[Biophp-dev] Fwd: BioPHP Project(s)

S Clark biophp-dev@bioinformatics.org
Wed, 10 Sep 2003 16:34:24 -0600

This is a message Serge and I got from Jesus Castagnetto.  Neither minded
me posting it to the main list for discussion, so here it is.

The summary of the discussion of the issues so far (my own interpretation,
at least) is that unification is already more or less in 
progress.  Of the "up to four" projects Jesus had seen reference
to, I know what's going on with at least three of them.

Hallgeir Bergum's project (the one at biophp.org) was to have
been a sequence annotation database, but due to circumstances
beyond his control he's been unable to work on it.

The other two are of course my own and Serge's GenePHP.  In essence,
we are two separate projects owing to the differences of approach,
but we're both nonetheless working towards unifying what we come
up with into a single "official" BioPHP codebase, even if our
own "personal" codebases and development styles are different.
(My personal goal right now, for example, is to combine the functionality
of Serge's original seq object and a bit of my own into a more
"object-orientationally correct" form - and hopefully make it
easy to interface with BioSQL tables at the same time.)

Serge and I both think that using PEAR for distribution would
be great, but neither of us (yet!) completely understand how
to make use of it, though I've been at least trying to stick
to PEAR coding standards and naming conventions as much as
possible.  I think PEAR is definitely in our future for
BioPHP distribution.

(Again, my interpretation of the discussion thus far - Apologies
to Serge and Jesus if I've mis-stated anything here...)

Public comments and suggestions are welcome.

----------  Forwarded Message  ----------

Subject: BioPHP Project(s)
Date: Friday 05 September 2003 05:11 pm
From: Jesus Castagnetto <jmcastagnetto@php.net>

I was looking to see if there was finally a project for PHP akin to the
BioPerl, BioJava, etc. and found out that at some point there were up to
four (!!!) different projects with the same name.

I kept looking and found out that some consolidation has taken place and
that one of the projects (ex genephp) seems to be in a more developed

Got the code from that project, but it seems to follow the old way of
doing things in PHP, i.e. get the code and put it somewhere in your
include_path, and hope that next time you download the next version and
replace the files you do not break something.

I have 2 questions to all of you:

1) Why not try and unify efforts and have one BioPHP project?

2) Have you considered using the installation, packaging, deployment
framework from PEAR (pear.php.net)?

PEAR is included w/ PHP (since 4.3.0), and makes life easier for the
developer and user, it is a cinch to install, upgrade or remove
packages, it has dependecy checking, and (soon) will support the concept
of channels.

The people at the PHPMath project (www.phpmath.com) will start using it,
the Horde project has some modules that are using it (pear.horder.org),

You do not need to follow the PEAR coding standards to use the
installation/packaging framework (although the naming coventions will
help to avoid clashes with other code).

Just some ideas. If you need more info let me know.

Jesus M. Castagnetto <jmcastagnetto@php.net>
Research: http://metallo.scripps.edu
Code: http://pear.php.net/account-info.php?handle=jmcastagnetto