Bioperl: RFI response, appendix (fwd)

[Georg Fuellen]

Thanks SteveC for getting the "Bioperl Object and Framework Requirements" 
together !!

Steve wrote,
>>>>>>>>
8. Highly fault-tolerant. 
...       It is preferrable to throw fatal exceptions when data
          inconsistencies or other serious problems are encountered,
          rather than generating warnings that cannot be
          programmatically handled, or relying on a polling mechanism,
          or relying on the software's inherent ability to accomodate
          the discrepency.
<<<<<<<<
As before, I'd suggest to prefer warnings to fatal exceptions.
Some of my runs take days (90 sequences, each 3000 nucleotides each,
are subjected to thousands of alignment calculations), and I don't wanna 
lose the end result b/c of some stupid exception. Fatal exceptions are OK
for small scripts, but not for larger applications, as long as there
is a reasonable way to handle them: garbage in, garbage out is OK for
me as long as warnings are issued.
>>>>>>>>
10. Ability to use individual components stand-alone or within a framework. 
...       This issue has not been adequately addressed with the Bioperl
          framework. At present, different versions (stand-alone or
          integrated) of selected components are generated by hand as
          needed. This is creates the problem of synchronizing the
          different versions as updates are released. This is a
          difficult problem and solutions are being considered.
<<<<<<<<
Which solution(s) do you envision ?
>>>>>>>>
11. Web-awareness.
...       Objects should be able to access information available via
          the web and should be able to present information to users
          via a web browser interface. Not every object needs to be
          web-savvy. For objects that do require a web interface, one
          should consider advantages and disadvantages of integrating
          or segregating the data processing code from the web
          interface code.
<<<<<<<<
My research code produces HTML directly; maybe I would consider BSML 
(Bioinformatic Sequence Markup Language)
http://www.topogen.com/bsml/ if I had to start again.

I like the suggested template POD for object methods at
http://www-genome.stanford.edu/perlOOP/bioperl/method_template_pod.txt

best wishes,
  georg
fuellen@techfak.uni-bielefeld.de
Univ. Bielefeld, Research Group in Practical Comp. Science
http://www.techfak.uni-bielefeld.de/bcd/welcome.html

SteveC wrote,
> I sent in my "Bioperl Object and Framework Requirements" text yesterday 
> to the Life Science Research group at the OMG. Here is a copy of my 
> message FYI. Note that feedback (to me) about these requirements is 
> still welcome.
> 
> Cheers,
> SteveC
> 
> 
> ---------- Forwarded message ----------
> Date: Mon, 9 Mar 1998 14:45:26 -0800 (PST)
> From: Steve A. Chervitz <sac@fafner.Stanford.EDU>
> To: lifesciences-td@omg.org
> Subject: RFI response, appendix
> 
> 
> Dear OMG,
> 
> This message contains response material for the Life Science Research 
> RFI (CORBAmed RFI4, corbamed/97-09-16).

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