[bip] Bioinformatics software design

[Nathan Harmston]

Hi,
The software will be for model validation and inference.....which I'm not to
sure on the details, I m hope to understand the methods when I start.

1) APIs: The problem with API's is that they should not change over
> the long term. I have seen this affect people with the Linux kernel
> and with Numerical Python to mainly a limited degree. One of the many
>

Would people suggest that the API should be similar to SciPy/NumPy? Would
people suggest this as a good example of a bioinformatics API thats easy to
use and learn. I was planning on making the API as Py3K compatible as
possible, and conforming to PEP8 as far as I can.


> 2) Tests: Certain basic tests can be useful while developing if core
> pieces will get changed. The main use that I really see for tests are
> for those rare, special and weird cases that you don't see everyday as
> well as porting to other environments (32 vs 64 bit). Also, there is
> some noise on the SciPy list because of the version of NOSE required
> to get those tests to work.


Hmm, I didnt think about the bit problem, Thanks. What testing suite would
people suggest is the best (no crusade/jihadist/flame comments please)?


>
> 3) Developing software. I found that developing for the web (two
> bioinformatics examples only for reference Student Interface to the
> Biology Workbench and NeuroPred) makes many things easier because you
> are limited to what can be provided. It does keep it easy to use and
> stay flexible as the User typically just 'points and clicks'. You can
> also change the underlying code such as fix bugs without having to
> make extensive releases because it will exist at a single place. Also,
> anyone with a web connection can use it wherever and whenever they
> want (obviously assuming server availability).


This project is going to be distributed as a package and while I totally
agree with your points that having a single place would simplify everything
(I think this is the future and maybe if web services were used and
maintained better, with a better indexing service, this software model would
really take off in bioinformatics). From researching Pyrex, it is
sub-optimal so we believe that Ctypes will be better. The plan is to
restrict the package to release on *nix machines (Linux, BSD and OS X). One
of the major requirements for this project will be speed and extendability
and ease of use and unfortunately Python only fullfills 2 of these
requirements.

Thanks

Nathan
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