Bioperl: RFI response, appendix (fwd)

Georg Fuellen fuellen@dali.Mathematik.Uni-Bielefeld.DE
Wed, 11 Mar 1998 22:31:28 +0000 (GMT)

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) if I had to start again.

I like the suggested template POD for object methods at

best wishes,
Univ. Bielefeld, Research Group in Practical Comp. Science

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:
> 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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