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Thread: Using Postgres to store genetic data

Using Postgres to store genetic data

From
Peter Hunsberger
Date:
We're looking at potentially using Postgres to store a variety of molecular and genetic data.  At this point I have a bunch of general questions which I can take to other lists if someone can tell me where they would be most appropriate:

1) are there groups or individuals already doing this that have things they can share?  I've seen the BLASTgres work and it needs rework to compile against 8.3 but might be potentially useful some of our forms of data;

2) if we do decided to implement our own data types where's the best place for discussion about such efforts?

3) Can anyone talk about what it would take to add columnar indexes to Postgres?  Where would be the best place for discussion about what this would take?

I can go into more details here if appropriate and if that will help...

--
Peter Hunsberger

Re: Using Postgres to store genetic data

From
Steve Crawford
Date:
Peter Hunsberger wrote:
> We're looking at potentially using Postgres to store a variety of
> molecular and genetic data.  At this point I have a bunch of general
> questions...

I don't know enough about your area of expertise to know if this is
useful, but I'd look at the Unison project to see what they are doing.
There are also videos/slides up from a recent San Francisco PUG meeting
at UCSF that might be of interest:

http://www.vimeo.com/3732938
http://www.slideshare.net/linuxpoet/unison-ucsf-sfpug

Re: Using Postgres to store genetic data

From
Peter Hunsberger
Date:
On Fri, Jul 10, 2009 at 4:02 PM, Steve Crawford
<scrawford@pinpointresearch.com> wrote:
>
> Peter Hunsberger wrote:
>>
>> We're looking at potentially using Postgres to store a variety of molecular and genetic data.  At this point I have
abunch of general questions... 
>
> I don't know enough about your area of expertise to know if this is useful, but I'd look at the Unison project to see
whatthey are doing. There are also videos/slides up from a recent San Francisco PUG meeting at UCSF that might be of
interest:
>
> http://www.vimeo.com/3732938
> http://www.slideshare.net/linuxpoet/unison-ucsf-sfpug
>

Looks like it may be somewhat applicable to my first question. Thanks.

Area of expertise is application architecture and design, focusing on
clinical systems for medical research these last 7 years or so and
medical in general for the last 15.  Adding the genomic and molecular
world to the mix is a new initiative. At the moment I've got enough
domain knowledge to be dangerous...

--
Peter Hunsberger

Re: Using Postgres to store genetic data

From
Martin Gainty
Date:
Peter-
if by 'dangerous' you mean employable then count me in!

Oracle is probably the only DB vendor which implements Clinical Informatics product
would like to hear about any Clinical Informatics offerings postgres would offer
I'm thinking a relational tree might work something like
Gene ->1..n-> Sequence(s) ->1..n-> GCATPermutations

thanks,
Martin Gainty
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> Date: Fri, 10 Jul 2009 21:56:09 -0500
> Subject: Re: [GENERAL] Using Postgres to store genetic data
> From: peter.hunsberger@gmail.com
> To: scrawford@pinpointresearch.com
> CC: pgsql-general@postgresql.org
>
> On Fri, Jul 10, 2009 at 4:02 PM, Steve Crawford
> <scrawford@pinpointresearch.com> wrote:
> >
> > Peter Hunsberger wrote:
> >>
> >> We're looking at potentially using Postgres to store a variety of molecular and genetic data.  At this point I have a bunch of general questions...
> >
> > I don't know enough about your area of expertise to know if this is useful, but I'd look at the Unison project to see what they are doing. There are also videos/slides up from a recent San Francisco PUG meeting at UCSF that might be of interest:
> >
> > http://www.vimeo.com/3732938
> > http://www.slideshare.net/linuxpoet/unison-ucsf-sfpug
> >
>
> Looks like it may be somewhat applicable to my first question. Thanks.
>
> Area of expertise is application architecture and design, focusing on
> clinical systems for medical research these last 7 years or so and
> medical in general for the last 15. Adding the genomic and molecular
> world to the mix is a new initiative. At the moment I've got enough
> domain knowledge to be dangerous...
>
> --
> Peter Hunsberger
>
> --
> Sent via pgsql-general mailing list (pgsql-general@postgresql.org)
> To make changes to your subscription:
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