[Biophp-dev] biophp status

[Nico Stuurman]

> >additional material).   It is really time to for biophp to get organized...
> 
> I think it would be great to bring BioPHP into the OBF fold.

Agree.  

> I think we could really leverage the BioSQL and MOBY platforms to enable 
> BioPHP
> to be a great web oriented library.

Don't know about MOBY (could you explain a little what this is for, or
give links or whatever?).  I worked a bit on BioSQL and wrote some code
to generate the BioSQL tables using the adodb
(http://php.weblogs.com/ADODB) RDBMS wrapper library ( see:
http://bioinformatics.org/cgi-bin/cvsweb.cgi/biophp/genephp/biosql-adodb.php).  I got a little disappointed in BioSQL because an insane amount of fields are set to 'NOT NULL', which does not make it, ehmm, versatile.  I hope I am overlooking something, but it would be nice to simply be able to write a simple php 'seq' object, containing only a sequence and not much else to a BioSQL database.  
In any case, biophp at this points really needs a good interface to a
RDBMS.

> I will probably contribute a few functions that calculate hydropathy, 
> amphipathicity, and some other protein properties. I have a few functions 
> to draw helical wheels and other data visualization kinds of things which I 
> might contribute later.

Great!  That is really stimulating.  Have a look at what is there and
how you can fit your code in.  We might as well all have (again) another
look at how the code should be structured, and your fresh insight will
be highly appreciated.


Best,

Nico




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> >Best,
> >
> >
> >Nico
> >
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