> I'd be interested in hearing everyone's views about the practicality of
> taking this approach, and any offers of help to actually do it :-)
Based on the requirements previously described, I will be building that with at
least one other (already hired/trained/fulltime) engineer. We are funded and
itching to get a prototype going.
I agree that the Base2(LIMS) GenePattern(analysis) approach works well, perhaps
I'll be working on the distributed query-aggregation code in the middle. We
have LOTS of experience with that -- in fact, we have already done that now to
share cancer specimens and ER extracts. I believe sharing microarray results
will be a similar endeavor, save the analysis part (thank you GenePatterns!)
--andy
http://www.jamia.org/cgi/content/abstract/14/4/527
-----Original Message-----
From: [EMAIL PROTECTED] on behalf of Tony Travis
Sent: Tue 12/11/2007 10:38 AM
To: BASE dev
Cc: Ulrich Harttig; Chris Evelo; Merce Crosas
Subject: Re: [basedb-devel] Open Source utils for sharing array results
Bob MacCallum wrote:
> Hi all,
>
> Following this with interest as we are putting together some Java tools to do
> on-the-fly analysis for web display on data stored in BASE2, through an API we
> have built on top of the BASE2 API. Perhaps we should have invested the time
> in plugin development instead, but that's another debate/story.
Hello, Bob.
In my opinion base2 is most appropriately used as a LIMS, for managing
and pre-processing raw data, but we want to be able to query multiple
base2 instances and analyse data using GenePattern or other 'external'
tools. Of course, this can already be done using the MeV plugin, but
attempting to do everything within the base2 plugin API is not the only
way forward. We used the RMA express plugin as a starting point to write
a plugin to use the JRI here at RRI, and Chris Evelo in Maastricht has
followed this up more recently. However, I think a BioMOBY compliant web
service for base2 could be useful because there are existing interfaces
in Taverna, for example, to utilise BioMOBY compatible web services, and
we are building a BioMOBY infrastructure for our NuGO project:
http://www.nugo.org
> [...]
> As someone who loads data from several labs and institutes around the world, I
> really doubt you can just point your software at a bunch of directories full
> of raw data files and expect to have all the data loaded in a meaningful way.
> It does unfortunately take some curation. Perhaps with Affy data you have
> less to worry about (ready-annotated probesets, only one channel, no dye swaps
> etc), but maybe you don't just have Affy? I doubt the experimental factor
> annotations will just fall into place without some curation.
In this respect, I've been talking to Merce Crosas at Harvard about Gary
King's 'dataverse, and its integration with GenePattern:
http://iic.harvard.edu/projects/gene-pattern.html
I think this might also be relevant to the type of data on numerous
biologist's desktop PC's that Andrew is attempting to organise. I see a
three-component model, including base2 (LIMS), GenePattern (Analysis)
and Dataverse (pre/post publication 'persistent' data repository).
I'd be interested in hearing everyone's views about the practicality of
taking this approach, and any offers of help to actually do it :-)
Tony.
--
Dr. A.J.Travis, | mailto:[EMAIL PROTECTED]
Rowett Research Institute, | http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn, | phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK. | fax:+44 (0)1224 716687
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