[bip] Bioinformatics examples (was[Fwd: Re: domain name for community site])

[Bruce Southey]

Hi,
(Changing the thread...)

I agree that we need to generate code examples (like Paulo's site at
http://python.genedrift.org) for doing simple things. But also we need
to have examples from the packages like BioPython and Corebio.

Also, does anyone know about 'Python for Bioinformatics (Chapman &
Hall/Crc Mathematical & Computational Biology) by  Sebastian Bassi' ?
It is meant to be available March 2008. From the publishers site:
"...Python for Bioinformatics provides an accessible introduction to
both the Python and BioPython languages. The book addresses advanced
topics, from web applications and XML to databases and version
control. In addition to useful appendices with reference material on
biological file formats, the book presents commented working code and
new programming techniques, such as error handling, functions, and
modules. It also includes source code as well as a companion CD-ROM
that contains a virtual machine with complete installation and a
working web server. "

Assuming that the source code is suitably licensed (i.e. BSD-like or
GPL v2 like), perhaps we can work related to this book?

Regards
Bruce



On 8/22/07, Titus Brown <titus at caltech.edu> wrote:
> -> In any case, there are a decent number of people on the Biopython
> -> mailing list interested in the same things that biology-in-python
> -> is interested in, so sending a email that way would be friendly and
> -> might bring in some good people.  I don't think there are any
> -> staunch defenders of the faith.
>
> I'm already chatting with two of the current main developers.
>
> One thing that came across quite clearly at the BoF was that even if
> many of us disliked what we'd see of BioPython, we didn't know what we
> *did* want to do.  There were a lot of ideas flung about, though, and
> hopefully they'll come up again in more concrete form.
>
> For the moment I'd prefer to think about code snippets and tutorials and
> getting some people involved in actually writing a bit of code.  At some
> point something will coalesce, I'm guessing, and then we can discuss
> melding it with BioPython, or releasing it as a series of small
> projects, or ...
>
> cheers,
> --titus
>
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