Hi, This sounds great! The Bioclipse project [1,2] is in the final phase towards releasing Bioclipse 2.0 and is using Equinox + Spring-DM [3]. Although it has not been a trivial path towards setting things up, we have now a powerful scriptable core (based on Javascript) and enjoy the features of OSGI and Spring.
As integration is a key issue for us we are very happy that both Taverna and Cytoscape are working in the same direction. If we can be of any assistance, just drop a note on the bioclipse-devel mailing list [4]. Cheers, Ola Spjuth Bioclipse coordinator [1] http://www.bioclipse.net/ [2] http://bioclipse.blogspot.com [3] http://wiki.bioclipse.net/index.php?title=Architecture [4] https://sourceforge.net/mail/?group_id=150681 On 30 maj 2009, at 02.29, Keiichiro Ono wrote: > Hi. > > This is a great news for us. Currently we are porting our software > (Cytoscape) to OSGi + Spring-DM framework: > > http://www.cytoscape.org/cgi-bin/moin.cgi/Cytoscape_3.0/Developer > > and if Taverna uses the same framework, it makes everything much > easier. One of our future plan is more sophisticated integration of > web services, including workflow support. We do not want to develop > everything from scratch, so we want to integrate it into our system. > However, since there are some overlap between Raven and OSGi based > package manager (we use custom version of Equinox P2), we do not know > how to handle this problem for now. But if both projects uses > OSGi+Spring DM, integration is much simpler. > > Thanks. > Kei > (Cytoscape Core Developer Team) > > > 2009/5/29 Stian Soiland-Reyes <[email protected]>: >> Hi! >> >> Taverna 2.x and the Taverna Platform (the API on which the Taverna >> Server is based) are currently two separate pieces of software. >> >> The Taverna Platform [1] is a branch of the code-base of the workflow >> engine (t2core), which has not yet been integrated into the Taverna >> Workbench 2.x (the graphical interface for designing and running >> workflows). The main reason for this has been that we wanted to >> mature >> the Platform and try it in other projects before committing to use it >> from the Workbench. >> >> The primary motivation for building the Taverna Platform was to >> make it >> easier to use Taverna code from other software, and to make it >> easier to >> extend Taverna. Additionally we wanted to solve some of the issues we >> and third party developers have had with classloaders and our plugin >> system Raven. Raven has been used by Taverna since Taverna 1.5 up >> to and >> including 2.0. >> >> The platform replaces the old Raven system (which was very closely >> related to Maven) with a new plugin-based solution (Raven 2) which >> makes >> the classloaders behave more like in a normal Java program, while >> keeping the separation between individual plugins. This means that in >> the Platform it would not be a problem if different activity/service >> implementations co-exists and depend on different/conflicting >> versions >> of dependencies such as Axis or JAXB. There are however industry >> standard ways to do this. >> >> As part of the Platform work, some of the APIs of the core workflow >> libraries had to be modified. As the platform is a fair amount of new >> work, introduces a new plugin/discovery system, and in addition had >> some >> unfinished pieces (such as activity implementations), we could not >> yet >> commit to moving the Taverna workbench to use the Taverna platform. >> >> After the release of Taverna workbench 2.0 important additional >> work for >> the graphical user interface was identified. We therefore started >> the >> user interface-centric work towards the upcoming Taverna workbench >> 2.1, >> but based on the pre-platform branch of t2core and Raven, which are >> largely unchanged since Taverna 2.0. >> >> The main new features of the 2.1 workbench will be GUI enhancements >> for >> service discovery, workflow editing, workflow invocation, reduced >> memory >> footprint (supporting larger data values) and support for >> provenance/intermediate values. Taverna Workbench 2.1 Beta 1 >> release is >> imminent. >> >> We have now had time to evaluate the Platform in projects and done a >> review of the codebase. One of these projects using the Platform is >> the >> Taverna Server, which allows remote execution of Taverna 2 workflows >> through a RESTful interface (in the same way as the Taverna Remote >> Execution Service did for Taverna 1). A beta version of Taverna >> Server >> will be released in June, and is currently used by the Shared >> Genomics >> project. >> >> This upcoming Taverna Server is built upon the second beta version of >> the platform (p0.1b2) , which we will also release during this >> summer. >> The work remaining for doing this release of the Platform is mainly >> to >> update the documentation, examples, JavaDocs and Maven archetypes >> to use >> the new versions. This version of the platform completes support for >> activity types like BioMoby, Soaplab and nested workflows. >> >> The platform has also successfully been used by a student to build a >> prototype portlet for executing workflows. >> >> Based upon this combined experience, we are planning to continue >> maintaining the majority of the Platform, e.g. the Platform API, >> although some minor modification might become necessary for later >> versions, such as for plugin definitions. >> >> We have however identified that some of the back-end components of >> the >> Platform would require extensive future maintenance from the project >> team. Our main goal is to continue to provide Taverna as a top class >> workflow environment, and we can't really justify spending too much >> developer time on maintaining bespoke code for which industry >> standard >> efforts could be used. >> >> An example of this is the Raven 2 plugin system which could be >> replaced >> by a standard system that would thus be less onerous to support. This >> approach would also offer a better sustainability path for the >> project. >> >> Thus the long-term plan if for us to replace the Platform Plugin >> system >> (Raven 2) with Spring Dynamic Modules [2] which uses OSGi [3] >> (which is >> used famously in Eclipse [4]). >> >> We have not yet decided on which OSGi implementation we will go >> for, but >> they do seem to be quite interchangeable (Eclipse Equinox, >> Knopflerfish, >> Apache Felix). Moving to OSGi would require additional >> modifications to >> the core and the workbench. >> >> This change to the Platform vs. using Raven 2 would take additional >> time >> and may impact plugin providers who are using the current Platform >> system, but we think that in the long run from a support and >> compliance >> perspective this is the right decision for the project. >> >> Your comments on this strategy are most appreciated and expected. >> >> Best Regards, >> The myGrid Taverna Team. >> >> >> >> >> [1] http://www.mygrid.org.uk/tools/developer-information/taverna-platform/ >> [2] http://www.springsource.org/osgi >> [3] http://www.osgi.org/ >> [4] http://www.eclipse.org/equinox/ >> >> >> -- >> Stian Soiland-Reyes, myGrid team >> School of Computer Science >> The University of Manchester >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity >> professionals. Meet >> the minds behind Google Creative Lab, Visual Complexity, >> Processing, & >> iPhoneDevCamp as they present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com >> _______________________________________________ >> taverna-hackers mailing list >> [email protected] >> Web site: http://www.taverna.org.uk >> Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ >> Developers Guide: http://www.mygrid.org.uk/tools/developer- >> information >> > > > > -- > Keiichiro Ono [email protected] > > Cytoscape Core Developer Team: http://www.cytoscape.org/ > UCSD Bioengineering Ideker Lab: http://chianti.ucsd.edu/idekerlab/ > > ------------------------------------------------------------------------------ > Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT > is a gathering of tech-side developers & brand creativity > professionals. Meet > the minds behind Google Creative Lab, Visual Complexity, Processing, & > iPhoneDevCamp as they present alongside digital heavyweights like > Barbarian > Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com > _______________________________________________ > taverna-hackers mailing list > [email protected] > Web site: http://www.taverna.org.uk > Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ > Developers Guide: http://www.mygrid.org.uk/tools/developer-information ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ taverna-hackers mailing list [email protected] Web site: http://www.taverna.org.uk Mailing lists: http://www.taverna.org.uk/taverna-mailing-lists/ Developers Guide: http://www.mygrid.org.uk/tools/developer-information
