[Bioperl-l] a project idea

[Jason Stajich]

I've talked to Martin about using Novella to interface with emboss - this
would be through AppLab I guess if I understand the objects correctly.  I
plan to start digging on this some this week but the more the merrier.

On Tue, 26 Jun 2001, Heikki Lehvaslaiho wrote:

> 
> I really think the next major step forward for bioperl is to get more
> external programs interfaced to it. 
> 
> Applab/Camballo, once it is works, is an excellent choice. The main
> problem with EMBOSS at the moment is that the output from its various
> programs is not standardized. I talked to Alan Bleasby (coordinator of
> EMBOSS project) the other day and they are right now working on it. We
> should know more in few weeks time.
> 
> 	-Heikki
> 
> 
> I talked to 
> 
> Martin Senger wrote:
> > 
> > > > I'd like to suggest the following.  Someone could design an interface
> > > > Bio::Tools::RunI which all these implementations can implement - something
> > > > like a bare minimum - parameters(), run(), output()  and handle checking
> > > > for executable in the path or specified dirs.
> > > >
> >    We worked quite hard on the BSA Analysis module - at the moment I am
> > convinced that it can handle almost all command-line driven tools. The
> > specification is quite straightforward and - the most important - it is
> > already implemented (AppLab project: http://industry.ebi.ac.uk/applab).
> >    As Juha said, I am working now on a non-valuetype flavour on this spec,
> > a project called NOVELLA ("NO-Valuetype Enhaced Liaison to the appLab
> > Analyses"). This will be ready in a couple of weeks. A
> > Novella-AppLab bridge server is ready now, I need some time to prepare a
> > Perl client. This will be a module BSA::Novella::Client - and the user
> > will not need to notice that she will be working with CORBA at all.
> >    Give me few days, then I will announce where you can get it and try it.
> > Then I will start questions and negotiations with BioCorba people
> > whether/how they want it as a part of BioCorba.
> > 
> > > >
> > > > Attachment to EMBOSS apps would also be an excellent next step.
> > >
> > > EMBOSS is currently working under the AppLab.
> > >
> >    See "cemballo" project: http://industry.ebi.ac.uk/cemballo (but I am
> > not sure now if the demo server is running and I am away till the end of
> > this week to restart it - but if it runs, it's a small miracle because I
> > started it in March as a demo, without any cronjob for restarting attached
> > to it yet :-)).
> > 
> >    Martin
> > 
> > --
> > Martin Senger
> > 
> > EMBL Outstation - Hinxton                Senger@EBI.ac.uk
> > European Bioinformatics Institute        Phone: (+44) 1223 494636
> > Wellcome Trust Genome Campus             (Switchboard:     494444)
> > Hinxton                                  Fax  : (+44) 1223 494468
> > Cambridge CB10 1SD
> > United Kingdom                           http://industry.ebi.ac.uk/~senger
> > 
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> 
> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
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Jason Stajich
jason@chg.mc.duke.edu
Center for Human Genetics
Duke University Medical Center 
http://www.chg.duke.edu/