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open-source software for bioinformatics (was Re: Unix vs Linux - the movie.)

Daniel Leonard leonard at alice.BCH.UMontreal.CA
Tue Aug 1 11:54:47 EST 2000

On Tue, 1 Aug 2000, Ted Byers wrote:

> Second, if a paper is to be published based primarily on the basis of a
> given program developed in the lab eporting the result, then I would rega=
> it as unprofessional if that program is not thoroughly documented.  While
> there are many ways to document software, UML provides a useful model for
> documenting software design.  If an application is properly documented, i=
> is not such a big problem to examine even a medium sized application of 5=
> kLOC.  Examining even a small program of only a few thousand lines of cod=
> can be a nightmare without proper documentation however.  And note, on su=
> a program, you would normally have a team developing it, the members of
> which will be reviewing each other's code.  It should also be noted that =
> most applications, most of the code involves the user interface and ought
> not to influence results produced by the algorithm that is actually
> responsible for the interesting scientific results.  I do this sort of th=

As a recent Comp. Sci. graduate, and future software engineer (I hope),
most of those UML diagrams are done before any code is written (like you
plan an experiment before doing it). So the documentation is done before
the program is written.

So someone having made a program and say "We did not have time to do the
documentation" could be look at suspiciously (unfortunatly, that is what
I do, well, for my personnal project, I think). Any serious program - and
more importantly, any BIG serious program - should have most of its
documentation done before any coding. While coding, some specs changes,
and the doc should reflect that. But I think, from what I have seen, that
some docs are done before, but that they are not updated to reflect the
current state of the project. As an example, the user manual of the game
StarCraft (Blizzard Entertainment) was finished (and I believe
printed) before the game was balanced by play-testing, so they had to put
addendums on the CD.

Hope that helps

Daniel L=E9onard

OGMP Informatics Division    E-Mail: leonard at bch.umontreal.ca
D=E9partement de Biochimie     Tel   : (514) 343-6111 ext 5149
Universit=E9 de Montr=E9al       Fax   : (514) 343-2210
Montr=E9al, Quebec             Office: Pavillon Principal G-312
Canada H3C 3J7               WWW   :

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