[DAS] Question about DAS clients and DAS registry servers

[Dan Bolser]

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?
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>
>
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