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From "James Carman" <>
Subject RE: Biological Object Model Project
Date Thu, 09 Jun 2005 00:12:50 GMT

I'm glad you like the idea.  I think there is a need for something like this
in the bioinformatics community.  

Well, I could start modeling some classes that I'm somewhat familiar with.
Unfortunately, though, I'm not a bioinformatician, so I'm not exactly the
person who should be doing the actual domain modeling.  What I (and many
others at ASF) can bring to the table is the infrastructure which allows the
objects to be stored/retrieved.  Maybe I could try to recruit some help from
some domain experts (bioinformaticians) to start developing the model.
Then, we could bring some subset of the finished product in as an ASF
incubator project.  How does that sound?  I was really just wanting to
figure out if ASF would be willing to host a project such as this one. 


-----Original Message-----
From: Sanjiva Weerawarana [] 
Sent: Wednesday, June 08, 2005 7:19 PM
Subject: Re: Biological Object Model Project

IMO its a great idea (assuming nothing like that exists) but how can ASF
help you given that the incubator is meant to bring in existing projects
with working code rather than ideas?


On Tue, 2005-06-07 at 18:35 -0400, James Carman wrote:
> All,
> 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.  I
> currently work with a product called GKP (Genomics Knowledge Platform)
> a company called Xteric and it works fairly well, but it is not open
> It's tough to get grant money from the government for software development
> if you're using something that's proprietary and not open source.  You
> exactly tell a university that they have to spend $1M on a software
> if they wish to use it for research.  Anyway, what is needed in the
> Genomics/Bioinformatics world is a common, standardized, open source
> model for us to develop applications against.  I understand that I'm
> supposed to have a working codebase, but this is still a vision for me.
> However, if we started a project, I think we could get some real experts
> (bioinformaticians) to contribute and work towards developing a standard
> platform.  Any thoughts?
> James Carman

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