away  
> though.
>
>
>>
>> I just noticed GI is actually in November though, by the way.
>
> There is also biology of genomes in May.
>
>>
>> On 7 Feb 2011, at 16:58, David Nix wrote:
>>
>>> Hmm...
>>>
>>> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml) 
>>> .  It's not the bay area and the organizers might already have a  
>>> set program.  There is a "Databases, Data Mining, Visualization  
>>> and Curation" session by Alex Bateman and Ting Wang though.
>>>
>>> -cheers, D
>>>
>>>
>>>
>>>
>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>
>>> Hi,
>>>
>>> Same for us here at UNC Charlotte.
>>>
>>> Meetings I'm attending next include two major plant science meetings
>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>
>>> David are there any other meetings you and your group are planning  
>>> to
>>> attend?
>>>
>>> The ideal setting would be a meeting where we can do outreach and  
>>> hold
>>> workshop event(s) for users, but also have a developers meeting  
>>> where we
>>> discuss future directions for the software, DAS spec, etc.
>>>
>>> Are there other meetings that would be a good fit?
>>>
>>> Best,
>>>
>>> Ann
>>>
>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>
>>>> Ah, that makes sense.
>>>>
>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah  
>>>> that would
>>>> attend an out of state meeting.  The bay area would be ideal  
>>>> (thanks Suzi!).
>>>> It might be best to make this part of a larger genomics/  
>>>> proteomics meeting to
>>>> start.  This would draw more folks who are interested in  
>>>> distributing their
>>>> own data and working DAS access into their own applications.  Are  
>>>> their any
>>>> appropriate upcoming meetings?
>>>>
>>>> -cheers, D
>>>>
>>>>
>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>  
>>>> wrote:
>>>>
>>>> Hi David,
>>>>
>>>> I guess one of the big reasons to want a proxy is it allows you  
>>>> to use DAS
>>>> sources you don't control, which is obviously potentially a  
>>>> really big benefit
>>>> with so many DAS/1 sources around. I don't know if this is what  
>>>> Jim is trying
>>>> to achieve though. In truth this has always been the difficulty  
>>>> with the
>>>> das/das2 tech divide really, with such a huge existing  
>>>> implementation base
>>>> there's a very high "activation energy" in switching!
>>>>
>>>> What was the issue with the ensembl servers?
>>>>
>>>> Jon and I have talked a few times about organising a DAS workshop  
>>>> in North
>>>> America, we just need someone to host (and to an extent fund) it.  
>>>> Do you have
>>>> any suggestions? Almost all of the attendees for our workshops  
>>>> are from
>>>> Europe, in fact lots are from Hinxton. So what sort of demand do  
>>>> you think
>>>> there would be stateside for such an event? Enough for a  
>>>> standalone workshop,
>>>> or more conducive to an add-on to or collaboration with another  
>>>> event?
>>>>
>>>> Maybe we can look into webcasting the talks? No idea how to go  
>>>> about this
>>>> though!
>>>>
>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>
>>>>> Hello Jim,
>>>>>
>>>>> If I make a suggestion.  If you're looking to visualize genomic  
>>>>> data in IGB,
>>>>> it would be best to use a DAS/2 server such as the Classic  
>>>>> (command line) or
>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.   
>>>>> DAS/2 is well
>>>>> suited to moving large amounts of sliced graph (gr, sgr,  
>>>>> bedgraph, wig, bar,
>>>>> useq...) and alignment data (ie BAM) to client apps.  We're  
>>>>> continuing to
>>>>> develop the GenoPub DAS/2 server with 5 year grant support from  
>>>>> NHLBI so
>>>>> expect continuing improvements (bulk uploading and file  
>>>>> conversion,
>>>>> annotation via ontologies, super group visibility settings,  
>>>>> additional file
>>>>> formats, etc.). See
>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2   
>>>>> and our paper
>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>
>>>>> GenoViz folks, correct me if I'm wrong here but I believe the  
>>>>> GenoViz DAS/2
>>>>> server supports  DAS xml datasets so moving data from a DAS/1  
>>>>> server to DAS/2
>>>>> wouldn't require any data reformatting.  Although for large  
>>>>> datasets, it's
>>>>> best to use one of the compressed binary data formats such as  
>>>>> bar, bam, or
>>>>> useq.
>>>>>
>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1  
>>>>> servers.  This works
>>>>> well for accessing their small annotation datasets (gene models:  
>>>>> refseq,
>>>>> knowngenes), but the graph distribution wasn't functional the  
>>>>> last I checked.
>>>>> The problem appeared to be from the server side.
>>>>>
>>>>> -cheers, David
>>>>>
>>>>> P.S. I wish I could attend the DAS workshop this year and show  
>>>>> you what we've
>>>>> been up to.  Any chance of getting a Skype conference call with  
>>>>> posted
>>>>> presentations?  Would be great if someone hosted a DAS Workshop  
>>>>> in the US.
>>>>>
>>>>>
>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>
>>>>> The core genomancer code is pretty stable, most of the recent  
>>>>> work is
>>>>> in plugins (and some work in the core to allow more extensive
>>>>> plugins).
>>>>>
>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>> the current head of the Trellis SVN repository -- you would just  
>>>>> need
>>>>> to add a web.xml config file with servlet parameters to get it  
>>>>> going in a
>>>>> servlet container like Tomcat, or alternatively run the built-in  
>>>>> Jetty server
>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in  
>>>>> code.
>>>>>
>>>>> But if the intent is to load DAS 1.x data into IGB, I don't  
>>>>> think you
>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>> that tab you can click the "Add" button to bring up a dialog  
>>>>> that lets
>>>>> you select "DAS" for the data source type, and enter the URL for  
>>>>> a DAS
>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>> server -- I haven't tried accessing data from any other DAS  
>>>>> servers
>>>>> recently.
>>>>>
>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>> discussion, to see if anyone currently working on IGB can add  
>>>>> any more
>>>>> info.
>>>>>
>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>
>>>>>> Hi all (but Gregg in particular!)
>>>>>>
>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of  
>>>>>> Trellis/Ivy
>>>>>> in the Genomancer project (http://code.google.com/p/ 
>>>>>> genomancer/) is
>>>>>> stable enough to use. We'd like to set up an in house DAS1->2  
>>>>>> proxy and
>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>> project at the moment, making me a little nervous about  
>>>>>> attempting to
>>>>>> use the code in a production(ish) setting.
>>>>>>
>>>>>> many thanks in advance,
>>>>>> Jim.
>>>>>>
>>>>>> --
>>>>>> -------------------------------------------------------------------
>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research  
>>>>>> Group
>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>> The University of Dundee is a Scottish Registered Charity, No.  
>>>>>> SC015096.
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The modern datacenter depends on network connectivity to access  
>>>> resources
>>>> and provide services. The best practices for maximizing a  
>>>> physical server's
>>>> connectivity to a physical network are well understood - see how  
>>>> these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>
>>> --
>>> Ann Loraine
>>> Associate Professor
>>> Dept. of Bioinformatics and Genomics, UNCC
>>> North Carolina Research Campus
>>> 600 Laureate Way
>>> Kannapolis, NC 28081
>>> 704-250-5750
>>> www.transvar.org
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> 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

