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
======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
_______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
_______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
