Mon, 5 May 1997 08:58:51 +0000 (GMT)
> > 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
Title is ok!!
> > 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
Regarding Java, I've appended some wild thoughts at the end, since this
is not in any way my area of expertise.
> 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.
Re Java, I hope that it will enable us one day to have a GUI-like
interface by way of the WWW-browser, but this opens a whole can of worms.
Last year I compiled the list of ``Java drawbacks'' that you can find below,
but I'd really suggest to say that Bioperl can win big from an interface
to Biojava stuff, and vice-versa this may be true well. I dunno whether
a generic object interface could help; last I heard some study saying
that simple concepts like Javabeans may outcompete COBRA really soon.
A prelimininary, biased, outdated, and ill-informed list of Java ``problems''...
<li> Java is less high-level, more restrictive, less efficient
<li> Java is strongly typed, but lacks templates
<li> Java links "too late", and collects garbage "too late"
<li> Java applet security problems are ``inherent'' in the design of the
language (but Perl is "catching up".. ;-) (((Hint at Penguin)))
<li> Java is not "Free Software"
<li> Java is too much "cutting edge"
<li> "Inferno"/"Limbo" is coming up anyway :-)
<li> Java is nice for designing user interfaces, while Perl
acts behind the scenes...