[Biococoa-dev] biococoa svn and everything

Scott Christley schristley at mac.com
Wed Sep 12 16:35:50 EDT 2007

That's the great thing about open source projects, they can sleep for  
awhile then wake up!  :-)

I'm currently in the process of integrating code for a paper I  
submitted to BMC Bioinformatics journal for finding ultraconserved  
elements; I've been making changes so that the code is more flexible  
and can be used for other analysis.  The pieces I'm putting in are:

BCCachedSequenceFile, some classes for handling very large sequence  
files, i.e. whole genomes, by not reading in the whole sequence into  
memory, but cache meta-data then read from the sequence file when  
sequence data is needed.

BCSuffixArray, implements a suffix array data structure, a memory  
efficient structure that allows for string matching operations.

BCMCP, this uses BCSuffixArray and BCCachedSequenceFile to perform  
the ultraconserved analysis which is essentially looking for longest  
common substrings across the whole genome for multiple organisms.

I have some gene expression related classes that I worked on a few  
months ago; some utility stuff like downloading data from NCBI GEO  
and parsing the SOFT file format, but I need to clean it up before  
committing it.  I'm not exactly sure where I'm going with this as it  
seems that R/Bioconductor is the main toolkit to use for statistical  
analysis of gene expression.

One of my interests is whole genome comparative analysis, so I intend  
to keep using BioCocoa and adding code to it; hopefully others find  
it useful!


On Sep 12, 2007, at 8:47 AM, Koen van der Drift wrote:

>> Is the BioCocoa project still "alive"? Don't get me wrong, I've
>> received the last mail from the mailing list in... may 2007! How many
>> people are involved?
> I don't think the project was ever officially shut down, however,  
> the people working on it about two years ago have moved on in their  
> lives, and have no more time to actively work on the project. There  
> were about 5 or 6 people actively involved. The current released  
> version 2.0 is more or less a good starting point to use in apps,  
> but there are also still many things unfinished or missing. So any  
> input is more than welcome!
> There was also some talk that macresearch.org would host the  
> project (giving us a lot of visibility), but I have not heard about  
> that in a long time.
> - Koen.
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