[Biococoa-dev] Fwd: Introducing myself

Craig Bateman craig at batemanspace.com
Tue Feb 24 17:31:23 EST 2009

I accidently dropped the list in my reply, so Scott was the only one that
got it.

---------- Forwarded message ----------
From: Craig Bateman <craig at batemanspace.com>
Date: Mon, Feb 23, 2009 at 2:01 AM
Subject: Re: [Biococoa-dev] Introducing myself
To: Scott Christley <schristley at mac.com>

Well, unfortunately I can't state what, in particular interests me about
genetics, mostly because I know so little.  I read the blind watchmaker and
was intrigued by the author's explanation of how genes work, and since then
have read other books about the human genome and the effects of certain
genes on human development, etc.  I guess I'm just vaguely interested in
genetics research because I want to know.  I certainly can't state that I'm
interested in any one sub-topic over any other.  In short, I've barely
scratched the surface, and want to learn so much more...

I am, however, an avid programmer, and was hoping that my vague interest in
the domain of genetics coupled with my years of writing software (banking
analysis software, but software all the same) would combine to provide a
great developer resource for the project.

As far as a "killer app" goes, I couldn't even guess what something like
that would look like for BioCocoa...  If you have some ideas I can certainly
bring something to light, but honestly I haven't a clue about how any of
this sequence information is actually used and/or what features in such an
app would be useful.

Unifying the BC*Sequence classes is a good idea, maybe I'll look at that
first as a tooth-cutting exercise.  Aside from that, I read a bit about
"shotgun" sequencing, which may not be what it's actually called, but where
overlapping bits of a sequence are used to assemble an entire sequence.

So I've got a lot to learn, but anything I can contribute to this project or
genetics/proteins/cancer/whatever research in general is a win in my book.

On Feb 22, 2009, at 11:16 PM, Scott Christley wrote:

 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 work.
> 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.
> cheers
> Scott
> 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
>> _______________________________________________
>> Biococoa-dev mailing list
>> Biococoa-dev at bioinformatics.org
>> http://www.bioinformatics.org/mailman/listinfo/biococoa-dev
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