[DAS] Personal genomics/Deploying a DAS server for Dummies/6 Easy steps

[Jonathan Warren]

On 12 Jan 2012, at 13:43, Dan Bolser wrote:

Hi Dan

Thanks for the feedback.

> That's great!
>
> Just last night I was looking for something that would fulfill this  
> requirement.
>
> One suggestion would be for authentication like I get with my Google,
> Flicker, Twitter, Facebook, etc. accounts. (Is this an open protocol
> for authentication, or did they each re-invent this wheel?)

>
> i.e. I want to be able to specifically grant access to my data by a
> known third party.
>
> e.g. GeneticGuru wants access to your GenotypeArchive account, allow  
> or deny?
>
For the situation where someone only wants themselves to access there  
own data for the moment they can just turn on their DAS server when  
they want to use it and not advertise their url. But if there is  
demand for people to be able to specify who can use it I can add some  
security to this.

We had large debates about how to implement security in DAS at the  
last couple of DAS workshops. In the end it was decided we would go  
with BASIC authentication and https requests and responses and people  
would have to trust DAS clients with their username and passwords.

The registry already supports this for the web service and I believe  
Andy J has implemented it in proserver as well. MyDAS if it doesn't  
already have it, can be easily modified to do so I think and it's on  
my list to do this for a writeback instance I'm setting up for genomic  
data anyway.

However the big fly in the ointment is that I'm pretty sure no clients  
support it at the moment however. I'm sure ensembl doesn't and I don't  
think Dalliance does, GBrowse doesn't? I think maybe Web Apollo does,  
but I haven't heard anything from those guys in ages? I hope I'm wrong  
on this though. Maybe Karyodas can implement it quickly???? http://mykaryoview.com

> Do any existing personal genotype archives have this kind of 'genotype
> server' service, or is DAS the first system to provide this
> functionality? Do you plan to build it into a dedicated service
> somewhere?
I'm in discussions about this with the powers that be at the moment.  
Problems would include massive memory usage if implemented this way  
and also legal issues around managing other peoples genomic data.  
Which is why the personal virtual machine in the cloud is something  
that is quite an elegant solution at the moment :) I would like the  
process for people to be even easier though and for setting up DAS  
sources in general.

>
>
> Cheers,
> Dan.
>
> On 12 January 2012 13:21, Jonathan Warren <jw12 at sanger.ac.uk> wrote:
>> Hi
>>
>> I've put some instructions for people with little or no technical  
>> ability
>> and no access to IT personnel or servers, to be able to publish there
>> genotype data from companies such as 23andme etc as a DAS source on  
>> the
>> amazon cloud.
>>
>> http://biodasman.wordpress.com/2012/01/12/easy-deployment-of-das-server-for-personal-genotype-data-to-the-amazon-cloud/
>>
>> All someone needs is a tab delimited text file from one of these  
>> companies,
>> a credit card and an internet connection. The instructions show  
>> them how to
>> set up and deploy their server to the cloud in 6 easy steps and  
>> then view
>> the data in Ensembl.
>>
>> Example server can be accessed from here
>> http://mychoiceofname.elasticbeanstalk.com/das/person1
>>
>> Any comments suggestions welcomed.
>>
>> Cheers
>>
>> Jonathan.
>>
>> Jonathan Warren
>> Senior Developer and DAS coordinator
>> blog: http://biodasman.wordpress.com/
>> jw12 at sanger.ac.uk
>> Ext: 2314
>> Telephone: 01223 492314
>>
>>
>>
>>
>>
>>
>>
>>
>>
>>
>> --
>> The Wellcome Trust Sanger Institute is operated by Genome  
>> ResearchLimited, a
>> charity registered in England with number 1021457 and acompany  
>> registered in
>> England with number 2742969, whose registeredoffice is 215 Euston  
>> Road,
>> London, NW1 2BE._______________________________________________
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>> DAS at lists.open-bio.org
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Jonathan Warren
Senior Developer and DAS coordinator
blog: http://biodasman.wordpress.com/
jw12 at sanger.ac.uk
Ext: 2314
Telephone: 01223 492314










-- 
 The Wellcome Trust Sanger Institute is operated by Genome Research 
 Limited, a charity registered in England with number 1021457 and a 
 company registered in England with number 2742969, whose registered 
 office is 215 Euston Road, London, NW1 2BE.