Here are a number of new features in the Workbench:

• Text Constant service allowing easier entry of large textual values
• Greater control over what is return from REST service
• Ability to use all the example values for a workflow run with one button
• Easier annotation of services and control over their list handling

Taverna 2.4.0 also includes the Command Line Tool that allows you to execute workflows outside of the Workbench. The Command Line Tool is available either as a stand-alone download or bundled with the Workbench.

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/254.

Known issues

Although Taverna 2.4.0 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=10260.

System requirements

Details of Taverna’s system requirements are available on-line.

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.

This release is a feature-complete version of the Taverna 2 Server that is provided as a basis for deployments of server-ized Taverna in a multi-user environment. This version of the Server is based on the Taverna 2.4 codebase. Detailed documentation for the Server is available on-line.

In addition to its improved performance, this release supports a number of new key features:

• Based on Taverna 2.4
• Multiple users, with strong separation between them.
• Limited persistence over service restarts, depending on exact deployment.
• Workflow run introspection capabilities; clients can ask the server what inputs they should supply and what outputs were provided.
• Workflow run termination notifications through multiple mechanisms (RSS feed, email, SMS, twitter, etc. depending on deployment).
• Security, both of access to the service and access by the workflow runs to other services.
• Administrative REST interface including resource accounting
• Streaming of large files both for download and upload.

This is in addition to the features supported by the previous version of Taverna 2 Server:

• Upload and Execution of arbitrary Taverna 2 workflows
• Access to Workflow’s Interim Output Files; no need to wait for the workflow to finish if the results are available sooner
• Safe File Management for handling results; workflows cannot interfere with each others files
• Simple mechanism for Removal of Expired Workflows
• Support for both RESTful and SOAP APIs, for easier tooling
• JMX-based Management API

A Ruby Gem for interfacing to the Server via its REST interface is available. A Virtual Machine and Demonstrator Interface will be released soon.

Specific Issues Addressed in This Release

• TAVSERV-224 Ability to pass configuration parameters to the command line
  executor
• TAVSERV-226 Odd webapp authentication behaviour!
• TAVSERV-228 Wrong title and missing documentation link on index page

Future improvements

There remain a number of known-missing features; notably these include access to:

• Provenance Database
• Workflow Execution Model

Installation

Download Taverna Server 2.4 war and follow the installation instructions.

• Taverna Server 2.4 war
  • MD5: 02ca855484dee31737264a8d80f8dcbc
• Taverna Server 2.4 war source code
  • MD5: ab3f73a2e584aa1caf8a41fe12f1b522
• Taverna Server 2.4 full distribution
  • MD5: 149bf8620071af931ae0893bd2c1928b

System Requirements

Operating system

The Server can currently be installed on Linux and MAC OS.

Java

You will need a Java 6 installation. You can download Java from Sun Microsystems.

WebApp container

You will need a suitable servlet container.

The Server has been developed using Tomcat 6.0.26 as the servlet container, but other versions of Tomcat are known to work (back to at least 6.0.20) and other containers may also function correctly as no Tomcat-specific APIs are used in the deployable code. We welcome feedback on which containers work, as well as on how to configure them (if they are not Tomcat versions).

This release is a feature-complete version of the Taverna 2 Server that is provided as a basis for deployments of server-ized Taverna in a multi-user environment. This version of the Server is based on the Taverna 2.3 codebase. Detailed documentation for the Server is available on-line.

In addition to its improved performance, this release supports a number of new key features:

• Based on Taverna 2.3
• Multiple users, with strong separation between them.
• Limited persistence over service restarts, depending on exact deployment.
• Workflow run introspection capabilities; clients can ask the server what inputs they should supply and what outputs were provided.
• Workflow run termination notifications through multiple mechanisms (RSS feed, email, SMS, twitter, etc. depending on deployment).
• Security, both of access to the service and access by the workflow runs to other services.
• Administrative REST interface including resource accounting
• Streaming of large files both for download and upload.

This is in addition to the features supported by the previous version of Taverna 2 Server:

• Upload and Execution of arbitrary Taverna 2 workflows
• Access to Workflow’s Interim Output Files; no need to wait for the workflow to finish if the results are available sooner
• Safe File Management for handling results; workflows cannot interfere with each others files
• Simple mechanism for Removal of Expired Workflows
• Support for both RESTful and SOAP APIs, for easier tooling
• JMX-based Management API

There remain a number of known-missing features; notably these include access to:

• Provenance Database
• Workflow Execution Model

A Ruby Gem for interfacing to the Server via its REST interface is available. A Virtual Machine and Demonstrator Interface will be released soon.

