[Biococoa-dev] BioCocoa 2.1.0 release

Peter Schols sweetcocoa at mac.com
Sat Oct 4 14:28:39 EDT 2008

Hi Scott,

Congratulations, it's really great to see that BioCocoa is alive!
Best wishes,


On 04 Oct 2008, at 05:25, Scott Christley wrote:

> Greetings,
> A new release of BioCocoa is now available; download is available  
> from the BioCocoa website  Below is some news about what is  
> available.  If you feel all excited and want to broadcast this all  
> around, I ask to maybe consider holding off for the moment :-)
> Part of this is a run-through to document all the steps required to  
> make a release, this will help in making periodic consistent  
> releases in the future.  For that purpose, it would be much more  
> helpful if people downloaded and prodded it and send back any  
> comments.  There are some things definitely missing, most notably  
> example programs to show off the library, and who knows what else.   
> This will give me a chance to walk through the process a few times,  
> and hopefully we will have a true release soon!
> enjoy!
> Scott
> http://www.bioinformatics.org/biococoa/
> BioCocoa 2.1.0 -- (found in Tags / 2.1.0)
> - New BCSuffixArray and BCMCP classes for constructing disk-based  
> suffix arrays of sequences and finding the maximum common prefixes  
> of sequences using those suffix arrays.  This is work based upon the  
> following publication:
> 	Scott Christley, Neil F. Lobo and Greg Madey.
> 	Multiple Organism Algorithm for Finding Ultraconserved Elements.
> 	BMC Bioinformatics, 9: 15, 2008.
> - New BCCachedSequenceFile and BCCachedFastaFile classes that allow  
> for reading sequence data without reading the whole sequence into  
> memory.  This is useful for working with very large sequences like  
> whole genomes.  A future release will support a BCCachedSequence  
> which provides a consistent sequence interface regardless of whether  
> the sequence is in memory or cached on disk.
> - File format can be explictly provided to BCSequenceReader using  
> BCFileFormat.
> - Documentation updates.
> - More complete port to GNUstep, all BCFoundation functionality  
> should be available.
> - Quad-fat binary supporting 32/64-bit and ppc/intel processors.
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