From ecerami at yahoo.com Sat Nov 15 14:14:21 2003 From: ecerami at yahoo.com (Ethan Cerami) Date: Sat Nov 15 14:10:41 2003 Subject: [DAS] Announcing JDAS Beta 1 Message-ID: <20031115191421.47267.qmail@web41503.mail.yahoo.com> Hello Everyone: I am writing to announce the availability of JDAS, Beta 1. JDAS is an open source Java client library for the DAS protocol. Features include: * Full support for DAS Commands: dsn, dna, sequence, entry_points, types, and features. * Easy access to the X-Das Status code and detailed error messages. * Easy access to the X-Das-Capabilities header. * Console logging feature for viewing all request/response data as it is transmitted over the wire. * XML validation for all DAS responses, and the ability to programmatically disable XML validation. * Fully documented API and several example applications to get you started. * Complete User Guide JDAS is available for download at: http://www.xmlbio.org/jdas/index.html Cheers, Ethan __________________________________ Do you Yahoo!? Protect your identity with Yahoo! Mail AddressGuard http://antispam.yahoo.com/whatsnewfree From lstein at cshl.edu Sat Nov 15 15:39:10 2003 From: lstein at cshl.edu (Lincoln Stein) Date: Sat Nov 15 15:35:38 2003 Subject: [DAS] Announcing JDAS Beta 1 In-Reply-To: <20031115191421.47267.qmail@web41503.mail.yahoo.com> References: <20031115191421.47267.qmail@web41503.mail.yahoo.com> Message-ID: <200311151539.10530.lstein@cshl.edu> Cool! Could you write up a short two-sentence announcement and I'll post it onto the News section of the DAS web site? Lincoln On Saturday 15 November 2003 02:14 pm, Ethan Cerami wrote: > Hello Everyone: > > I am writing to announce the availability of JDAS, > Beta 1. > > JDAS is an open source Java client library for the DAS > protocol. Features include: > > * Full support for DAS Commands: dsn, dna, sequence, > entry_points, types, and features. > * Easy access to the X-Das Status code and detailed > error messages. > * Easy access to the X-Das-Capabilities header. > * Console logging feature for viewing all > request/response data as it is transmitted over the > wire. > * XML validation for all DAS responses, and the > ability to programmatically disable XML validation. > * Fully documented API and several example > applications to get you started. > * Complete User Guide > > JDAS is available for download at: > http://www.xmlbio.org/jdas/index.html > > Cheers, > > Ethan > > > > __________________________________ > Do you Yahoo!? > Protect your identity with Yahoo! Mail AddressGuard > http://antispam.yahoo.com/whatsnewfree > _______________________________________________ > DAS mailing list > DAS@biodas.org > http://biodas.org/mailman/listinfo/das -- Lincoln Stein lstein@cshl.edu Cold Spring Harbor Laboratory 1 Bungtown Road Cold Spring Harbor, NY 11724 (516) 367-8380 (voice) (516) 367-8389 (fax) From stefan.weckx at ua.ac.be Tue Nov 18 12:12:14 2003 From: stefan.weckx at ua.ac.be (Stefan Weckx) Date: Tue Nov 18 12:06:07 2003 Subject: [DAS] links Message-ID: <3FBA52EE.3070008@ua.ac.be> Hi all, a question about the web links generated for annotations using LDAS. It seems that by default the weblink is opened in the same window as is used to browse eg. Ensembl (so after viewing the extra info on our server, one has to click the back button to go back to the ContigView). Is there any way to change settings so that the link is opened in a new window? thanks Stefan -- =========================================== Stefan Weckx Bioinformatics Unit Department of Molecular Genetics VIB8 University of Antwerp Universiteitsplein 1 B-2610 Antwerpen Belgium tel: + 32 3 820 2336 fax: + 32 3 820 2541 mail: stefan.weckx@ua.ac.be url: http://molgen-www.uia.ac.be/bioinfo =========================================== From avc at sanger.ac.uk Tue Nov 18 12:26:09 2003 From: avc at sanger.ac.uk (Tony Cox) Date: Tue Nov 18 12:22:24 2003 Subject: [DAS] links In-Reply-To: <3FBA52EE.3070008@ua.ac.be> References: <3FBA52EE.3070008@ua.ac.be> Message-ID: On Tue, 18 Nov 2003, Stefan Weckx wrote: +>Hi all, +> +>a question about the web links generated for annotations using LDAS. It +>seems that by default the weblink is opened in the same window as is +>used to browse eg. Ensembl (so after viewing the extra info on our +>server, one has to click the back button to go back to the ContigView). +>Is there any way to change settings so that the link is opened in a new +>window? Hi Stefan, For Ensembl tracks that use the LDAS stylesheet support the link for the features can be set in the individual LDAS datasource configuration file - and it is simply a matter of including TARGET="new" in the Href. For internally configured Ensembl DAS track the link can be similarly modified in the Ensembl species configuration files. regards Tony +> +>thanks +> +>Stefan +> +>-- +>=========================================== +>Stefan Weckx +>Bioinformatics Unit +>Department of Molecular Genetics VIB8 +>University of Antwerp +>Universiteitsplein 1 +>B-2610 Antwerpen +>Belgium +> +>tel: + 32 3 820 2336 +>fax: + 32 3 820 2541 +>mail: stefan.weckx@ua.ac.be +>url: http://molgen-www.uia.ac.be/bioinfo +>=========================================== +> +> +>_______________________________________________ +>DAS mailing list +>DAS@biodas.org +>http://biodas.org/mailman/listinfo/das +> ****************************************************** Tony Cox Email:avc@sanger.ac.uk Sanger Institute WWW:www.sanger.ac.uk Wellcome Trust Genome Campus Head,Software Services Hinxton Tel: +44 1223 834244 Cambs. CB10 1SA Fax: +44 1223 494919 ****************************************************** From stefan.weckx at ua.ac.be Tue Nov 18 15:21:14 2003 From: stefan.weckx at ua.ac.be (Stefan Weckx) Date: Tue Nov 18 15:17:27 2003 Subject: [DAS] links References: <3FBA52EE.3070008@ua.ac.be> Message-ID: <000d01c3ae11$871c6d10$85bc0b51@desktop> Hi Tony, To be sure: with the LDAS configuration file, do you mean the *.conf file in the .../httpd/conf/das.conf directory? there is the [LINKS] section with the URL to link to (eg: default = http://our.annotationserver.org), but it seems I can't figure the right syntax to add the target=new. There is no real "href" as in basic html, so what's the trick to add the target=new there? Or am I looking at the wrong place? thanks Stefan > > Hi Stefan, > > For Ensembl tracks that use the LDAS stylesheet support the link for the > features can be set in the individual LDAS datasource configuration file - and > it is simply a matter of including TARGET="new" in the Href. > > For internally configured Ensembl DAS track the link can be similarly modified > in the Ensembl species configuration files. From dag at sonsorol.org Thu Nov 20 10:38:23 2003 From: dag at sonsorol.org (Chris Dagdigian) Date: Fri Nov 21 08:14:06 2003 Subject: [DAS] Total OBF server shutdown Saturday November 22nd (all day EDT timezone) Message-ID: <3FBCDFEF.1010807@sonsorol.org> Hi folks, Apologies for the massive cross-posting. Our CVS, mailing list and web servers are located in a Cambridge, MA USA datacenter belonging to Wyeth Resarch. Genetics Institute (which became part of Wyeth) has supported our signficant internet bandwidth and hosting needs for many years since the earliest versions of our open source efforts. Since I have to do this massive cross-post anyway I figured it was a good time to thank them again in public. The real reason for this message is to announce a 1-day period of significant server downtime. The office floor & datacenter in the building where our servers are hosted is going to have a planned electrical shutdown (including emergency and backup power circuits) from 10am - 6pm on Saturday November 22nd. I'll be manually bringing down our servers sometime before the 10am deadline. The time estimate is conservative. In the event that the facilty work takes less time than expected I'll probably take advantage of the window to perform some server upgrades and failed disk replacements. For any questions/concerns or if you notice a server or service that is still not available after the 22nd please contact me directly at 'chris@bioteam.net' or 1-617-877-5498. Regards, Chris From ak at ebi.ac.uk Fri Nov 28 11:46:45 2003 From: ak at ebi.ac.uk (Andreas Kahari) Date: Fri Nov 28 11:53:17 2003 Subject: [DAS] ProServer, a pluggable DAS server, Bio::SeqIO support added Message-ID: <20031128164645.GA27626@ebi.ac.uk> Hi lists (sorry for the cross-posting), This for those of you who are interested in DAS but not aware of ProServer: ProServer is a DAS server implementation written in Perl by Roger Pettett at the Sanger Institute, here outside Cambridge in the UK. It builds on top of ideas from Tony Cox, also at the Sanger Institute. The point with ProServer is that it is pluggable, so that any data source may be used as a source to serve DAS features from, as long as there is source adaptor and a transport module for it. There are source adaptors already written for a number of types of sources, and they are fairly easy to extend to other types of sources or transports (I recently wrote a toy "wgetz" transport module from the already existing "getz" module which is used by the Swissprot source adaptor). Other DAS servers often requires you to create a dedicated database of DAS data. I thought it might be of interest to a couple of you to note that you now also can serve features or sequence data from any type of file that Bio::SeqIO can read. This, of course, is only of interest to people with smallish amount of data since queries are looked up sequentially in the files (unless the Bio::DB::Flat support in the code is used, which reduces the lookup time but which doesn't support all formats). ProServer is part of the Bio-Das2 module in the biodas CVS repository: http://cvs.bioperl.org/cgi-bin/viewcvs/viewcvs.cgi/Bio-Das2/?cvsroot=biodas Cheers, Andreas -- |(--)| Andreas K?h?ri |<><>| |-)(-| EMBL, European Bioinformatics Institute |><><| |(--)| Wellcome Trust Genome Campus, Hinxton |<><>| |-)(-| Cambridge, CB10 1SD |><><| |(--)| United Kingdom |<><>|