From dalke at dalkescientific.com Mon Nov 21 13:22:24 2005 From: dalke at dalkescientific.com (Andrew Dalke) Date: Mon Nov 21 13:28:47 2005 Subject: [DAS] Just checking if this Message-ID: is alive. Andrew dalke@dalkescientific.com From allenday at ucla.edu Mon Nov 21 13:37:22 2005 From: allenday at ucla.edu (Allen Day) Date: Mon Nov 21 14:36:03 2005 Subject: [DAS] Just checking if this In-Reply-To: References: Message-ID: it's alive! On Mon, 21 Nov 2005, Andrew Dalke wrote: > is alive. > > Andrew > dalke@dalkescientific.com > > _______________________________________________ > DAS mailing list > DAS@biodas.org > http://biodas.org/mailman/listinfo/das > From tomc at cs.uoregon.edu Mon Nov 21 14:22:29 2005 From: tomc at cs.uoregon.edu (Tom Conlin) Date: Mon Nov 21 14:39:25 2005 Subject: [DAS] Just checking if this In-Reply-To: References: Message-ID: <43821E75.1040904@cs.uoregon.edu> Andrew Dalke wrote: > is alive. > > Andrew > dalke@dalkescientific.com > > _______________________________________________ > DAS mailing list > DAS@biodas.org > http://biodas.org/mailman/listinfo/das in a quantum sort of way ... by looking you have changed it's state. -- ... nice weather eh tomc@cs.uoregon.edu From Steve_Chervitz at affymetrix.com Mon Nov 28 17:55:28 2005 From: Steve_Chervitz at affymetrix.com (Chervitz, Steve) Date: Mon Nov 28 18:05:18 2005 Subject: [DAS] DAS/1 vs DAS/2 discussion list In-Reply-To: Message-ID: 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" > Date: Mon, 21 Nov 2005 09:24:37 -0800 > To: Andrew Dalke , DAS/2 > 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@portal.open-bio.org > [mailto:das2-bounces@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@dalkescientific.com >> >> _______________________________________________ >> DAS2 mailing list >> DAS2@portal.open-bio.org >> http://portal.open-bio.org/mailman/listinfo/das2 > > _______________________________________________ > DAS2 mailing list > DAS2@portal.open-bio.org > http://portal.open-bio.org/mailman/listinfo/das2