[Biophp-dev] biophp status

[Can Tran]

At 05:29 PM 3/10/2004, you wrote:
>>I was wondering what the status of biophp was?
>
>As far as I know biophp is in a very rudimentary stage.  There is some 
>code written by Serge (with additions by Sean and me) that still need a 
>lot of work to become a easily usable library.  Then there is also still 
>the problem of two code bases  (one at Sourceforge, one at 
>bioinformatics.org, the second one basically contains the first with some 
>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.
I think we could really leverage the BioSQL and MOBY platforms to enable 
BioPHP
to be a great web oriented library.



>>I am the project manager for TCDB, a membrane transport protein 
>>classification database.
>>http://tcdb.ucsd.edu
>>beta site is http://mtpas.ucsd.edu
>>I have written many classes and functions dedicated to the analysis of 
>>membrane proteins.
>
>Great, what language did you use?  I'd be interested to discus how you set 
>up your database structure, not in the least since I might start a 
>database system for classifying coiled-coil proteins.


All of the web pages in TCDB use PHP. The classification scheme is encoded 
within an adjacency list. It's essentially a sparse directed graph. If 
you'd like to know more, you can email me off the list.


>>With a little hacking, I can get my functions to work with BioPHP.
>>Is that something that you would be interested in?
>
>That would be great.  For now, it would be best to check-out the cvs from 
>bioinformatics.org and add your contributions there.  Work is currently 
>being done in the 'genephp' directory.

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.


>Best,
>
>
>Nico
>
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