From jw12 at sanger.ac.uk Wed Jan 7 11:58:24 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Wed, 07 Jan 2009 16:58:24 +0000 Subject: [DAS] emai addresses and the das registry Message-ID: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> Hi Due to security and spam considerations: I was wondering what DAS users would think of www.dasregistry.org asking people if they want their email addresses made public as a contact for their sources? If people say no - then the registry would for example: set the maintainer field of the source to a link back to the registry, which would be a submission form where people could indirectly email the source maintainer? Thus avoiding anyone other than the registry needing to know the maintainers real email address? Any opinions or recommendations for how this could be done are welcomed. Cheers Jonathan. -- 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 dan.bolser at gmail.com Mon Jan 12 07:11:43 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jan 2009 12:11:43 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers Message-ID: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Hi all, I'm relatively new to DAS, and I have been playing with setting up a DAS server using Dazzle. Now that I have created my reference and annotation data sources, naturally enough I would like to start browsing and visualizing the data. So... Q1) Which DAS client do you recommend for a beginner working with Dazzle? I am working in a Linux OS, and I am looking at gene predictions on a chromosome as well as 'similarity' features between the chromosome and several 'clones' from a closely related organism. To organize my research into the various clients available, I created the following page on Wikipedia: http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients That table is still quite rough, so please feel free to contribute information there. I put the table into a sub-page of the DAS page so that sites like http://www.biodas.org/ can easily 'transclude' this information. I'm not sure if that's sensible or not yet, so let me know what you think. Since we are exploring the various possibilities of using DAS with our projects, is it possible to set up a local (private) DAS registry server? This would be useful for testing purposes, especially as we may be initially working with unpublished data. Q2) What steps are required for setting up a local or a secure DAS registry? Thanks very much for any help with the above two questions. Dan P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange data encoding that I don't understand? I've seen more than one page that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - Should I go ahead and delete this pages? From jw12 at sanger.ac.uk Mon Jan 12 07:53:09 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 12:53:09 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Message-ID: <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> Hi Dan Thanks for putting up the table - I'll add some info to it shortly. The dasregistry source code is downloadable using subversion at http://www.derkholm.net/svn/repos/dasregistry/trunk/ You will also need a mysql instance set up. I can send you some info on that if you wish. There are many dependencies and configurations needed- so it may take a while to set up a fully fledged version - it may be better to experiment with your sources using the real one - I'll help you out if you need clarification on anything such as error messages and logs. Or is it that you don't want to release your data to the world and only want an in house version? I think I would recomment using ensembl to connect to your sources in the first instance - but if you want the client to sit on your desktop/local server then maybe GBrowse (this is for genomic annotations obvioyusly)? On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: > Hi all, > > I'm relatively new to DAS, and I have been playing with setting up a > DAS server using Dazzle. Now that I have created my reference and > annotation data sources, naturally enough I would like to start > browsing and visualizing the data. So... > > Q1) Which DAS client do you recommend for a beginner working with Dazzle? > > > I am working in a Linux OS, and I am looking at gene predictions on a > chromosome as well as 'similarity' features between the chromosome and > several 'clones' from a closely related organism. > > To organize my research into the various clients available, I created > the following page on Wikipedia: > > http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > > > That table is still quite rough, so please feel free to contribute > information there. I put the table into a sub-page of the DAS page so > that sites like http://www.biodas.org/ can easily 'transclude' this > information. I'm not sure if that's sensible or not yet, so let me > know what you think. > > > Since we are exploring the various possibilities of using DAS with our > projects, is it possible to set up a local (private) DAS registry > server? This would be useful for testing purposes, especially as we > may be initially working with unpublished data. > > Q2) What steps are required for setting up a local or a secure DAS registry? > > > Thanks very much for any help with the above two questions. > > Dan > > P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > data encoding that I don't understand? I've seen more than one page > that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > Should I go ahead and delete this pages? > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das -- 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 Mon Jan 12 07:57:57 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 12:57:57 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Message-ID: <1231765077.7515.160.camel@deskpro20727.dynamic.sanger.ac.uk> You can just put the table onto biodas.org if you wish dan? On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: > > chromosome as well as 'similarity' features between the chromosome > and -- 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 andy.jenkinson at ebi.ac.uk Mon Jan 12 08:05:32 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 12 Jan 2009 13:05:32 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Message-ID: <496B401C.5070305@ebi.ac.uk> Hi Dan, DAS clients tend to be different depending on the type of data you're looking at, and have different capabilities. For example, Ensembl is a well supported client for (mostly) genomic data, and implements all the most recent developments such as the DAS registry (via the sources command). However it makes no use of reference servers, instead all reference data is stored locally in a database. Dasty is more focussed on protein data. GBrowse is another genomic client, but IIRC does not know about the DAS registry. Regarding setting up a local DAS registry, what is this for? If for instance you were using Ensembl, any server that implements the sources command can potentially be a "registry" from a programmatic point of view, so unless you want to have a manual process where you can use a GUI to register a souce, you probably don't need to implement a copy of the real thing. Looks like the biodas wiki has been getting spammed, must have started recently. I'll talk to the admins about sorting it out. We'll probably need to update the registration process. Cheers, Andy Dan Bolser wrote: > Hi all, > > I'm relatively new to DAS, and I have been playing with setting up a > DAS server using Dazzle. Now that I have created my reference and > annotation data sources, naturally enough I would like to start > browsing and visualizing the data. So... > > Q1) Which DAS client do you recommend for a beginner working with Dazzle? > > > I am working in a Linux OS, and I am looking at gene predictions on a > chromosome as well as 'similarity' features between the chromosome and > several 'clones' from a closely related organism. > > To organize my research into the various clients available, I created > the following page on Wikipedia: > > http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > > > That table is still quite rough, so please feel free to contribute > information there. I put the table into a sub-page of the DAS page so > that sites like http://www.biodas.org/ can easily 'transclude' this > information. I'm not sure if that's sensible or not yet, so let me > know what you think. > > > Since we are exploring the various possibilities of using DAS with our > projects, is it possible to set up a local (private) DAS registry > server? This would be useful for testing purposes, especially as we > may be initially working with unpublished data. > > Q2) What steps are required for setting up a local or a secure DAS registry? > > > Thanks very much for any help with the above two questions. > > Dan > > P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > data encoding that I don't understand? I've seen more than one page > that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > Should I go ahead and delete this pages? > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From - Mon From dan.bolser at gmail.com Mon Jan 12 08:21:05 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jan 2009 13:21:05 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> Message-ID: <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> Hi Jonathan, Thanks very much for your reply. My comments are inline below: 2009/1/12 Jonathan Warren : > Hi Dan > > Thanks for putting up the table - I'll add some info to it shortly. Cheers, that would be great! > The dasregistry source code is downloadable using subversion at > http://www.derkholm.net/svn/repos/dasregistry/trunk/ > > You will also need a mysql instance set up. I can send you some info on > that if you wish. Please provide as much information as possible! :-D > There are many dependencies and configurations needed- so it may take a > while to set up a fully fledged version - it may be better to experiment > with your sources using the real one - I'll help you out if you need > clarification on anything such as error messages and logs. Or is it that > you don't want to release your data to the world and only want an in > house version? Yes. In the long run we will be making all our data publicly available, however, for R&D purposes