From dan.bolser at gmail.com Tue Nov 2 06:14:23 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 2 Nov 2010 10:14:23 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk> References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk> Message-ID: Here is how I thought it would work (please let me know if this sounds about right, or if I made some mistakes in my understanding of the way DAS writeback will work): 1) I was thinking that the ProServer DAS server should (or at least could) implement the DAS writeback extension. 2) The genome browser client (or some other client) would talk to the DAS server using the DAS writeback protocol once a comment was added (i.e. I'm relying on a sensible client that can 'properly' handle comments). 3) I expect that ProServer will offload the job of actually storing the comment on a datasource adaptor. 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading feature data from the wiki to also write feature data there too. (Comments are just features right?) 5) You could then use either the genome browser client (or some other client) or the wiki directly to add and/or edit comments. i.e. the wiki is just another feature editing client / DAS datasource. I like this solution because I think 'community annotation' should be in the 'community', not on some server behind closed doors somewhere (somehow a wiki 'feels' more 'open' to me than some bespoke database x). There are plenty of wikis that could be used as back ends, and 'wiki' is a good way to do community annotation. They handle issues related to provenance, QC, versioning, authorship, motivation, publicising, publication, etc., etc. Again, MediaWiki is a good choice, because their is a lot of development for that platform, and I can easily imagine tagging, 'micro-publication' and syndication extensions being leveraged for this kind of data. Does it sound reasonable? Cheers, Dan. BioWiki conference: http://www.nettab.org/2010/ On 30 October 2010 12:41, Andy Jenkinson wrote: > Hi Dan, > > Sounds interesting. How do you see that working? > > Cheers, > Andy > > On 29 Oct 2010, at 16:28, Dan Bolser wrote: > >> My thinking was that the DASWiki approach could also support the DAS >> writeback extension. >> >> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >> wrote: >>> Hello There, >>> >>> I have been working in an extension to DAS1.6 called >>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow >>> to create new versions of an existing feature. So, putting new notes into a >>> feature is just a creation of a new version of the feature. The server >>> implementation of the writeback extends MyDas >>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>> We are close to release the plugin for Dasty3 to use the writeback server, >>> however this first client is a protein client, and so far there is not a >>> development for a genome client with DAS writeback capability, but I am >>> quite interested in this. >>> I hope to be able to announce the release of the writeback client in Dasty3 >>> in a few days, so you will be able to see it working and see if this >>> approach goes in the same direction of what you are looking for. >>> >>> Regards, >>> >>> Gustavo. >>> >>> 2010/10/29 Dan Bolser >>>> >>>> Hi Bob, >>>> >>>> This is a nice idea. In my spare time I've been working on running a >>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>> runs Wikipedia). >>>> >>>> In theory, you could have a comments track that was pulled in from the >>>> 'DASWiki', and clicking the details link would take you to the wiki >>>> page to edit the comment. Going back to the GBrowse, you would then >>>> see the updated data from the wiki page. It wouldn't be too hard to >>>> have a similar workflow for adding new comments. >>>> >>>> I saw a talk from some people at KeyGene who are doing something >>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>> query reports for specific regions). You can see the talk here: >>>> >>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>> ** >>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>> >>>> >>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>> prototype is here: >>>> >>>> http://das.referata.com/wiki/Main_Page >>>> >>>> >>>> Kick me a few times and I'll get the underlying code into shape. A >>>> year or two back I did have a working prototype based on a MediaWiki >>>> ProServer adaptor. >>>> >>>> >>>> If you are interested in community annotation should think about attending >>>> this: >>>> >>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>> http://www.nettab.org/2010/ >>>> >>>> >>>> Cheers, >>>> Dan. >>>> >>>> On 26 October 2010 20:31, Bob Muller wrote: >>>>> We are working with a small research project that doesn't have funds for >>>>> a full-scale database for features, so they want to know: >>>>> >>>>> How difficult would it be to add a comment section editable by users to >>>>> gbrowse? ?When you click on a feature in gbrowse it shows a detail page for >>>>> that feature, is there any way we could enable edits that could be written >>>>> back to the underlying mysql database that gbrowse runs on? >>>>> >>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>> entered through GBrowse as a way to annotate their genome. I'd be interested >>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>> >>>>> ? --Bob Muller, TAIR (www.arabidopsis.org) >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>> contest >>>>> Create new apps & games for the Nokia N8 for consumers in ?U.S. and >>>>> Canada >>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>> marketing >>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse at lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> DAS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> >>> >>> -- >>> Gustavo Adolfo Salazar Orejuela >>> >> >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das > > From andy.jenkinson at ebi.ac.uk Tue Nov 2 09:07:15 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 2 Nov 2010 13:07:15 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk> Message-ID: Hi Dan, Now I see what you mean - basically the wiki and DAS source have the same data/comments, and there are two ways to enter it (writeback inside the client OR the wiki itself). This sounds good and certainly feasible. I guess there will be details about the format the comments take in the Wiki, but I'm sure it would work. I agree that the great thing about an approach like this (and DAS writeback's "independent" architecture) is the open model. This, and the fact that it would also be possible to have the comments propagated into multiple clients (the usual DAS distributed approach) make things much more appealing than just a single isolated database of user comments. It's probably worth looking at the provenance/users aspect of the wiki integration to see how this can work with writeback. Gustavo can say more about how writeback handles user tracking I expect, but authentication is often the most difficult thing when it comes to implementing these things, I find. Specifically in this case: "when I edit something in the client, can people see who made the edit on the wiki itself, and if so is the process by which that happens secure?" I definitely encourage you to look further into it and am keen to find out how you get on. Cheers, Andy On 2 Nov 2010, at 10:14, Dan Bolser wrote: > Here is how I thought it would work (please let me know if this sounds > about right, or if I made some mistakes in my understanding of the way > DAS writeback will work): > > 1) I was thinking that the ProServer DAS server should (or at least > could) implement the DAS writeback extension. > > 2) The genome browser client (or some other client) would talk to the > DAS server using the DAS writeback protocol once a comment was added > (i.e. I'm relying on a sensible client that can 'properly' handle > comments). > > 3) I expect that ProServer will offload