From mauricio at open-bio.org Wed Nov 4 16:16:17 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Wed, 04 Nov 2009 15:16:17 -0600 Subject: [DAS] The DAS wiki In-Reply-To: <2c8757af0909250058j70ac0c8em882bce3babc70361@mail.gmail.com> References: <2c8757af0909250058j70ac0c8em882bce3babc70361@mail.gmail.com> Message-ID: <4AF1EF21.7070306@open-bio.org> GeSHiHighlight is now enabled for BioDAS wiki. Next time send this kind of requests to support at helpdesk.open-bio.org so they don't get lost. Regards, Mauricio. Dan Bolser wrote: > Please can you install a syntax highlighting extension on the wiki? > > * http://www.mediawiki.org/wiki/Category:Syntax_highlighting_extensions > ** http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi > > > This should help maintain snippets of code on the wiki. > > > Cheers, > Dan. > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From jw12 at sanger.ac.uk Thu Nov 26 09:57:35 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 26 Nov 2009 14:57:35 +0000 Subject: [DAS] DAS workshop 7th-9th April 2010 Message-ID: We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part then please email me jw12 at sanger.ac.uk The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: http://www.dasregistry.org/course.jsp If you would like to present then please send a short summary of what you would like to talk about. Thanks Jonathan. Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- 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 mauricio at open-bio.org Thu Nov 26 16:45:43 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Thu, 26 Nov 2009 15:45:43 -0600 Subject: [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <4B0EF707.6080202@open-bio.org> Hi Jonathan, Any chance it can be webcasted? I'm sure it would attract a lot of remote attendees ;) Regards, Mauricio. Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here > at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If > you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st > day for beginners, 2nd for both beginners and advanced users, 3rd day > for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what > you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > > From christoph.gille at charite.de Fri Nov 27 02:40:42 2009 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 27 Nov 2009 08:40:42 +0100 Subject: [DAS] DAS Workshop In-Reply-To: References: Message-ID: > We are considering running a Distributed Annotation System workshop Great, I would like to come and could prepare a presentation on a work which has been submitted as a poster by Rafael Jimenez and me to the VizBi 2010: "Visualization of sequence features with Dasty and STRAP" Protein sequence features such as post-translational modifications of amino acids, cleavage sites, catalytic site residues and ligand binding sites, are recorded by data curators from all over the world and stored in public databases. The collections of sequence features are accessible via DAS servers. Here we present two sequence feature viewers - Dasty http://www.ebi.ac.uk/dasty/ and STRAP http://www.bioinformatics.org/strap/ . They are complementary in several aspects, therefore, they can be used in concert. Both have in common that they load sequence features from any registered DAS server and display the up-to-data information along the amino acid sequence. Dasty gives a clear and compact overview of sequence features of one single amino acid sequence. An outstanding feature is the ability to re-arrange the information using the mouse. To compare sequence features of two homologous proteins or to display sequence features of one protein in the context of a sequence alignment or 3D-structure the user can activate the "STRAP"-button in the Dasty view. In the multiple sequence alignment panel of STRAP, the residues with sequence features are underlined. Textural information is not directly shown due to the limited space, but pops up as a balloon message instead. For structural biologists we also provide the ability to highlight the sequence features on the 3D-model of the protein itself or on a related PDB entry, see http://3d-alignment.eu/. Christoph From suzi at berkeleybop.org Sun Nov 29 23:03:09 2009 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 29 Nov 2009 20:03:09 -0800 Subject: [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <3AD3C819-4BAA-4D90-B141-9611F48C5CAD@ berkeleybop.org> I/we (Gregg) would be interested in attending. We'd present an update on the collaborative, web-based version of Apollo. We will be working with Ian Holmes and Mitch Skinner using JBrowse for basic display. -S On Nov 26, 2009, at 6:57 AM, Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice 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 david.nix at hci.utah.edu Mon Nov 30 12:46:30 2009 From: david.nix at hci.utah.edu (David Nix) Date: Mon, 30 Nov 2009 10:46:30 -0700 Subject: [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: Message-ID: Jonathan, I would be interested in attending and presenting the work our group has done with the GenoViz DAS/2 framework (public/ private security model, FLEX webapp front end/ relational database back end, new pre indexed binary file archives for massive scale Next Gen data distribution). -cheers, David -- David Austin Nix, PhD | HCI Bioinformatics | Huntsman Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc: 801.587.4611 | Fx: 801.585.6458 | david.nix at hci.utah.edu | Skype/iChat: LiveNix | http://bioserver.hci.utah.edu On 11/26/09 7:57 AM, "Jonathan Warren" wrote: > We are considering running a Distributed Annotation System workshop > here at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If > you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st > day for beginners, 2nd for both beginners and advanced users, 3rd day > for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what > you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > From mauricio at open-bio.org Wed Nov 4 21:16:17 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Wed, 04 Nov 2009 15:16:17 -0600 Subject: [DAS] The DAS wiki In-Reply-To: <2c8757af0909250058j70ac0c8em882bce3babc70361@mail.gmail.com> References: <2c8757af0909250058j70ac0c8em882bce3babc70361@mail.gmail.com> Message-ID: <4AF1EF21.7070306@open-bio.org> GeSHiHighlight is now enabled for BioDAS wiki. Next time send this kind of