The Taverna Team are pleased to announce the release of the first in the line of the new Taverna 2 Server series – Taverna 2 Server Release 1.

Taverna Server manages the running of workflows, making the results of workflow runs available to users, tools, web pages and portals.  The Server can be installed locally or remotely from where it is used.

Taverna 2 Server Release 1 features:

* Runs Taverna 2 workflows
* Calls the Taverna Command Line 2.2.0
* Has both REST and SOAP interfaces
* All functionality available through both interfaces
* Manages files for workflows
* Make files, read files, delete files
* Create subdirectories, list directory contents
* Can download a whole directory structure as a single ZIP archive
* Tidies up when workflow runs expire
* Expiry time fully configurable
* Can force immediate deletion of a workflow run

Taverna 2 Server Release 1 currently only runs on Linux and Mac OS. If you wish to run Taverna 2 Server Release 1 on a Windows or other
operating system, then you should install it as a virtual machine (see below).

Taverna 2 Server Release 1 can, of course, be accessed by clients using other operating systems, such as Windows.

Taverna 2 Web Demonstrator Client Interface

The Taverna 2 Web Demonstrator client interface is an small example of how Web pages can run workflows on a Taverna 2 Server.  Although it is not intended to be a fully-functional robust Web interface to the Server, it does expose some of the Server’s capabilities. The Demonstrator uses a Ruby gem for accessing the Server’s REST interface.

Taverna 2 Ruby gem

The DataViewer Tool 2.2.0 is the updated version of the older DataViewer Tool that used to be shipped together with the Taverna Workbench 1.x. It has now been updated to use of the Taverna 2.x codebase (most notably data renderers for displaying various data types) and is available as a separate download as well. The functionality of the Tool remained almost the same as in the previous 1.x version.

The DataViewer Tool is available to download from:
http://www.taverna.org.uk/download/associated-tools/dataviewer-tool/

For more details, see the release notes at:
http://www.taverna.org.uk/download/associated-tools/dataviewer-tool/release-notes/

NCBI Entrez Utilities service set provides access to NCBI’s EGQuery, ESummary, EInfo, ELink, ESearch, ESpell, EPost and EFetch utilities.

Chemistry Web service set contains a set of Web services for chemistry provided by ChemSpider, ChEBI and PubChem.

You can add a set of services to the list of available services in the Service Panel in the Taverna Workbench by right clicking on “Available Services” and selecting “Import services” and then pointing to the service set description file contained in the service set pack.

To install the plugins, in the Taverna Workbench go to Advanced -> Updates and plugins -> Find new plugins, select the plugin you wish to install from the list and click “Install” button. You may have to restart Taverna to make sure the new plugin is installed properly.

• T2-1514 – Previous runs have data inverted when displayed
• T2-1515 – Expansion triangles are missing in top-level data and invocations
• T2-1516 – Split pane jumps around

To install the patch:

1. Start Taverna 2.2.0. It is best to install the patch when no workflows are being edited or run.
2. Click “Advanced” on the top menu and select “Updates and plugins”; the Updates and plugins dialog will appear.
3. Click “Find updates” within the dialog.  You should now see that updates are available for “Workbench”.
4. Select “Workbench” and then click the “Update” button on the right hand side.  The Taverna user interface may be unresponsive while the update is downloaded.  *Do not quit Taverna*.  When the update has finished, Taverna will show a dialog warning that the update will not take effect until Taverna is restarted.
5. Restart Taverna and it will now be at version 2.2.1.

Note that the title bar will still say Taverna 2.2.0.

If you have any problems with the patch, or any other issues with
Taverna, then please contact support@mygrid.org.uk.

• Keynote 4: Thinking Outside the Box: How Cloud, Grid, and Service Can Make Us Smarter? Ian Foster
• SERVICES Tutorial 4: Services Computing in Biomedical Science. Wei Tan, Ravi Madduri
• SCC: Co-Taverna: A Tool Supporting Collaborative Scientific Workflows. Jia Zhang.
• ICWS Confucius: A Scientific Collaboration System Using Collaborative Scientific Workflows. Jia Zhang, Daniel Kuc, Shiyong Lu

Prof. Jia Zhang from Northern Illinois University also has a NSF project “Collaborative Research: A Collaborative Scientific Workflow Composition Tool Supporting Scientific Collaboration” that uses Taverna as the implementation tool.

Taverna 2.2.0 includes improvements to the Workbench user interface and gives users greater control over the workflow engine. Here are a few of the new features in the Workbench:

• Loading and sharing of service sets
• Ability to load and edit workflows that contain services that are offline
• Reporting on the state of the workflow
• Tabular representation of a workflow run
• Retrying and parallelization of service calls
• Consistent representation of the intermediate and workflow results
• Pause/resume/cancel of a running workflow

Taverna 2.2.0 also includes the Command Line Tool that allows you to execute workflows outside of the Workbench. The Command Line Tool is available either bundled with the Workbench or as a separate download.

Tutorials and examples

Tutorials for Taverna are available under the Taverna 2.x documentation.

Example workflows can be found under the Starter pack tab in the myExperiment perspective of the Workbench.  They can also be downloaded from the myExperiment Web site at http://www.myexperiment.org/packs/122.

Known issues

Although Taverna 2.2.0 contains many improvements there are some known issues with it. These are detailed in known-issues.txt in the download bundle. An updated and more detailed list can be found in our issue tracker Jira at:
http://www.mygrid.org.uk/dev/issues/secure/IssueNavigator.jspa?mode=hide&requestId=10171.

Taverna and Java

Taverna requires the Java Runtime Environment (JRE) version 5 or 6 from Sun. No other versions of Java have been tested.

Java on Linux

Some Operating Systems, such as Ubuntu, come with the Gnu GCJ version of Java that cannot be used to run Taverna due to bugs in GCJ.

To download Sun Java 6 for Ubuntu, start a Terminal and type the following:

sudo apt-get install sun-java6-jre

and follow the instructions. You might also have to switch the default Java installation by running something like

sudo update-java-alternatives -s java-6-sun

Read more details about Taverna’s system requirements, in particular how to set the location of the Graphviz binary dot if needed.

Licence and source code

Taverna is distributed under the LGPL 2.1 licence.

The source code for Taverna can be retrieved from our Subversion repository.  We also recommend you to sign up to the taverna-hackers mailing list if you are a developer.

Reporting problems

If you find any problems that are not listed in known-issues.txt, then please send them to the taverna-users or taverna-hackers mailing lists. Our support team is monitoring the mailing lists and will try to respond to questions as soon as possible.

If you prefer not to subscribe to our mailing lists, you can send your questions directly to support@mygrid.org.uk and a member of our support team will respond to your inquiries.