Installation

Download Taverna Server 2.3 war and follow the installation instructions.

• Taverna Server 2.3 war
  • MD5: 4ace507cbbc7f7224bf7ad6419a25598
• Taverna Server 2.3 war source code
  • MD5: b43aff472c915d407928bf9311f15a7d

System Requirements

Operating system

The Server can currently be installed on Linux and MAC OS.

Java

You will need a Java 6 installation. You can download Java from Sun Microsystems.

WebApp container

You will need a suitable servlet container.

The Server has been developed using Tomcat 6.0.26 as the servlet container, but other versions of Tomcat are known to work (back to at least 6.0.20) and other containers may also function correctly as no Tomcat-specific APIs are used in the deployable code. We welcome feedback on which containers work, as well as on how to configure them (if they are not Tomcat versions).

SCUFL2 is the proposed new mechanism for specifying Taverna workflows, and forms the basis for our current development work on Taverna 3. SCUFL2 adopts Linked Data technology and preservation methodologies to create a platform-independent workflow language that can be inspected, modified, created and executed.

SCUFL2 comes with a Java API that can be used for programmatic access to read and write SCUFL2 workflow bundles. A workflow bundle is a structured ZIP file with the workflow definitions included as RDF/XML documents.

The workflow structure is defined using an OWL ontology and annotated with URIs so that third parties can form semantic statements about any component of a SCUFL2 workflow, for example to state that a particular service produces outputs of a certain type, or that a data link was added by a specific researcher.

Version 0.9.2 of the SCUFL2 is the first public beta release of the Java API for working with SCUFL2 workflow bundles. The main features are:

• Standalone Java library, no external dependencies (optional dependency on JAXB)
• Import Taverna 2 workflows (.t2flow)
• Import/export SCUFL2 workflow bundles (.wfbundle)
• API for inspecting, creating and modifying workflow structures (JavaDoc)

The API has also experimental support for importing Taverna 1 workflows (SCUFL 1) and performing structural validation of a workflow. Note that the API does not provide a way to execute the workflow (Taverna 3 platform will do this) and does not currently implement export to t2flow.

The team have provided a set of example SCUFL2 programs to show how the API can be used. Here is an extract from ServiceTypes.java, which shows which service types (WSDL, Beanshell, etc) have been used in a workflow:

Set types = new LinkedHashSet();
WorkflowBundleIO io = new WorkflowBundleIO();
File file = new File(filepath);
WorkflowBundle wfBundle = io.readBundle(file, null);
for (Profile profile : wfBundle.getProfiles()) {
  for (Activity activity : profile.getActivities()) {
    types.add(activity.getConfigurableType().toASCIIString());
  }
}

Note that this is a beta release of the API. Based on your feedback, we might be have to do minor changes to some methods or the Workflow Bundle file format for the 1.0 release, but will try to keep such changes to a minimum.

The myGrid team welcome developers to try SCUFL2 and contact us on the taverna-hackers mailing list with feedback, suggestions, bug reports, and most importantly, how they use or would like to use SCUFL2.

Quick links:

• http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2
• http://www.mygrid.org.uk/dev/wiki/display/developer/SCUFL2+API
• http://taverna.googlecode.com/svn/scufl2/ or
  https://github.com/mygrid/scufl2
• https://github.com/mygrid/scufl2-examples
• http://mygrid.github.com/scufl2/api/0.9/

The Collaborations Workshop will be held on 21-22 March at Queen’s College, Oxford.

Registration is now open (http://bit.ly/CW12Reg).

For more information, visit the Collaborations Workshop website.

Meet with researchers and software developers

A fresh perspective can help solve problems or come up with new ideas. The workshop brings together researchers from a wide range of disciplines, and software developers with experience of working for the research community. It is this variety of backgrounds that makes the workshop productive.

To see who’s attending, visit the website.

You control the agenda

The workshop is split into a series of discussion sessions. As a delegate, you can nominate topics for discussion: anything from a problem specific to your research, to an issue that affects the entire research community. We will then discuss the topic and try to find solutions.