the job of actually storing > the comment on a datasource adaptor. > > 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading > feature data from the wiki to also write feature data there too. > (Comments are just features right?) > > 5) You could then use either the genome browser client (or some other > client) or the wiki directly to add and/or edit comments. i.e. the > wiki is just another feature editing client / DAS datasource. > > > I like this solution because I think 'community annotation' should be > in the 'community', not on some server behind closed doors somewhere > (somehow a wiki 'feels' more 'open' to me than some bespoke database > x). There are plenty of wikis that could be used as back ends, and > 'wiki' is a good way to do community annotation. They handle issues > related to provenance, QC, versioning, authorship, motivation, > publicising, publication, etc., etc. Again, MediaWiki is a good > choice, because their is a lot of development for that platform, and I > can easily imagine tagging, 'micro-publication' and syndication > extensions being leveraged for this kind of data. > > > Does it sound reasonable? > > > Cheers, > Dan. > > BioWiki conference: > http://www.nettab.org/2010/ > > > On 30 October 2010 12:41, Andy Jenkinson wrote: >> Hi Dan, >> >> Sounds interesting. How do you see that working? >> >> Cheers, >> Andy >> >> On 29 Oct 2010, at 16:28, Dan Bolser wrote: >> >>> My thinking was that the DASWiki approach could also support the DAS >>> writeback extension. >>> >>> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >>> wrote: >>>> Hello There, >>>> >>>> I have been working in an extension to DAS1.6 called >>>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow >>>> to create new versions of an existing feature. So, putting new notes into a >>>> feature is just a creation of a new version of the feature. The server >>>> implementation of the writeback extends MyDas >>>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>>> We are close to release the plugin for Dasty3 to use the writeback server, >>>> however this first client is a protein client, and so far there is not a >>>> development for a genome client with DAS writeback capability, but I am >>>> quite interested in this. >>>> I hope to be able to announce the release of the writeback client in Dasty3 >>>> in a few days, so you will be able to see it working and see if this >>>> approach goes in the same direction of what you are looking for. >>>> >>>> Regards, >>>> >>>> Gustavo. >>>> >>>> 2010/10/29 Dan Bolser >>>>> >>>>> Hi Bob, >>>>> >>>>> This is a nice idea. In my spare time I've been working on running a >>>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>>> runs Wikipedia). >>>>> >>>>> In theory, you could have a comments track that was pulled in from the >>>>> 'DASWiki', and clicking the details link would take you to the wiki >>>>> page to edit the comment. Going back to the GBrowse, you would then >>>>> see the updated data from the wiki page. It wouldn't be too hard to >>>>> have a similar workflow for adding new comments. >>>>> >>>>> I saw a talk from some people at KeyGene who are doing something >>>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>>> query reports for specific regions). You can see the talk here: >>>>> >>>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>>> ** >>>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>>> >>>>> >>>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>>> prototype is here: >>>>> >>>>> http://das.referata.com/wiki/Main_Page >>>>> >>>>> >>>>> Kick me a few times and I'll get the underlying code into shape. A >>>>> year or two back I did have a working prototype based on a MediaWiki >>>>> ProServer adaptor. >>>>> >>>>> >>>>> If you are interested in community annotation should think about attending >>>>> this: >>>>> >>>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>>> http://www.nettab.org/2010/ >>>>> >>>>> >>>>> Cheers, >>>>> Dan. >>>>> >>>>> On 26 October 2010 20:31, Bob Muller wrote: >>>>>> We are working with a small research project that doesn't have funds for >>>>>> a full-scale database for features, so they want to know: >>>>>> >>>>>> How difficult would it be to add a comment section editable by users to >>>>>> gbrowse? When you click on a feature in gbrowse it shows a detail page for >>>>>> that feature, is there any way we could enable edits that could be written >>>>>> back to the underlying mysql database that gbrowse runs on? >>>>>> >>>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>>> entered through GBrowse as a way to annotate their genome. I'd be interested >>>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>>> >>>>>> --Bob Muller, TAIR (www.arabidopsis.org) >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>>> contest >>>>>> Create new apps & games for the Nokia N8 for consumers in U.S. and >>>>>> Canada >>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>>> marketing >>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse at lists.sourceforge.net >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>> >>>>> _______________________________________________ >>>>> DAS mailing list >>>>> DAS at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/das >>>> >>>> >>>> >>>> -- >>>> Gustavo Adolfo Salazar Orejuela >>>> >>> >>> _______________________________________________ >>> DAS mailing list >>> DAS at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/das >> >> From dan.bolser at gmail.com Tue Nov 2 09:28:12 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 2 Nov 2010 13:28:12 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk>

Message-ID: Thanks for the encouragement Andy! Yup, I need to look in detail at the DAS writeback specification. I remember Gustavo talking a couple of years back, asking people to work together on features like these (rather than all competing on similar but probably mutually exclusive methods). I really value that sentiment. Cheers, Dan. On 2 November 2010 13:07, Andy Jenkinson wrote: > Hi Dan, > > Now I see what you mean - basically the wiki and DAS source have the same data/comments, and there are two ways to enter it (writeback inside the client OR the wiki itself). This sounds good and certainly feasible. I guess there will be details about the format the comments take in the Wiki, but I'm sure it would work. I agree that the great thing about an approach like this (and DAS writeback's "independent" architecture) is the open model. This, and the fact that it would also be possible to have the comments propagated into multiple clients (the usual DAS distributed approach) make things much more appealing than just a single isolated database of user comments. > > It's probably worth looking at the provenance/users aspect of the wiki integration to see how this can work with writeback. Gustavo can say more about how writeback handles user tracking I expect, but authentication is often the most difficult thing when it comes to implementing these things, I find. Specifically in this case: "when I edit something in the client, can people see who made the edit on the wiki itself, and if so is the process by which that happens secure?" > > I definitely encourage you to look further into it and am keen to find out how you get on. > > Cheers, > Andy > > On 2 Nov 2010, at 10:14, Dan Bolser wrote: > >> Here is how I thought it would work (please let me know if this sounds >> about right, or if I made some mistakes in my understanding of the way >> DAS writeback will work): >> >> 1) I was thinking that the ProServer DAS server should (or at least >> could) implement the DAS writeback extension. >> >> 2) The genome browser client (or some other client) would talk to the >> DAS server using the DAS writeback protocol once a comment was added >> (i.e. I'm relying on a sensible client that can 'properly' handle >> comments). >> >> 3) I expect that ProServer will offload the job