and leading up to publication of the source data we would like to experiment with an in-house registry. Also, I think it would be a convenient administrative / organizational tool for us. i.e. to keep track of the various data sources (experimental or otherwise) that are being developed in-house. > I think I would recomment using ensembl to connect to your sources in > the first instance - but if you want the client to sit on your > desktop/local server then maybe GBrowse (this is for genomic annotations > obvioyusly)? Sorry for my ignorance, but can I ask if you mean that I should use ensembl remotely (on some server 'out there') and point it at my local reference / annotation server? The problem is again that both are internal, with no outfacing interface. In any case, its clear that I need to read more about ensembl, so feel free to ignore this question. In another email you said: "You can just put the table onto biodas.org if you wish..." I see this point. I am never sure how 'external' wikis should interact with Wikipedia when overlapping data is available in both. In this case I thought I'd edit WP, but please feel free to move the table to somewhere within biodas.org - I wasn't immediately sure where to put it, which is partly why I picked WP. Thanks very much for the information above, Dan. > On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: >> Hi all, >> >> I'm relatively new to DAS, and I have been playing with setting up a >> DAS server using Dazzle. Now that I have created my reference and >> annotation data sources, naturally enough I would like to start >> browsing and visualizing the data. So... >> >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? >> >> >> I am working in a Linux OS, and I am looking at gene predictions on a >> chromosome as well as 'similarity' features between the chromosome and >> several 'clones' from a closely related organism. >> >> To organize my research into the various clients available, I created >> the following page on Wikipedia: >> >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients >> >> >> That table is still quite rough, so please feel free to contribute >> information there. I put the table into a sub-page of the DAS page so >> that sites like http://www.biodas.org/ can easily 'transclude' this >> information. I'm not sure if that's sensible or not yet, so let me >> know what you think. >> >> >> Since we are exploring the various possibilities of using DAS with our >> projects, is it possible to set up a local (private) DAS registry >> server? This would be useful for testing purposes, especially as we >> may be initially working with unpublished data. >> >> Q2) What steps are required for setting up a local or a secure DAS registry? >> >> >> Thanks very much for any help with the above two questions. >> >> Dan >> >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange >> data encoding that I don't understand? I've seen more than one page >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - >> Should I go ahead and delete this pages? >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das > > > > -- > 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 dan.bolser at gmail.com Mon Jan 12 08:34:35 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jan 2009 13:34:35 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <496B401C.5070305@ebi.ac.uk> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <496B401C.5070305@ebi.ac.uk> Message-ID: <2c8757af0901120534s79ab269cuc5504bef05d27faa@mail.gmail.com> 2009/1/12 Andy Jenkinson : > Hi Dan, > > DAS clients tend to be different depending on the type of data you're > looking at, and have different capabilities. For example, Ensembl is a well > supported client for (mostly) genomic data, and implements all the most > recent developments such as the DAS registry (via the sources command). > However it makes no use of reference servers, instead all reference data is > stored locally in a database. Dasty is more focussed on protein data. > GBrowse is another genomic client, but IIRC does not know about the DAS > registry. > > Regarding setting up a local DAS registry, what is this for? If for instance > you were using Ensembl, any server that implements the sources command can > potentially be a "registry" from a programmatic point of view, so unless you > want to have a manual process where you can use a GUI to register a souce, > you probably don't need to implement a copy of the real thing. I see what you mean, but what I'm calling 'in-house' could potentially comprise several different servers at several different locations. The theory is that they would all be part of a private 'consortium', which would ultimately become part of the DAS registry proper. In so far as we would like to keep track of the different DAS servers that we have 'in-house', I thought a registry could be a good solution. > Looks like the biodas wiki has been getting spammed, must have started > recently. I'll talk to the admins about sorting it out. We'll probably need > to update the registration process. On several wikis using a 'captcha', I found that the following set rules strikes the right balance between keeping spam down and allowing unrestrictive access to users: 0) Any user can edit the wiki, because registration puts people off. 1) On any edit, present any anonymous user with a captcha. 2) Registration requires a captcha. 3) Never present a registered user with a captcha. In the MediaWiki config that looks like this: // Fix the default captcha behaviour $wgGroupPermissions['*' ]['skipcaptcha'] = false; $wgGroupPermissions['user' ]['skipcaptcha'] = true; $wgGroupPermissions['autoconfirmed']['skipcaptcha'] = true; $wgGroupPermissions['bot' ]['skipcaptcha'] = true; // registered bots $wgGroupPermissions['sysop' ]['skipcaptcha'] = true; $wgCaptchaTriggers['edit'] = true; $wgCaptchaTriggers['create'] = true; $wgCaptchaTriggers['createaccount'] = true; (all other permissions having their default values) Thanks for the info above, Dan. > Cheers, > Andy > > Dan Bolser wrote: >> >> Hi all, >> >> I'm relatively new to DAS, and I have been playing with setting up a >> DAS server using Dazzle. Now that I have created my reference and >> annotation data sources, naturally enough I would like to start >> browsing and visualizing the data. So... >> >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? >> >> >> I am working in a Linux OS, and I am looking at gene predictions on a >> chromosome as well as 'similarity' features between the chromosome and >> several 'clones' from a closely related organism. >> >> To organize my research into the various clients available, I created >> the following page on Wikipedia: >> >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients >> >> >> That table is still quite rough, so please feel free to contribute >> information there. I put the table into a sub-page of the DAS page so >> that sites like http://www.biodas.org/ can easily 'transclude' this >> information. I'm not sure if that's sensible or not yet, so let me >> know what you think. >> >> >> Since we are exploring the various possibilities of using DAS with our >> projects, is it possible to set up a local (private) DAS registry >> server? This would be useful for testing purposes, especially as we >> may be initially working with unpublished data. >> >> Q2) What steps are required for setting up a local or a secure DAS >> registry? >> >> >> Thanks very much for any help with the above two questions. >> >> Dan >> >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange >> data encoding that I don't understand? I've seen more than one page >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - >> Should I go ahead and delete this pages? >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das >> From - Mon > From andy.jenkinson at ebi.ac.uk Mon Jan 12 09:06:55 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 12 Jan 2009 14:06:55 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> Message-ID: <496B4E7F.1030901@ebi.ac.uk> Dan Bolser wrote: > 2009/1/12 Jonathan Warren : >> I think I would recomment using ensembl to connect to your sources in >> the first instance - but if you want the client to sit on your >> desktop/local server then maybe GBrowse (this is for genomic annotations >> obvioyusly)? > > Sorry for my ignorance, but can I ask if you mean that I should use > ensembl remotely (on some server 'out there') and point it at my local > reference / annotation server? The problem is again that both are > internal, with no outfacing interface. In any case, its clear that I > need to read more about ensembl, so feel free to ignore this question. It would depend on which genomes you are interested in. If Ensembl (or another Ensembl-powered site) supports your genomes, you could it to display your DAS annotations provided the DAS servers are accessible to the Ensembl servers. If not, you would have to set up an independent local Ensembl installation containing your reference genome data. Something similar would be required for GBrowse, but I suspect Ensembl is more complicated. Current visual genomic DAS clients tend not to use DAS reference servers for sequence data. Rather they have taken to storing this data locally. From jw12 at sanger.ac.uk Mon Jan 12 09:10:51 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 14:10:51 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> Message-ID: <1231769451.7515.174.camel@deskpro20727.dynamic.sanger.ac.uk> Ok if your sources are in-house then I'd use GBrowse as it's easier to set up and you can point it at both a das reference server and annotation server (which I don't think you can do with ensembl). GBrowse can also be set up to be a DAS source itself just by setting the mapmaster in the configuration file. Note: GBrowse is perl based and the registry is Java (servlets and JSP) based. Also note that most of the clients you list on the table use DAS 1.