[Biophp-dev] biophp status

[Serge Gregorio]

Regarding OBF, I remember making inquiries last April and May 2003, but got no reply.  My thinking now is, let's just continue developing BioPHP to the point that OBF *cannot afford* to ignore it.  =)

Regards,

Serge

--------- Original Message ---------

DATE: Wed, 10 Mar 2004 19:11:41
From: Can Tran <can@ucsd.edu>
To: biophp-dev@bioinformatics.org

>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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>
>
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