BioWidget meeting

Steven E. Brenner
Thu, 1 May 1997 16:26:19 +0900 (JST)

> I recieved a message from Alan Robinson, the organizer of the EBI 
> BioWidget meeting, asking if I would be willing to give a to give a talk 
> on Bioperl. I told him yes and that it might be tag-team style talk. I'm 
> perfectly willing to split the talk with any of you who will be there. If 
> I'm the only speaker, I could touch on the Bioperl work you all have done 
> in addition to talking about my own work.

Good.  He told me a couple days ago that he'd penciled in 30 minutes which
could be broken into 2 x 15 minutes.

> We need to submit a title ASAP and an abstract by 18 May. Since 
> this is going to be a community effort, how does this sound for a title:
> "Bioperl: Object-Oriented Perl Modules for Bioinformatics". It's general 
> since the content of the talk is still not nailed down. I'll try to come 
> up with an initial outline/abstract soon. If any of you have specific 
> suggestions for the plan of the talk, i.e., what should definitely be 
> included/excluded, let me know.  

Title sounds good.  The contents will depend on who else can make it --
parts (3 and 4) below will be longer or shorter depending on who can
speak.  I would propose that the following main topics be covered: 

1) What's Perl, why's it good for biology.  Why not all Java?
   Georg has written a lot of good stuff about this.  We probably do 
   want to explictly mention advantages of Perl over Java for some tasks.
2) What's the Bioperl project trying to do?
   A) First, core modules which can be a standard currency for which
      everyone can write their functions to operate on.  This means that
      different people's functions can be linked together without always
      writing conversion routines.  They also allow for complex yet
      maintainable programs
   B) Later, lots of functions to operate on these modules

3) What's been written, explicitly and what's planned
   A) Bio::PreSeq   
      Discuss basic functions/interface.  Modification to be included 
      in Bio::Seq.  Example of usage to do something really cool 
      very easily.  Bio::SeqBig (?) - superset of Bio::Seq to support
      all sorts of NCBI annotation, etc.
   B) Bio::UnixAln
      Discuss basic functions/interface.  Example of usage to do something
      really cool really easily
   C) Bio::Struct
      ...still on the drawing board.  Volunteers wanted!

4) SteveC's own code and perspectives.