[Bioperl-pipeline] Starting the Pipeline with ensembl
Peter Kos
kos@rite.or.jp" <kos@rite.or.jp
Thu, 22 Aug 2002 16:49:02 +0900
Hi, Elia
Thank you for the advice, I will follow that.
Meanwhile I have looked at the web pages of the pipeline. At first
glimpse it seemed scary for me to have the jobs in a relational
database and the resulting data in an OO database. I understand that
these are pretty simple everyday things for you though. I am sorry
that your two papers on the databases have not been published yet.
To be honest, I have always been a bit afraid of EnsEMBL. I have seen
presentations from Tim on this project a couple of times and it
always seemed some extremely complex thing, not for the size of our
"Bioinformatics Center" as I call my desk.
I had considered ACeDB because you can start with a whatever small
primitive schema; Bioperl is getting close to it via AcePerl and
Ace.pm; and GFF format (also from Tim, as I know) is also getting
closer to it in the v.2 specification and also supported in Bioperl.
I downloaded the ACeDB program, and played a bit with the demo
database, and I found that nice. I think it is getting a kind of
standard.
I will now try to find, download, study and investigate ensembl. If I
can make it ignorant enough (forgetting about introns, chromosomes,
ESTs and other trendy eucaryotic features) and still flexible to put
our special stuff there, then it still may be 100% perfect for me.
Especially if there is someone giving advice in case I get stuck.
So, thank you. I will shout out when I am getting stuck.
Best regards
Peter
On Thursday, August 22, 2002 1:36 PM, Elia Stupka
[SMTP:elia@fugu-sg.org] wrote:
> > What I WANT to do, however, is to create an automatic annotation,
> > at least make an EMBL formatted file-set with useful information
and
> > perhaps dump the whole thing into an ACeDB.
>
> We can definitely help you with this, please start off by looking
at
> the
> download and install instructions at
> http://www.fugu-sg.org/bioperl-pipeline/bioperl-pipeline-
> install.html
>
> and let me know how far you manage to go. We'll be happy to assist
> you
> once you are not sure how to proceed, or if you see functionality
> missing,etc.
>
> If you want to get the job done fast, I would suggest you to use
> our
> pipeline with our templates and install also the ensembl database
as
> a way
> to store the data, rather than AceDB (which at the moment we
haven't
> used)
>
> Elia
>
> ********************************
> * http://www.fugu-sg.org/~elia *
> * tel: +65 6874 1467 *
> * mobile: +65 9030 7613 *
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> ********************************
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..................................................................
..........
Peter B. Kos, Ph.D.
Molecular Microbiology and Genetics Lab.
Research Institute of Innovative Technology for the Earth (RITE)
9-2 Kizugawadai, Kizu-cho, Soraku-gun,
Kyoto 619-0292 JAPAN
Phone: +81-774-75-2308
Fax: +81-774-75-2321
E-mail: kos@rite.or.jp