of actually storing >> the comment on a datasource adaptor. >> >> 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading >> feature data from the wiki to also write feature data there too. >> (Comments are just features right?) >> >> 5) You could then use either the genome browser client (or some other >> client) or the wiki directly to add and/or edit comments. i.e. the >> wiki is just another feature editing client / DAS datasource. >> >> >> I like this solution because I think 'community annotation' should be >> in the 'community', not on some server behind closed doors somewhere >> (somehow a wiki 'feels' more 'open' to me than some bespoke database >> x). There are plenty of wikis that could be used as back ends, and >> 'wiki' is a good way to do community annotation. They handle issues >> related to provenance, QC, versioning, authorship, motivation, >> publicising, publication, etc., etc. Again, MediaWiki is a good >> choice, because their is a lot of development for that platform, and I >> can easily imagine tagging, 'micro-publication' and syndication >> extensions being leveraged for this kind of data. >> >> >> Does it sound reasonable? >> >> >> Cheers, >> Dan. >> >> BioWiki conference: >> http://www.nettab.org/2010/ >> >> >> On 30 October 2010 12:41, Andy Jenkinson wrote: >>> Hi Dan, >>> >>> Sounds interesting. How do you see that working? >>> >>> Cheers, >>> Andy >>> >>> On 29 Oct 2010, at 16:28, Dan Bolser wrote: >>> >>>> My thinking was that the DASWiki approach could also support the DAS >>>> writeback extension. >>>> >>>> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >>>> wrote: >>>>> Hello There, >>>>> >>>>> I have been working in an extension to DAS1.6 called >>>>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow >>>>> to create new versions of an existing feature. So, putting new notes into a >>>>> feature is just a creation of a new version of the feature. The server >>>>> implementation of the writeback extends MyDas >>>>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>>>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>>>> We are close to release the plugin for Dasty3 to use the writeback server, >>>>> however this first client is a protein client, and so far there is not a >>>>> development for a genome client with DAS writeback capability, but I am >>>>> quite interested in this. >>>>> I hope to be able to announce the release of the writeback client in Dasty3 >>>>> in a few days, so you will be able to see it working and see if this >>>>> approach goes in the same direction of what you are looking for. >>>>> >>>>> Regards, >>>>> >>>>> Gustavo. >>>>> >>>>> 2010/10/29 Dan Bolser >>>>>> >>>>>> Hi Bob, >>>>>> >>>>>> This is a nice idea. In my spare time I've been working on running a >>>>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>>>> runs Wikipedia). >>>>>> >>>>>> In theory, you could have a comments track that was pulled in from the >>>>>> 'DASWiki', and clicking the details link would take you to the wiki >>>>>> page to edit the comment. Going back to the GBrowse, you would then >>>>>> see the updated data from the wiki page. It wouldn't be too hard to >>>>>> have a similar workflow for adding new comments. >>>>>> >>>>>> I saw a talk from some people at KeyGene who are doing something >>>>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>>>> query reports for specific regions). You can see the talk here: >>>>>> >>>>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>>>> ** >>>>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>>>> >>>>>> >>>>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>>>> prototype is here: >>>>>> >>>>>> http://das.referata.com/wiki/Main_Page >>>>>> >>>>>> >>>>>> Kick me a few times and I'll get the underlying code into shape. A >>>>>> year or two back I did have a working prototype based on a MediaWiki >>>>>> ProServer adaptor. >>>>>> >>>>>> >>>>>> If you are interested in community annotation should think about attending >>>>>> this: >>>>>> >>>>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>>>> http://www.nettab.org/2010/ >>>>>> >>>>>> >>>>>> Cheers, >>>>>> Dan. >>>>>> >>>>>> On 26 October 2010 20:31, Bob Muller wrote: >>>>>>> We are working with a small research project that doesn't have funds for >>>>>>> a full-scale database for features, so they want to know: >>>>>>> >>>>>>> How difficult would it be to add a comment section editable by users to >>>>>>> gbrowse? ?When you click on a feature in gbrowse it shows a detail page for >>>>>>> that feature, is there any way we could enable edits that could be written >>>>>>> back to the underlying mysql database that gbrowse runs on? >>>>>>> >>>>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>>>> entered through GBrowse as a way to annotate their genome. I'd be interested >>>>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>>>> >>>>>>> ? --Bob Muller, TAIR (www.arabidopsis.org) >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>>>> contest >>>>>>> Create new apps & games for the Nokia N8 for consumers in ?U.S. and >>>>>>> Canada >>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>>>> marketing >>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse at lists.sourceforge.net >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> DAS mailing list >>>>>> DAS at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>> >>>>> >>>>> >>>>> -- >>>>> Gustavo Adolfo Salazar Orejuela >>>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> DAS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> > > From ljgarcia at ebi.ac.uk Tue Nov 2 11:51:07 2010 From: ljgarcia at ebi.ac.uk (Leyla Garcia) Date: Tue, 02 Nov 2010 15:51:07 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk>

Message-ID: <4CD0336B.2050602@ebi.ac.uk> Hi Dan, There will be a writeback client, a Dasty 3 plugin soon. So, your Wiki approach will be a client as well? It would be nice, and it would also give people more possibilities. Actually, I think it would be possible to configure the same writeback server for both clients. Have you thought to add some other functionalities related to DAS besides those provided by the writeback? We plan to extend the writeback idea with some folksnomy-based facilities. This project is just starting so I will let you know more in a while. That idea could be interesting for you too. Leyla On 02/11/2010 13:28, Dan Bolser wrote: > Thanks for the encouragement Andy! > > Yup, I need to look in detail at the DAS writeback specification. > > I remember Gustavo talking a couple of years back, asking people to > work together on features like these (rather than all competing on > similar but probably mutually exclusive methods). I really value that > sentiment. > > > Cheers, > Dan. > > On 2 November 2010 13:07, Andy Jenkinson wrote: >> Hi Dan, >> >> Now I see what you mean - basically the wiki and DAS source have the same data/comments, and there are two ways to enter it (writeback inside the client OR the wiki itself). This sounds good and certainly feasible. I guess there will be details about the format the comments take in the Wiki, but I'm sure it would work. I agree that the great thing about an approach like this (and DAS writeback's "independent" architecture) is the open model. This, and the fact that it would also be possible to have the comments propagated into multiple clients (the usual DAS distributed approach) make things much more appealing than just a single isolated database of user comments. >> >> It's probably worth looking at the provenance/users aspect of the wiki integration to see how this can work with writeback. Gustavo can say more about how writeback handles user tracking I expect, but authentication is often the most difficult thing when it comes to implementing these things, I find. Specifically in this case: "when I edit something in the client, can people see who made the edit on the wiki itself, and if so is the process by which that