Pack: Taverna 2.1 beta 2

Created at: 02/07/09 @ 12:51:12      Last updated: 03/07/09 @ 15:39:08
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Title: Taverna 2.1 beta 2


Information Description

Taverna workbench 2.1 beta 2

Due to user response to Taverna 2 workbench, major improvements have been made to the user interface of Taverna 2.1 Beta 2 workbench.  Many of these are described below.

Installing

Choose your download from the list of links in this pack depending on your operating system.

Windows

If you have administrator rights on your machine, you can download the Windows installer (taverna-workbench-2.1.b2-installer.exe). A wizard should guide you through the installation to C:\Program files and add Taverna to the Start menu. If you don't have a recent Java, the wizard will also help you install the newest Java from Sun.

If you do not have administrator rights, you can download the Windows archive (taverna-workbench-2.1.b2.exe) - this is simply a self-extracting 7zip archive. You can place the extracted folder wherever you like. Start Taverna by double clicking on taverna.exe.

If you need to make any changes to the Java parameters, such as the amount of memory allocated (by default the minimum of 300 MB or 50% of free memory), or are a developer interested in debug messages, use taverna-debug.bat instead of the executable. 

Mac OS X

Download the OS X disk image (taverna-workbench-2.1.b2.dmg). After opening the disk image, a Finder window should appear. You can then drag the Taverna application into your Application folder, or wherever you prefer to keep the application. Double-click on the installed application (not the one in the disk image) to start Taverna.

Linux

Download the Linux archive (taverna-workbench-2.1.b2.tar.gz) and unpack it using tar zxfv averna-workbench-2.1.b2.tar.gz  or by double-clicking it in your desktop environment.  Make sure check that you have both SUN Java 1.6 JRE and Graphviz installed.

Place the extracted folder wherever you like, start a terminal, and run ./taverna to start Taverna. If you have any problems, double-check that you are using the correct java by running java -version

Tutorials and examples

See the Example workflows pack for example workflows.
 
See tutorial.html in the tutorial folder of your download for an introduction on how to build a workflow using Taverna 2. 

Known issues

As this is a beta, there are some known issues which will be fixed for the Taverna 2.1 release. These are detailed in known-issues.txt in the download. An updated and more detailed list can be found in our issue tracker Jira.

Taverna and Java

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

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 requirements, in particular how to set the location of the Graphviz binary dot if needed.

Licence and source code

Taverna is distributed under the licence LGPL 2.1.
 
The source code for Taverna can be retrieved from our Subversion repository  - we also really recommend you to sign up to the taverna-hackers mailing list if you are a developer. If you want to download the source code used for this release, download taverna-workbench-2.1.b2-src.zip from below.

New improvements

Although Taverna 2.1 beta 2 brings about many improvement, future improvements are planned for 2.1 and future versions, especially in the viewing of results.

Overall organization
The workflow explorer has been moved from the right-hand side of Taverna workbench to below the service panel.
 
Service panel
The service panel replaces the activity palette of Taverna 2 workbench.  It has a simplified and more familiar interface.
 
The services are now organized so that Service templates i.e. services that always require configuration such as Beanshell, are grouped together.
 
The tree used to display the services is more natural, with service-type specific organization within the branches.
 
The service panel allows filtered search of services.  Type in text to search on and the service panel will just show the matching services. Note that it may match on attributes of the services that are not immediately visibile.
 
The service panel automatically saves the set of service providers that are loaded.  This means that if you add a new WSDL then it will be there the next time you start Taverna.
 
Service providers can be removed from the service panel.
 
Adding services to the workflow
You can now add services to the current workflow by right-clicking on the service in the service panel.  You can still drag-and-drop the service into either the workflow explorer or the workflow diagram.
 
If the service that you add needs to be configured, then the configuration panel for that type of service will automatically pop-up.
 
Workflow creation
You can now use all of the necessary workflow creation and editing functions from within the workflow explorer.  Merges and control links (for run after specification) are now shown in the workflow explorer.
 
Merges can now be configured to control the order in which the data arriving is combined.
 
Objects in the workflow explorer and workflow diagram can be configured by right-clicking on them.
 
Data link creation is more intelligent so that it does not allow the creation of loops.
 
The workflow diagram can now be scrolled using standard scrollbars.
 
Run dialog
The run dialog has been changed so that a graphical representation of the workflow and information about the ports, including example values is shown.  The mechanism for entering input values for ports has been made more user-friendly.
 
The dialog "remembers" the values used for previous runs of the workflow.
 
Results viewing
The results view now shows when all the data has arrived at an output (the port turns grey) and also gives an indication of whether the workflow is still running.
 
The number of iterations of a service during the run is shown in the top right of the service.
 
If any calls to a service fail, then the service is shown in red and the number of failures shown in the bottom right of the service.
 
Intermediate results of a service can be examined by clicking on the service.  The input and output values for each iteration of the service can be examined.  The results for several services can be viewed at the same time (in separate windows).
 
You can zoom and scroll within the monitored view of the workflow run.
 
Data storage
The storing of the values passed between services has been made more efficient.  The values are now stored, if necessary, in a database. Because of the in-memory caching used, there is negligible impact on workflow runtime whilst allowing the handling of larger datasets.

Reporting problems

If you find any problems that are not listed in known-issues.txt, then please send them to the mailing list taverna-hackers. 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, you can send your questions to support@mygrid.org.uk and a member of our support team will be responding to your inquiries.
  
 
myGrid team,
University of Manchester

2nd July 2009

 

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