[Biojava-l] Running apps with Java

Schreiber, Mark mark.schreiber at agresearch.co.nz
Mon Aug 11 12:59:46 EDT 2003

Hi -

I know this has come up a few times on the list but I'm not sure we have
ever come to any agreement on it so I'm going to raise it again as I
think it is important.

What is the best way to invoke a native bioinformatics program in Java.
People have reported that controlling processes directly has been patchy
in Java, is this still the case or have JVMs evolved? If not then what
is the alternative? Wrapping the program in a perl or python webservice?
If this was the prefered method then we could borrow quite a bit from
the Bio::Pipeline::Runnable package.

Ultimately the reason for asking is that J2EE (particularly the message
driven beans) would make for a pretty good pipelining system (drawing on
all its inherent transaction control, roll back etc). My expectation
would be that biojava could exist server side to provide parsing support
and possibly connection to BioSQL although J2EE could also do that
without biojava. It would also be useful in local EJBs (no serialization
slowdown) to do some manipulation of sequence data. The only missing
component is some kind of BioRunnable that could reliably kick off the
jobs and capture the output for parsing with the biojava parsers.

Any thoughts?

- Mark

Mark Schreiber PhD
AgResearch Joint Bioinformatics Institute
School of Biological Sciences
Universtity of Auckland
3a Symonds St
Private Bag 92-019 Auckland New Zealand
PH:   +64 9 3737599 ext 84290
FAX:  +64 9 3737414

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