happens secure?" >> >> I definitely encourage you to look further into it and am keen to find out how you get on. >> >> Cheers, >> Andy >> >> On 2 Nov 2010, at 10:14, Dan Bolser wrote: >> >>> Here is how I thought it would work (please let me know if this sounds >>> about right, or if I made some mistakes in my understanding of the way >>> DAS writeback will work): >>> >>> 1) I was thinking that the ProServer DAS server should (or at least >>> could) implement the DAS writeback extension. >>> >>> 2) The genome browser client (or some other client) would talk to the >>> DAS server using the DAS writeback protocol once a comment was added >>> (i.e. I'm relying on a sensible client that can 'properly' handle >>> comments). >>> >>> 3) I expect that ProServer will offload the job of actually storing >>> the comment on a datasource adaptor. >>> >>> 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading >>> feature data from the wiki to also write feature data there too. >>> (Comments are just features right?) >>> >>> 5) You could then use either the genome browser client (or some other >>> client) or the wiki directly to add and/or edit comments. i.e. the >>> wiki is just another feature editing client / DAS datasource. >>> >>> >>> I like this solution because I think 'community annotation' should be >>> in the 'community', not on some server behind closed doors somewhere >>> (somehow a wiki 'feels' more 'open' to me than some bespoke database >>> x). There are plenty of wikis that could be used as back ends, and >>> 'wiki' is a good way to do community annotation. They handle issues >>> related to provenance, QC, versioning, authorship, motivation, >>> publicising, publication, etc., etc. Again, MediaWiki is a good >>> choice, because their is a lot of development for that platform, and I >>> can easily imagine tagging, 'micro-publication' and syndication >>> extensions being leveraged for this kind of data. >>> >>> >>> Does it sound reasonable? >>> >>> >>> Cheers, >>> Dan. >>> >>> BioWiki conference: >>> http://www.nettab.org/2010/ >>> >>> >>> On 30 October 2010 12:41, Andy Jenkinson wrote: >>>> Hi Dan, >>>> >>>> Sounds interesting. How do you see that working? >>>> >>>> Cheers, >>>> Andy >>>> >>>> On 29 Oct 2010, at 16:28, Dan Bolser wrote: >>>> >>>>> My thinking was that the DASWiki approach could also support the DAS >>>>> writeback extension. >>>>> >>>>> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >>>>> wrote: >>>>>> Hello There, >>>>>> >>>>>> I have been working in an extension to DAS1.6 called >>>>>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow >>>>>> to create new versions of an existing feature. So, putting new notes into a >>>>>> feature is just a creation of a new version of the feature. The server >>>>>> implementation of the writeback extends MyDas >>>>>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>>>>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>>>>> We are close to release the plugin for Dasty3 to use the writeback server, >>>>>> however this first client is a protein client, and so far there is not a >>>>>> development for a genome client with DAS writeback capability, but I am >>>>>> quite interested in this. >>>>>> I hope to be able to announce the release of the writeback client in Dasty3 >>>>>> in a few days, so you will be able to see it working and see if this >>>>>> approach goes in the same direction of what you are looking for. >>>>>> >>>>>> Regards, >>>>>> >>>>>> Gustavo. >>>>>> >>>>>> 2010/10/29 Dan Bolser >>>>>>> Hi Bob, >>>>>>> >>>>>>> This is a nice idea. In my spare time I've been working on running a >>>>>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>>>>> runs Wikipedia). >>>>>>> >>>>>>> In theory, you could have a comments track that was pulled in from the >>>>>>> 'DASWiki', and clicking the details link would take you to the wiki >>>>>>> page to edit the comment. Going back to the GBrowse, you would then >>>>>>> see the updated data from the wiki page. It wouldn't be too hard to >>>>>>> have a similar workflow for adding new comments. >>>>>>> >>>>>>> I saw a talk from some people at KeyGene who are doing something >>>>>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>>>>> query reports for specific regions). You can see the talk here: >>>>>>> >>>>>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>>>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>>>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>>>>> ** >>>>>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>>>>> >>>>>>> >>>>>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>>>>> prototype is here: >>>>>>> >>>>>>> http://das.referata.com/wiki/Main_Page >>>>>>> >>>>>>> >>>>>>> Kick me a few times and I'll get the underlying code into shape. A >>>>>>> year or two back I did have a working prototype based on a MediaWiki >>>>>>> ProServer adaptor. >>>>>>> >>>>>>> >>>>>>> If you are interested in community annotation should think about attending >>>>>>> this: >>>>>>> >>>>>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>>>>> http://www.nettab.org/2010/ >>>>>>> >>>>>>> >>>>>>> Cheers, >>>>>>> Dan. >>>>>>> >>>>>>> On 26 October 2010 20:31, Bob Muller wrote: >>>>>>>> We are working with a small research project that doesn't have funds for >>>>>>>> a full-scale database for features, so they want to know: >>>>>>>> >>>>>>>> How difficult would it be to add a comment section editable by users to >>>>>>>> gbrowse? When you click on a feature in gbrowse it shows a detail page for >>>>>>>> that feature, is there any way we could enable edits that could be written >>>>>>>> back to the underlying mysql database that gbrowse runs on? >>>>>>>> >>>>>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>>>>> entered through GBrowse as a way to annotate their genome. I'd be interested >>>>>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>>>>> >>>>>>>> --Bob Muller, TAIR (www.arabidopsis.org) >>>>>>>> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>>>>> contest >>>>>>>> Create new apps& games for the Nokia N8 for consumers in U.S. and >>>>>>>> Canada >>>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>>>>> marketing >>>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>>>>> _______________________________________________ >>>>>>>> Gmod-gbrowse mailing list >>>>>>>> Gmod-gbrowse at lists.sourceforge.net >>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>>> >>>>>>> _______________________________________________ >>>>>>> DAS mailing list >>>>>>> DAS at lists.open-bio.org >>>>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>>> >>>>>> >>>>>> -- >>>>>> Gustavo Adolfo Salazar Orejuela >>>>>> >>>>> _______________________________________________ >>>>> DAS mailing list >>>>> DAS at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/das >>>> >> > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das From bernatgel at gmail.com Tue Nov 2 12:15:42 2010 From: bernatgel at gmail.com (Bernat Gel) Date: Tue, 2 Nov 2010 17:15:42 +0100 Subject: [DAS] easyDAS presentation Message-ID: Hi all, We are happy to announce that the first public version of easyDAS is finally available. easyDAS is a web application for the automatic creation of DAS sources hosted at the EBI. To create a new source, upload a data file (currently GFF or other "tabular files" (CSV, etc)), define some properties of the new source and data (selecting a coordinates system, assigning ontology terms to the different feature types) and click on Finish. A new source (1.6 compliant) will be available and ready to use. Although there's currently no hard limit on the number of features, it's feasible to create new sources only up to 100k features. You can find easyDAS at http://http://www.ebi.ac.uk/panda-srv/easydas/ This is the fist public version and any feedback will be welcome! Cheers Bernat Gel From jw12 at sanger.ac.uk Fri Nov 19 05:45:14 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Fri, 