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From ljgarcia at ebi.ac.uk  Mon Feb 21 13:27:05 2011
From: ljgarcia at ebi.ac.uk (Leyla Garcia)
Date: Mon, 21 Feb 2011 13:27:05 +0000
Subject: [DAS] DAS client libraries
In-Reply-To: <3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
	<3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
Message-ID: <4D626829.3060302@ebi.ac.uk>

Hi All,

I need to know what DAS client libraries are available. So far I am 
aware of JsDAS and Bio::DAS::Lite but still do not know more about them.
If you have a DAS client library, could you please send me this information?

Client Library Name
Web page
Language
Platform
Clients built upon it
Main advantages
Known restrictions/disadvantages
Currently supported (yes/no, who)
Current version
DAS spec supported

Thanks,

Leyla


From thomas.a.down at gmail.com  Mon Feb 21 13:44:55 2011
From: thomas.a.down at gmail.com (Thomas Down)
Date: Mon, 21 Feb 2011 13:44:55 +0000
Subject: [DAS] DAS client libraries
In-Reply-To: <4D626829.3060302@ebi.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>
	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>
	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
	<3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
	<4D626829.3060302@ebi.ac.uk>
Message-ID: <AANLkTikFPOVe4evUYXHWLJfFPj7TEQPhc5Y3nkCGmMdZ@mail.gmail.com>

On Mon, Feb 21, 2011 at 1:27 PM, Leyla Garcia <ljgarcia at ebi.ac.uk> wrote:

> Hi All,
>
> I need to know what DAS client libraries are available. So far I am aware
> of JsDAS and Bio::DAS::Lite but still do not know more about them.
> If you have a DAS client library, could you please send me this
> information?
>

Well, it hasn't really been "sold" as a library, but it is open source (BSD
license) and would be fairly easy to separate out if another client wanted
to use it, so:


> Client Library Name
>

das.js


> Web page
>

http://github.com/dasmoth/dalliance


> Language
>

Javascript


> Platform
>

Modern web browsers, plus IE8+.


> Clients built upon it
>

Dalliance


> Main advantages


Very lightweight.
No external dependencies
Designed for asynchronous operation.
Can do cross-origin fetching (including credentialed CORS) on most browsers.
Empirical testing suggests it's pretty tolerant of any DAS XML "in the wild"
at the moment.


> Known restrictions/disadvantages
>

Missing support for a few things we don't currently use in Dalliance (e.g.
DSN requests, structure extension, etc.).
Currently not easy to cancel in-flight requests (although that's something
we're working on).


> Currently supported (yes/no, who)
>

Yes, file a ticket in Github or e-mail me.


> Current version
>

Linked to Dalliance releases, current version is 0.5.7 (0.6 should be out in
the next few days, but doesn't have any major changes to the DAS backend).


> DAS spec supported
>

1.5, 1.6

           Thomas.


From jw12 at sanger.ac.uk  Mon Feb 21 14:45:14 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 21 Feb 2011 14:45:14 +0000
Subject: [DAS] DAS client libraries
In-Reply-To: <4D626829.3060302@ebi.ac.uk>
References: <C97572B9.7D42%david.nix@hci.utah.edu>	<DE869BD3-D60F-4565-91D0-1B2B988AB6C9@ebi.ac.uk>	<2CCD61A5-E971-4E5D-B174-89D7D6215A37@berkeleybop.org>
	<3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
	<4D626829.3060302@ebi.ac.uk>
Message-ID: <0847ADF7-D140-46D8-B223-8A98FEB45688@sanger.ac.uk>


On 21 Feb 2011, at 13:27, Leyla Garcia wrote:

> Hi All,
>
> I need to know what DAS client libraries are available. So far I am  
> aware of JsDAS and Bio::DAS::Lite but still do not know more about  
> them.
> If you have a DAS client library, could you please send me this  
> information?
>
> Client Library Name

Dasobert
> Web page

http://www.spice-3d.org/dasobert/
> Language
Java
> Platform
> Clients built upon it

Spice, DAS Registry, Jalview.....

> Main advantages
Java ? :)


> Known restrictions/disadvantages

Have to read code or find in docs how to access xml attributes and  
elements as hash based not method/object.
Probably needs more documentation and support for asynchronous requests.

> Currently supported (yes/no, who)

yes - though development has been allied to the DAS Registry over the  
last 3 years and mostly validation so not all that useful for "normal  
clients". Jonathan Warren
Hence reason for discussion about Dasobert on day 3 of this years  
workshop- do we want to go with JAXB generated classes? What do we do  
with Dasobert now?
> Current version

http://www.derkholm.net/svn/repos/dasobert/trunk/ has some 1.6 support  
and has moved to using Lists rather than arrays[ ] for old version  
with arrays use oldTrunk under branches.

