[Bioperl-l] medperl, something kinda like bioperl

[Robert Buels]

Hi Spiros,

This is a fine idea.  My most important piece of advice is to keep the 
code loosely coupled and flexible.

Don't try to make big monolithic distributions like Bioperl.  Keep the 
code as loosely-coupled as possible: think carefully before making 
something be a subclass of something else, or have some other kind of 
direct dependency upon it.  Things change.  Coding practices change. 
Technology changes too, both on the bio/med side, *and* on the code side.

For the project to stay healthy for the long haul, it needs to stay easy 
for people to wrap their minds around the codebase, and then work on it: 
developers need to be able to focus their efforts on the code that they 
are interested in without having to worry about huge amounts of other 
code.  For this to be possible, the various parts of the codebase need 
to stay organized and compartmentalized, with minimal, 
well-characterized dependency relationships between them.

Good luck!

Rob


Spiros Denaxas wrote:
> Hello,
> 
> I am sending this email here since I consider all people that contribute
> and/or follow the bioperl project as the best starting point for advice on a
> new project I am currently planning ; my apologies if its considered
> off-topic.
> 
> While the bioinformatics community has greatly benefitted from the Perl
> community, with the shining example of bioperl, the medical community is
> sadly a bit behind. I am currently employed in a public health /
> epidemiology environment and have under numerous occasions discovered
> opportunities to contribute code to CPAN that has made my life easier. I
> know I am not alone, but a very quick search on CPAN for related modules
> form the medical / biomedical domain does not return much for now.
> 
> I recently gave a presentation at the London Perl Workshop [1] and while
> creating it, I thought, would it be useful to have something similar to
> bioperl for modules which largely contribute to the medical /
> epidemiological domain? I was thinking of creating something like medperl,
> alas similar to bioperl, but in a very very simple form. It would serve as a
> reference point to the (albeit small) numbers of modules that are currently
> on CPAN and will also hopefully urge people to contribute some of their code
> along the way.
> 
> So I would like to request your advice on:
> 
> a) Can you think of any reasons for not doing this?
> b) Does anybody know of something similar?
> c) Does anybody feel like they could contribute?
> 
> Regards,
> Spiros Denaxas
> 
> [1]
> http://www.slideshare.net/spirosd/perl-cures-coronary-heart-disease-lpw2010
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>