Just looking a little further into Oliver's issue, the following may
Effectively, it seems that we could use the Java Help example and do
something similar for versions of libsbml. So, if I was to create a
Java web start application using libsbml, I could write something
similar to the following in my jnlp doc...
<extension name="libsbml3_3_1" href="http://www.sbml.org/jws/3_3_1/libsbml.jnlp
So, I would be downloading the appropriate version of libsbml from
sbml.org, where the contents of libsbml.jnlp would look a little like
<?xml version="1.0" encoding="utf-8"?>
<jnlp spec="1.0+" codebase="http://www.sbml.org/jws/3_3_1"
<resources os="Mac OS X">
The production of libsbml.jnlp and the appropriate three jar files
would only have to be done once per release of libsbml, and then all
of us can deploy our stuff using Java Web Start with the minimum of
Obviously this is pseudo code, and issues would arise from this. But
I'd guess that less issues would arise from this than from duplicating
the entire libsbml effort to produce a pure Java version.
Manchester Centre for Integrative Systems Biology
Manchester Interdisciplinary Biocentre
University of Manchester
Manchester M1 7DN
On 19 May 2009, at 00:25, Oliver Ruebenacker wrote:
> Hello Mike, All,
> Users click on a link on our website and Java Webstart selects the
> appropriate binary among three options: Windows, Mac and Linux.
> We have a person responsible for deployment (Fei Gao) who has been
> doing this for years and I am assuming she is on top of it.
> Meanwhile, I developed a stand-alone application (SyBiL) that uses
> libSBML and deployed it myself on our website, also using Java
> Webstart. You need to have binaries for Win, Mac and Linux in the same
> version you use for development. If the application needs access to
> the file system (ours do), all JAR files need to be signed.
> In principle, it is not hard to do. In practical terms, it can be
> painful, because you either redeploy (upload to webspace and download
> again with your browser) all files together, which can take time if
> your application is large, or you try to redeploy only the files that
> need updating and easily pick the wrong ones. If you fail to suppress
> caching, this can create artificial version conflicts and other
> irreproducible behaviour.
> Of course, if you are willing to invest the work, you can do things
> like set up a local webspace on the same computer you use for
> development, or set up some clever automatation.
> And, of course, this requires that three binaries are enough to
> cover all users you intend to have, and that you have the means to
> test deployment of every one of them. Maybe true these days, but who
> knows how that will be in the future.
> Take care
> On Mon, May 18, 2009 at 6:13 PM, Michael Hucka <firstname.lastname@example.org>
>> So, here's a question for you. The Virtual Cell group has
>> (I imagine) one of the biggest Java code bases -- so what
>> happens now, with the current native binary version of
>> libSBML? How much trouble has it been to use in VCell?
>>>>>>> On 18 May 2009, Oliver Ruebenacker <email@example.com> wrote:
>> curoli> Have you ever tried to deploy across different
>> curoli> platforms?
>> curoli> A pure Java version can easily be deployed across
>> curoli> platforms without change (ideally). However, if
>> curoli> you depend on binaries, you need to provide
>> curoli> different ones for each platform. If a system
>> curoli> already has the binary installed but in a version
>> curoli> incompatible with your software, then you have a
>> curoli> problem. You can still run it in a cage such as
>> curoli> with Java Webstart, but that is infinitely harder
>> curoli> to deploy and debug than just putting a pure Java
>> curoli> application in a JAR for download.
>> curoli> The JNI approach also prevents you from avoiding
>> curoli> redundancies, for example, libSBML needs native
>> curoli> XML support, and your application may need Java
>> curoli> XML support in addition to that.
>> curoli> Take care Oliver
>> To manage your libsbml-development list subscription, visit
>> For a web interface to the libsbml-development mailing list, visit
>> For questions or feedback about the libsbml-development list,
>> contact firstname.lastname@example.org
> Oliver Ruebenacker, Computational Cell Biologist
> BioPAX Integration at Virtual Cell (http://vcell.org/biopax)
> Center for Cell Analysis and Modeling
> To manage your libsbml-development list subscription, visit
> For a web interface to the libsbml-development mailing list, visit
> For questions or feedback about the libsbml-development list,
> contact email@example.com
To manage your libsbml-development list subscription, visit
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