* whereas IGB uses DAS2. There are far more das sources available for DAS1 than 2 but some efforts are being made at allowing them to communicate with each other. On Mon, 2009-01-12 at 13:21 +0000, Dan Bolser wrote: > Hi Jonathan, > > Thanks very much for your reply. My comments are inline below: > > > 2009/1/12 Jonathan Warren : > > Hi Dan > > > > Thanks for putting up the table - I'll add some info to it shortly. > > Cheers, that would be great! > > > > The dasregistry source code is downloadable using subversion at > > http://www.derkholm.net/svn/repos/dasregistry/trunk/ > > > > You will also need a mysql instance set up. I can send you some info on > > that if you wish. > > Please provide as much information as possible! :-D > > > > There are many dependencies and configurations needed- so it may take a > > while to set up a fully fledged version - it may be better to experiment > > with your sources using the real one - I'll help you out if you need > > clarification on anything such as error messages and logs. Or is it that > > you don't want to release your data to the world and only want an in > > house version? > > Yes. In the long run we will be making all our data publicly > available, however, for R&D purposes and leading up to publication of > the source data we would like to experiment with an in-house registry. > Also, I think it would be a convenient administrative / organizational > tool for us. i.e. to keep track of the various data sources > (experimental or otherwise) that are being developed in-house. > > > > I think I would recomment using ensembl to connect to your sources in > > the first instance - but if you want the client to sit on your > > desktop/local server then maybe GBrowse (this is for genomic annotations > > obvioyusly)? > > Sorry for my ignorance, but can I ask if you mean that I should use > ensembl remotely (on some server 'out there') and point it at my local > reference / annotation server? The problem is again that both are > internal, with no outfacing interface. In any case, its clear that I > need to read more about ensembl, so feel free to ignore this question. > > > In another email you said: "You can just put the table onto biodas.org > if you wish..." > > I see this point. I am never sure how 'external' wikis should interact > with Wikipedia when overlapping data is available in both. In this > case I thought I'd edit WP, but please feel free to move the table to > somewhere within biodas.org - I wasn't immediately sure where to put > it, which is partly why I picked WP. > > > Thanks very much for the information above, > > Dan. > > > On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: > >> Hi all, > >> > >> I'm relatively new to DAS, and I have been playing with setting up a > >> DAS server using Dazzle. Now that I have created my reference and > >> annotation data sources, naturally enough I would like to start > >> browsing and visualizing the data. So... > >> > >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? > >> > >> > >> I am working in a Linux OS, and I am looking at gene predictions on a > >> chromosome as well as 'similarity' features between the chromosome and > >> several 'clones' from a closely related organism. > >> > >> To organize my research into the various clients available, I created > >> the following page on Wikipedia: > >> > >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > >> > >> > >> That table is still quite rough, so please feel free to contribute > >> information there. I put the table into a sub-page of the DAS page so > >> that sites like http://www.biodas.org/ can easily 'transclude' this > >> information. I'm not sure if that's sensible or not yet, so let me > >> know what you think. > >> > >> > >> Since we are exploring the various possibilities of using DAS with our > >> projects, is it possible to set up a local (private) DAS registry > >> server? This would be useful for testing purposes, especially as we > >> may be initially working with unpublished data. > >> > >> Q2) What steps are required for setting up a local or a secure DAS registry? > >> > >> > >> Thanks very much for any help with the above two questions. > >> > >> Dan > >> > >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > >> data encoding that I don't understand? I've seen more than one page > >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > >> Should I go ahead and delete this pages? > >> _______________________________________________ > >> DAS mailing list > >> DAS at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/das > > > > > > > > -- > > 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. > > -- 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 andy.jenkinson at ebi.ac.uk Mon Jan 12 09:24:13 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 12 Jan 2009 14:24:13 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <1231769451.7515.174.camel@deskpro20727.dynamic.sanger.ac.uk> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> <1231769451.7515.174.camel@deskpro20727.dynamic.sanger.ac.uk> Message-ID: <496B528D.9070305@ebi.ac.uk> Agreed, gbrowse is probably your easiest solution. I'm not sure what stage of development GBrowse 2 is at, it might be worth playing around with when it's released? Jonathan Warren wrote: > Ok if your sources are in-house then I'd use GBrowse as it's easier to > set up and you can point it at both a das reference server and > annotation server (which I don't think you can do with ensembl). GBrowse > can also be set up to be a DAS source itself just by setting the > mapmaster in the configuration file. Note: GBrowse is perl based and the > registry is Java (servlets and JSP) based. Also note that most of the > clients you list on the table use DAS 1.* whereas IGB uses DAS2. There > are far more das sources available for DAS1 than 2 but some efforts are > being made at allowing them to communicate with each other. > > > > > On Mon, 2009-01-12 at 13:21 +0000, Dan Bolser wrote: >> Hi Jonathan, >> >> Thanks very much for your reply. My comments are inline below: >> >> >> 2009/1/12 Jonathan Warren : >>> Hi Dan >>> >>> Thanks for putting up the table - I'll add some info to it shortly. >> Cheers, that would be great! >> >> >>> The dasregistry source code is downloadable using subversion at >>> http://www.derkholm.net/svn/repos/dasregistry/trunk/ >>> >>> You will also need a mysql instance set up. I can send you some info on >>> that if you wish. >> Please provide as much information as possible! :-D >> >> >>> There are many dependencies and configurations needed- so it may take a >>> while to set up a fully fledged version - it may be better to experiment >>> with your sources using the real one - I'll help you out if you need >>> clarification on anything such as error messages and logs. Or is it that >>> you don't want to release your data to the world and only want an in >>> house version? >> Yes. In the long run we will be making all our data publicly >> available, however, for R&D purposes and leading up to publication of >> the source data we would like to experiment with an in-house registry. >> Also, I think it would be a convenient administrative / organizational >> tool for us. i.e. to keep track of the various data sources >> (experimental or otherwise) that are being developed in-house. >> >> >>> I think I would recomment using ensembl to connect to your sources in >>> the first instance - but if you want the client to sit on your >>> desktop/local server then maybe GBrowse (this is for genomic annotations >>> obvioyusly)? >> Sorry for my ignorance, but can I ask if you mean that I should use >> ensembl remotely (on some server 'out there') and point it at my local >> reference / annotation server? The problem is again that both are >> internal, with no outfacing interface. In any case, its clear that I >> need to read more about ensembl, so feel free to ignore this question. >> >> >> In another email you said: "You can just put the table onto biodas.org >> if you wish..." >> >> I see this point. I am never sure how 'external' wikis should interact >> with Wikipedia when overlapping data is available in both. In this >> case I thought I'd edit WP, but please feel free to move the table to >> somewhere within biodas.org - I wasn't immediately sure where to put >> it, which is partly why I picked WP. >> >> >> Thanks very much for the information above, >> >> Dan. >> >>> On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: >>>> Hi all, >>>> >>>> I'm relatively new to DAS, and I have been playing with setting up a >>>> DAS server using Dazzle. Now that I have created my reference and >>>> annotation data sources, naturally enough I would like to start >>>> browsing and visualizing the data. So... >>>> >>>> Q1) Which DAS client do you recommend for a beginner working with Dazzle? >>>> >>>> >>>> I am working in a Linux OS, and I am looking at gene predictions on a >>>> chromosome as well as 'similarity' features between the chromosome and >>>> several 'clones' from a closely related organism. >>>> >>>> To organize my research into the various clients available, I created >>>> the following page on Wikipedia: >>>> >>>> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients >>>> >>>> >>>> That table is still quite rough, so please feel free to contribute >>>> information there. I put the table into a sub-page of the DAS page so >>>> that sites like http://www.biodas.org/ can easily 'transclude' this >>>> information. I'm not sure if that's sensible or not yet, so let me >>>> know what you think. >>>> >>>> >>>> Since we are exploring the various possibilities of using DAS with our >>>> projects, is it possible to set up a local (private) DAS registry >>>> server? This would be useful for testing purposes, especially as we >>>> may be initially working with unpublished data. >>>> >>>> Q2) What steps are required for setting up a local or a secure DAS registry? >>>> >>>> >>>> Thanks very much for any help with the above two questions. >>>> >>>> Dan >>>> >>>> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange >>>> data encoding that I don't understand? I've seen more than one page >>>> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - >>>> Should I go ahead and delete this pages? >>>> _______________________________________________ >>>> DAS mailing list >>>> DAS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> >>> -- >>> 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 Mon Jan 12 09:40:59 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 14:40:59 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120534s79ab269cuc5504bef05d27faa@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <496B401C.5070305@ebi.ac.uk> <2c8757af0901120534s79ab269cuc5504bef05d27faa@mail.gmail.com> Message-ID: <1231771259.7515.176.camel@deskpro20727.dynamic.sanger.ac.uk> Dan - have you any timescales in mind for setting up an internal registry? I am looking at the DAS documentation available at the moment and could write a DASRegistry doc. Are you happy with using eclipse, jsp and servlets in tomcat or resin containers? On Mon, 2009-01-12 at 13:34 +0000, Dan Bolser wrote: > 2009/1/12 Andy Jenkinson : > > Hi Dan, > > > > DAS clients tend to be different depending on the type of data you're > > looking at, and have different capabilities. For example, Ensembl is a well > > supported client for (mostly) genomic data, and implements all the most > > recent developments such as the DAS registry (via the sources command). > > However it makes no use of reference servers, instead all reference data is > > stored locally in a database. Dasty is more focussed on protein data. > > GBrowse is another genomic client, but IIRC does not know about the DAS > > registry. > > > > Regarding setting up a local DAS registry, what is this for? If for instance > > you were using Ensembl, any server that implements the sources command can > > potentially be a "registry" from a programmatic point of view, so unless you > > want to have a manual process where you can use a GUI to register a souce, > > you probably don't need to implement a copy of the real thing. > > I see what you mean, but what I'm calling 'in-house' could potentially > comprise several different servers at several different locations. The > theory is that they would all be part of a private 'consortium', which > would ultimately become part of the DAS registry proper. In so far as > we would like to keep track of the different DAS servers that we have > 'in-house', I thought a registry could be a good solution. > > > > Looks like the biodas wiki has been getting spammed, must have started > > recently. I'll talk to the admins about sorting it out. We'll probably need > > to update the registration process. > > On several wikis using a 'captcha', I found that the following set > rules strikes the right balance between keeping spam down and allowing > unrestrictive access to users: > > 0) Any user can edit the wiki, because registration puts people off. > 1) On any edit, present any anonymous user with a captcha. > 2) Registration requires a captcha. > 3) Never present a registered user with a captcha. > > In the MediaWiki config that looks like this: > > // Fix the default captcha behaviour > $wgGroupPermissions['*' ]['skipcaptcha'] = false; > $wgGroupPermissions['user' ]['skipcaptcha'] = true; > $wgGroupPermissions['autoconfirmed']['skipcaptcha'] = true; > $wgGroupPermissions['bot' ]['skipcaptcha'] = true; // registered bots > $wgGroupPermissions['sysop' ]['skipcaptcha'] = true; > > $wgCaptchaTriggers['edit'] = true; > $wgCaptchaTriggers['create'] = true; > $wgCaptchaTriggers['createaccount'] = true; > > (all other permissions having their default values) > > > Thanks for the info above, > Dan. > > > Cheers, > > Andy > > > > Dan Bolser wrote: > >> > >> Hi all, > >> > >> I'm relatively new to DAS, and I have been playing with setting up a > >> DAS server using Dazzle. Now that I have created my reference and > >> annotation data sources, naturally enough I would like to start > >> browsing and visualizing the data. So... > >> > >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? > >> > >> > >> I am working in a Linux OS, and I am looking at gene predictions on a > >> chromosome as well as 'similarity' features between the chromosome and > >> several 'clones' from a closely related organism. > >> > >> To organize my research into the various clients available, I created > >> the following page on Wikipedia: > >> > >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > >> > >> > >> That table is still quite rough, so please feel free to contribute > >> information there. I put the table into a sub-page of the DAS page so > >> that sites like http://www.biodas.org/ can easily 'transclude' this > >> information. I'm not sure if that's sensible or not yet, so let me > >> know what you think. > >> > >> > >> Since we are exploring the various possibilities of using DAS with our > >> projects, is it possible to set up a local (private) DAS registry > >> server? This would be useful for testing purposes, especially as we > >> may be initially working with unpublished data. > >> > >> Q2) What steps are required for setting up a local or a secure DAS > >> registry? > >> > >> > >> Thanks very much for any help with the above two questions. > >> > >> Dan > >> > >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > >> data encoding that I don't understand? I've seen more than one page > >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > >> Should I go ahead and delete this pages? > >> _______________________________________________ > >> DAS mailing list > >> DAS at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/das > >> From - Mon > > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das -- 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 Mon Jan 12 11:10:31 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 16:10:31 +0000 Subject: [DAS] Register soon for DAS workshop Message-ID: <1231776631.7515.193.camel@deskpro20727.dynamic.sanger.ac.uk> Just a reminder that registrations for the DAS workshop will be closing on the 1st of Feb (just over 2 weeks). Please register at http://www.dasregistry.org/course.jsp if you are interested. -- 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 Mon Jan 12 11:40:36 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 16:40:36 +0000 Subject: [DAS] DAS Registry validation Message-ID: <1231778436.7515.206.camel@deskpro20727.dynamic.sanger.ac.uk> The registry has been updated to a more strict validation mechanism using RelaxNG and may start to give warnings on validation pages when tested. Later it's our intention for newly registered sources to conform to this validation process whereas old sources will validate. If a source does not validate and you think it should - please get in touch as this may not be perfect yet. The validation pages can be found at: http://www.dasregistry.org/validation/ documentation for how to use these documents in your own software will be available in the next few weeks. Thanks Jonathan. -- 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 fsk at sanger.ac.uk Mon Jan 12 12:03:53 2009 From: fsk at sanger.ac.uk (Felix Kokocinski) Date: Mon, 12 Jan 2009 17:03:53 +0000 Subject: [DAS] emai addresses and the das registry In-Reply-To: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> References: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> Message-ID: <496B77F9.9000208@sanger.ac.uk> Hi Jonathan, I believe this would be a good thing and should be applied for ALL sources. You could display the name of the maintainer on the showdetails page, so people know who they are contacting, but then just use a form for email contact, without displaying the address. Cheers, Felix. Jonathan Warren wrote: > Hi > > Due to security and spam considerations: > > I was wondering what DAS users would think of www.dasregistry.org asking > people if they want their email addresses made public as a contact for > their sources? If people say no - then the registry would for example: > set the maintainer field of the source to a link back to the registry, > which would be a submission form where people could indirectly email the > source maintainer? Thus avoiding anyone other than the registry needing > to know the maintainers real email address? > > Any opinions or recommendations for how this could be done are welcomed. > > Cheers > > Jonathan. > > > -- 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 haslam at embl.de Tue Jan 13 08:30:56 2009 From: haslam at embl.de (Niall Haslam) Date: Tue, 13 Jan 2009 14:30:56 +0100 Subject: [DAS] emai addresses and the das registry In-Reply-To: <496B77F9.9000208@sanger.ac.uk> References: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> <496B77F9.9000208@sanger.ac.uk> Message-ID: <200901131430.57055.haslam@embl.de> On Monday 12 January 2009 18:03, Felix Kokocinski wrote: > Hi Jonathan, > > I believe this would be a good thing and should be applied for ALL sources. > You could display the name of the maintainer on the showdetails page, so > people know who they are contacting, but then just use a form for email > contact, without displaying the address. Just to agree with what Felix said I think its important to be able to contact the owners of the DAS sources. I think the e.mail form solution you mentioned would be fine. Niall. > Cheers, Felix. > > Jonathan Warren wrote: > > Hi > > > > Due to security and spam considerations: > > > > I was wondering what DAS users would think of www.dasregistry.org asking > > people if they want their email addresses made public as a contact for > > their sources? If people say no - then the registry would for example: > > set the maintainer field of the source to a link back to the registry, > > which would be a submission form where people could indirectly email the > > source maintainer? Thus avoiding anyone other than the registry needing > > to know the maintainers real email address? > > > > Any opinions or recommendations for how this could be done are welcomed. > > > > Cheers > > > > Jonathan. From jw12 at sanger.ac.uk Thu Jan 29 05:25:40 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 29 Jan 2009 10:25:40 +0000 Subject: [DAS] closing this week: Registrations for DAS workshop Message-ID: <45CCAF09-2A37-4257-B904-A6230BC449FC@sanger.ac.uk> 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 2009 DAS workshop (8,9,10th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.dasregistry.org/course.jsp 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. Closing date for registration is 1st Feb 2009. If you register now you can change the details of your registration any time up until this closing date. Please register early as places will be limited. -- 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 Wed Jan 7 16:58:24 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Wed, 07 Jan 2009 16:58:24 +0000 Subject: [DAS] emai addresses and the das registry Message-ID: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> Hi Due to security and spam considerations: I was wondering what DAS users