[aventis.com]:Re: [Biophp-dev] BioPHP CVS access?

Frederic.Fleche at sanofi-aventis.com Frederic.Fleche at sanofi-aventis.com
Fri Nov 17 03:54:55 EST 2006

Hi all,

Just to let you know that I am still interested in Biophp since I still use it.
I use it to parse the alignments between mRNA and genomic sequences performed by Spidey and to draw the represention of the alignment : Very useful to see the differences between mRNA from Ensembl and REFseq.
By the way I am planning to launch the website www.bioinformatics.fr that will be a place to share knowledge related to the broad field of biocomputing so everyone will be welcome to visit this fresh place.
I am also involved in the Google groups group4bioinformatics that is about Technical question in bioinformatics so you are also welcome to join it.
I am PHP addicted so I hope that the Biophp project will be kept alive.



-----Message d'origine-----
De : biophp-dev-bounces+frederic.fleche=aventis.com at bioinformatics.org
[mailto:biophp-dev-bounces+frederic.fleche=aventis.com at bioinformatics.or
g]De la part de mail-lists+biophpdev at dogphilosophy.net
Envoyé : Friday, November 17, 2006 05:50
À : Bioinformatics for PHP
Objet : [aventis.com]:Re: [Biophp-dev] BioPHP CVS access?

On Wednesday 15 November 2006 21:01, C T wrote:
> I was trying to access the following URLs today, but unable to view the
> BioPHP CVS at all:
> Is it possible for you to send these to me in a zip file or something? I am
> trying to develop a new website for geneticists at www.genome.ws and
> integrating php code (from biophp.org and your files for php BLAST) for the
> website.
> Please let me know and if you have any other useful tools for the proposed
> website I have in mind
> Thanks,
> Vittle B.

I'm not seeing anything at www.genome.ws at the moment.  What kind of site 
will it be?  (Doesn't actually MATTER, I'm just curious).

By odd coincidence, I finally (after a couple of years now) ended up in a
position to play a little with the code again - I just dusted off the NCBI 
BLAST query code to query a set of sequences.  Looks like it's still 
working - guess NCBI hasn't messed with the API much.

I can send you a zip of the entire CVS tree (the whole thing's about 18k as a 
bzip'd tarball) if you'd like, either via email or ftp or whatever.  

For anyone else still on the mailing list wondering if this project is dead - 
nearly, but not totally.  More like comatose with the possibility of eventual 
return to activity.  

A few painful years of a somewhat life-devouring job kept me away from being 
able to do much of anything here except discard the spam trying to get to the 
list and approve a slow trickle of subscription requests.  Apologies to 
everyone who subscribed and ended up annoyed at the silence.

Now that I've escaped Dilbertland and fortuitously managed to end up back in 
school again working on my Microbiology degree, I at least now have good
cause to spend some more time dusting this stuff off and working on it
again if I can get some time between classes.

Anybody else still on the list and still interested in this project?  Given 
that it looks like GenePHP/BioPHP has been more active and has the biophp.org 
domain the name probably ought to be changed, though.  Perhaps something like
"PHPBioFetch" since as it stands now the working code primarily deals with 
reading, parsing, and fetching biological data (rather than analyzing it)?

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