19 Nov 2010 10:45:14 +0000 Subject: [DAS] DAS Position available at the Sanger Message-ID: A great opportunity is available for a DAS Perl developer at the Sanger. To apply please go to this link https://jobs.sanger.ac.uk/wd/plsql/wd_portal.show_job?p_web_site_id=1764&p_web_page_id=116385 Brief summary below: Senior Ensembl Web Developer - DAS Support Salary from ?27316 to ?37690 pa dependent on experience We are seeking a highly motivated Senior Perl Web Developer to develop and maintain DAS (Distributed Annotation System) infrastructure for the Ensembl project, along with developing web displays for DAS data. DAS is a client server technology for delivering annotation on genomic sequence, genes and other biological features, in a standardised XML format. It enables users to display their own data in the Ensembl browser, facilitating research and collaboration, and allows embedding of Ensembl data within other software. The position is in the Ensembl web team working on the Ensembl sites (http://www.ensembl.org/ ). The scope of the role includes all aspects of DAS technology from client and server development to graphical display. You will be working closely with other members of the Ensembl web team to integrate DAS into our large scale object-oriented web application. The role involves interaction with other projects at the Wellcome Trust Sanger Institute (WTSI) and the European Bioinformatics Institute (EBI), the WTSI web team and the external DAS community. Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- 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 jw12 at sanger.ac.uk Thu Nov 25 10:58:33 2010 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 25 Nov 2010 15:58:33 +0000 Subject: [DAS] DAS Workshop 2011 Dates Message-ID: <915EC394-E26C-4595-978A-15F3764207AF@sanger.ac.uk> Hi Just a heads up that the current dates for the next DAS workshop held at the Sanger/EBI will be Wednesday 2nd, Thursday 3rd and Friday 4th March 2011. We will endeavour to confirm these dates and give more details shortly. Thanks Jonathan Warren Senior Developer and DAS coordinator blog: http://biodasman.wordpress.com/ jw12 at sanger.ac.uk Ext: 2314 Telephone: 01223 492314 -- 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 David.Nix at hci.utah.edu Thu Nov 25 11:31:59 2010 From: David.Nix at hci.utah.edu (David Nix) Date: Thu, 25 Nov 2010 09:31:59 -0700 Subject: [DAS] Bam file support in GenoPub DAS/2 -> IGB In-Reply-To: Message-ID: Hello Thomas, FYI. Finally have this up and running. -cheers, D ------ Forwarded Message From: David Nix Date: Wed, 24 Nov 2010 19:58:33 -0700 To: Brett Milash , Ying Sun , Gholson Lyon , Sean Tavtigian , Russell Bell , Barry Moore , M Hobbs , Reid Robison , Richard Clark , Tonya DiSera , Karin Chen , Bradley Katz , Brenda Bass , "W. Evan Johnson" Conversation: Bam file support in GenoPub DAS/2 -> IGB Subject: Bam file support in GenoPub DAS/2 -> IGB Hello Folks, I've finally worked out what I believe are all the bugs and have enabled bam alignment file support for GenoPub DAS/2 distribution to IGB. (IGB currently supports local desktop BAM file loading.) You'll have to use http://bioserver.hci.utah.edu/IGB/igb_exe.jar or a build off the current head. IGB 6.4 won't work since I had to modify a critical utility. I'll switch over the web start links in a couple weeks after running some more tests. If you want to install the modified server download the archive from http://bioserver.hci.utah.edu/IGB/ das2server-genopub_0.2.zip . To upload bam files use the Picard tools (http://picard.sourceforge.net) to sort your bam file by coordinate, build an index, and validate both. Then upload both the xxx.bam and it's corresponding xxx.bam.bai index file simultaneously into the same Annotation in GenoPub. Note, the C based SamTools seem to generate bam and bai files that don't always pass the java based Picard validation so be sure to run the Picard ValidateSamFile app before uploading to GenoPub. Let me know if you run into any bugs or odd behavior. -cheers, D [cid:3373522319_21881239] ------ End of Forwarded Message [DAS] 1.6 draft 7 Thomas Down thomas.a.down at gmail.com Thu Sep 23 10:44:05 EDT 2010 Previous message: [DAS] 1.6 draft 7 Next message: [DAS] 1.6 draft 7 Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] Hi David, Just getting in touch to let you know that we're very interested in getting big piles of sequencing data onto genome browsers, and are certainly interested in alternative formats. My current thoughts are that -- at least for what we're doing -- a slightly more concise XML schema, plus richer control of server-side summarization/binning (think maxbins++) might be the sweet spot, but very interested to see other options as well. Also, just to check... are you currently gzipping your DAS XML? This makes a *huge* (at least 10-fold, potentially more) difference, and while I agree it's still not quite optimal, this has got us a long way so far. It's possible to negotiate compression purely in the HTTP layer (using the Accept-Encoding header), so doesn't necessarily impact the DAS spec at all. Best wishes, Thomas. On Wed, Sep 22, 2010 at 9:33 PM, David Nix wrote: > Bugger, that's unfortunate. Without alternative formats, it is impossible > to distribute genomic data from next generation sequencing and microarray > experiments in a timely manner. Even then, the data transfer is very slow > due to the <2MB/s bandwidth limitation. > > I wonder if folks should be encouraged to use DAS/2 for genomic data > distribution and DAS/1 for everything else? There seems to be a great > reluctance to add alternative formats to DAS/1. I can understand the > advantages of having a standardized data distribution format. Unfortunately > this won't work for us, even compressed, DAS GFF XML is about 100x larger > than some of the other binary genomic data formats such as bar and useq. > > I'm afraid DAS is going to get left behind as other data distribution > models are adopted that can accommodate the ever growing density of genomic > data. > > What do you think? > > -cheers, D > > On 9/22/10 10:51 AM, "Andy Jenkinson" wrote: > > Hi David, > > It is not part of DAS 1.6 but was discussed at the DAS workshop. During the > workshop we had some discussion on the topic and came up with a couple of > sensible proposals for an extension to 1.6 to cover it. If my memory serves > me we agreed on an outline proposal, and there is a write up on > http://www.biodas.org/wiki/DAS1.6E (courtesy of Gregg? Is that correct?) > but as far as I know there are no implementations as yet. > > Cheers, > Andy > > On 22 Sep 2010, at 17:17, David Nix wrote: > > > Hello Andy, > > > > I'm looking at the latest and trying to find out if alternative file > formats were added to 1.6? Can one respond to DAS/1 queries with binary > data formats or is it still XML? If the later, any time frame for when this > will be added? > > > > -cheers, D > > > > -- > > David Austin Nix, PhD | Bioinformatics Shared Resource | 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 | WebSite: http://bioserver.hci.utah.edu | DAS/2: > http://bioserver.hci.utah.edu:8080/DAS2DB/genome > > > > > > > > On 9/22/10 9:44 AM, "Andy Jenkinson" wrote: > > > > Hi all, > > > > I have updated the 1.6 specification to draft 7 in light of recent > discussions on the list: > > 1. All features in a parent/part hierarchy must be returned if any > overlap a query segment. > > 2. The alignment command is back to extension status, in anticipation of > a revamp (see the 1.6E page on the wiki). > > > > Also in this draft is a previous change that was missed: the start and > end attributes of a SEGMENT element in the features, types and entry_points > commands are now optional. This makes it possible for servers without access > to detailed information about the segments they are annotating to comply > with the specification. Previously, it was impossible for such servers