[Biophp-dev] but where is the code?

biophp-dev@bioinformatics.org biophp-dev@bioinformatics.org
Mon, 14 Apr 2003 13:23:57 -0600

Glad to see people interested in the project...

However, the project is only about 1 month old (and the mailing
list only about 2 weeks old) so we're naturally still in the
very early stages.  Much of the work being done currently is 
focussed on parsing/interpreting XML-format information pulled
from NCBI's databases (EUtils and, soon after, the online BLAST
databases), but a GenBank parser isn't going to be far behind, I

On Saturday 12 April 2003 11:04 am, nicos@itsa.ucsf.edu wrote:
> Sorry to sound impatient (and not being hindered by having all the mails
> on this list), but - if available - I would use some of the code you seem
> to be proposing right away.  Together with some friends I am running a
> generalized database project geared towards molecular biology labs
> (http://phplabware.sf.net).  It provides an easy and extensible interface
> to an SQL database and plugin code can enhance its functionality.
> For a rudimentary plasmid database, we started writing a very simple
> genbank parser
> (http://cvs.sourceforge.net/cgi-bin/viewcvs.cgi/phplabware/phplabware/plug
> ins/gb_plugin.php?rev=1.1&content-type=text/vnd.viewcvs-markup), but I
> would reuse (better) code anytime if available.  The alternative would
> be, of course, to use bioperl, but it would be much nicer and easier to
> use php code.
> So, if there is any code and or idea about structuring the objects out
> there, make it known so that wok can be done.
> Best,
> Nico