http://blog.gmane.org/gmane.science.biology.biodas hourly 1 1901-01-01T00:00+00:00 http://gmane.org/img/gmane-25t.png http://gmane.org http://comments.gmane.org/gmane.science.biology.biodas/602 <pre>http://das.ensembl.org/das/sources now contains a non redundant list of ensembl das sources that points to archived ensembl instances using the new sources document specification and conforms to the 1.6 specification way of specifying data source uris http://www.biodas.org/documents/spec-1.6.html#uris. This document is hosted by the Sanger but not maintained by the ensembl project itself. The DAS data sources it points to are hosted by the ensembl project however. Any issues/suggestions then let me know. Cheers Jonathan. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk </pre> Jonathan Warren 2012-04-12T11:50:51 http://comments.gmane.org/gmane.science.biology.biodas/601 <pre>Thanks to all those who attended the DAS workshop this year it was a great year in terms of developer outcomes and we hope the tutorials on day 1 were useful for new users. There is a section on the workshop page with outcomes of the workshop http://www.biodas.org/wiki/DASWorkshop2012#Outcomes_from_workshop_2012 please feel free to add further links and information there. Thanks to David for all the great pictures available here http://www.flickr.com/photos/davidmam/sets/72157629110016398/ looks to me like we were having a good time :) I'd personally like to thank the other tutors many of whom put in extra hours outside of work to make this a successful workshop. New users who attended the workshop my be interested to know that talks from last years workshop that illustrate how DAS is being used in the wider community are available as video links from here: http://www.biodas.org/wiki/DASWorkshop2011#Day_2 Thanks again Jonathan. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasma</pre> Jonathan Warren 2012-03-13T13:34:34 http://comments.gmane.org/gmane.science.biology.biodas/596 <pre> Hi Jonathan and everyone. I noticed that there are several topics listed on the developer day under 'developments since last meeting' for which there is no proposer (authentication/encryption in proserver is the one that caught my eye). Who is going to talk about those topics ? Jim. </pre> Jim Procter 2012-02-22T11:08:53 http://comments.gmane.org/gmane.science.biology.biodas/594 <pre>Hi If you are intending to come to the DAS workshop this year can you register soon as we would like to get an idea of numbers for the 3 respective days (1st day tutorials and short talks, 2nd and 3rd day developers hackathon). This will then enable us to start firming up the schedule for the 3 days. If you are not intending to come to the workshop can I ask for some feedback that may help us entice you in the future? Many thanks Jonathan. See workshop email for you convenience below: DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This work</pre> Jonathan Warren 2012-01-20T10:41:18 http://comments.gmane.org/gmane.science.biology.biodas/582 <pre>Hi, Given a set of features in DAS format, what is the easiest way to generate GFF3 format? Can most DAS server implementation be persuaded to serve GFF3 in response to DAS feature requests? Cheers, Dan. </pre> Dan Bolser 2012-01-12T18:09:48 http://comments.gmane.org/gmane.science.biology.biodas/577 <pre>Hi I've put some instructions for people with little or no technical ability and no access to IT personnel or servers, to be able to publish there genotype data from companies such as 23andme etc as a DAS source on the amazon cloud. http://biodasman.wordpress.com/2012/01/12/easy-deployment-of-das-server-for-personal-genotype-data-to-the-amazon-cloud/ All someone needs is a tab delimited text file from one of these companies, a credit card and an internet connection. The instructions show them how to set up and deploy their server to the cloud in 6 easy steps and then view the data in Ensembl. Example server can be accessed from here http://mychoiceofname.elasticbeanstalk.com/das/person1 Any comments suggestions welcomed. Cheers Jonathan. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2012-01-12T13:21:14 http://comments.gmane.org/gmane.science.biology.biodas/576 <pre>After some discussions and partly due to a lack of volunteers for talks we have decided to modify the DAS workshop format this year. The first day as per previous years will be tutorials and talks for new users of DAS. The second and third day will be for DAS developers as a hackathon to facilitate the implementation and updating of clients, servers and libraries to implement the latest 1.6E specifications. Thus for this year we are dispensing with the second day of talks which will hopefully be back in some form next year. The workshop registration page and registrations will be updated to reflect this change soon. Any comments or suggestions please let us know. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2012-01-11T14:20:54 http://comments.gmane.org/gmane.science.biology.biodas/575 <pre>DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Learn of and contribute to current developments in DAS such as: DAS in the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative annotation projects, DAS alternative formats. