[Biococoa-dev] project alive?

Scott Christley schristley at mac.com
Mon Sep 22 17:07:16 EDT 2008

Hello Alex,

Yes, the project is still alive; however, many of the original  
developers have moved on to other things (though they might still be  
lurking on the list), so there is not much active development.  I've  
been putting in code related to my research, e.g. suffix arrays, plus  
I have a bunch of local modifications dealing with managing gene  
expression data.  I've recently tried getting the documentation in  

I haven't used BCSequenceAlignment but from looking at the code, it  
doesn't look like much is there.  Duplicating existing work on  
sequence alignment is probably not the best use of resources, better  
to add wrapper and handlers to BioCocoa for other tools.

By alignment visualization, do you mean something like JalView which  
gives a graphical output of CLUSTAL?

I'm happy to take any of your changes and merge them back into the  


On Sep 22, 2008, at 1:47 PM, Alexander K. Hudek wrote:

> Hash: SHA1
> I'm playing around with BioCocoa for an alignment visualization
> application. It appears the project is no longer under active
> development? Is there still interesting in continuing development? I'm
> very new to Objective-C and Cocoa, but I'm not opposed to helping out.
> I've already had to modify the sequence reader class to allow it to
> read sequences with gap characters, although I'm not sure if this was
> the intended use of SequenceReader. Also, it looks like
> BCSequenceAlignment is very far from being finished. Is this correct?
> Regards,
> Alex
> Alexander K. Hudek
> School of Computer Science, University of Waterloo
> 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada
> Phone: +1 519 888 4567 x37886  Fax: +1 519 885 1208
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