to > respond in a compliant fashion to requests in which the client does not > specify a start/end position. > > > > If my understanding is correct, no further changes to the specification > are anticipated which means we can consider this the final draft... > > > > See here for details: > > http://www.biodas.org/wiki/DAS1.6 > > > > Cheers, > > Andy > > _______________________________________________ > > DAS mailing list > > DAS at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/das > > > > > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > Previous message: [DAS] 1.6 draft 7 Next message: [DAS] 1.6 draft 7 Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] More information about the DAS mailing list -------------- next part -------------- A non-text attachment was scrubbed... Name: image.png Type: image/png Size: 286654 bytes Desc: image.png URL: From dan.bolser at gmail.com Tue Nov 2 10:14:23 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 2 Nov 2010 10:14:23 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk> References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk> Message-ID: Here is how I thought it would work (please let me know if this sounds about right, or if I made some mistakes in my understanding of the way DAS writeback will work): 1) I was thinking that the ProServer DAS server should (or at least could) implement the DAS writeback extension. 2) The genome browser client (or some other client) would talk to the DAS server using the DAS writeback protocol once a comment was added (i.e. I'm relying on a sensible client that can 'properly' handle comments). 3) I expect that ProServer will offload the job of actually storing the comment on a datasource adaptor. 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading feature data from the wiki to also write feature data there too. (Comments are just features right?) 5) You could then use either the genome browser client (or some other client) or the wiki directly to add and/or edit comments. i.e. the wiki is just another feature editing client / DAS datasource. I like this solution because I think 'community annotation' should be in the 'community', not on some server behind closed doors somewhere (somehow a wiki 'feels' more 'open' to me than some bespoke database x). There are plenty of wikis that could be used as back ends, and 'wiki' is a good way to do community annotation. They handle issues related to provenance, QC, versioning, authorship, motivation, publicising, publication, etc., etc. Again, MediaWiki is a good choice, because their is a lot of development for that platform, and I can easily imagine tagging, 'micro-publication' and syndication extensions being leveraged for this kind of data. Does it sound reasonable? Cheers, Dan. BioWiki conference: http://www.nettab.org/2010/ On 30 October 2010 12:41, Andy Jenkinson wrote: > Hi Dan, > > Sounds interesting. How do you see that working? > > Cheers, > Andy > > On 29 Oct 2010, at 16:28, Dan Bolser wrote: > >> My thinking was that the DASWiki approach could also support the DAS >> writeback extension. >> >> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >> wrote: >>> Hello There, >>> >>> I have been working in an extension to DAS1.6 called >>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow >>> to create new versions of an existing feature. So, putting new notes into a >>> feature is just a creation of a new version of the feature. The server >>> implementation of the writeback extends MyDas >>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>> We are close to release the plugin for Dasty3 to use the writeback server, >>> however this first client is a protein client, and so far there is not a >>> development for a genome client with DAS writeback capability, but I am >>> quite interested in this. >>> I hope to be able to announce the release of the writeback client in Dasty3 >>> in a few days, so you will be able to see it working and see if this >>> approach goes in the same direction of what you are looking for. >>> >>> Regards, >>> >>> Gustavo. >>> >>> 2010/10/29 Dan Bolser >>>> >>>> Hi Bob, >>>> >>>> This is a nice idea. In my spare time I've been working on running a >>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>> runs Wikipedia). >>>> >>>> In theory, you could have a comments track that was pulled in from the >>>> 'DASWiki', and clicking the details link would take you to the wiki >>>> page to edit the comment. Going back to the GBrowse, you would then >>>> see the updated data from the wiki page. It wouldn't be too hard to >>>> have a similar workflow for adding new comments. >>>> >>>> I saw a talk from some people at KeyGene who are doing something >>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>> query reports for specific regions). You can see the talk here: >>>> >>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>> ** >>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>> >>>> >>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>> prototype is here: >>>> >>>> http://das.referata.com/wiki/Main_Page >>>> >>>> >>>> Kick me a few times and I'll get the underlying code into shape. A >>>> year or two back I did have a working prototype based on a MediaWiki >>>> ProServer adaptor. >>>> >>>> >>>> If you are interested in community annotation should think about attending >>>> this: >>>> >>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>> http://www.nettab.org/2010/ >>>> >>>> >>>> Cheers, >>>> Dan. >>>> >>>> On 26 October 2010 20:31, Bob Muller wrote: >>>>> We are working with a small research project that doesn't have funds for >>>>> a full-scale database for features, so they want to know: >>>>> >>>>> How difficult would it be to add a comment section editable by users to >>>>> gbrowse? ?When you click on a feature in gbrowse it shows a detail page for >>>>> that feature, is there any way we could enable edits that could be written >>>>> back to the underlying mysql database that gbrowse runs on? >>>>> >>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>> entered through GBrowse as a way to annotate their genome. I'd be interested >>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>> >>>>> ? --Bob Muller, TAIR (www.arabidopsis.org) >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>> contest >>>>> Create new apps & games for the Nokia N8 for consumers in ?U.S. and >>>>> Canada >>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>> marketing >>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>> _______________________________________________ >>>>> Gmod-gbrowse mailing list >>>>> Gmod-gbrowse at lists.sourceforge.net >>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> DAS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> >>> >>> -- >>> Gustavo Adolfo Salazar Orejuela >>> >> >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das > > From andy.jenkinson at ebi.ac.uk Tue Nov 2 13:07:15 2010 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Tue, 2 Nov 2010 13:07:15 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk> Message-ID: Hi Dan, Now I see what you mean - basically the wiki and DAS source have the same data/comments, and there are two ways to enter it (writeback inside the client OR the wiki itself). This sounds good and certainly feasible. I guess there will be details about the format the comments take in the Wiki, but I'm sure it would work. I agree that the great thing about an approach like this (and DAS writeback's "independent" architecture) is the open model. This, and the fact that it would also be possible to have the comments propagated into multiple clients (the usual DAS distributed approach) make things much more appealing than just a single isolated database of user comments. It's probably worth looking at the provenance/users aspect of the wiki integration to see how this can work with writeback. Gustavo can say more about how writeback handles user