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

[Nico Stuurman]

Here too.  I used quite a few parts of biophp (including the primer3  
interface I contributed) in selecting primers for genome-wide RNAi  
libraries that I designed.

I find the stuff in biophp/genephp very useful.  It would be nice to  
expand on it, document it well, and bring all the scattered biophp  
stuff that apparently can be found all over the internet, together in  
one place.

Best,

Nico


On Nov 17, 2006, at 12:54 AM, <Frederic.Fleche at sanofi-aventis.com>  
<Frederic.Fleche at sanofi-aventis.com> wrote:

> 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.
>
> Regards,
>
> Fred
>
> -----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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