[Bioperl-l] "Project OpenLab" (working title)

[Fernan Aguero]

+----[ Jay Hannah <jay at jays.net> (27.May.2006 15:15):
|
| Hola --

Hola!

| We've been kicking around this idea for a few months now. I'm threatening to start coding. Once I do I might not sleep for a few weeks so I thought I'd solicit feedback now. :)
| 
|    "Project OpenLab":
|    http://omaha.pm.org/kwiki/?BioPerl
| 
| - Does any such project already exist? 

mmm ... maybe ... both GUS (Genomics Unified Schema:
gusdb.org, though not developed around bioperl) and GMOD
(Generic Model Organism Database: gmod.org) provide you with 
i) RDBMS storage
ii) a Perl object layer
iii) a web app framework

Though certainly overkill for the needs you describe
in the wiki, they can be customized to work in the way you
describe or at least serve as a guide.

| - If there's no other obvious choice already bent to BioPerl / BioPerl DB / BioSQL, I'll probably be writing the web framework in Perl's Template Toolkit. The server is Linux, Apache, mySQL (BioPerl DBs). 

Have you considered Perl Catalyst? It has the benefits of
allowing you to work with bioperl modules naturally (it's
Perl!) a choice of templating toolkits (Template Toolkit, Mason,
among others) and will provide you with an almost ready to
go controller/url dispatcher.

| - I'll be using BioPerl objects for the persistence layer as much as possible. Where not possible I'll ask this list about my patches/additions/ugly hackery.
| - I'll be discussing my back office tables like "users" that don't belong in bioperl-db; and my questions about new tables that might belong there on the BioSQL-l mailing list.
| - I'm not a computer language zealot (usually), so I'm open to out-of-the-box ideas from anyone.
| - I'm a biology newb with a long Perl/database/web/e-commerce background, so please feel free to point out any bio idiocy I engage in.
| 
| Thanks for your time,
| 
| j
|
+----]

Good luck,

Fernan