biococoa at bioworxx.com
Fri Sep 22 05:01:30 EDT 2006
> 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?
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