[Biojava-dev] Microarray code

[Michael Heuer]

Hello David,

There is a wiki up at

> http://hume.ccgb.umn.edu:8668/space/BiojavaExpr

and a page on the MAGE wiki at

> https://www.cbil.upenn.edu/magewiki/index.php/MGED%20and%20biojava

to discuss gene expression support in biojava.  The former would probably
be a good place to document what you've built.

I have started committing to the subversion repository at

> http://www.derkholm.net/svn/repos/biojava-expr/

but to be honest the only thing there so far is a library for source code
generation.

I would suggest committing to a separate project in the subversion
repository then hopefully over time as I start committing more useful
bits to biojava-expr we can merge things there.

For what it's worth, the open-bio folks are open to creating a subversion
repository on the open-bio hardware as part of the new hardware migration
you may have recently received a notice about, so whatever gets committed
to derkholm.net should be easily migrate-able to open-bio hardware when
it is ready.

   michael


On Sun, 20 Feb 2005, David Huen wrote:

> Dear colleagues,
> I am now finalising a body of code that does microarray quantitation
> with an algorithm of my own and  also a program that simulates microarray
> images for pipeline validation.   As the code appears to work both on
> simulated and real-world data, I would like to publish it and and make a
> public alpha release soon.
>
> I would like it to become part of Biojava but committed under another
> hierarchy than org.biojava.* (I have my own stupidly snazzy name for it
> but hey, that's half the fun of doing code :-).  It shares almost nothing
> with the existing codebase.  It runs under Java 1.4 and uses JAI and some
> Jakarta code and the backported Java 5 synchronisation library.  Parts of
> it are also rather hacked to take data from our internal pipeline and will
> probably need work to make it suitable for other pipelines but as I don't
> know how others do this kind of thang, I would not even know where to
> start on that.  It will probably not work out of the box for you but could
> be beaten into shape in a week or two of hacking and scripting.
>
> Could I have a decision on your willingness to host this codebase
> post-publication?
>
> Regards,
> David Huen
>
> -----
>
> David Huen, Ph.D.              Email: smh1008 at cus.cam.ac.uk
> Dept. of Genetics              Fax  : +44 1223 333992
> University of Cambridge        Phone: +44 1223 766748/333982
> Cambridge, CB2 3EH
> U.K.
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