[Bioperl-l] a project idea

[Heikki Lehvaslaiho]

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
> 
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> European Bioinformatics Institute        Phone: (+44) 1223 494636
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> 
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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
___ _/_/_/_/_/________________________________________________________