tracking I expect, but authentication is often the most difficult thing when it comes to implementing these things, I find. Specifically in this case: "when I edit something in the client, can people see who made the edit on the wiki itself, and if so is the process by which that happens secure?" I definitely encourage you to look further into it and am keen to find out how you get on. Cheers, Andy On 2 Nov 2010, at 10:14, Dan Bolser wrote: > Here is how I thought it would work (please let me know if this sounds > about right, or if I made some mistakes in my understanding of the way > DAS writeback will work): > > 1) I was thinking that the ProServer DAS server should (or at least > could) implement the DAS writeback extension. > > 2) The genome browser client (or some other client) would talk to the > DAS server using the DAS writeback protocol once a comment was added > (i.e. I'm relying on a sensible client that can 'properly' handle > comments). > > 3) I expect that ProServer will offload the job of actually storing > the comment on a datasource adaptor. > > 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading > feature data from the wiki to also write feature data there too. > (Comments are just features right?) > > 5) You could then use either the genome browser client (or some other > client) or the wiki directly to add and/or edit comments. i.e. the > wiki is just another feature editing client / DAS datasource. > > > I like this solution because I think 'community annotation' should be > in the 'community', not on some server behind closed doors somewhere > (somehow a wiki 'feels' more 'open' to me than some bespoke database > x). There are plenty of wikis that could be used as back ends, and > 'wiki' is a good way to do community annotation. They handle issues > related to provenance, QC, versioning, authorship, motivation, > publicising, publication, etc., etc. Again, MediaWiki is a good > choice, because their is a lot of development for that platform, and I > can easily imagine tagging, 'micro-publication' and syndication > extensions being leveraged for this kind of data. > > > Does it sound reasonable? > > > Cheers, > Dan. > > BioWiki conference: > http://www.nettab.org/2010/ > > > On 30 October 2010 12:41, Andy Jenkinson wrote: >> Hi Dan, >> >> Sounds interesting. How do you see that working? >> >> Cheers, >> Andy >> >> On 29 Oct 2010, at 16:28, Dan Bolser wrote: >> >>> My thinking was that the DASWiki approach could also support the DAS >>> writeback extension. >>> >>> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >>> wrote: >>>> Hello There, >>>> >>>> I have been working in an extension to DAS1.6 called >>>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow >>>> to create new versions of an existing feature. So, putting new notes into a >>>> feature is just a creation of a new version of the feature. The server >>>> implementation of the writeback extends MyDas >>>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>>> We are close to release the plugin for Dasty3 to use the writeback server, >>>> however this first client is a protein client, and so far there is not a >>>> development for a genome client with DAS writeback capability, but I am >>>> quite interested in this. >>>> I hope to be able to announce the release of the writeback client in Dasty3 >>>> in a few days, so you will be able to see it working and see if this >>>> approach goes in the same direction of what you are looking for. >>>> >>>> Regards, >>>> >>>> Gustavo. >>>> >>>> 2010/10/29 Dan Bolser >>>>> >>>>> Hi Bob, >>>>> >>>>> This is a nice idea. In my spare time I've been working on running a >>>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>>> runs Wikipedia). >>>>> >>>>> In theory, you could have a comments track that was pulled in from the >>>>> 'DASWiki', and clicking the details link would take you to the wiki >>>>> page to edit the comment. Going back to the GBrowse, you would then >>>>> see the updated data from the wiki page. It wouldn't be too hard to >>>>> have a similar workflow for adding new comments. >>>>> >>>>> I saw a talk from some people at KeyGene who are doing something >>>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>>> query reports for specific regions). You can see the talk here: >>>>> >>>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>>> ** >>>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>>> >>>>> >>>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>>> prototype is here: >>>>> >>>>> http://das.referata.com/wiki/Main_Page >>>>> >>>>> >>>>> Kick me a few times and I'll get the underlying code into shape. A >>>>> year or two back I did have a working prototype based on a MediaWiki >>>>> ProServer adaptor. >>>>> >>>>> >>>>> If you are interested in community annotation should think about attending >>>>> this: >>>>> >>>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>>> http://www.nettab.org/2010/ >>>>> >>>>> >>>>> Cheers, >>>>> Dan. >>>>> >>>>> On 26 October 2010 20:31, Bob Muller wrote: >>>>>> We are working with a small research project that doesn't have funds for >>>>>> a full-scale database for features, so they want to know: >>>>>> >>>>>> How difficult would it be to add a comment section editable by users to >>>>>> gbrowse? When you click on a feature in gbrowse it shows a detail page for >>>>>> that feature, is there any way we could enable edits that could be written >>>>>> back to the underlying mysql database that gbrowse runs on? >>>>>> >>>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>>> entered through GBrowse as a way to annotate their genome. I'd be interested >>>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>>> >>>>>> --Bob Muller, TAIR (www.arabidopsis.org) >>>>>> >>>>>> >>>>>> ------------------------------------------------------------------------------ >>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>>> contest >>>>>> Create new apps & games for the Nokia N8 for consumers in U.S. and >>>>>> Canada >>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>>> marketing >>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>>> _______________________________________________ >>>>>> Gmod-gbrowse mailing list >>>>>> Gmod-gbrowse at lists.sourceforge.net >>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>> >>>>> >>>>> _______________________________________________ >>>>> DAS mailing list >>>>> DAS at lists.open-bio.org >>>>> http://lists.open-bio.org/mailman/listinfo/das >>>> >>>> >>>> >>>> -- >>>> Gustavo Adolfo Salazar Orejuela >>>> >>> >>> _______________________________________________ >>> DAS mailing list >>> DAS at lists.open-bio.org >>> http://lists.open-bio.org/mailman/listinfo/das >> >> From dan.bolser at gmail.com Tue Nov 2 13:28:12 2010 From: dan.bolser at gmail.com (Dan Bolser) Date: Tue, 2 Nov 2010 13:28:12 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk>

