[Biococoa-dev] project alive?

Koen van der Drift kvddrift at earthlink.net
Tue Sep 23 14:08:10 EDT 2008

Hi Alex,

A slick sequence alignment tool would be the "Killer App" for BioCocoa! It would be great if you were able to use the framework for that. Annotations are still in an immature stage so that would need attention as well. As with some of the other original developers, I am also unable to spent much time on BioCocoa, but a fresh injection may change that.

Welcome to the team, and if you'd like you can join the LinkedIn group.

- Koen.

-----Original Message-----
>From: "Alexander K. Hudek" <akhudek at cs.uwaterloo.ca>
>Sent: Sep 22, 2008 6:47 PM
>To: Scott Christley <schristley at mac.com>
>Cc: biococoa-dev at bioinformatics.org
>Subject: Re: [Biococoa-dev] project alive?
>I'm initially working on a slightly more flexible version of the Vista  
>alignment tool (or similarly the SinicView tool) while I wait for  
>research results to compute. This is in part to learn Cocoa  
>programming and in part because I find both tools to be very clumsy  
>and lacking in their ability to easily add custom annotation tracks.  
>Ultimately, I'd like an easy to extend platform for both evaluating  
>alignments and visualizing them in various ways. Too many of these  
>sorts of tools are extremely customized to one particular data source.
>It isn't a major priority for me, but I figure that it's better to  
>build functionality into a tool like this rather than create one shot  
>command line tools as I've currently been doing. If I get somewhere  
>useful with this, I'll be sure to send back changes and relevant  
>On 2008-09-22, at 5:07 PM, Scott Christley wrote:
>> 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 order.
>> 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  
>> source.
>> cheers
>> Scott
>> 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
>>> Version: GnuPG v1.4.8 (Darwin)
>>> QHIAn2CmkZqifAaUIX3wZ0RO0wg3maRr
>>> =utoz
>>> -----END PGP SIGNATURE-----
>>> _______________________________________________
>>> Biococoa-dev mailing list
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>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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