[Gmod-help] Building a GMOD database for transcriptome data

[Scott Cain]

Hello Vared,

I don't recall any projects that are quite like yours, though it does
seem like a reasonable thing to do with GMOD tools.  There are some
transcriptome projects that use Chado and Tripal and it seems like the
creation of a database like that could be scripted fairly easily for a
core facility.  Another option would be to provide a Amazon Web
Service or VMWare machine with the data for one project to a customer
(I'm currently working on an AMI that you could clone for each data
set).

For further research, I'd suggest asking on the Chado and Tripal
mailing lists, as there might be people already working on something
like this that I'm not aware of:

  gmod-schema at lists.sourceforge.net

and

  gmod-tripal at lists.sourceforge.net

Please let us know if we can provide more information.

Scott



2011/7/11 Vered Caspi <veredcc at exchange.bgu.ac.il>:
> Hello,
>
> I am head of a small bioinformatics core facility. We have recently started
> to perform NGS data analysis services for our customers. Now we want to be
> able to create a web-accessible database for each customer, and I thought
> GMOD may be a good platform.
>
> Our current projects have to do with transcriptome sequencing of novel
> eukaryotic organisms (plants, arthropods, other). Typically, several RNA
> libraries from different tissues or conditions are sequenced. We mix all of
> them for de novo assembly, annotate the achieved 'reference' transcriptome,
> in some cases compare to other genomes, and eventually perform differential
> expression analysis between the libraries.
>
> We would like to allow our users, at the end of the analysis, to query their
> transcriptome, see the raw as well as processed data per gene or contig, see
> the gene structure, differential expression results, run blast against their
> transcriptome etc.
>
> I will be happy to know if you can recommend on example projects that used
> GMOD for a similar purpose, and if you have a documentation on a suggested
> pipeline for the database development.
>
> Thank you in advance,
>
>                                     Vered Caspi
>
> http://bioinfo.bgu.ac.il



-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research