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From "James Carman" <>
Subject RE: Biological Object Model Project
Date Wed, 08 Jun 2005 11:49:41 GMT
>From what I understand, the BioJava project doesn't really provide
persistence for biological objects, which is something that I would want in
a model/platform.  My idea is to use something like Hibernate or JDO to
actually persist the data.  Also, the last "recent update" for BioJava was
from May 2004.  I would think that a platform should allow you to store your
objects into a persistent storage mechanism (RDBMS).  Once you have a
persistable model in place, then you write utilities which can operate on
it.  Granted, I haven't used BioJava that much.  I'm just going by what I
see from the JavaDocs and I could be very wrong.

-----Original Message-----
From: Jukka Zitting [] 
Sent: Wednesday, June 08, 2005 2:10 AM
Subject: Re: Biological Object Model Project


James Carman wrote:
> I would like to start a biological object model process (I need to come up
> with a catchier name) and I think ASF would be a great place for it.

Have you looked at the Open Bioinformatics Foundation 
( They are not ASF, but they have a working, 
actively used and evolving codebase that already forms a de-facto 
standard platform for open source bioinformatics.


Jukka Zitting

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