[Biococoa-dev] Introducing myself

Scott Christley schristley at mac.com
Mon Feb 23 02:16:25 EST 2009

Hello Craig,

The coding I've been doing lately is primarily related to the research  
I'm doing, so from this sense it doesn't necessarily go fast.  My long- 
term goal is to add some advanced analysis techniques into BioCocoa.

One of the key things I would like to do is make the sequence and  
cached sequence class correspond in their interface.  The cached  
sequence class is important to do large scale analysis on large  
genomes, because they are too big to load completely into memory.   
This is something that BioCocoa can offer above other toolkits like  
BioPerl and BioPython, high performance and large scale analysis.

What interests you about genetics?  Much of the algorithms in  
genetics, bioinformatics and so on are still being developed, even  
things like assembly of genomes is not a "done" technology.  If you  
have a  specific interest area, then I can help lay out a series of  
tasks that would be both highly useful and be interesting algorithmic  

Koen is right, the todo list is still accurate, and those are  
certainly useful enhancements to make.  And the creation of a "killer  
app" is definitely desired, especially to bring these advanced  
analysis techniques together into an easy-to-use GUI and/or command  
line applications that biologists can use.


On Feb 21, 2009, at 12:43 PM, Craig Bateman wrote:

> I'm an experienced software engineer looking for an open source mac  
> project to contribute to, and I'm recently very interested in  
> genetics.  So BioCocoa seemed an obvious choice.
> I looked at the To Do list, and fear that 2+ years later it must be  
> out of date unless there's just nobody left working on this  
> project.  Is it officially dead?  There hasn't been a lot of  
> movement on this list in the past few months since the 2.1.0 "non"- 
> release.  I've checked out the source and will start digging now to  
> get a feel for what's here and how it works.  What/where are the  
> primary missing pieces? Has all the 1.x functionality been  
> incorporated to 2.1?  Is anything on the todo list still up for  
> doing?  Should I be looking at the framework itself or the  
> applications?
> Anyway, to whoever is still alive on this project, let me know how  
> and where I can help and I'll be glad to.
> Thanks,
> Craig Bateman
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> Biococoa-dev at bioinformatics.org
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