would think of www.dasregistry.org asking people if they want their email addresses made public as a contact for their sources? If people say no - then the registry would for example: set the maintainer field of the source to a link back to the registry, which would be a submission form where people could indirectly email the source maintainer? Thus avoiding anyone other than the registry needing to know the maintainers real email address? Any opinions or recommendations for how this could be done are welcomed. Cheers Jonathan. -- 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 dan.bolser at gmail.com Mon Jan 12 12:11:43 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jan 2009 12:11:43 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers Message-ID: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Hi all, I'm relatively new to DAS, and I have been playing with setting up a DAS server using Dazzle. Now that I have created my reference and annotation data sources, naturally enough I would like to start browsing and visualizing the data. So... Q1) Which DAS client do you recommend for a beginner working with Dazzle? I am working in a Linux OS, and I am looking at gene predictions on a chromosome as well as 'similarity' features between the chromosome and several 'clones' from a closely related organism. To organize my research into the various clients available, I created the following page on Wikipedia: http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients That table is still quite rough, so please feel free to contribute information there. I put the table into a sub-page of the DAS page so that sites like http://www.biodas.org/ can easily 'transclude' this information. I'm not sure if that's sensible or not yet, so let me know what you think. Since we are exploring the various possibilities of using DAS with our projects, is it possible to set up a local (private) DAS registry server? This would be useful for testing purposes, especially as we may be initially working with unpublished data. Q2) What steps are required for setting up a local or a secure DAS registry? Thanks very much for any help with the above two questions. Dan P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange data encoding that I don't understand? I've seen more than one page that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - Should I go ahead and delete this pages? From jw12 at sanger.ac.uk Mon Jan 12 12:53:09 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 12:53:09 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Message-ID: <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> Hi Dan Thanks for putting up the table - I'll add some info to it shortly. The dasregistry source code is downloadable using subversion at http://www.derkholm.net/svn/repos/dasregistry/trunk/ You will also need a mysql instance set up. I can send you some info on that if you wish. There are many dependencies and configurations needed- so it may take a while to set up a fully fledged version - it may be better to experiment with your sources using the real one - I'll help you out if you need clarification on anything such as error messages and logs. Or is it that you don't want to release your data to the world and only want an in house version? I think I would recomment using ensembl to connect to your sources in the first instance - but if you want the client to sit on your desktop/local server then maybe GBrowse (this is for genomic annotations obvioyusly)? On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: > Hi all, > > I'm relatively new to DAS, and I have been playing with setting up a > DAS server using Dazzle. Now that I have created my reference and > annotation data sources, naturally enough I would like to start > browsing and visualizing the data. So... > > Q1) Which DAS client do you recommend for a beginner working with Dazzle? > > > I am working in a Linux OS, and I am looking at gene predictions on a > chromosome as well as 'similarity' features between the chromosome and > several 'clones' from a closely related organism. > > To organize my research into the various clients available, I created > the following page on Wikipedia: > > http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > > > That table is still quite rough, so please feel free to contribute > information there. I put the table into a sub-page of the DAS page so > that sites like http://www.biodas.org/ can easily 'transclude' this > information. I'm not sure if that's sensible or not yet, so let me > know what you think. > > > Since we are exploring the various possibilities of using DAS with our > projects, is it possible to set up a local (private) DAS registry > server? This would be useful for testing purposes, especially as we > may be initially working with unpublished data. > > Q2) What steps are required for setting up a local or a secure DAS registry? > > > Thanks very much for any help with the above two questions. > > Dan > > P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > data encoding that I don't understand? I've seen more than one page > that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > Should I go ahead and delete this pages? > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das -- 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 Mon Jan 12 12:57:57 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 12:57:57 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Message-ID: <1231765077.7515.160.camel@deskpro20727.dynamic.sanger.ac.uk> You can just put the table onto biodas.org if you wish dan? On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: > > chromosome as well as 'similarity' features between the chromosome > and -- 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 andy.jenkinson at ebi.ac.uk Mon Jan 12 13:05:32 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 12 Jan 2009 13:05:32 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> Message-ID: <496B401C.5070305@ebi.ac.uk> Hi Dan, DAS clients tend to be different depending on the type of data you're looking at, and have different capabilities. For example, Ensembl is a well supported client for (mostly) genomic data, and implements all the most recent developments such as the DAS registry (via the sources command). However it makes no use of reference servers, instead all reference data is stored locally in a database. Dasty is more focussed on protein data. GBrowse is another genomic client, but IIRC does not know about the DAS registry. Regarding setting up a local DAS registry, what is this for? If for instance you were using Ensembl, any server that implements the sources command can potentially be a "registry" from a programmatic point of view, so unless you want to have a manual process where you can use a GUI to register a souce, you probably don't need to implement a copy of the real thing. Looks like the biodas wiki has been getting spammed, must have started recently. I'll talk to the admins about sorting it out. We'll probably need to update the registration process. Cheers, Andy Dan Bolser wrote: > Hi all, > > I'm relatively new to DAS, and I have been playing with setting up a > DAS server using Dazzle. Now that I have created my reference and > annotation data sources, naturally enough I would like to start > browsing and visualizing the data. So... > > Q1) Which DAS client do you recommend for a beginner working with Dazzle? > > > I am working in a Linux OS, and I am looking at gene predictions on a > chromosome as well as 'similarity' features between the chromosome and > several 'clones' from a closely related organism. > > To organize my research into the various clients available, I created > the following page on Wikipedia: > > http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > > > That table is still quite rough, so please feel free to contribute > information there. I put the table into a sub-page of the DAS page so > that sites like http://www.biodas.org/ can easily 'transclude' this > information. I'm not sure if that's sensible or not yet, so let me > know what you think. > > > Since we are exploring the various possibilities of using DAS with our > projects, is it possible to set up a local (private) DAS registry > server? This would be useful for testing purposes, especially as we > may be initially working with unpublished data. > > Q2) What steps are required for setting up a local or a secure DAS registry? > > > Thanks very much for any help with the above two questions. > > Dan > > P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > data encoding that I don't understand? I've seen more than one page > that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > Should I go ahead and delete this pages? > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das > From - Mon From dan.bolser at gmail.com Mon Jan 12 13:21:05 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jan 2009 13:21:05 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> Message-ID: <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> Hi Jonathan, Thanks very much for your reply. My comments are inline below: 2009/1/12 Jonathan Warren : > Hi Dan > > Thanks for putting up the table - I'll add some info to it shortly. Cheers, that would be great! > The dasregistry source code is downloadable using subversion at > http://www.derkholm.net/svn/repos/dasregistry/trunk/ > > You will also need a mysql instance set up. I can send you some info on > that if you wish. Please provide as much information as possible! :-D > There are many dependencies and configurations needed- so it may take a > while to set up a fully fledged version - it may be better to experiment > with your sources using the real one - I'll help you out if you need > clarification on anything such as error messages and logs. Or is it that > you don't want to release your data to the world and only want an in > house version? Yes. In the long run we will be making all our data publicly available, however, for R&D purposes and leading up to publication of the source data we would like to experiment with an in-house registry. Also, I think it would be a convenient administrative / organizational tool for us. i.e. to keep track of the various data sources (experimental or otherwise) that are being developed in-house. > I think I would