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 10 February 2012 - 12:00. If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren&lt; at &gt;sanger.ac.uk Many th</pre> Jonathan Warren 2012-01-05T09:49:02 http://comments.gmane.org/gmane.science.biology.biodas/574 <pre>Hi DAS people. I intend to circulate to other email lists the DAS workshop email just sent. If anyone has suggestions as to other email lists to post it to or would like to forward this email on to them (saves me registering on lots of lists :) ) then please do (but let me know so I don't duplicate posts). List I intend to use are: gmod biojava ensembl bioperl Sanger/EBI campus We could do with it being circulated around less developer focused lists e.g. plant focused user groups? More general biology lists? Suggestions? Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2012-01-05T09:57:05 http://comments.gmane.org/gmane.science.biology.biodas/575 <pre>DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Learn of and contribute to current developments in DAS such as: DAS in the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative annotation projects, DAS alternative formats. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 10 February 2012 - 12:00. If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren&lt; at &gt;sanger.ac.uk Many th</pre> Jonathan Warren 2012-01-05T09:49:02 http://comments.gmane.org/gmane.science.biology.biodas/574 <pre>Hi DAS people. I intend to circulate to other email lists the DAS workshop email just sent. If anyone has suggestions as to other email lists to post it to or would like to forward this email on to them (saves me registering on lots of lists :) ) then please do (but let me know so I don't duplicate posts). List I intend to use are: gmod biojava ensembl bioperl Sanger/EBI campus We could do with it being circulated around less developer focused lists e.g. plant focused user groups? More general biology lists? Suggestions? Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2012-01-05T09:57:05 http://comments.gmane.org/gmane.science.biology.biodas/575 <pre>DAS is currently being used to share annotations on genomes, protein alignments, structural and interaction information. If you are interested in sharing biological information the DAS workshop below may be of interest to you. Learn of and contribute to current developments in DAS such as: DAS in the cloud, DAS for Genotype Data, DAS searching, DAS for collaborative annotation projects, DAS alternative formats. Registration is open for the 2012 DAS workshop (27-29 February) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.ebi.ac.uk/training/onsite/120227_DAS.html and register via the web link at the bottom of the page. This workshop will cater for novice to expert DAS users as each day is optional. Please register early as places will be limited. Registration closes 10 February 2012 - 12:00. If you are interested in giving a 15 minute talk on the second day please email Jonathan Warren using jonathan.warren&lt; at &gt;sanger.ac.uk Many th</pre> Jonathan Warren 2012-01-05T09:49:02 http://comments.gmane.org/gmane.science.biology.biodas/574 <pre>Hi DAS people. I intend to circulate to other email lists the DAS workshop email just sent. If anyone has suggestions as to other email lists to post it to or would like to forward this email on to them (saves me registering on lots of lists :) ) then please do (but let me know so I don't duplicate posts). List I intend to use are: gmod biojava ensembl bioperl Sanger/EBI campus We could do with it being circulated around less developer focused lists e.g. plant focused user groups? More general biology lists? Suggestions? Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2012-01-05T09:57:05 http://comments.gmane.org/gmane.science.biology.biodas/573 <pre>Please register at the link below if you are coming to the 2012 DAS workshop at the Sanger/EBI genome campus, Hinxton, Cambridge UK. http://www.ebi.ac.uk/training/onsite/120227_DAS.html If you would like to give a talk about work you have done/are doing with DAS please email me. Many thanks Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2011-12-20T11:49:19 http://comments.gmane.org/gmane.science.biology.biodas/572 <pre>If a client has the X-DAS-Version set to DAS/1.6E in the request header the Sanger DAS sources at http://das.sanger.ac.uk/das/sources will respond with 1.6 style XML responses. If no header is set for this or it does not contain the number 6 the DAS 1.53E xml responses will be returned (with the exception of about 10 data sources that are labelled 1.6E with a property in the sources response (&lt;PROP name="spec" value="DAS/1.6E"/&gt;). In the future I hope that more genomic DAS clients will move to support DAS 1.6 but in the meantime this is the Sanger solution to backwards compatibility issues which normally will only effect data sources with groups/parent/parts. This way we can also support the clients that do offer support for DAS 1.6. Any problems or suggestion as always feel free to email