[Biojava-l] Running apps with Java

Tue Aug 12 22:48:48 EDT 2003

Running on a remote machine (ie where the service is located by something like JNDI) might be best left to something like J2EE message driven beans or something similar. For good old biojava we should probably focus (at first) on local. After all once the local running service is working it can be made available in a client that is registered on JNDI, the client could be local or remote. Getting serious JNDI dependencies in biojava might be a bit heacy (at least for 1.4).

- mark

	-----Original Message----- 
	From: Francois Pepin [mailto:fpepin at cs.mcgill.ca] 
	Sent: Tue 12/08/2003 4:47 a.m. 
	To: Tom Oinn 
	Cc: biojava-l 
	Subject: Re: [Biojava-l] Running apps with Java

	What do other people think about something like that?

	We've basically got 2 problems here, running apps on the same machine
	and running them on a remote machine.

	If you can run apps on a remote machine, then you can obviously run them
	on the local machine. But the machinery to do that is often pretty heavy
	(as compared to just calling the command line).

	I'm not sure if I'd want to have to depend on that machinery just
	because I want to my dingy little application to call blast once.

	I personally think that both problems should be handled independently.

	If you're calling remote machines, you're often in heavy computation
	land, so you need something robust and that can support a workflow
	system. You don't care if you have to install 3 applications on the
	server and a client on all of the machines.

	If you're calling a local application, you usually just want to do light
	stuff and be done with it. You've got a JVM and your executable and you
	don't want to have to install anything else in there.

	At this point we're basically been using the following:
	-BioOpera for the heavy computations
	(http://www.inf.ethz.ch/personal/bausch/bioopera/main.html)
	-Nasty java for the command line (creates a shell script and deletes it
	later)
	-We also have an ssh implementation of Java for remote command-line
	execution. It's useful to call Linux apps from Windows. But it's based
	on the MindTerm code which isn't licensed for commercial use (and
	conflicts with the LGPL).

	I think that biojava should have a nice way to calling local apps, and
	leave the heavy-duty stuff to someone else (and then get a client to
	call that someone else).

	Francois

	On Mon, 2003-08-11 at 11:26, Tom Oinn wrote:
	> 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...
	>
	> http://industry.ebi.ac.uk/soaplab/
	> http://taverna.sf.net
	> http://freefluo.sf.net
	>
	> 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.
	>
	> Cheers,
	>
	> 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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