[Bioperl-l] medperl, something kinda like bioperl

[Spiros Denaxas]

On Mon, Jan 31, 2011 at 11:46 PM, Robert Buels <rmb32 at cornell.edu> wrote:

> 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
>
>
>
Hello Rob,

thanks for the feedback. It will be definitely a learning experience for me
as well. I'm planing on setting up some sort of public resource for people
to have a look at and discuss / make a plan before actual coding gets done.
Will keep you posted.

thanks
Spiros


> 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
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>>
>