me. Thanks Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2011-12-20T10:48:20 http://comments.gmane.org/gmane.science.biology.biodas/563 <pre>Hi As the 2012 DAS workshop is coming up at the end of February we would like to hear from people using DAS. We would be really grateful to receive just a short email from anyone using DAS or developing DAS with a brief summary about their project and how DAS fits in, especially if you have not spoken at the DAS workshops at any time. Please also say if you would be interested in giving a short presentation at the workshop in February even if you are not sure if you could make it. Previous years the presentations have been 15 minutes with 5 minutes for questions - however this year we intend to be more flexible and so if you would prefer to give a "lightning talk" of just 5 minutes to update people or give them a brief overview that will be fine. Links to the previous years talks can be found here http://www.biodas.org/wiki/DASWorkshop2011#Day_2 I must emphasise - please give us a summary even if you are not interested in giving a talk as we would like to know what is going on out </pre> Jonathan Warren 2011-11-17T12:11:14 http://comments.gmane.org/gmane.science.biology.biodas/562 <pre>I forgot to add: If you are interested in giving a talk please reply by the 1st of December (2 weeks from now) as we will need to start organising the format of this years workshop. Many thanks Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2011-11-17T12:15:35 http://comments.gmane.org/gmane.science.biology.biodas/559 <pre>Hi There are at least 4 of us meeting up on the Sanger/EBI genome campus (Thursday 1st December) to write some code for the new Java DAS library (JDAS http://code.google.com/p/jdas/). The main focus will be on making sure the new library has all the "essential" capabilities of the old Dasobert library and some new features. We would like to extend an open invitation to Java developers in the DAS community. If you would like to attend and contribute then please drop me a line. We would be especially interested in having someone with expertise/interest in DAS structure or Alignment clients. If you have any suggestions or burning needs for support to be included in the JDAS library you can also write to me or post to the list. For inclusion (some of which has/will be implemented by 1 December): Support for concurrency (Threads and queue management). Support for alignment and structure queries/responses. JSON support. Writeback functionality (xml and JSON). Registry sources filtering support</pre> Jonathan Warren 2011-11-02T15:57:15 http://comments.gmane.org/gmane.science.biology.biodas/558 <pre>Dear Colleagues, on behalf of the other co-authors, I am pleased to announce that the paper describing myKaryoView, a light weight client for visualization of personal genomics data, is now published in PLoS One. The article is open access and we welcome any feedback. You can access it here: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0026345 Best wishes, Manuel Manuel Corpas, PhD Tel:      +44.122349.2372 Web:    http://manuelcorpas.com/about/ Twitter: &lt; at &gt;manuelcorpas </pre> Manuel Corpas 2011-10-31T22:23:57 http://comments.gmane.org/gmane.science.biology.biodas/555 <pre>Hi I've started a wiki page for the DAS workshop 2012 preliminarily scheduled for 27-29th Feb 2012. Subject to funding. http://www.biodas.org/wiki/DASWorkshop2012 The page is currently split into 3 sections 1)Recent developments since the last DAS workshop 2) Suggestions for Developer Discussions on Developers Day 3) Possible DAS related talks. To kick things off I've added to some of those topics. Please feel free to add some suggestions and/or email to the list. I'd also be very interested in hearing from people who would be interested in attending, either as a new user for the tutorials or a seasoned DAS developer. This will enable us to make informed decisions about how the 2012 workshop should be organised. For the last couple of years the workshop has been a 3 day event with the first day consisting of tutorials, the second had talks and the third a developer discussions day. As many of last years talks are available on the web we may change the format so there are a reduced nu</pre> Jonathan Warren 2011-10-20T11:26:15 http://comments.gmane.org/gmane.science.biology.biodas/554 <pre>The DAS registry and Sanger DAS sources will be unavailable from Friday midday (GMT) through the weekend. This is because the Sanger Data Centre is being shut down for essential maintenance. I'm pretty sure this will affect the EBI DAS sources also. But someone from the EBI may want to confirm this? We are working on a solution so that a read only version of the Sanger DAS data and Registry will be available when there are future shutdowns, but this facility is not currently available. Sorry for any inconvenience caused. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12&lt; at &gt;sanger.ac.uk Ext: 2314 Telephone: 01223 492314 </pre> Jonathan Warren 2011-10-20T09:27:56 Search the mailing list at Gmane query http://search.gmane.org/?group=$group=gmane.science.biology.biodas