To install the patch

1. Start Taverna 2.1. 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 three parts of Taverna. You need to install all three updates for Taverna to be patched correctly. Do *not* restart Taverna until all three updates are installed.
4. Choose “Compatibility” and then click “update” on the right. 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. Do not restart Taverna yet. “Compatibility” should now show that it is version 2.1.1
5. Update “Services” and then update “Workbench” in a similar manner
6. Restart Taverna.

Note that the title bar will still say Taverna 2.1.0

The Taverna 2.1.1 Patch includes the following fixes

Credential Manager/Security

The Credential Manager now checks if it is running as a headless process and so decides whether to pop up a password dialog. (T2-698)

The default truststore password on Java 6 Sun Leopard (”changeme”) is now checked for. (T2-1094)

The Credential Manager password dialog is now recognised as a master password provider. (T2-1133)

Beanshell and R services

Beanshell and R prevented users from creating an input and an output port with the same name. This check has been removed. (T2-1127)

Beanshell and R previously allowed users to create ports with invalid names. This is no longer allowed. (T2-1129)

A problem with R services not saving changes to the script was fixed. (T2-1145)

Engine

Two concurrency problems were fixed that, in some cases, prevented a large number of iterations over nested workflows running correctly on some Java Virtual Machines (T2-1124 and T2-1137)

A range of cheminformatics services will be made available for use in the Taverna 2.1 Workbench in addition to workflows showing how they can be used in data analyses. The results from cheminformatics workflows will be shared by the use of blogs to provide a notebook record of data analyses.

The ChemTaverna project will also investigate how laboratory instrumentation can be controlled in workflows for use in closed-loop optimization experiments to enhance the performance of analytical instruments.

Tutorial overview, registration details and programme are available on-line.

• Copy/paste, shortcuts, undo/redo, drag and drop
• Animated workflow diagram
• Remembers added/removed services
• Secure Web services support
• Up-to-date R support
• Intermediate values during workflow runs
• myExperiment integration
• Excel and csv spreadsheet support

Taverna 2.1 has been designed to improve the user-experience, the range of available services, include support for more industry standards, and ease the design and execution of workflows.

To enable the plugin, go to Advanced -> Updates and plugins. Click on Find new plugins. Tick the box for Taverna 2 Spreadsheet 0.2.0 and click Close.

When you restart Taverna 2.1 Beta 2, you will have a new type of Service Template called SpreadsheetImport. To import a spreadsheet into your workflow, simply add the SpreadsheetImport service to your workflow (either drag it from the service panel into the Workflow Diagram or Explorer, or right-click on it in the Service Panel and select Add to workflow).

When you add the service to your workflow, you can configure how it deals with the rows and columns from the spreadsheet:

• select which rows and columns to output
• how to deal with empty cells
• whether to include the header row, and
• what name to use for the data from a given column

A SpreadsheetImport service takes as input the file path or URL to an Excel spreadsheet. It has an output port for each selected column; data for the selected rows of the column is output from the port in row order.

Press release

New videos show how researchers use advanced technology

New videos showing how JISC is helping researchers achieve faster, better and different research through virtual research environments have just been released at http://www.youtube.com/user/JISCmedia

The videos feature projects from JISC’s virtual research environment (VRE) programme, which is trying to find ways to connect people and speed up research processes across disciplines. These include astronomy, physics, electronics, chemistry and the study of ancient documents.

Case studies from the e-infrastructure programme are also online, showing how normal it is for researchers to use advanced internet technology when they work with other institutions and internationally.

Dr Mike Fraser of Oxford University, who led the e-infrastructure project, said: “We have used story-telling and videos to remove the mystery from e-infrastructure and demonstrate that its use can now be considered normal within many subject areas.”

JISC’s VRE programme manager Frederique van Till explained: “Virtual research environments really speed up the whole chain, and in some ways that makes the work for researchers much faster because it’s easier to get to the resources and the people. It also allows them to branch out into areas they could never have done before by using this new technology.”

Projects featured in the videos include VRE’s in archaeology, the study of documents and manuscripts, collaborative research events on the web and the MyExperiment social networking site for scientists.

Professor Mike Fulford from Reading University, who features in two of the videos, describes the impact of JISC’s work in archaeology project as “simply a revolution.”

He said: “I used to be a Luddite; the technology was all new to me. But now it’s like an umbilical cord – I can’t do without it.”

The VRE programme is now entering its third phase with a more modular approach aimed at making VRE’s work more effectively between different universities and colleges.

Watch the videos of the VRE projects and see e-infrastructures in action at http://www.youtube.com/user/JISCmedia

Explore audio and video from all of the VRE programme phases at http://www.jisc.ac.uk/whatwedo/programmes/vre/outputs

Listen to Frederique van Till, JISC VRE programme manager, discussing the latest phase of the programme at http://www.jisc.ac.uk/news/stories/2009/06/podcast82frederiquevantill