[Biojava-l] HOWTO doc v1: taking BioSQL + bioperl-db + bioperl and rolling a relational "biosql" database

Chris Dagdigian dag@sonsorol.org
Fri, 17 May 2002 16:52:01 -0400

Hi folks,

One of the cooler things that came out of the OBF hackathon held in 
Arizona/Capetown was seeing so many groups and projects agree on a 
cross-platform/cross-project way to access flatfile, SQL and web-based 
databases and resources.

It turns out that when you put OBF developers in the same city, give 
them a wireless network to plug their laptops into and keep the beer and 
pizza flowing what you end up with is really productive, clever & usable 

This is probably a great time to plug BOSC :) The next time that a 
sizeable number of Open Bio affiliated developers, project leaders and 
users will be together in one city with wireless network access etc. 
will be BOSC/ISMB coming up in August. Anyone planning to attend ISMB 
this year should think about coming to Edmonton a few days early to 
participate in the Bioinformatics Open Source Conference ('BOSC'). More 
info is online at http://open-bio.org/bosc2002/

That's the good news. The bad news is that most of the cool stuff being 
cooked up by the various OBF-affiliated developers has not really made 
it very far onto our websites and documentation. I don't think that 
people who are not actively monitoring various dev lists and 
open-bio-l@open-bio.org have really gotten a chance to hear about this 
stuff. {another reason to come to BOSC and meet folks in person...}

On that note I've been itching to try out some of the "bioSQL" stuff 
that the group had come up with. That opportunity came this week when I 
was able to spend a day trying to build a MySQL-based system on a new 
linux server.

I ended up using code and scripts from the following projects/repositories:

o obf-common/biosql-schema
o boperl/bioperl-db
o bioperl/bioperl-live

The end result was that it took me about a day to build the database and 
load ~307MB worth of Swissprot sequences into it.

The whole point of this email is that I ended up taking notes during the 
process and put together a diary/howto guide that explains what I had to do.

The URL is http://bioteam.net/dag/BioTeam-HOWTO-1-BIOSQL.html

I'd be interested in feedback and suggestions on how to improve the 


Chris Dagdigian, <dag@sonsorol.org>
Independent life science IT & research computing consulting
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
Work: http://BioTeam.net PGP KeyID: 83D4310E  Yahoo IM: craffi