> DAS spec supported
1.53/1.6
>
> Thanks,
>
> Leyla
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From David.Nix at hci.utah.edu  Tue Feb 22 16:05:54 2011
From: David.Nix at hci.utah.edu (David Nix)
Date: Tue, 22 Feb 2011 09:05:54 -0700
Subject: [DAS] US DAS workshop
In-Reply-To: <3767ED24-B484-42E8-A1A7-36238A895D6E@sanger.ac.uk>
Message-ID: <C9892CF2.8047%david.nix@hci.utah.edu>

Sounds good Jonathan,

Thanks for pursuing this.  I would agree, there isn't a huge demand for a general workshop (just yet) in the US.  Most bioinformatics folks I know just haven't heard about DAS.  And even when I explain it to them the don't understand it nor appreciate what a common language for data distribution can do.  That will hopefully change....

Folks might not have heard but the SRA has been cut.  http://www.ncbi.nlm.nih.gov/sra for the official announcement and http://seqanswers.com/forums/showthread.php?t=9431 for a thread on SeqAnswers.  This is the primary data repository for all things related to next generation sequencing in the US. It's not clear where folks are going to put their fastq and bam files.  It's kind of ridiculous how fragmented the data repository problem has become. Here are the recommendations for where folks should bury, I mean send their data in the US:

[cid:3381210354_50664721]

Ouch!  Each of these repositories has their own methods of encoding meta data and distributing primary data and analysis. The data distribution problem is becoming intractable.

I think we (DAS folks) should speak up loud and clear and make sure that DAS is considered as a technology to link these disparate island of information.

-cheers, D




On 2/21/11 5:13 AM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:

So the current situation as far as I can see is that we have at least
two offers of venues to host a possible DAS workshop in the US. One
east coast and one west coast? Which is great.
However, at the moment we have no funding and we are not sure what
format the workshop should be.

I think Andy and myself are keen for this to happen in some way. Maybe
(after this workshop in the UK next week) we can come up with a short
5-10 question doodle poll that can be sent around to relevant email
lists in the US to get an idea of the likely attendance numbers, best
location, format and likely background of attendees etc.

This email discussion on the list hasn't convinced me that there is a
massive demand for a general workshop - however I would hope that at
the least Andy and myself would be able to come over and have a
developers meeting with the current active DAS developers..... So it
would be good to see what might come back from this doodle poll?

As a related topic: We are hoping to video many of the presentations
at the workshop next week to be made available shortly after over the
web. As always the tutorials and presentations will be available
online from the biodas wiki:
http://www.biodas.org/wiki/DASWorkshop2011

Hope to see some of you soon.

Thanks

Jonathan.


On 7 Feb 2011, at 18:00, Suzanna Lewis wrote:

>
> On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:
>
>> Might we add on to the end/beginning of GI instead of running
>> concurrently (assuming CSHL can oblige)?
>
> David Stewart is pretty open to this kind of thing given enough
> forewarning.
>
>> Perhaps we can consider running a workshop at ISMB next year
>> (California?) should interest be sufficient for an event at GI or
>> the like this year?
>
> ISMB is in California next year? Didn't know that. 2012 is far away
> though.
>
>
>>
>> I just noticed GI is actually in November though, by the way.
>
> There is also biology of genomes in May.
>
>>
>> On 7 Feb 2011, at 16:58, David Nix wrote:
>>
>>> Hmm...
>>>
>>> There's the Genome Informatics meeting in August at CSHL ( http://meetings.cshl.edu/meetings/info11.shtml)
>>> .  It's not the bay area and the organizers might already have a
>>> set program.  There is a "Databases, Data Mining, Visualization
>>> and Curation" session by Alex Bateman and Ting Wang though.
>>>
>>> -cheers, D
>>>
>>>
>>>
>>>
>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>
>>> Hi,
>>>
>>> Same for us here at UNC Charlotte.
>>>
>>> Meetings I'm attending next include two major plant science meetings
>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>
>>> David are there any other meetings you and your group are planning
>>> to
>>> attend?
>>>
>>> The ideal setting would be a meeting where we can do outreach and
>>> hold
>>> workshop event(s) for users, but also have a developers meeting
>>> where we
>>> discuss future directions for the software, DAS spec, etc.
>>>
>>> Are there other meetings that would be a good fit?
>>>
>>> Best,
>>>
>>> Ann
>>>
>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>
>>>> Ah, that makes sense.
>>>>
>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah
>>>> that would
>>>> attend an out of state meeting.  The bay area would be ideal
>>>> (thanks Suzi!).
>>>> It might be best to make this part of a larger genomics/
>>>> proteomics meeting to
>>>> start.  This would draw more folks who are interested in
>>>> distributing their
>>>> own data and working DAS access into their own applications.  Are
>>>> their any
>>>> appropriate upcoming meetings?
>>>>
>>>> -cheers, D
>>>>
>>>>
>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>
>>>> wrote:
>>>>
>>>> Hi David,
>>>>
>>>> I guess one of the big reasons to want a proxy is it allows you
>>>> to use DAS
>>>> sources you don't control, which is obviously potentially a
>>>> really big benefit
>>>> with so many DAS/1 sources around. I don't know if this is what
>>>> Jim is trying
>>>> to achieve though. In truth this has always been the difficulty
>>>> with the
>>>> das/das2 tech divide really, with such a huge existing
>>>> implementation base
>>>> there's a very high "activation energy" in switching!
>>>>
>>>> What was the issue with the ensembl servers?
>>>>
>>>> Jon and I have talked a few times about organising a DAS workshop
>>>> in North
>>>> America, we just need someone to host (and to an extent fund) it.
>>>> Do you have
>>>> any suggestions? Almost all of the attendees for our workshops
>>>> are from
>>>> Europe, in fact lots are from Hinxton. So what sort of demand do
>>>> you think
>>>> there would be stateside for such an event? Enough for a
>>>> standalone workshop,
>>>> or more conducive to an add-on to or collaboration with another
>>>> event?
>>>>
>>>> Maybe we can look into webcasting the talks? No idea how to go
>>>> about this
>>>> though!
>>>>
>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>
>>>>> Hello Jim,
>>>>>
>>>>> If I make a suggestion.  If you're looking to visualize genomic
>>>>> data in IGB,
>>>>> it would be best to use a DAS/2 server such as the Classic
>>>>> (command line) or
>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.
>>>>> DAS/2 is well
>>>>> suited to moving large amounts of sliced graph (gr, sgr,
>>>>> bedgraph, wig, bar,
>>>>> useq...) and alignment data (ie BAM) to client apps.  We're
>>>>> continuing to
>>>>> develop the GenoPub DAS/2 server with 5 year grant support from
>>>>> NHLBI so
>>>>> expect continuing improvements (bulk uploading and file
>>>>> conversion,
>>>>> annotation via ontologies, super group visibility settings,
>>>>> additional file
>>>>> formats, etc.). See
>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2
>>>>> and our paper
>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>
>>>>> GenoViz folks, correct me if I'm wrong here but I believe the
>>>>> GenoViz DAS/2
>>>>> server supports  DAS xml datasets so moving data from a DAS/1
>>>>> server to DAS/2
>>>>> wouldn't require any data reformatting.  Although for large
>>>>> datasets, it's
>>>>> best to use one of the compressed binary data formats such as
>>>>> bar, bam, or
>>>>> useq.
>>>>>
>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1
>>>>> servers.  This works
>>>>> well for accessing their small annotation datasets (gene models:
>>>>> refseq,
>>>>> knowngenes), but the graph distribution wasn't functional the
>>>>> last I checked.
>>>>> The problem appeared to be from the server side.
>>>>>
>>>>> -cheers, David
>>>>>
>>>>> P.S. I wish I could attend the DAS workshop this year and show
>>>>> you what we've
>>>>> been up to.  Any chance of getting a Skype conference call with
>>>>> posted
>>>>> presentations?  Would be great if someone hosted a DAS Workshop
>>>>> in the US.
>>>>>
>>>>>
>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>
>>>>> The core genomancer code is pretty stable, most of the recent
>>>>> work is
>>>>> in plugins (and some work in the core to allow more extensive
>>>>> plugins).
>>>>>
>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>> the current head of the Trellis SVN repository -- you would just
>>>>> need
>>>>> to add a web.xml config file with servlet parameters to get it
>>>>> going in a
>>>>> servlet container like Tomcat, or alternatively run the built-in
>>>>> Jetty server
>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in
>>>>> code.
>>>>>
>>>>> But if the intent is to load DAS 1.x data into IGB, I don't
>>>>> think you
>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>> that tab you can click the "Add" button to bring up a dialog
>>>>> that lets
>>>>> you select "DAS" for the data source type, and enter the URL for
>>>>> a DAS
>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>> server -- I haven't tried accessing data from any other DAS
>>>>> servers
>>>>> recently.
>>>>>
>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>> discussion, to see if anyone currently working on IGB can add
>>>>> any more
>>>>> info.
>>>>>
>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>
>>>>>> Hi all (but Gregg in particular!)
>>>>>>
>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of
>>>>>> Trellis/Ivy
>>>>>> in the Genomancer project (http://code.google.com/p/
>>>>>> genomancer/) is
>>>>>> stable enough to use. We'd like to set up an in house DAS1->2
>>>>>> proxy and
>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>> project at the moment, making me a little nervous about
>>>>>> attempting to
>>>>>> use the code in a production(ish) setting.
>>>>>>
>>>>>> many thanks in advance,
>>>>>> Jim.
>>>>>>
>>>>>> --
>>>>>> -------------------------------------------------------------------
>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research
>>>>>> Group
>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>> The University of Dundee is a Scottish Registered Charity, No.
>>>>>> SC015096.
>>>>>>
>>>>>> _______________________________________________
>>>>>> 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
>>>>>
>>>>>
>>>>> _______________________________________________
>>>>> DAS mailing list
>>>>> DAS at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>
>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> The modern datacenter depends on network connectivity to access
>>>> resources
>>>> and provide services. The best practices for maximizing a
>>>> physical server's
>>>> connectivity to a physical network are well understood - see how
>>>> these
>>>> rules translate into the virtual world?
>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>> _______________________________________________
>>>> Genoviz-devel mailing list
>>>> Genoviz-devel at lists.sourceforge.net
>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>
>>> --
>>> Ann Loraine
>>> Associate Professor
>>> Dept. of Bioinformatics and Genomics, UNCC
>>> North Carolina Research Campus
>>> 600 Laureate Way
>>> Kannapolis, NC 28081
>>> 704-250-5750
>>> www.transvar.org
>>>
>>>
>>>
>>
>>
>> _______________________________________________
>> 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

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









--
 The Wellcome Trust Sanger Institute is operated by Genome Research
 Limited, a charity registered in England with number 1021457 and a
 company registered in England with number 2742969, whose registered
 office is 215 Euston Road, London, NW1 2BE.
_______________________________________________
DAS mailing list
DAS at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/das

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From andy.jenkinson at ebi.ac.uk  Tue Feb 22 18:10:11 2011
From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson)
Date: Tue, 22 Feb 2011 18:10:11 +0000
Subject: [DAS] US DAS workshop
In-Reply-To: <C9894D75.70F4%aloraine@uncc.edu>
References: <C9894D75.70F4%aloraine@uncc.edu>
Message-ID: <CFF23102-D83E-4D1E-9799-58744A8C13ED@ebi.ac.uk>

Just to add, the EBI will continue to support its SRA:
http://www.ebi.ac.uk/ena/SRA_announcement_Feb_2011.pdf

I have not heard of any DDBJ (also part of INSDC) plans to stop accepting submissions either. Is the availability of bandwidth workable for submissions at either of these? They should continue to sync as normal. I hear the east-west coast bandwidth isn't too great anyway, and the transatlantic link is OK.

