During the conference people were to be particularly struck with the simplicity of RightField, and the fact that it allows scientists to continue to use their favourite data tool – Spreadsheets – unimpeded, without having any unfamiliar new tools or technologies imposed upon them. They also liked that the spreadsheets created by RightField carry the all the ontology and term information around within them, all of which can be retrieved any time, long into the future, directly from the spreadsheet alone.

We think this tweet from the conference sums things up rather nicely:

• Data integration methods and tools
• Ontologies, semantic modeling
• Data representation model and reasoning
• Semantic workflows

The semantic workflows section included a talk by Dr Paolo Missier called “Workflows, experimental findings, and their provenance: towards semantically rich linked data and method sharing for collaborative science”. The talk covers:

• Workflow and their provenance
• Janus: workflows + provenance + semantics for Taverna
• The W3C PROV Semantic data model for provenance
• Extending PROV with patterns to capture workflow structure
• Packaging and sharing: data + methods + provenance
• Research Objects in the Wf4Ever project
• Data Packages in the DataONE project

Reproducibility in principle underpins the scientific method. For an experimental finding to be reproducible its materials must be available and its methods clear, accurate and transparent. In this talk I will explore the reality of reproducibility in computational science, focusing on methods that use workflows. I will discuss what we mean by reproducibility; differentiate between the preservation and conservation of workflows; sketch the role provenance has to play; and point to a growing number of initiatives that aim to make in silico science reproducible, including our own first steps towards a reproducibility framework based on Research Objects. Although technical infrastructure helps towards the utopian ideal of truly reproducible science it is social factors that define the reality.

The talk is available as

• Powerpoint, or
• PDF

The funding is flexible, and can be used to pay for travel to conferences, setting up and running workshops, and starting new collaborations. In return for funding, Fellows keep the Software Sustainability Institute up to date with the latest news from their discipline. More information about the Fellowship is available on the Fellowship page.

The Software Sustainability Institute is a national facility for cultivating world-class research through software. It comprises experts from the universities of Edinburgh, Manchester, Oxford and Southampton.

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.

Simon Jupp, Julie Klein, Panagiotis Moulos, Joost Schanstra and Robert Stevens: Ontologies Come of Age with the iKUP Browser

Congratulations to all involved. The iKUP Browser can be seen online.

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.