Message-ID: Thanks for the encouragement Andy! Yup, I need to look in detail at the DAS writeback specification. I remember Gustavo talking a couple of years back, asking people to work together on features like these (rather than all competing on similar but probably mutually exclusive methods). I really value that sentiment. Cheers, Dan. On 2 November 2010 13:07, Andy Jenkinson wrote: > Hi Dan, > > Now I see what you mean - basically the wiki and DAS source have the same data/comments, and there are two ways to enter it (writeback inside the client OR the wiki itself). This sounds good and certainly feasible. I guess there will be details about the format the comments take in the Wiki, but I'm sure it would work. I agree that the great thing about an approach like this (and DAS writeback's "independent" architecture) is the open model. This, and the fact that it would also be possible to have the comments propagated into multiple clients (the usual DAS distributed approach) make things much more appealing than just a single isolated database of user comments. > > It's probably worth looking at the provenance/users aspect of the wiki integration to see how this can work with writeback. Gustavo can say more about how writeback handles user tracking I expect, but authentication is often the most difficult thing when it comes to implementing these things, I find. Specifically in this case: "when I edit something in the client, can people see who made the edit on the wiki itself, and if so is the process by which that happens secure?" > > I definitely encourage you to look further into it and am keen to find out how you get on. > > Cheers, > Andy > > On 2 Nov 2010, at 10:14, Dan Bolser wrote: > >> Here is how I thought it would work (please let me know if this sounds >> about right, or if I made some mistakes in my understanding of the way >> DAS writeback will work): >> >> 1) I was thinking that the ProServer DAS server should (or at least >> could) implement the DAS writeback extension. >> >> 2) The genome browser client (or some other client) would talk to the >> DAS server using the DAS writeback protocol once a comment was added >> (i.e. I'm relying on a sensible client that can 'properly' handle >> comments). >> >> 3) I expect that ProServer will offload the job of actually storing >> the comment on a datasource adaptor. >> >> 4) I thought I'd extend the MediaWiki adaptor that I wrote for reading >> feature data from the wiki to also write feature data there too. >> (Comments are just features right?) >> >> 5) You could then use either the genome browser client (or some other >> client) or the wiki directly to add and/or edit comments. i.e. the >> wiki is just another feature editing client / DAS datasource. >> >> >> I like this solution because I think 'community annotation' should be >> in the 'community', not on some server behind closed doors somewhere >> (somehow a wiki 'feels' more 'open' to me than some bespoke database >> x). There are plenty of wikis that could be used as back ends, and >> 'wiki' is a good way to do community annotation. They handle issues >> related to provenance, QC, versioning, authorship, motivation, >> publicising, publication, etc., etc. Again, MediaWiki is a good >> choice, because their is a lot of development for that platform, and I >> can easily imagine tagging, 'micro-publication' and syndication >> extensions being leveraged for this kind of data. >> >> >> Does it sound reasonable? >> >> >> Cheers, >> Dan. >> >> BioWiki conference: >> http://www.nettab.org/2010/ >> >> >> On 30 October 2010 12:41, Andy Jenkinson wrote: >>> Hi Dan, >>> >>> Sounds interesting. How do you see that working? >>> >>> Cheers, >>> Andy >>> >>> On 29 Oct 2010, at 16:28, Dan Bolser wrote: >>> >>>> My thinking was that the DASWiki approach could also support the DAS >>>> writeback extension. >>>> >>>> On 29 October 2010 11:58, Gustavo Adolfo Salazar Orejuela >>>> wrote: >>>>> Hello There, >>>>> >>>>> I have been working in an extension to DAS1.6 called >>>>> writeback(http://www.biodas.org/wiki/DAS1.6E#DAS_writeback), this will allow >>>>> to create new versions of an existing feature. So, putting new notes into a >>>>> feature is just a creation of a new version of the feature. The server >>>>> implementation of the writeback extends MyDas >>>>> (http://code.google.com/p/mydas/) and you can get a mydas+writebackk >>>>> datasource by SVN (https://mydas.googlecode.com/svn/writeback-datasource). >>>>> We are close to release the plugin for Dasty3 to use the writeback server, >>>>> however this first client is a protein client, and so far there is not a >>>>> development for a genome client with DAS writeback capability, but I am >>>>> quite interested in this. >>>>> I hope to be able to announce the release of the writeback client in Dasty3 >>>>> in a few days, so you will be able to see it working and see if this >>>>> approach goes in the same direction of what you are looking for. >>>>> >>>>> Regards, >>>>> >>>>> Gustavo. >>>>> >>>>> 2010/10/29 Dan Bolser >>>>>> >>>>>> Hi Bob, >>>>>> >>>>>> This is a nice idea. In my spare time I've been working on running a >>>>>> DAS server from a MediaWiki data source. (MediaWiki is the wiki that >>>>>> runs Wikipedia). >>>>>> >>>>>> In theory, you could have a comments track that was pulled in from the >>>>>> 'DASWiki', and clicking the details link would take you to the wiki >>>>>> page to edit the comment. Going back to the GBrowse, you would then >>>>>> see the updated data from the wiki page. It wouldn't be too hard to >>>>>> have a similar workflow for adding new comments. >>>>>> >>>>>> I saw a talk from some people at KeyGene who are doing something >>>>>> similar (loading DAS into a wiki and linking it to GBrowse to generate >>>>>> query reports for specific regions). You can see the talk here: >>>>>> >>>>>> SMWCon Fall 2010 / Sunday / Rudi van Bavel >>>>>> * http://semantic-mediawiki.org/wiki/SMWCon_Fall_2010#Program >>>>>> ** https://docs.google.com/present/view?id=dg56kh6m_344gh2dg72g >>>>>> ** >>>>>> http://srv-hrl-32.web.pwo.ou.nl//informatica/SMWCon/Van%20Bavel%20bulk%20loading.wmv >>>>>> >>>>>> >>>>>> If anyone wants to take what I have done so far, my (sadly neglected) >>>>>> prototype is here: >>>>>> >>>>>> http://das.referata.com/wiki/Main_Page >>>>>> >>>>>> >>>>>> Kick me a few times and I'll get the underlying code into shape. A >>>>>> year or two back I did have a working prototype based on a MediaWiki >>>>>> ProServer adaptor. >>>>>> >>>>>> >>>>>> If you are interested in community annotation should think about attending >>>>>> this: >>>>>> >>>>>> Joint NETTAB 2010 and BBCC 2010 workshops focused on Biological Wikis: >>>>>> http://www.nettab.org/2010/ >>>>>> >>>>>> >>>>>> Cheers, >>>>>> Dan. >>>>>> >>>>>> On 26 October 2010 20:31, Bob Muller wrote: >>>>>>> We are working with a small research project that doesn't have funds for >>>>>>> a full-scale database for features, so they want to know: >>>>>>> >>>>>>> How difficult would it be to add a comment section editable by users to >>>>>>> gbrowse? ?When you click on a feature in gbrowse it shows a detail page for >>>>>>> that feature, is there any way we could enable edits that could be written >>>>>>> back to the underlying mysql database that gbrowse runs on? >>>>>>> >>>>>>> Their idea is to use the SeqFeature::Store database to hold "comments" >>>>>>> entered through GBrowse as a way to annotate their genome. I'd be interested >>>>>>> in whether this is possible in GBrowse 1.7 or in 2.x. >>>>>>> >>>>>>> ? --Bob Muller, TAIR (www.arabidopsis.org) >>>>>>> >>>>>>> >>>>>>> ------------------------------------------------------------------------------ >>>>>>> Nokia and AT&T present the 2010 Calling All Innovators-North America >>>>>>> contest >>>>>>> Create new apps & games for the Nokia N8 for consumers in ?U.S. and >>>>>>> Canada >>>>>>> $10 million total in prizes - $4M cash, 500 devices, nearly $6M in >>>>>>> marketing >>>>>>> Develop with Nokia Qt SDK, Web Runtime, or Java and Publish to Ovi Store >>>>>>> http://p.sf.net/sfu/nokia-dev2dev >>>>>>> _______________________________________________ >>>>>>> Gmod-gbrowse mailing list >>>>>>> Gmod-gbrowse at lists.sourceforge.net >>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-gbrowse >>>>>>> >>>>>> >>>>>> _______________________________________________ >>>>>> DAS mailing list >>>>>> DAS at lists.open-bio.org >>>>>> http://lists.open-bio.org/mailman/listinfo/das >>>>> >>>>> >>>>> >>>>> -- >>>>> Gustavo Adolfo Salazar Orejuela >>>>> >>>> >>>> _______________________________________________ >>>> DAS mailing list >>>> DAS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> > > From ljgarcia at ebi.ac.uk Tue Nov 2 15:51:07 2010 From: ljgarcia at ebi.ac.uk (Leyla Garcia) Date: Tue, 02 Nov 2010 15:51:07 +0000 Subject: [DAS] [Gmod-gbrowse] Adding comments to a gbrowse database In-Reply-To: References: <4CC71E8F.8020802@stanford.edu> <6631318A-5425-417F-8220-4627B0116C36@ebi.ac.uk>