[Biococoa-dev] biococoa svn and everything

Peter Schols sweetcocoa at mac.com
Fri Sep 21 03:57:36 EDT 2007

Hi Scott,

Great to see the BioCocoa project being alive again!
I would be happy to share admin access or give it to someone else

While I'm quite busy with Undercover these days (and with a new  
microscopy app we are developing), I'm still very interested in  
BioCocoa and my (probably naive) dream is that I will become an  
active member again in the future. So while I don't have time to  
contribute code to the project at this time, I'd be very interested  
in helping out with smaller things and with spreading the word. I  
think the NAR article is a great idea, btw.

best wishes,


On 19 Sep 2007, at 21:32, Scott Christley wrote:

> 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.
> cheers
> Scott
> 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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