[Biojava-l] Running apps with Java

Tom Oinn tmo at ebi.ac.uk
Mon Aug 11 17:26:24 EDT 2003

Hi there,

Apologies for the slight plug, but at the EBI we've been working on 
something that might be of interest to people trying to do this. We have 
a system called Soaplab that can be used to expose command line tools as 
web services (trivial to then consume) and another project Taverna which 
focuses on workflow construction and execution using FreeFluo (open 
source workflow enactor written by some of our collaborators at 
Southampton). The URLs for these are...


As an example, we have all of EMBOSS in this system here and can build 
complex workflows (we're using it for work on genetic disease in 
collaboration with some biologists in Newcastle University), there's a 
graphical workflow construction environment, it's all pretty much there. 
Ongoing work of course (aren't they always?) but usable in its current 
form. Anyway, sorry if this is off topic too much, we are actually 
planning to contribute parts of Soaplab's clients into BioJava in the 
same way as we have for BioPerl, and similarly so for the workflow 
engine if that's desirable.


Tom Oinn (work above is by Martin Senger, myself and the rest of the 
Taverna project team), I've cc'd Martin on this email, he's the author 
of Soaplab.

Schreiber, Mark wrote:
> 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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