[Biococoa-dev] Greetings

Scott Christley schristley at mac.com
Thu Sep 21 17:49:49 EDT 2006

Hello all,

I first became aware of BioCocoa at the 2005 WWDC, at the time I was  
just starting to get involved in biology simulations and  
bioinformatics with my PhD; now that I'm deep in it, I would like to  
contribute code I've developed.  I wasn't able to make it to the  
recent WWDC, but congratulations to the EnzymeX guys!

One thing I am interested in is GNUstep support.  From looking at the  
archives, I may be opening a can of worms but onward I go.  Why I am  
interested in GNUstep is because I use both platforms.  Specifically  
my Mac tends to be my development platform and for visualization, but  
when I kick off a bunch of simulations or do some heavy computation,  
I pass it over to the computer cluster which tends to be 64bit  
Opteron processors running Linux, so I use GNUstep there.

My understanding from reading the mailing list archives is that  
optimizations to use CoreFoundation is what killed GNUstep  
compatibility.  Are people still interested in this, if I were to  
tackle this issue, supporting both platforms in a clean way and  
maintaining the compatibility?  From looking at the code, I think  
many of the differences can be handled with careful macros, keeping  
CoreFoundation speed on Mac but OpenStep code for GNUstep.

As for BioCocoa itself, with some of the work I've been doing I've  
been writing various parsers as well as playing around with some  
ideas, and I've thought well if I do all this work it would be nice  
to make it available.  I could just start my own project, but maybe  
it would be good to add this into BioCocoa.  Anyways, these are the  
ideas I'm thinking:

* Gene expression data, currently Affymextric data sets that can be  
gotten from GEO.  Parser to load in the data, form links with  
ontology, genes, etc.

* Ontologies, I have a plain parser for OBO which seems to be  
becoming a standard format.  There is also the OWL variants which is  
semi-handled by XML parsing.

* Web Services, I've mainly been playing around with web services  
provided by NCBI, EBI, and KEGG.

This all falls under the general idea of integration of multiple data  
sources for doing bioinformatic analysis and simulations.  I have  
some other ideas as well but this is a good start.

Let me know what you think.


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