[Biococoa-dev] biococoa svn and everything

Scott Christley schristley at mac.com
Wed Sep 19 15:32:02 EDT 2007

Hello Charles!

I'm not sure if I'm nominating myself to be project leader, seems a  
bit ambitious for somebody new to the community, but I certainly have  
the time and (most importantly) the desire to move BioCocoa forward.   
What I worry about mostly is not losing the ability to add new  
developers if and when they come along, I remember that I tried to  
send an email to Peter Schols from bioinformatics.org and it went  
into a black hole, I had to find another email to reach him.  He was  
responsive though (thanks Peter if you are out there) once I got the  
email right, but if he has moved on maybe it would be good to give  
some others admin access to the project?

You are exactly right that there are a lot of avenues that can be  
taken.  I keep thinking to myself that BioCocoa can differentiate  
itself by providing functionality not provided by the other packages  
like BioPerl and BioJava.  Not sure what a "killer" app would be, one  
thing that I think would be very cool though is a desktop genome  
browser (versus the web-based ones) which integrates all the genome  
information with analysis tools.

Has anybody thought about putting an article together and submit to  
Nucleic Acids Research journal?  Might be a good way to get a little  
awareness as well as have a solid reference that research articles  
can point to.


On Sep 13, 2007, at 12:48 PM, Charles Parnot wrote:

> Hi there!
> I was one of the people that did the "moving on" thing
> I think there is a pretty strong basis in the framework, at least  
> for the export/import tools, and then for the basics BCSequence  
> stuff. I did set up the initial test suite, which I think would  
> need to be updated and extended.
> When the project went into hibernation mode, the status was (at  
> least from my point of view):
> * in search of a project leader, that would have some basic amount  
> of time to make decision as to where to go, and do some coding too
> * needing a "killer" app to wrap the framework and put it to use.  
> This is the only way things would be tested in the real world by  
> real users. The killer app can be a simple sequence editor that  
> expose as much as possible of the underlying framework
> * a design decision has to be made to allow 2 aspects of the  
> framework to coexist: a core framework that provides the basic  
> functionality; an extension mechanisms that allows people to easily  
> contribute additional more specialized functionality (we had some  
> talks for instance with Phil Seibel about how the NSImage and  
> NSImageRepresentation design could inspire something. But really  
> more thoughts need to be put into that, and nothing has been  
> decided). The idea is that not everybody will be interested in the  
> specialized stuff, so having optional modules would be a good thing.
> * one of the feature that was in the works was to add annotation/ 
> feature to the basic BCSequence class
> so, a big roadmap, with lots of avenues ;-)
> And yes, if things start moving again, or a project leader self  
> nominates, that would certainly warrant a post on macresearch.  
> Hosting the project is also still a possibility, but that would  
> mean some additional work for the project leader too in setting  
> things up and maintaining it, as well as some kind of commitment  
> for a reasonable amount of time.
> charles
> On Sep 12, 2007, at 5:47 AM, Koen van der Drift wrote:
>>> Is the BioCocoa project still "alive"? Don't get me wrong, I've
>>> received the last mail from the mailing list in... may 2007! How  
>>> many
>>> people are involved?
>> I don't think the project was ever officially shut down, however,  
>> the people working on it about two years ago have moved on in  
>> their lives, and have no more time to actively work on the  
>> project. There were about 5 or 6 people actively involved. The  
>> current released version 2.0 is more or less a good starting point  
>> to use in apps, but there are also still many things unfinished or  
>> missing. So any input is more than welcome!
>> There was also some talk that macresearch.org would host the  
>> project (giving us a lot of visibility), but I have not heard  
>> about that in a long time.
>> - Koen.
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> https://bioinformatics.org/mailman/listinfo/biococoa-dev
> --
> Xgrid-at-Stanford
> Help science move fast forward:
> http://cmgm.stanford.edu/~cparnot/xgrid-stanford
> Charles Parnot
> charles.parnot at gmail.com

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