[Bioperl-pipeline] Starting the Pipeline with ensembl

[Peter Kos]

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        *
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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