recomment using ensembl to connect to your sources in > the first instance - but if you want the client to sit on your > desktop/local server then maybe GBrowse (this is for genomic annotations > obvioyusly)? Sorry for my ignorance, but can I ask if you mean that I should use ensembl remotely (on some server 'out there') and point it at my local reference / annotation server? The problem is again that both are internal, with no outfacing interface. In any case, its clear that I need to read more about ensembl, so feel free to ignore this question. In another email you said: "You can just put the table onto biodas.org if you wish..." I see this point. I am never sure how 'external' wikis should interact with Wikipedia when overlapping data is available in both. In this case I thought I'd edit WP, but please feel free to move the table to somewhere within biodas.org - I wasn't immediately sure where to put it, which is partly why I picked WP. Thanks very much for the information above, Dan. > On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: >> Hi all, >> >> I'm relatively new to DAS, and I have been playing with setting up a >> DAS server using Dazzle. Now that I have created my reference and >> annotation data sources, naturally enough I would like to start >> browsing and visualizing the data. So... >> >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? >> >> >> I am working in a Linux OS, and I am looking at gene predictions on a >> chromosome as well as 'similarity' features between the chromosome and >> several 'clones' from a closely related organism. >> >> To organize my research into the various clients available, I created >> the following page on Wikipedia: >> >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients >> >> >> That table is still quite rough, so please feel free to contribute >> information there. I put the table into a sub-page of the DAS page so >> that sites like http://www.biodas.org/ can easily 'transclude' this >> information. I'm not sure if that's sensible or not yet, so let me >> know what you think. >> >> >> Since we are exploring the various possibilities of using DAS with our >> projects, is it possible to set up a local (private) DAS registry >> server? This would be useful for testing purposes, especially as we >> may be initially working with unpublished data. >> >> Q2) What steps are required for setting up a local or a secure DAS registry? >> >> >> Thanks very much for any help with the above two questions. >> >> Dan >> >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange >> data encoding that I don't understand? I've seen more than one page >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - >> Should I go ahead and delete this pages? >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das > > > > -- > 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 dan.bolser at gmail.com Mon Jan 12 13:34:35 2009 From: dan.bolser at gmail.com (Dan Bolser) Date: Mon, 12 Jan 2009 13:34:35 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <496B401C.5070305@ebi.ac.uk> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <496B401C.5070305@ebi.ac.uk> Message-ID: <2c8757af0901120534s79ab269cuc5504bef05d27faa@mail.gmail.com> 2009/1/12 Andy Jenkinson : > Hi Dan, > > DAS clients tend to be different depending on the type of data you're > looking at, and have different capabilities. For example, Ensembl is a well > supported client for (mostly) genomic data, and implements all the most > recent developments such as the DAS registry (via the sources command). > However it makes no use of reference servers, instead all reference data is > stored locally in a database. Dasty is more focussed on protein data. > GBrowse is another genomic client, but IIRC does not know about the DAS > registry. > > Regarding setting up a local DAS registry, what is this for? If for instance > you were using Ensembl, any server that implements the sources command can > potentially be a "registry" from a programmatic point of view, so unless you > want to have a manual process where you can use a GUI to register a souce, > you probably don't need to implement a copy of the real thing. I see what you mean, but what I'm calling 'in-house' could potentially comprise several different servers at several different locations. The theory is that they would all be part of a private 'consortium', which would ultimately become part of the DAS registry proper. In so far as we would like to keep track of the different DAS servers that we have 'in-house', I thought a registry could be a good solution. > Looks like the biodas wiki has been getting spammed, must have started > recently. I'll talk to the admins about sorting it out. We'll probably need > to update the registration process. On several wikis using a 'captcha', I found that the following set rules strikes the right balance between keeping spam down and allowing unrestrictive access to users: 0) Any user can edit the wiki, because registration puts people off. 1) On any edit, present any anonymous user with a captcha. 2) Registration requires a captcha. 3) Never present a registered user with a captcha. In the MediaWiki config that looks like this: // Fix the default captcha behaviour $wgGroupPermissions['*' ]['skipcaptcha'] = false; $wgGroupPermissions['user' ]['skipcaptcha'] = true; $wgGroupPermissions['autoconfirmed']['skipcaptcha'] = true; $wgGroupPermissions['bot' ]['skipcaptcha'] = true; // registered bots $wgGroupPermissions['sysop' ]['skipcaptcha'] = true; $wgCaptchaTriggers['edit'] = true; $wgCaptchaTriggers['create'] = true; $wgCaptchaTriggers['createaccount'] = true; (all other permissions having their default values) Thanks for the info above, Dan. > Cheers, > Andy > > Dan Bolser wrote: >> >> Hi all, >> >> I'm relatively new to DAS, and I have been playing with setting up a >> DAS server using Dazzle. Now that I have created my reference and >> annotation data sources, naturally enough I would like to start >> browsing and visualizing the data. So... >> >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? >> >> >> I am working in a Linux OS, and I am looking at gene predictions on a >> chromosome as well as 'similarity' features between the chromosome and >> several 'clones' from a closely related organism. >> >> To organize my research into the various clients available, I created >> the following page on Wikipedia: >> >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients >> >> >> That table is still quite rough, so please feel free to contribute >> information there. I put the table into a sub-page of the DAS page so >> that sites like http://www.biodas.org/ can easily 'transclude' this >> information. I'm not sure if that's sensible or not yet, so let me >> know what you think. >> >> >> Since we are exploring the various possibilities of using DAS with our >> projects, is it possible to set up a local (private) DAS registry >> server? This would be useful for testing purposes, especially as we >> may be initially working with unpublished data. >> >> Q2) What steps are required for setting up a local or a secure DAS >> registry? >> >> >> Thanks very much for any help with the above two questions. >> >> Dan >> >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange >> data encoding that I don't understand? I've seen more than one page >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - >> Should I go ahead and delete this pages? >> _______________________________________________ >> DAS mailing list >> DAS at lists.open-bio.org >> http://lists.open-bio.org/mailman/listinfo/das >> From - Mon > From andy.jenkinson at ebi.ac.uk Mon Jan 12 14:06:55 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 12 Jan 2009 14:06:55 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> Message-ID: <496B4E7F.1030901@ebi.ac.uk> Dan Bolser wrote: > 2009/1/12 Jonathan Warren : >> I think I would recomment using ensembl to connect to your sources in >> the first instance - but if you want the client to sit on your >> desktop/local server then maybe GBrowse (this is for genomic annotations >> obvioyusly)? > > Sorry for my ignorance, but can I ask if you mean that I should use > ensembl remotely (on some server 'out there') and point it at my local > reference / annotation server? The problem is again that both are > internal, with no outfacing interface. In any case, its clear that I > need to read more about ensembl, so feel free to ignore this question. It would depend on which genomes you are interested in. If Ensembl (or another Ensembl-powered site) supports your genomes, you could it to display your DAS annotations provided the DAS servers are accessible to the Ensembl servers. If not, you would have to set up an independent local Ensembl installation containing your reference genome data. Something similar would be required for GBrowse, but I suspect Ensembl is more complicated. Current visual genomic DAS clients tend not to use DAS reference servers for sequence data. Rather they have taken to storing this data locally. From jw12 at sanger.ac.uk Mon Jan 12 14:10:51 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 14:10:51 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> Message-ID: <1231769451.7515.174.camel@deskpro20727.dynamic.sanger.ac.uk> Ok if your sources are in-house then I'd use GBrowse as it's easier to set up and you can point it at both a das reference server and annotation server (which I don't think you can do with ensembl). GBrowse can also be set up to be a DAS source itself just by setting the mapmaster in the configuration file. Note: GBrowse is perl based and the registry is Java (servlets and JSP) based. Also note that most of the clients you list on the table use DAS 1.