[Biococoa-dev] biococoa svn and everything

Alexander Griekspoor mekentosj at gmail.com
Thu Oct 11 05:22:51 EDT 2007

Hi guys,

I just had a look "corebio" without capitals does the trick. Scott,  
it's great to see that someone is willing to pick things up again  
(and even has time for a change ;-). Like Peter I still hope to  
contribute again one day but it won't be anywhere soon. Still, if I  
can help out with small things let me know as well. Perhaps could we  
use the biococoa mailinglist again for questions and comments like  
these? That way we are all kept in the loop and we could jump in if  
time permits to help out with certain things.

On 11-okt-2007, at 9:50, Peter Schols wrote:

> Hi Scott,
> As I did not setup the Wiki myself (I think Koen did), I'm not sure  
> about the password (I'm sorry). It might be something like CoreBio,  
> but I'll put Koen and Alex in CC, maybe they still remember... ;-)
> best wishes,
> Peter
> On 10 Oct 2007, at 23:21, Scott Christley wrote:
>> Hello Peter,
>> Are you able to give me access to the wiki?  It appears to need a  
>> password for editing.
>> thanks
>> Scott
>> On Sep 21, 2007, at 3:57 AM, Peter Schols wrote:
>>> 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,
>>> Peter
>>> 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
>>>> _______________________________________________
>>>> Biococoa-dev mailing list
>>>> Biococoa-dev at bioinformatics.org
>>>> https://bioinformatics.org/mailman/listinfo/biococoa-dev

                ** Alexander Griekspoor  PhD **
		  EMBL Outstation - Hinxton,
          European Bioinformatics Institute,
		  Rebholz Textmining group

	  Wellcome Trust Genome Campus,
              Cambridge, CB10 1SD, UK
                    Tel:  + 44 1223 492 605
                   Fax:  + 44 1223 492 468
                  Web: http://www.mekentosj.com

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