On 22 Feb 2011, at 16:24, Ann Loraine wrote:

> The announcement says we can deposit RNA-Seq and epigenomic data to GEO and
> transcript assemblies to GenBank/TSA.
> 
> Will GEO capture and make available the FASTQ files? (Or some other format
> for reads?)
> 
> I like how easy GEO makes it to do a bulk download of CEL files.
> 
> Will it provide the same easy method for accessing FASTQ?
> 
> Tools in common use (e.g., bowtie, tophat) are changing at a lightning pace
> and it's important to have access to the "raw" sequence data well into the
> future. 
> 
> 
> On 2/22/11 11:05 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
> 
>> Sounds good Jonathan,
>> 
>> Thanks for pursuing this.  I would agree, there isn't a huge demand for a
>> general workshop (just yet) in the US.  Most bioinformatics folks I know just
>> haven't heard about DAS.  And even when I explain it to them the don't
>> understand it nor appreciate what a common language for data distribution can
>> do.  That will hopefully change....
>> 
>> Folks might not have heard but the SRA has been cut.
>> http://www.ncbi.nlm.nih.gov/sra for the official announcement and
>> http://seqanswers.com/forums/showthread.php?t=9431 for a thread on SeqAnswers.
>> This is the primary data repository for all things related to next generation
>> sequencing in the US. It's not clear where folks are going to put their fastq
>> and bam files.  It's kind of ridiculous how fragmented the data repository
>> problem has become. Here are the recommendations for where folks should bury,
>> I mean send their data in the US:
>> 
>> [cid:3381210354_50664721]
>> 
>> Ouch!  Each of these repositories has their own methods of encoding meta data
>> and distributing primary data and analysis. The data distribution problem is
>> becoming intractable.
>> 
>> I think we (DAS folks) should speak up loud and clear and make sure that DAS
>> is considered as a technology to link these disparate island of information.
>> 
>> -cheers, D
>> 
>> 
>> 
>> 
>> On 2/21/11 5:13 AM, "Jonathan Warren" <jw12 at sanger.ac.uk> wrote:
>> 
>> So the current situation as far as I can see is that we have at least
>> two offers of venues to host a possible DAS workshop in the US. One
>> east coast and one west coast? Which is great.
>> However, at the moment we have no funding and we are not sure what
>> format the workshop should be.
>> 
>> I think Andy and myself are keen for this to happen in some way. Maybe
>> (after this workshop in the UK next week) we can come up with a short
>> 5-10 question doodle poll that can be sent around to relevant email
>> lists in the US to get an idea of the likely attendance numbers, best
>> location, format and likely background of attendees etc.
>> 
>> This email discussion on the list hasn't convinced me that there is a
>> massive demand for a general workshop - however I would hope that at
>> the least Andy and myself would be able to come over and have a
>> developers meeting with the current active DAS developers..... So it
>> would be good to see what might come back from this doodle poll?
>> 
>> As a related topic: We are hoping to video many of the presentations
>> at the workshop next week to be made available shortly after over the
>> web. As always the tutorials and presentations will be available
>> online from the biodas wiki:
>> http://www.biodas.org/wiki/DASWorkshop2011
>> 
>> Hope to see some of you soon.
>> 
>> Thanks
>> 
>> Jonathan.
>> 
>> 
>> On 7 Feb 2011, at 18:00, Suzanna Lewis wrote:
>> 
>>> 
>>> On Feb 7, 2011, at 9:57 AM, Andy Jenkinson wrote:
>>> 
>>>> Might we add on to the end/beginning of GI instead of running
>>>> concurrently (assuming CSHL can oblige)?
>>> 
>>> David Stewart is pretty open to this kind of thing given enough
>>> forewarning.
>>> 
>>>> Perhaps we can consider running a workshop at ISMB next year
>>>> (California?) should interest be sufficient for an event at GI or
>>>> the like this year?
>>> 
>>> ISMB is in California next year? Didn't know that. 2012 is far away
>>> though.
>>> 
>>> 
>>>> 
>>>> I just noticed GI is actually in November though, by the way.
>>> 
>>> There is also biology of genomes in May.
>>> 
>>>> 
>>>> On 7 Feb 2011, at 16:58, David Nix wrote:
>>>> 
>>>>> Hmm...
>>>>> 
>>>>> There's the Genome Informatics meeting in August at CSHL (
>>>>> http://meetings.cshl.edu/meetings/info11.shtml)
>>>>> .  It's not the bay area and the organizers might already have a
>>>>> set program.  There is a "Databases, Data Mining, Visualization
>>>>> and Curation" session by Alex Bateman and Ting Wang though.
>>>>> 
>>>>> -cheers, D
>>>>> 
>>>>> 
>>>>> 
>>>>> 
>>>>> On 2/7/11 9:25 AM, "Ann Loraine" <aloraine at uncc.edu> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Same for us here at UNC Charlotte.
>>>>> 
>>>>> Meetings I'm attending next include two major plant science meetings
>>>>> (Arabidopsis and ASPB) and possibly ISMB in Vienna.
>>>>> 
>>>>> David are there any other meetings you and your group are planning
>>>>> to
>>>>> attend?
>>>>> 
>>>>> The ideal setting would be a meeting where we can do outreach and
>>>>> hold
>>>>> workshop event(s) for users, but also have a developers meeting
>>>>> where we
>>>>> discuss future directions for the software, DAS spec, etc.
>>>>> 
>>>>> Are there other meetings that would be a good fit?
>>>>> 
>>>>> Best,
>>>>> 
>>>>> Ann
>>>>> 
>>>>> On 2/7/11 10:58 AM, "David Nix" <David.Nix at hci.utah.edu> wrote:
>>>>> 
>>>>>> Ah, that makes sense.
>>>>>> 
>>>>>> As for a US meeting, there are 3 or 4 folks here at the U of Utah
>>>>>> that would
>>>>>> attend an out of state meeting.  The bay area would be ideal
>>>>>> (thanks Suzi!).
>>>>>> It might be best to make this part of a larger genomics/
>>>>>> proteomics meeting to
>>>>>> start.  This would draw more folks who are interested in
>>>>>> distributing their
>>>>>> own data and working DAS access into their own applications.  Are
>>>>>> their any
>>>>>> appropriate upcoming meetings?
>>>>>> 
>>>>>> -cheers, D
>>>>>> 
>>>>>> 
>>>>>> On 2/4/11 1:57 PM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk>
>>>>>> wrote:
>>>>>> 
>>>>>> Hi David,
>>>>>> 
>>>>>> I guess one of the big reasons to want a proxy is it allows you
>>>>>> to use DAS
>>>>>> sources you don't control, which is obviously potentially a
>>>>>> really big benefit
>>>>>> with so many DAS/1 sources around. I don't know if this is what
>>>>>> Jim is trying
>>>>>> to achieve though. In truth this has always been the difficulty
>>>>>> with the
>>>>>> das/das2 tech divide really, with such a huge existing
>>>>>> implementation base
>>>>>> there's a very high "activation energy" in switching!
>>>>>> 
>>>>>> What was the issue with the ensembl servers?
>>>>>> 
>>>>>> Jon and I have talked a few times about organising a DAS workshop
>>>>>> in North
>>>>>> America, we just need someone to host (and to an extent fund) it.
>>>>>> Do you have
>>>>>> any suggestions? Almost all of the attendees for our workshops
>>>>>> are from
>>>>>> Europe, in fact lots are from Hinxton. So what sort of demand do
>>>>>> you think