* whereas IGB uses DAS2. There are far more das sources available for DAS1 than 2 but some efforts are being made at allowing them to communicate with each other. On Mon, 2009-01-12 at 13:21 +0000, Dan Bolser wrote: > Hi Jonathan, > > Thanks very much for your reply. My comments are inline below: > > > 2009/1/12 Jonathan Warren : > > Hi Dan > > > > Thanks for putting up the table - I'll add some info to it shortly. > > Cheers, that would be great! > > > > The dasregistry source code is downloadable using subversion at > > http://www.derkholm.net/svn/repos/dasregistry/trunk/ > > > > You will also need a mysql instance set up. I can send you some info on > > that if you wish. > > Please provide as much information as possible! :-D > > > > There are many dependencies and configurations needed- so it may take a > > while to set up a fully fledged version - it may be better to experiment > > with your sources using the real one - I'll help you out if you need > > clarification on anything such as error messages and logs. Or is it that > > you don't want to release your data to the world and only want an in > > house version? > > Yes. In the long run we will be making all our data publicly > available, however, for R&D purposes and leading up to publication of > the source data we would like to experiment with an in-house registry. > Also, I think it would be a convenient administrative / organizational > tool for us. i.e. to keep track of the various data sources > (experimental or otherwise) that are being developed in-house. > > > > I think I would recomment using ensembl to connect to your sources in > > the first instance - but if you want the client to sit on your > > desktop/local server then maybe GBrowse (this is for genomic annotations > > obvioyusly)? > > Sorry for my ignorance, but can I ask if you mean that I should use > ensembl remotely (on some server 'out there') and point it at my local > reference / annotation server? The problem is again that both are > internal, with no outfacing interface. In any case, its clear that I > need to read more about ensembl, so feel free to ignore this question. > > > In another email you said: "You can just put the table onto biodas.org > if you wish..." > > I see this point. I am never sure how 'external' wikis should interact > with Wikipedia when overlapping data is available in both. In this > case I thought I'd edit WP, but please feel free to move the table to > somewhere within biodas.org - I wasn't immediately sure where to put > it, which is partly why I picked WP. > > > Thanks very much for the information above, > > Dan. > > > On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: > >> Hi all, > >> > >> I'm relatively new to DAS, and I have been playing with setting up a > >> DAS server using Dazzle. Now that I have created my reference and > >> annotation data sources, naturally enough I would like to start > >> browsing and visualizing the data. So... > >> > >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? > >> > >> > >> I am working in a Linux OS, and I am looking at gene predictions on a > >> chromosome as well as 'similarity' features between the chromosome and > >> several 'clones' from a closely related organism. > >> > >> To organize my research into the various clients available, I created > >> the following page on Wikipedia: > >> > >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > >> > >> > >> That table is still quite rough, so please feel free to contribute > >> information there. I put the table into a sub-page of the DAS page so > >> that sites like http://www.biodas.org/ can easily 'transclude' this > >> information. I'm not sure if that's sensible or not yet, so let me > >> know what you think. > >> > >> > >> Since we are exploring the various possibilities of using DAS with our > >> projects, is it possible to set up a local (private) DAS registry > >> server? This would be useful for testing purposes, especially as we > >> may be initially working with unpublished data. > >> > >> Q2) What steps are required for setting up a local or a secure DAS registry? > >> > >> > >> Thanks very much for any help with the above two questions. > >> > >> Dan > >> > >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > >> data encoding that I don't understand? I've seen more than one page > >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > >> Should I go ahead and delete this pages? > >> _______________________________________________ > >> DAS mailing list > >> DAS at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/das > > > > > > > > -- > > 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. > > -- 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 andy.jenkinson at ebi.ac.uk Mon Jan 12 14:24:13 2009 From: andy.jenkinson at ebi.ac.uk (Andy Jenkinson) Date: Mon, 12 Jan 2009 14:24:13 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <1231769451.7515.174.camel@deskpro20727.dynamic.sanger.ac.uk> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <1231764789.7515.158.camel@deskpro20727.dynamic.sanger.ac.uk> <2c8757af0901120521t5366fe4djda7981a644f5db8b@mail.gmail.com> <1231769451.7515.174.camel@deskpro20727.dynamic.sanger.ac.uk> Message-ID: <496B528D.9070305@ebi.ac.uk> Agreed, gbrowse is probably your easiest solution. I'm not sure what stage of development GBrowse 2 is at, it might be worth playing around with when it's released? Jonathan Warren wrote: > Ok if your sources are in-house then I'd use GBrowse as it's easier to > set up and you can point it at both a das reference server and > annotation server (which I don't think you can do with ensembl). GBrowse > can also be set up to be a DAS source itself just by setting the > mapmaster in the configuration file. Note: GBrowse is perl based and the > registry is Java (servlets and JSP) based. Also note that most of the > clients you list on the table use DAS 1.* whereas IGB uses DAS2. There > are far more das sources available for DAS1 than 2 but some efforts are > being made at allowing them to communicate with each other. > > > > > On Mon, 2009-01-12 at 13:21 +0000, Dan Bolser wrote: >> Hi Jonathan, >> >> Thanks very much for your reply. My comments are inline below: >> >> >> 2009/1/12 Jonathan Warren : >>> Hi Dan >>> >>> Thanks for putting up the table - I'll add some info to it shortly. >> Cheers, that would be great! >> >> >>> The dasregistry source code is downloadable using subversion at >>> http://www.derkholm.net/svn/repos/dasregistry/trunk/ >>> >>> You will also need a mysql instance set up. I can send you some info on >>> that if you wish. >> Please provide as much information as possible! :-D >> >> >>> There are many dependencies and configurations needed- so it may take a >>> while to set up a fully fledged version - it may be better to experiment >>> with your sources using the real one - I'll help you out if you need >>> clarification on anything such as error messages and logs. Or is it that >>> you don't want to release your data to the world and only want an in >>> house version? >> Yes. In the long run we will be making all our data publicly >> available, however, for R&D purposes and leading up to publication of >> the source data we would like to experiment with an in-house registry. >> Also, I think it would be a convenient administrative / organizational >> tool for us. i.e. to keep track of the various data sources >> (experimental or otherwise) that are being developed in-house. >> >> >>> I think I would recomment using ensembl to connect to your sources in >>> the first instance - but if you want the client to sit on your >>> desktop/local server then maybe GBrowse (this is for genomic annotations >>> obvioyusly)? >> Sorry for my ignorance, but can I ask if you mean that I should use >> ensembl remotely (on some server 'out there') and point it at my local >> reference / annotation server? The problem is again that both are >> internal, with no outfacing interface. In any case, its clear that I >> need to read more about ensembl, so feel free to ignore this question. >> >> >> In another email you said: "You can just put the table onto biodas.org >> if you wish..." >> >> I see this point. I am never sure how 'external' wikis should interact >> with Wikipedia when overlapping data is available in both. In this >> case I thought I'd edit WP, but please feel free to move the table to >> somewhere within biodas.org - I wasn't immediately sure where to put >> it, which is partly why I picked WP. >> >> >> Thanks very much for the information above, >> >> Dan. >> >>> On Mon, 2009-01-12 at 12:11 +0000, Dan Bolser wrote: >>>> Hi all, >>>> >>>> I'm relatively new to DAS, and I have been playing with setting up a >>>> DAS server using Dazzle. Now that I have created my reference and >>>> annotation data sources, naturally enough I would like to start >>>> browsing and visualizing the data. So... >>>> >>>> Q1) Which DAS client do you recommend for a beginner working with Dazzle? >>>> >>>> >>>> I am working in a Linux OS, and I am looking at gene predictions on a >>>> chromosome as well as 'similarity' features between the chromosome and >>>> several 'clones' from a closely related organism. >>>> >>>> To organize my research into the various clients available, I created >>>> the following page on Wikipedia: >>>> >>>> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients >>>> >>>> >>>> That table is still quite rough, so please feel free to contribute >>>> information there. I put the table into a sub-page of the DAS page so >>>> that sites like http://www.biodas.org/ can easily 'transclude' this >>>> information. I'm not sure if that's sensible or not yet, so let me >>>> know what you think. >>>> >>>> >>>> Since we are exploring the various possibilities of using DAS with our >>>> projects, is it possible to set up a local (private) DAS registry >>>> server? This would be useful for testing purposes, especially as we >>>> may be initially working with unpublished data. >>>> >>>> Q2) What steps are required for setting up a local or a secure DAS registry? >>>> >>>> >>>> Thanks very much for any help with the above two questions. >>>> >>>> Dan >>>> >>>> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange >>>> data encoding that I don't understand? I've seen more than one page >>>> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - >>>> Should I go ahead and delete this pages? >>>> _______________________________________________ >>>> DAS mailing list >>>> DAS at lists.open-bio.org >>>> http://lists.open-bio.org/mailman/listinfo/das >>> >>> >>> -- >>> 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 Mon Jan 12 14:40:59 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 14:40:59 +0000 Subject: [DAS] Question about DAS clients and DAS registry servers In-Reply-To: <2c8757af0901120534s79ab269cuc5504bef05d27faa@mail.gmail.com> References: <2c8757af0901120411v4a0f63e9p64b169945c606b85@mail.gmail.com> <496B401C.5070305@ebi.ac.uk> <2c8757af0901120534s79ab269cuc5504bef05d27faa@mail.gmail.com> Message-ID: <1231771259.7515.176.camel@deskpro20727.dynamic.sanger.ac.uk> Dan - have you any timescales in mind for setting up an internal registry? I am looking at the DAS documentation available at the moment and could write a DASRegistry doc. Are you happy with using eclipse, jsp and servlets in tomcat or resin containers? On Mon, 2009-01-12 at 13:34 +0000, Dan Bolser wrote: > 2009/1/12 Andy Jenkinson : > > Hi Dan, > > > > DAS clients tend to be different depending on the type of data you're > > looking at, and have different capabilities. For example, Ensembl is a well > > supported client for (mostly) genomic data, and implements all the most > > recent developments such as the DAS registry (via the sources command). > > However it makes no use of reference servers, instead all reference data is > > stored locally in a database. Dasty is more focussed on protein data. > > GBrowse is another genomic client, but IIRC does not know about the DAS > > registry. > > > > Regarding setting up a local DAS registry, what is this for? If for instance > > you were using Ensembl, any server that implements the sources command can > > potentially be a "registry" from a programmatic point of view, so unless you > > want to have a manual process where you can use a GUI to register a souce, > > you probably don't need to implement a copy of the real thing. > > I see what you mean, but what I'm calling 'in-house' could potentially > comprise several different servers at several different locations. The > theory is that they would all be part of a private 'consortium', which > would ultimately become part of the DAS registry proper. In so far as > we would like to keep track of the different DAS servers that we have > 'in-house', I thought a registry could be a good solution. > > > > Looks like the biodas wiki has been getting spammed, must have started > > recently. I'll talk to the admins about sorting it out. We'll probably need > > to update the registration process. > > On several wikis using a 'captcha', I found that the following set > rules strikes the right balance between keeping spam down and allowing > unrestrictive access to users: > > 0) Any user can edit the wiki, because registration puts people off. > 1) On any edit, present any anonymous user with a captcha. > 2) Registration requires a captcha. > 3) Never present a registered user with a captcha. > > In the MediaWiki config that looks like this: > > // Fix the default captcha behaviour > $wgGroupPermissions['*' ]['skipcaptcha'] = false; > $wgGroupPermissions['user' ]['skipcaptcha'] = true; > $wgGroupPermissions['autoconfirmed']['skipcaptcha'] = true; > $wgGroupPermissions['bot' ]['skipcaptcha'] = true; // registered bots > $wgGroupPermissions['sysop' ]['skipcaptcha'] = true; > > $wgCaptchaTriggers['edit'] = true; > $wgCaptchaTriggers['create'] = true; > $wgCaptchaTriggers['createaccount'] = true; > > (all other permissions having their default values) > > > Thanks for the info above, > Dan. > > > Cheers, > > Andy > > > > Dan Bolser wrote: > >> > >> Hi all, > >> > >> I'm relatively new to DAS, and I have been playing with setting up a > >> DAS server using Dazzle. Now that I have created my reference and > >> annotation data sources, naturally enough I would like to start > >> browsing and visualizing the data. So... > >> > >> Q1) Which DAS client do you recommend for a beginner working with Dazzle? > >> > >> > >> I am working in a Linux OS, and I am looking at gene predictions on a > >> chromosome as well as 'similarity' features between the chromosome and > >> several 'clones' from a closely related organism. > >> > >> To organize my research into the various clients available, I created > >> the following page on Wikipedia: > >> > >> http://en.wikipedia.org/wiki/Distributed_Annotation_System/Clients > >> > >> > >> That table is still quite rough, so please feel free to contribute > >> information there. I put the table into a sub-page of the DAS page so > >> that sites like http://www.biodas.org/ can easily 'transclude' this > >> information. I'm not sure if that's sensible or not yet, so let me > >> know what you think. > >> > >> > >> Since we are exploring the various possibilities of using DAS with our > >> projects, is it possible to set up a local (private) DAS registry > >> server? This would be useful for testing purposes, especially as we > >> may be initially working with unpublished data. > >> > >> Q2) What steps are required for setting up a local or a secure DAS > >> registry? > >> > >> > >> Thanks very much for any help with the above two questions. > >> > >> Dan > >> > >> P.S. Is this spam? http://www.biodas.org/wiki/Smother or some strange > >> data encoding that I don't understand? I've seen more than one page > >> that looks like this. e.g. http://www.biodas.org/wiki/Selflessnesss - > >> Should I go ahead and delete this pages? > >> _______________________________________________ > >> DAS mailing list > >> DAS at lists.open-bio.org > >> http://lists.open-bio.org/mailman/listinfo/das > >> From - Mon > > > _______________________________________________ > DAS mailing list > DAS at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/das -- 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 Mon Jan 12 16:10:31 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 16:10:31 +0000 Subject: [DAS] Register soon for DAS workshop Message-ID: <1231776631.7515.193.camel@deskpro20727.dynamic.sanger.ac.uk> Just a reminder that registrations for the DAS workshop will be closing on the 1st of Feb (just over 2 weeks). Please register at http://www.dasregistry.org/course.jsp if you are interested. -- 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 Mon Jan 12 16:40:36 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Mon, 12 Jan 2009 16:40:36 +0000 Subject: [DAS] DAS Registry validation Message-ID: <1231778436.7515.206.camel@deskpro20727.dynamic.sanger.ac.uk> The registry has been updated to a more strict validation mechanism using RelaxNG and may start to give warnings on validation pages when tested. Later it's our intention for newly registered sources to conform to this validation process whereas old sources will validate. If a source does not validate and you think it should - please get in touch as this may not be perfect yet. The validation pages can be found at: http://www.dasregistry.org/validation/ documentation for how to use these documents in your own software will be available in the next few weeks. Thanks Jonathan. -- 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 fsk at sanger.ac.uk Mon Jan 12 17:03:53 2009 From: fsk at sanger.ac.uk (Felix Kokocinski) Date: Mon, 12 Jan 2009 17:03:53 +0000 Subject: [DAS] emai addresses and the das registry In-Reply-To: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> References: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> Message-ID: <496B77F9.9000208@sanger.ac.uk> Hi Jonathan, I believe this would be a good thing and should be applied for ALL sources. You could display the name of the maintainer on the showdetails page, so people know who they are contacting, but then just use a form for email contact, without displaying the address. Cheers, Felix. Jonathan Warren wrote: > Hi > > Due to security and spam considerations: > > I was wondering what DAS users would think of www.dasregistry.org asking > people if they want their email addresses made public as a contact for > their sources? If people say no - then the registry would for example: > set the maintainer field of the source to a link back to the registry, > which would be a submission form where people could indirectly email the > source maintainer? Thus avoiding anyone other than the registry needing > to know the maintainers real email address? > > Any opinions or recommendations for how this could be done are welcomed. > > Cheers > > Jonathan. > > > -- 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 haslam at embl.de Tue Jan 13 13:30:56 2009 From: haslam at embl.de (Niall Haslam) Date: Tue, 13 Jan 2009 14:30:56 +0100 Subject: [DAS] emai addresses and the das registry In-Reply-To: <496B77F9.9000208@sanger.ac.uk> References: <1231347504.7515.110.camel@deskpro20727.dynamic.sanger.ac.uk> <496B77F9.9000208@sanger.ac.uk> Message-ID: <200901131430.57055.haslam@embl.de> On Monday 12 January 2009 18:03, Felix Kokocinski wrote: > Hi Jonathan, > > I believe this would be a good thing and should be applied for ALL sources. > You could display the name of the maintainer on the showdetails page, so > people know who they are contacting, but then just use a form for email > contact, without displaying the address. Just to agree with what Felix said I think its important to be able to contact the owners of the DAS sources. I think the e.mail form solution you mentioned would be fine. Niall. > Cheers, Felix. > > Jonathan Warren wrote: > > Hi > > > > Due to security and spam considerations: > > > > I was wondering what DAS users would think of www.dasregistry.org asking > > people if they want their email addresses made public as a contact for > > their sources? If people say no - then the registry would for example: > > set the maintainer field of the source to a link back to the registry, > > which would be a submission form where people could indirectly email the > > source maintainer? Thus avoiding anyone other than the registry needing > > to know the maintainers real email address? > > > > Any opinions or recommendations for how this could be done are welcomed. > > > > Cheers > > > > Jonathan. From jw12 at sanger.ac.uk Thu Jan 29 10:25:40 2009 From: jw12 at sanger.ac.uk (Jonathan Warren) Date: Thu, 29 Jan 2009 10:25:40 +0000 Subject: [DAS] closing this week: Registrations for DAS workshop Message-ID: <45CCAF09-2A37-4257-B904-A6230BC449FC@sanger.ac.uk> 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 2009 DAS workshop (8,9,10th March) at the Genome Campus, Hinxton UK. If you are interested in attending, please find out more by going to http://www.dasregistry.org/course.jsp 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. Closing date for registration is 1st Feb 2009. If you register now you can change the details of your registration any time up until this closing date. Please register early as places will be limited. -- 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.