[Biophp-dev] Re: [Genephp-news] Biophp, where is it and where does it go?

[Nico Stuurman]

> Omigosh!!!  Did you or did you not receive a previous reply to your email?  

Nope, sorry.

> Project Updates:
> 
> 1) Cayte has submitted a revised glycan.inc.php last December but which I haven't finished reviewing.

Great, why not put in cvs so that everyone can use it, work with it,
modify it, enjoy it?

> 2) Jesus has volunteered someone to PEAR-ify BioPHP 1.0 (as found in SF's CVS).  As of early February, it's still underway.

Ehm, why that version?  Sean and I made some pretty nice enhancements to
that code, so why not work with that?  It really would be so much more
fun if we could all work with the same code base...

> 3) Dominik Gehl contributed some enhancements to etc.inc.php last January.

Great.  Why do we not see this in cvs (or anywhere else for that
matter)?  If we do not start all using cvs, then how do we work together
on code?  What is the strategy here?

> I didn't restart the CVS.  It was already there since April last year.  The absence of your code (and Sean's) was a result of my failed attempt to update it (due to some technical problems at SF I suppose).

Strange, I strongly recall having the cvs on biophp and sourceforge in
sync (even have an email here from Sean from July 2003 stating that he
contributed files to both the cvs at sourceforge and
bioinformatics.org).  Am I delusional?

In any case, this all still leaves us with the exact same problem that I
have been complaining about for more than a year now: we are not working
on the same code base.  I must confess that I am getting pretty tired of
that now, so unless there is a strong commitment from everyone to work
with one and the same codebase at one and the same place (I don't care
where), I am simply going to work with the cvs at bioinformatics.org
(actually started doing that last week, everything is right there, right
now, for all to use/modify/trash/criticize/whatever), and invite
everyone who wants to contribute code to a biophp library to do the
same.  

I simply would like to use a decent biophp library and - in the absence
of sufficient functionality - contribute to such a thing whenever I
can.  And it would really be fun to do that with a couple of people, so
why does that turn out to be so difficult?  


Best,


Nico


> 
> Quo vadis?  I intend to resume writing code this April-May (my summer break). 
> 
> First stop would be to integrate everything that has been written so far (which constitutes the "core features" of BioPHP, which unavoidably overlaps with BioXXX).
> 
> Next, I feel like working on features that distinguish BioPHP from the other BioXXX.  (Yes, I'm getting tired hearing, "Why reinvent the wheel?" from people around me.)
> 
> Earlier, I thought about modules for protein tertiary and quaternary structures, which other BioXXX do not have, which explained my interest in PDB and MMCIF.
> 
> But right now, I'm thinking along the lines of a PHP solution to integrating biological databases (see article by Lincoln Stein, Nature Reviews, May 2003), perhaps even a PHP implementation of BioMoby (biomoby.org).  I figured this whole web services thing plays very much to the strength of PHP.  
> 
> This is partly influenced by a project I'm working on right now with IRRI and CGIAR on data interoperability.
> 
> These are just some of my thoughts.  I'd very much welcome any suggestions on how to proceed from here. 
> 
> Regards,
> 
> Serge
> 
> 
> Need a new email address that people can remember
> Check out the new EudoraMail at
> http://www.eudoramail.com
> 
> 
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