[DAS] Question about DAS clients and DAS registry servers

[Dan Bolser]

2009/1/12 Andy Jenkinson <andy.jenkinson at 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.

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?
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>