[Biococoa-dev] [BiO Mail] BioCocoa, Leopard etc

[Alexander Griekspoor]

Hi Peter,

Unfortunately the BioCocoa project is no longer (very) active due to a  
lack of time and to some extent need by the core developers. That  
doesn't mean it's completely dead but what is missing is one or two  
people who very actively like to push the project forward and which  
have a need for a BioCocoa framework and the time to develop it. So  
for instance it's indeed not pushed forward to 10.5, but you should be  
easily able to checkout the project change the target SDK to 10.4 or  
10.5 in XCode.

I don't know what formats Vector NTI support, and what it is you wish  
to convert exactly. We have a simple GCK read method but it only takes  
the sequence (not the vector map). Since the GCK file format is closed  
(and binary) it won't be easy to get all data out that you might wish,  
unless you're only interested in the raw sequence.

If you are still interested Koen should probably be able to help you  
out with the CVS issue.

Finally, regarding 4Peaks and contigs, we'd love to do that one day if  
time permits, we'll do our best.
Best wishes,
Alex & Tom
Mek & Tosj

On 26 jan 2008, at 16:57, Peter Ulvskov wrote:

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> The sender is user Peter Ulvskov <p.ulvskov at dias.kvl.dk>.
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> >.
> ----------------------------------------------------------------------------
> Dear Alexander,
>
> I hope that you can spare the time for a few questions:
>
> I have signed up at bioinformatics.org because of BioCocoa. My new
> username/password works fine for login, but I am rejected when I do  
> this:
> export CVSROOT=':ext:Ulvskov at bioinformatics.org:/cvsroot'
> cvs checkout BioCocoa -P
> ...and enter my password
> Does it take more than signing up at bioinformatics.org to download
> BioCocoa?
>
> I then did the download manually, and got the 10.3.9 SDK error,  
> which raises
> the question whether BioCocoa is an active project? Are efforts  
> being made at
> moving BioCocoa forward to 10.5? What does it entail changing the  
> SDK to
> Leopard (in other words, can I do this myself)?
>
> Finally, the problem I wanted to solve using BioCocoa is writing a  
> file
> conversion utility which will convert Gene Construction Kit files to  
> Vector NTI
> files. Is it correct that BioCocoa will help me get there?
>
> By the way, one of the reasons why Vector NTI is making its way into  
> the lab
> (under Windows XP (ouch!) on our Intel Macs) is the need for a contig
> assembly program. Judging from your FAQ-page at Mekentosj, this is  
> one of
> the most frequently requested features for 4Peaks. Any chance that  
> you will
> be swayed by the prayers?
>
> Thanks for your time, best regards,
>
> Peter
>
> (My Bioinformatics.Org username is Ulvskov.)
>
>
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**********************************************
          ** Alexander Griekspoor  PhD **
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           mekentosj.com

            EnzymeX - To cut or not to cut
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