[Biococoa-dev] project alive?

[Alexander K. Hudek]

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  
classes.

Regards,

Alex

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:
>
>> -----BEGIN PGP SIGNED MESSAGE-----
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>> 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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>> Biococoa-dev at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev

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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