To see the discussion topics that have been suggested so far, visit the website.

Everything is flexible

Everything about the workshop is flexible. Delegates control what they talk about. If someone wants time to present results, time will be found. If more time is needed for a discussion, it will be added.

To see the agenda, visit the website.

Everything is open

Information on the planning of the workshop, the agenda items, the presentations, the reporting-back sessions, and post-workshop progress will all be available on the CW12 website.

For more information, visit the Collaborations Workshop website, or send us an email (info@software.ac.uk).

The Software Sustainability Institute

The Software Sustainability Institute is a national facility for building better software. We are funded by the EPSRC, with additional funding from JISC, and are based at the universities of Edinburgh, Manchester and Southampton.

For more information, visit the Institute’s website.

Sponsors

This year, our gold sponsor is Digital Social Research, which maximises the uptake, use and impact of new digital technologies across the social science community.

We are also sponsored by the SeIUCCR project, which is a network of Community Champions who advocate the use of e-Infrastructures in their research, and the DevCSI project, which helps software developers
realise their full potential.

The course will provide an introduction to using Galaxy and Taverna in Next Generation analysis and will highlight the increasing requirements for reproducible workflows when performing high-throughput informatics research.

For more details and to register please see the Nowgen Web site:
http://www.nowgen.org.uk/facilities/events/event.php?id=30

SADI is a set of standards-compliant best practices that simplify interoperability between semantic Web services. The SADI codebase make it easy for people to deploy services that adhere to the SADI framework practices. The SADI plugin allows semantic services to be accessed from Taverna. The plugin has been developed by the SADI team (with the support of the Genome Canada Bioinformatics Platform).

The SADI plugin is available as a prototype plugin. For details on how to install plugins see:
http://www.mygrid.org.uk/dev/wiki/display/taverna/Installing+plugins

Documentation on the SADI plugin, including a link to a tutorial on SlideShare is available on the SADI wiki:
http://code.google.com/p/sadi/wiki/TavernaPlugin

If you have any problems or questions about the SADI plugin or need help, please contact sadi-discuss@googlegroups.com

This workshop will be on the 14-15th November 2011 and held in Manchester, UK. Full details of the IMPACT/myGrid Hackathon and online registration can be found on the wiki at:

http://impact-mygrid-taverna-hackathon.wikispaces.com/

Registration for this event is free, however there is a ‘no-show’ fee for those who book but who do not turn up.

Summary of the event:

This free workshop will showcase how scientific workflows can be used in digitisation and related fields. Using a number of tools developed in the IMPACT project the workshop will explore how they interact within the Taverna platform and will then lead exploration of some advanced use cases and technical challenges.

The workshop aims to bring together technical staff – ‘developers’ and ‘implementers’, rather than ‘practitioners’ in order to encourage the further development of the tools and investigate new solutions and features that could be developed in the near future for the benefit of the wider community.

The workshop will be run by the technical staff of the IMPACT project in conjunction with the Taverna developers.

Biodiversity science is the study of plants and animals that inhabit our planet and the environments they live in. Amid growing concerns over the extinction rate of certain species as their natural habitats are increasingly destroyed, and with biodiversity becoming as important as climate change on the political agenda, this new research project could not be more timely.

Starting in September 2011, the three-year project called Biodiversity Virtual e‑Laboratory (BioVeL) will establish an international e-Laboratory – the first of its kind in Europe – that will allow biodiversity scientists to jointly tackle diverse research challenges.

Experts from Cardiff University along with 15 partners from institutions across Europe, hope that when completed, the BioVeL e-Laboratory will, for the first time, give scientists access to multiple data, analysis and computing resources for biodiversity science through a robust e-Science infrastructure.

Coordinator of the project, Alex Hardisty of the School of Computer Science and Informatics, Cardiff, commented: “The outcomes from this project will improve the study of biodiversity. All scientists will benefit directly from the tools, knowledge and expertise assembled in this infrastructure, offering the promise of new opportunities to more easily research substantial biodiversity problems with societal impact.”

Ranked by the European Commission (EC) as top of its class from more than 60 proposals, BioVeL is funded under the EC’s FP7 e-Infrastructures programme to support the creation of the European Research Area.

For further information on the BioVeL project, visit http://www.biovel.eu/