[DAS2] DAS/1 vs DAS/2 discussion list

[Steve Chervitz]

The DAS/1 list is still open and working. I updated biodas.org to reflect
this and set up a special page to inform people about which list to use:

http://biodas.org/documents/biodas-lists.html

Subscribers on the DAS/1 list have not been automatically added to the DAS/2
list. They must actively subscribe themselves here:

http://biodas.org/mailman/listinfo/das2

Steve


> From: "Helt,Gregg" <Gregg_Helt at affymetrix.com>
> Date: Mon, 21 Nov 2005 09:24:37 -0800
> To: Andrew Dalke <dalke at dalkescientific.com>, DAS/2 <das2 at portal.open-bio.org>
> Conversation: [DAS2] Getting individual features in DAS/1
> Subject: RE: [DAS2] Getting individual features in DAS/1
> 
> We need to discuss at today's meeting.  I don't think the original DAS
> list should be closed, but rather continue to serve as a list to discuss
> the DAS/1 protocol and implementations, and the DAS2 mailing list should
> focus on DAS/2.  If we mix DAS/1 and DAS/2 discussions in the same
> mailing list I think it's going to lead to a lot of confusion.
> 
> gregg
> 
>> -----Original Message-----
>> From: das2-bounces at portal.open-bio.org
> [mailto:das2-bounces at portal.open-
>> bio.org] On Behalf Of Andrew Dalke
>> Sent: Monday, November 21, 2005 9:09 AM
>> To: DAS/2
>> Subject: Re: [DAS2] Getting individual features in DAS/1
>> 
>> Has anyone answered Ilari's question?
>> 
>> I never used DAS/1 enough to answer it myself.
>> 
>> If the normal DAS list is closed, is this the right place for DAS/1
>> questions?
>> 
>> 
>> On Nov 18, 2005, at 4:22 PM, Ilari Scheinin wrote:
>> 
>>> This mail is not really about DAS/2, but the web site says the
>>> original DAS mailing list is now closed.
>>> 
>>> I am setting up a DAS server that serves CGH data from my database
> to
>>> a visualization software, which in my case is gbrowse. I've already
>>> set up Dazzle that serves the reference data from a local copy of
>>> Ensembl. I need to be able to select individual CGH experiments to
> be
>>> visualized, and as the measurements from a single CGH experiment
> cover
>>> the entire genome, this cannot of course be done by specifying a
>>> segment along with the features command.
>>> 
>>> I noticed that there is a feature_id option for getting the features
>>> in DAS/1.5, but on a closer look, it seems to work by getting the
>>> segment that the specified feature corresponds to, and then getting
>>> all features from that segment. My next approach was to use the
>>> feature type to distinguish between different CGH experiments. As
> all
>>> my data is of the type CGH, I thought that I could use spare this
>>> piece of information for identifying purposes.
>>> 
>>> First I tried the generic seqfeature plugin. I created a database
> for
>>> it with some test data. However, getting features by type does not
>>> seem to work. I always get all the features from the segment in
>>> question.
>>> 
>>> Next I tried the LDAS plugin. Again I created a compatible database
>>> with some test data. I must have done something wrong the the data
>>> file I imported to the database, because getting the features does
> not
>>> work. I can get the feature types, but trying to get the features
>>> gives me an ERRORSEGMENT error.
>>> 
>>> I thought that before I go further, it might be useful to ask
> whether
>>> my approach seems reasonable, or is there a better way to achieve
> what
>>> I am trying to do? What should I do to be able to visualize
> individual
>>> CGH profiles?
>>> 
>>> I'm grateful for any advice,
>>> Ilari
>> 
>> Andrew
>> dalke at dalkescientific.com
>> 
>> _______________________________________________
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> 
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