[BioC] MAGE-ML reading

Vincent Carey 525-2265 stvjc at channing.harvard.edu
Fri Apr 1 22:34:15 CEST 2005

> I would like to read MAGE-ML, but I have not been able to get SJava to
> install on MacOS.  Are there other options to read MAGE-ML besides
> RMAGEML (which requires SJava)?

There is a version of SJava that ports to Mac OSX.  It is made
available by Simon Urbanek


I have not tried it with R 2.0.1.  This version of SJava
lacks some important features of SJava_0.67-3 which is known
to work with RMAGEML.  You may have to modify the RMAGEML
source a bit to get it to install with this old version of
SJava -- you may have to relax the SJava version dependency.
And this may lead to problems.  But I think it is worth a

You could parse and process the MAGE-ML using the XML package.
If you had a clear and fairly restricted set of elements that you
needed to grab, this might be very effective.

The nice thing about RMAGEML is that it can in principle
reflect anything in the MAGE-OM as captured by the java MAGEstk.
RMAGEML has the resources to translate elements of MAGE-OM directly
into elements of marray class instances.

There is also a perl MAGEstk, I believe.  One might get an
interface through RSPerl.

Please keep us informed of successes and failures in using
MAGEML documents with Bioconductor.

> Thanks,
> Sean
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