[Biophp-dev] Ok. Im new Hows the deal?

biophp-dev@bioinformatics.org biophp-dev@bioinformatics.org
Tue, 22 Apr 2003 20:32:14 PST

I think it would be real nice to bring Sean's and Serge's code together
into a start of something real nice.  It will be very stimulating to
actually have some code that is doing something usefull.  

I suggest to bring all the files together in a single directory on one of 
the cvs servers (genephp on sourceforge or biophp on the bioinformatics
one, I don't care which one, sourceforge is a very reliable server,
biophp is the catchier name).  Having them all in one directory is simply 
a good initial organization and a simple 'cvs update' will give you a
nice library of (hopefully) working biophp scripts.  Splitting them out
by author is not a good idea, because it will not be the organization in
which the files will work together.  Simply put, let's immediately put
that code to work and let's structure everything such that it is easy to use.  

Don't be scared about others doing stuff to your files, cvs is extremely
nice (once you get used to it), and you will be able to retrieve every
version of the file that ever existed. cvs will also take care of people
working on the same file at the same time.   

I am really looking forward to seeing this all move to something nice.
Once Serge has made the easier constructor for his seqdb class (that does 
not need index files) I am going to use the code in the phplabware
project and help write more parsers.

Just my 2 cents..


On Tue, 22 Apr 2003 21:32:36 -0500 Andrés Pinzón wrote:

> OK,  initially i come from the bio-side (i'm biologyst), but i also come
> from the C++-side, and of course, from the PHP/computing-side, here in
> Colombia!
> How's the organization here?, i mean i've been taking a look at the
> scripts
> at biophp, but i can not realize if someone is in charge of something in
> particular. This is my first time with CVS and that stuff  (so i'm gettin
> used to), i`ve been also looking at the genbank's ANSI.1, and trying to
> realize how the parser could be ("any help will help").
> How's the deal with genephp? R those different projects why aren`t they
> unified? Anyway im going to take alook
> Seeu
> Thanx 4 everything
> ----- Original Message -----
> From: "Dong Gregorio" <d.gregorio@eudoramail.com>
> To: <biophp-dev@bioinformatics.org>
> Sent: Tuesday, April 22, 2003 3:48 AM
> Subject: Re: [Biophp-dev] Ok. Im new Hows the deal?
> > Welcome, Mr. Pinzon!  Well, I guess we're all new here so
> > feel free to butt in the discussion.  Maybe you can tell
> > us where you're coming from (the PHP/computing side, the
> > Bio side, etc.), for starters.  =)
> >
> > No, my apologies, Sean.  I think I was the one who was
> > distracted...  Or maybe it's both (of us)?
> >
> > You can check the site out at http://genephp.sourceforge.net.
> >
> > I must stress that everything there is still fluid and under
> development.
> As for the labels "biophp" and "genephp", to me
> > it's the same thing.  As they say, a rose is still a
> > rose by whatever name.  Looking forward to "merge" the code
> > with you guys in the not-so-distant future.  =)
> >
> > Cheers!
> >
> > Serge
> >
> > --
> >
> > On Tue, 22 Apr 2003 00:36:38
> >  S Clark wrote:
> > >Ah, yes, Serge had sent me some documentation in MS Word format...
> > >
> > >I hadn't realized that all this time genephp
> > >already had a page on sourceforge...tells you how distracted
> > >I've been lately.
> > >
> > >I hadn't seen the code itself yet, but so far the plan is that
> > >developers will each have their own "subsection" for their own
> > >code while we work out how to structure the "core" biophp modules.
> > >I would have no problem keeping a CVS mirror of GenePHP available
> > >if desired, though it may not be necessary since it's hosted
> > >on SourceForge.
> > >
> > >I'll be adding genephp to the links page, assuming, or course,
> > >that Serge doesn't mind (I would assume not!).  I will be doing a
> > >bit of updating (uploading the "utility" classes for sending POST
> > >queries and the "generic" filehandle xml parser class) tomorrow
> > >(well, really "later today" in my timezone), so I'll add the link
> > >then.
> > >
> > >Sean
> >
> >
> >
> > Need a new email address that people can remember
> > Check out the new EudoraMail at
> > http://www.eudoramail.com
> > _______________________________________________
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> > Biophp-dev@bioinformatics.org
> > https://bioinformatics.org/mailman/listinfo/biophp-dev
> >
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