[Biococoa-dev] Greetings

Philipp Seibel biococoa at bioworxx.com
Fri Sep 22 05:01:30 EDT 2006

Hey Scott,
> 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!

Nice to hear, contributions are welcome of course:-).

> 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.

Sounds interesting, in my opinion it would make sense to make as much  
as possible GNUstep compatible.

> 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.

So i'm thinking of building a RNA Framework for BioCocoa so i think  
it would make sense if you could make a Microarray framework  
containing your code. So organizing code for different bioinformatic  
areas in different frameworks would be a good solution, i think. Like  
eg. the apple quartz.framework.

> 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.

I think it sounds promising :-). Btw. do you have support for MAGE-ML?



More information about the Biococoa-dev mailing list