[pyphy] Re: phylogenetic python

[J.W. Bizzaro]

Jeffrey Chang wrote:

> I believe I have some code related to Phylip connectivity that may be
> useful for PyPhy.  I would be happy to try and integrate that with the
> rest of the project.

Hi Jeff!  Great.

Hej Thomas, are you still alive? :-)

> Unfortunately, the "theopenlab" web server seems to
> be down now, so I cannot grab a copy of the code to see how
> useful/feasible it would be.  When it comes back up, I'll take a closer
> look at it.

I just noticed that myself.  One of our guys was trying to upgrade Apache for
PHP, and something must have gone wrong.  I'm looking into it.

> 
> If I can contribute code, then I will need a CVS account.  Since I doubt
> you will let me have the username "jeff" ;), I will take "jchang".

I'll set one up for "jchang" and get back to you.

> BTW, PSB accepted my proposal to do a python tutorial.  Looks like
> interest in python is picking up in the bioinformatics community!

That's good to hear.  There has been some skepticism about Python for
bioinformatics, with many people I know thinking that Perl and Java are the
accepted standards.  Of course Python has shown itself to be better suited for
scientific programming, and physicists have accepted it as there standard, and
possibly a replacement for FORTRAN.

Konrad Hinsen gave a tutorial on scientific Python and has a Web page on the
subject.  Maybe you'd like to check them out for your tutorial:

    http://starship.python.net/crew/hinsen/


Cheers.
Jeff
-- 
                   +------------------------------------+
                   |                                    |
                   |           J.W. Bizzaro             |
                   |      jeff@theopenlab.uml.edu       |
                   |                                    |
                   |       THE OPEN COLLABORATORY       |
                   |    FOR MOLECULAR BIOINFORMATICS    |
                   |                                    |
                   |     http://theopenlab.uml.edu/     |
                   |                                    |
                   +------------------------------------+