>>>>>> there would be stateside for such an event? Enough for a
>>>>>> standalone workshop,
>>>>>> or more conducive to an add-on to or collaboration with another
>>>>>> event?
>>>>>> 
>>>>>> Maybe we can look into webcasting the talks? No idea how to go
>>>>>> about this
>>>>>> though!
>>>>>> 
>>>>>> On 4 Feb 2011, at 19:13, David Nix wrote:
>>>>>> 
>>>>>>> Hello Jim,
>>>>>>> 
>>>>>>> If I make a suggestion.  If you're looking to visualize genomic
>>>>>>> data in IGB,
>>>>>>> it would be best to use a DAS/2 server such as the Classic
>>>>>>> (command line) or
>>>>>>> GenoPub (web app/ relational database) GenoViz DAS/2 server.
>>>>>>> DAS/2 is well
>>>>>>> suited to moving large amounts of sliced graph (gr, sgr,
>>>>>>> bedgraph, wig, bar,
>>>>>>> useq...) and alignment data (ie BAM) to client apps.  We're
>>>>>>> continuing to
>>>>>>> develop the GenoPub DAS/2 server with 5 year grant support from
>>>>>>> NHLBI so
>>>>>>> expect continuing improvements (bulk uploading and file
>>>>>>> conversion,
>>>>>>> annotation via ontologies, super group visibility settings,
>>>>>>> additional file
>>>>>>> formats, etc.). See
>>>>>>> http://bioserver.hci.utah.edu/BioInfo/index.php/Software:DAS2
>>>>>>> and our paper
>>>>>>> http://www.biomedcentral.com/1471-2105/11/455
>>>>>>> 
>>>>>>> GenoViz folks, correct me if I'm wrong here but I believe the
>>>>>>> GenoViz DAS/2
>>>>>>> server supports  DAS xml datasets so moving data from a DAS/1
>>>>>>> server to DAS/2
>>>>>>> wouldn't require any data reformatting.  Although for large
>>>>>>> datasets, it's
>>>>>>> best to use one of the compressed binary data formats such as
>>>>>>> bar, bam, or
>>>>>>> useq.
>>>>>>> 
>>>>>>> IGB comes pre configured with the UCSC and Ensembl DAS/1
>>>>>>> servers.  This works
>>>>>>> well for accessing their small annotation datasets (gene models:
>>>>>>> refseq,
>>>>>>> knowngenes), but the graph distribution wasn't functional the
>>>>>>> last I checked.
>>>>>>> The problem appeared to be from the server side.
>>>>>>> 
>>>>>>> -cheers, David
>>>>>>> 
>>>>>>> P.S. I wish I could attend the DAS workshop this year and show
>>>>>>> you what we've
>>>>>>> been up to.  Any chance of getting a Skype conference call with
>>>>>>> posted
>>>>>>> presentations?  Would be great if someone hosted a DAS Workshop
>>>>>>> in the US.
>>>>>>> 
>>>>>>> 
>>>>>>> On 2/4/11 8:19 AM, "Gregg Helt" <gregghelt at gmail.com> wrote:
>>>>>>> 
>>>>>>> The core genomancer code is pretty stable, most of the recent
>>>>>>> work is
>>>>>>> in plugins (and some work in the core to allow more extensive
>>>>>>> plugins).
>>>>>>> 
>>>>>>> You should be able to get a working DAS1-->DAS2 proxy running from
>>>>>>> the current head of the Trellis SVN repository -- you would just
>>>>>>> need
>>>>>>> to add a web.xml config file with servlet parameters to get it
>>>>>>> going in a
>>>>>>> servlet container like Tomcat, or alternatively run the built-in
>>>>>>> Jetty server
>>>>>>> (ExampleJettyDas2Server) and edit servlet parameters directly in
>>>>>>> code.
>>>>>>> 
>>>>>>> But if the intent is to load DAS 1.x data into IGB, I don't
>>>>>>> think you
>>>>>>> need to use Trellis.  Th latest IGB (6.4.1 loaded via WebStart)
>>>>>>> already supports DAS 1.5 access.  In the "Data Access" tab, under
>>>>>>> "Choose Data Sources and Data Sets" section click the "Configure"
>>>>>>> button.  This brings up a window with a "Data Sources" tab, and in
>>>>>>> that tab you can click the "Add" button to bring up a dialog
>>>>>>> that lets
>>>>>>> you select "DAS" for the data source type, and enter the URL for
>>>>>>> a DAS
>>>>>>> server.  This worked fine for loading data from the UCSC DAS 1.5
>>>>>>> server -- I haven't tried accessing data from any other DAS
>>>>>>> servers
>>>>>>> recently.
>>>>>>> 
>>>>>>> I'm forwarding to the genoviz-devel list for IGB developments and
>>>>>>> discussion, to see if anyone currently working on IGB can add
>>>>>>> any more
>>>>>>> info.
>>>>>>> 
>>>>>>> On Tue, Feb 1, 2011 at 7:51 AM, Jim Procter
>>>>>>> <jprocter at compbio.dundee.ac.uk> wrote:
>>>>>>>> 
>>>>>>>> Hi all (but Gregg in particular!)
>>>>>>>> 
>>>>>>>> I was wondering whether the DAS1 to DAS2 proxy component of
>>>>>>>> Trellis/Ivy
>>>>>>>> in the Genomancer project (http://code.google.com/p/
>>>>>>>> genomancer/) is
>>>>>>>> stable enough to use. We'd like to set up an in house DAS1->2
>>>>>>>> proxy and
>>>>>>>> it looks like there's a moderate amount of commit activity in the
>>>>>>>> project at the moment, making me a little nervous about
>>>>>>>> attempting to
>>>>>>>> use the code in a production(ish) setting.
>>>>>>>> 
>>>>>>>> many thanks in advance,
>>>>>>>> Jim.
>>>>>>>> 
>>>>>>>> --
>>>>>>>> -------------------------------------------------------------------
>>>>>>>> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research
>>>>>>>> Group
>>>>>>>> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
>>>>>>>> The University of Dundee is a Scottish Registered Charity, No.
>>>>>>>> SC015096.
>>>>>>>> 
>>>>>>>> _______________________________________________
>>>>>>>> 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
>>>>>>> 
>>>>>>> 
>>>>>>> _______________________________________________
>>>>>>> DAS mailing list
>>>>>>> DAS at lists.open-bio.org
>>>>>>> http://lists.open-bio.org/mailman/listinfo/das
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> --------------------------------------------------------------------------
>>>>>> ----
>>>>>> The modern datacenter depends on network connectivity to access
>>>>>> resources
>>>>>> and provide services. The best practices for maximizing a
>>>>>> physical server's
>>>>>> connectivity to a physical network are well understood - see how
>>>>>> these
>>>>>> rules translate into the virtual world?
>>>>>> http://p.sf.net/sfu/oracle-sfdevnlfb
>>>>>> _______________________________________________
>>>>>> Genoviz-devel mailing list
>>>>>> Genoviz-devel at lists.sourceforge.net
>>>>>> https://lists.sourceforge.net/lists/listinfo/genoviz-devel
>>>>> 
>>>>> --
>>>>> Ann Loraine
>>>>> Associate Professor
>>>>> Dept. of Bioinformatics and Genomics, UNCC
>>>>> North Carolina Research Campus
>>>>> 600 Laureate Way
>>>>> Kannapolis, NC 28081
>>>>> 704-250-5750
>>>>> www.transvar.org
>>>>> 
>>>>> 
>>>>> 
>>>> 
>>>> 
>>>> _______________________________________________
>>>> 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
>> 
>> Jonathan Warren
>> Senior Developer and DAS coordinator
>> blog: http://biodasman.wordpress.com/
>> jw12 at sanger.ac.uk
>> Ext: 2314
>> Telephone: 01223 492314
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> 
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome Research
>> Limited, a charity registered in England with number 1021457 and a
>> company registered in England with number 2742969, whose registered
>> office is 215 Euston Road, London, NW1 2BE.
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>> 
> 
> -- 
> Ann Loraine
> Associate Professor
> Dept. of Bioinformatics and Genomics, UNCC
> North Carolina Research Campus
> 600 Laureate Way
> Kannapolis, NC 28081
> 704-250-5750
> www.transvar.org
> 




From jzhang at ximpleware.com  Sat Feb 26 01:25:55 2011
From: jzhang at ximpleware.com (jimmy Zhang)
Date: Fri, 25 Feb 2011 17:25:55 -0800
Subject: [DAS] [ANN]VTD-XML 2.10
In-Reply-To: <E0CA4C49-6C87-4222-B82E-F71CECD51916@sanger.ac.uk>
References: <E0CA4C49-6C87-4222-B82E-F71CECD51916@sanger.ac.uk>
Message-ID: <241E9E98F7494B2CB7492D06DC172C2D@JimmyZhangPC>

VTD-XML 2.10 is now released. It can be downloaded at
https://sourceforge.net/projects/vtd-xml/files/vtd-xml/ximpleware_2.10/.
This release includes a number of new features and enhancement.

* The core API of VTD-XML has been expanded. Users can now perform
cut/paste/insert on an empty element.
* This release also adds the support of deeper location cache support for
parsing and indexing. This feature is useful for application performance
tuning for
processing various XML documents.
* The java version also added support for processing zip and gzip files.
Direct processing of httpURL based XML is enhanced.
* Extended Java version now support Iso-8859-10~16 encoding.
* A full featured C++ port is released.
* C version of VTD-XML now make use of thread local storage to achieve
thread safety for multi-threaded application.
* There are also a number of bugs fixed. Special thanks to Jozef Aerts, John
Sillers, Chris Tornau and a number of other users for input and suggestions



From aroberts at broadinstitute.org  Mon Feb 28 18:34:10 2011
From: aroberts at broadinstitute.org (Andrew Roberts)
Date: Mon, 28 Feb 2011 13:34:10 -0500
Subject: [DAS] RELAX NG schema for "sequence" command
Message-ID: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>

Hello,

	I'm working on some validations, and I think I may have found an  
error in sequence.rng (www.dasregistry.org/validation1.6/ 
sequence.rng).  It appears that this schema makes no provision for the  
actual text data that belongs to the sequence element (i.e. the bases  
themselves).  Is this a known issue?

