Ola,

There are many ways to make a system modular.  One (but not only ) way is
OSGI .  As OSGI is a Java framework, we adopted different way to achieve
modularity in Opentox, which does not depend on particular language, and a
model might be implemented in any language and run anywhere in the internet,
not necessary on one single server.

Within a Java service, I agree with your suggestion (although for
performance and stability reasons I would prefer not  to allow dynamically
plugged modules on a production server ...).  In any way, we need to spend
more efforts on this.

Regards,
Nina

On 23 February 2011 23:46, Ola Spjuth <ola.spjuth at farmbio.uu.se> wrote:

> Nina,
>
> This is more a general question rather than to get something existing out.
> It would be nice to be able to as easy as possible set up OpenTox services
> in a plugin-fashion, without having to recompile a complete server instance
> each time. For our future projects and models this would be valuable, and my
> proposal is to do this as an extensible server-side solution based on a
> dynamic module system, such as OSGi. Users could then develop models as
> plugins, which could be dynamically linked at runtime to a running server
> instance.
>
> Cheers,
>
> /Ola
>
>
> On 22 feb 2011, at 07.46, Nina Jeliazkova wrote:
>
> > On 22 February 2011 08:43, Nina Jeliazkova <jeliazkova.nina at gmail.com>
> wrote:
> >> On 22 February 2011 00:05, Barry Hardy <barry.hardy at douglasconnect.com>
> wrote:
> >>> Was discussing this topic with Ola and we both agreed we should open it
> up
> >>> for discussion to OpenTox developers.  Your feedback to Ola very
> welcome!
> >>>
> >>> Barry
> >>>
> >>>
> >>> On 20 feb 2011, at 19.18, Barry Hardy wrote:
> >>>
> >>>>  Thanks Ola.
> >>>>
> >>>>  I had a thought/question - you/Egon made initial progress on getting
> >>>>  OpenTox services talking to Bioclipse client; what about the reverse
> >>>>  problem: what would be needed for data, algs, models in Bioclipse to
> >>>>  talk with OpenTox?
> >>>
> >>> Hi,
> >>>
> >>> Me and Lars at AZ thought about it too and agreed it would be nice
> project.
> >>> However I think it requires some work, but I don´t know the status of
> the
> >>> latest OpenTox frameworks for publishing models online. Are there any
> SDKs
> >>> available for this? The AMBIT server seems more a proof-of-concept than
> an
> >>> actual framework to use (needs to be recompiled for adding services).
> >>> ToxOtis is more for clients if I understand it correctly. Does it exist
> some
> >>> thing like SADI has for building services
> >>> (http://sadiframework.org/content/getting-involved/)? A plugin for
> Protege
> >>> or Java service skeleton would be very nice to have...?The best way
> would be
> >>> if it would be possible to drop services into a container (such as
> copying a
> >>> WAR file into tomcat) and the application server would set up the rest
> for
> >>> you. If nothing like this exist then I propose a solution based on OSGi
> for
> >>> dynamically adding models to a running server instance. Maybe you can
> >>> elaborate on the current status of things?
> >>>
> >>
> >> There is an initial implementation of such a skeleton at
> >>
> >>
> https://ambit.svn.sourceforge.net/svnroot/ambit/branches/opentox/opentox-demoserver
> >>
> >> Not completed though.
> >>
> >> If we decided this is a priority, it needs only few touches to be
> >> completed as a skeleton code.
> >>
> >
> > Could you tell if there are algorithms/models in Bioclipse ,
> > additional to those, available via CDK ?  For example , adding
> > anything that implements CDK IMolecular Descriptor interface in ambit
> > services is as easy as adding one configuration line with descriptor
> > class name.
> >
> > Same for all Weka machine learning models.
> >
> > Regards,
> > Nina
> >
> >> Regards,
> >> Nina
> >>
> >>> Cheers,
> >>>
> >>> /Ola
> >>>
> >>>
> >>>
> >>> _______________________________________________
> >>> Development mailing list
> >>> Development at opentox.org
> >>> http://www.opentox.org/mailman/listinfo/development
> >>>
> >>
>
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