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
