[Bioperl-l] complexity?

[Jason Stajich]

This is a common complaint about the toolkit.  It seems too hard to
understand all the components for new comers.  We have tried to strike a
balance between the sophistication and ease of use, sometimes we fall too
far on one side or the other.

I'm not sure the best way to convey all the information - there are
class diagrams available on the website and each module should have
documentation on how it works.  The tutorial walks through
the use of a lot of the modules, but we've not got a great
narrative written just yet.  Understanding the whole picture might seem
overwhelming, but focus on what you need to do - then ask questions on the
list - and we can try and point you towards what are the right tools for
the job.  Some work is going on to provide some more formal and concise
documentation for a large part of the toolkit, but of course that takes
time and we all do this in our little bit of it that is free.

The Variation objects are part of Heikki and Josep's mutation( say
variation when talking about human data...=) toolkit that they you can
read more about at http://www.ebi.ac.uk/mutations/

-jason

On Mon, 22 Apr 2002, Liu, Mingyi wrote:

> Hi, Jason,
>
> Thanks for fill me in on these new developments.  Unfortunately it also made
> me realize that it might take a while for me to get a good understanding of
> the full picture.  After all, bioperl's a huge, tightly interwined package
> that I do not yet understand all of its structure and philosophy behind it.
> BTW, I just found that the Transcript module, Variation module are also not
> written out (except for their locations)?  I would appreciate it if you
> could fill me in on responsibilities for each module to be implemented and
> timeline expected in the future.
>
> Best,
>
> Mingyi
>

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu