[DAS] Question about DAS clients and DAS registry servers

[Andy Jenkinson]

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 <jw12 at sanger.ac.uk>:
>>> 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.
>>>
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