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
>>> 
>>> 
>>> 
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>>