[Biococoa-dev] BioCocoa 2.1.0 release

Alexander Griekspoor mekentosj at gmail.com
Sat Oct 4 05:17:58 EDT 2008

Awesome work, well done.

On Sat, Oct 4, 2008 at 4:25 AM, Scott Christley <schristley at mac.com> 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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         ** Alexander Griekspoor  PhD **

 Papers - Your Personal Library of Science
 2007 Winner of the Apple Design Awards
         Best Mac OS X Scientific Solution

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