	If not, I think the solution is to add a <text/> element inside the  
sequence element.  Line 10 should read,

                 <attribute name="start"><data type="integer"></data></ 
attribute><attribute name="stop"><data type="integer"></data></ 
attribute><optional><attribute name="version"><text></text></ 
attribute></optional><optional><attribute name="label"><text></text></ 
attribute></optional><text/></element>

Cheers,

Andrew


From jw12 at sanger.ac.uk  Mon Feb 28 18:52:00 2011
From: jw12 at sanger.ac.uk (Jonathan Warren)
Date: Mon, 28 Feb 2011 18:52:00 +0000
Subject: [DAS] RELAX NG schema for "sequence" command
In-Reply-To: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>
References: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>
Message-ID: <51BE8FEB-E4B6-4931-BFD6-79BE35A6F171@sanger.ac.uk>

Hi
Welcome to the DAS list :)
I'm guessing that when I made an edit on Friday I inadvertently  
deleted or moved the text element to the wrong place!
Ill check it.

Thanks for the info!


On 28 Feb 2011, at 18:34, Andrew Roberts wrote:

> Hello,
>
> 	I'm working on some validations, and I think I may have found an  
> error in sequence.rng (www.dasregistry.org/validation1.6/ 
> sequence.rng).  It appears that this schema makes no provision for  
> the actual text data that belongs to the sequence element (i.e. the  
> bases themselves).  Is this a known issue?
>
> 	If not, I think the solution is to add a <text/> element inside the  
> sequence element.  Line 10 should read,
>
>                <attribute name="start"><data type="integer"></data></ 
> attribute><attribute name="stop"><data type="integer"></data></ 
> attribute><optional><attribute name="version"><text></text></ 
> attribute></optional><optional><attribute name="label"><text></ 
> text></attribute></optional><text/></element>
>
> Cheers,
>
> Andrew
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das

Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314









-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE. 


From ljgarcia at ebi.ac.uk  Mon Feb 28 19:38:43 2011
From: ljgarcia at ebi.ac.uk (ljgarcia at ebi.ac.uk)
Date: Mon, 28 Feb 2011 19:38:43 -0000 (UTC)
Subject: [DAS] RELAX NG schema for "sequence" command
In-Reply-To: <51BE8FEB-E4B6-4931-BFD6-79BE35A6F171@sanger.ac.uk>
References: <0F015AE7-09D7-4F4D-B547-353830FD82A2@broadinstitute.org>
	<51BE8FEB-E4B6-4931-BFD6-79BE35A6F171@sanger.ac.uk>
Message-ID: <58547.86.9.203.124.1298921923.squirrel@webmail.ebi.ac.uk>

Hi,

Rafael and I also noted it this afternoon. We used trang in order to
transform sequence.rng into sequence.xsd, then we used Jaxb and we got
nothing about the content. However, a while ago we did the same procedure
and it worked. We were wondering what could it be.

Jonathan, please let us know when you update the rng schema.

Thanks,

Leyla

> Hi
> Welcome to the DAS list :)
> I'm guessing that when I made an edit on Friday I inadvertently
> deleted or moved the text element to the wrong place!
> Ill check it.
>
> Thanks for the info!
>
>
> On 28 Feb 2011, at 18:34, Andrew Roberts wrote:
>
>> Hello,
>>
>> 	I'm working on some validations, and I think I may have found an
>> error in sequence.rng (www.dasregistry.org/validation1.6/
>> sequence.rng).  It appears that this schema makes no provision for
>> the actual text data that belongs to the sequence element (i.e. the
>> bases themselves).  Is this a known issue?
>>
>> 	If not, I think the solution is to add a <text/> element inside the
>> sequence element.  Line 10 should read,
>>
>>                <attribute name="start"><data type="integer"></data></
>> attribute><attribute name="stop"><data type="integer"></data></
>> attribute><optional><attribute name="version"><text></text></
>> attribute></optional><optional><attribute name="label"><text></
>> text></attribute></optional><text/></element>
>>
>> Cheers,
>>
>> Andrew
>> _______________________________________________
>> DAS mailing list
>> DAS at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/das
>
> Jonathan Warren
> Senior Developer and DAS coordinator
> blog: http://biodasman.wordpress.com/
> jw12 at sanger.ac.uk
> Ext: 2314
> Telephone: 01223 492314
>
>
>
>
>
>
>
>
>
> --
>  The Wellcome Trust Sanger Institute is operated by Genome Research
>  Limited, a charity registered in England with number 1021457 and a
>  company registered in England with number 2742969, whose registered
>  office is 215 Euston Road, London, NW1 2BE.
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>




From thomas.a.down at gmail.com  Mon Feb 28 21:17:43 2011
From: thomas.a.down at gmail.com (Thomas Down)
Date: Mon, 28 Feb 2011 21:17:43 +0000
Subject: [DAS] Announcing Dalliance 0.6
Message-ID: <AANLkTikrz0F+RcTSMX8YJOnPfMPER2ffXu-Dn2NJrFC-@mail.gmail.com>

I'm very pleased to announce the latest release of Dalliance, an interactive
genome viewer and DAS client for the web.  You can try the latest release in
any modern web browser here:

            http://www.biodalliance.org/

Major improvements since version 0.5 include:

         - Better DAS/1.6 support, including complex features defined using
the PART/PARENT system.
         - Keyboard navigation improvements (in particular, tap space to
toggle instantly between two zoom levels).
         - Direct export of the current display in SVG or PDF format.
         - Binary data support: you can now directly add bigwig or bigbed
data to the browser (see http://www.biodalliance.org/bin.html).

As always, comments and suggestions welcome!

                   Thomas Down.