requests to support at helpdesk.open-bio.org so they don't get lost. Regards, Mauricio. Dan Bolser wrote: > Please can you install a syntax highlighting extension on the wiki? > > * http://www.mediawiki.org/wiki/Category:Syntax_highlighting_extensions > ** http://www.mediawiki.org/wiki/Extension:SyntaxHighlight_GeSHi > > > This should help maintain snippets of code on the wiki. > > > Cheers, > Dan. > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From jw12 at sanger.ac.uk Thu Nov 26 14:57:35 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 26 Nov 2009 14:57:35 +0000 Subject: [DAS] DAS workshop 7th-9th April 2010 Message-ID: We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part then please email me jw12 at sanger.ac.uk The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: http://www.dasregistry.org/course.jsp If you would like to present then please send a short summary of what you would like to talk about. Thanks Jonathan. Jonathan Warren Senior Developer and DAS coordinator jw12 at sanger.ac.uk -- 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 mauricio at open-bio.org Thu Nov 26 21:45:43 2009 From: mauricio at open-bio.org (Mauricio Herrera Cuadra) Date: Thu, 26 Nov 2009 15:45:43 -0600 Subject: [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <4B0EF707.6080202@open-bio.org> Hi Jonathan, Any chance it can be webcasted? I'm sure it would attract a lot of remote attendees ;) Regards, Mauricio. Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here > at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If > you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st > day for beginners, 2nd for both beginners and advanced users, 3rd day > for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what > you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > > From christoph.gille at charite.de Fri Nov 27 07:40:42 2009 From: christoph.gille at charite.de (Dr. Christoph Gille) Date: Fri, 27 Nov 2009 08:40:42 +0100 Subject: [DAS] DAS Workshop In-Reply-To: References: Message-ID: > We are considering running a Distributed Annotation System workshop Great, I would like to come and could prepare a presentation on a work which has been submitted as a poster by Rafael Jimenez and me to the VizBi 2010: "Visualization of sequence features with Dasty and STRAP" Protein sequence features such as post-translational modifications of amino acids, cleavage sites, catalytic site residues and ligand binding sites, are recorded by data curators from all over the world and stored in public databases. The collections of sequence features are accessible via DAS servers. Here we present two sequence feature viewers - Dasty http://www.ebi.ac.uk/dasty/ and STRAP http://www.bioinformatics.org/strap/ . They are complementary in several aspects, therefore, they can be used in concert. Both have in common that they load sequence features from any registered DAS server and display the up-to-data information along the amino acid sequence. Dasty gives a clear and compact overview of sequence features of one single amino acid sequence. An outstanding feature is the ability to re-arrange the information using the mouse. To compare sequence features of two homologous proteins or to display sequence features of one protein in the context of a sequence alignment or 3D-structure the user can activate the "STRAP"-button in the Dasty view. In the multiple sequence alignment panel of STRAP, the residues with sequence features are underlined. Textural information is not directly shown due to the limited space, but pops up as a balloon message instead. For structural biologists we also provide the ability to highlight the sequence features on the 3D-model of the protein itself or on a related PDB entry, see http://3d-alignment.eu/. Christoph From suzi at berkeleybop.org Mon Nov 30 04:03:09 2009 From: suzi at berkeleybop.org (Suzanna Lewis) Date: Sun, 29 Nov 2009 20:03:09 -0800 Subject: [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: References: Message-ID: <3AD3C819-4BAA-4D90-B141-9611F48C5CAD@ berkeleybop.org> I/we (Gregg) would be interested in attending. We'd present an update on the collaborative, web-based version of Apollo. We will be working with Ian Holmes and Mitch Skinner using JBrowse for basic display. -S On Nov 26, 2009, at 6:57 AM, Jonathan Warren wrote: > We are considering running a Distributed Annotation System workshop here at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st day for beginners, 2nd for both beginners and advanced users, 3rd day for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome ResearchLimited, a charity registered in England with number 1021457 and acompany registered in England with number 2742969, whose registeredoffice 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 david.nix at hci.utah.edu Mon Nov 30 17:46:30 2009 From: david.nix at hci.utah.edu (David Nix) Date: Mon, 30 Nov 2009 10:46:30 -0700 Subject: [DAS] DAS workshop 7th-9th April 2010 In-Reply-To: Message-ID: Jonathan, I would be interested in attending and presenting the work our group has done with the GenoViz DAS/2 framework (public/ private security model, FLEX webapp front end/ relational database back end, new pre indexed binary file archives for massive scale Next Gen data distribution). -cheers, David -- David Austin Nix, PhD | HCI Bioinformatics | Huntsman Cancer Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc: 801.587.4611 | Fx: 801.585.6458 | david.nix at hci.utah.edu | Skype/iChat: LiveNix | http://bioserver.hci.utah.edu On 11/26/09 7:57 AM, "Jonathan Warren" wrote: > We are considering running a Distributed Annotation System workshop > here at the Sanger/EBI in the UK subject to decent demand. > The workshop will be held from Wednesday 7th-Friday 9th April 2010. If > you would be interested in attending either to present or just take part > then please email me jw12 at sanger.ac.uk > > The format of the workshop is likely to be similar to last years (1st > day for beginners, 2nd for both beginners and advanced users, 3rd day > for advanced), information for which can be found here: > http://www.dasregistry.org/course.jsp > > If you would like to present then please send a short summary of what > you would like to talk about. > > Thanks > > Jonathan. > > Jonathan Warren > Senior Developer and DAS coordinator > jw12 at sanger.ac.uk > > > > > > > >