Paper: SADI, SHARE, and the in silico scientific method

The SADI, SHARE, and the in silico scientific method paper by Mark D Wilkinson, Luke McCarthy, Benjamin Vandervalk, David Withers, Edward Kawas and Soroush Samadian is available online at

Best Demonstration of Semantic Technologies award

Congratulations to Luke who won the Best Demonstration of Semantic Technologies award at the SWAT4LS workshop in Berlin for his demo of the SPARQL assist Language-neutral query composer! Update 2010-01-06: Slides are now available online.

Leveraging of Semantic Web Services for Practical Application: Creating Transferable Methodology with SADI Case Studies

A presentation of several use cases for the SADI framework and the SHARE client by Alexandre Riazanov at AWOSS2010

SPARQL Assist Language-Neutral Query Composer

I’ll be presenting a demo of our SPARQL Assist Language-Neutral Query Composer at SWAT4LS 2010 in Berlin next week.The slides are available on SlideShare: SPARQL Assist Language-Neutral Query Composer.

Download the SPARQL Assist distribution. You can also explore the customized CardioSHARE-specific demo at

New version of SPARQL Assist.  See SPARQL Assist 0.1.2 for details.

A technical(ish) introduction to the SADI Semantic Web Service Framework

SADI Technical Introduction  Written by Alexandre Riazanov, a programmer who recently joined the C-BRASS project at the University of New Brunswick, Saint John (Dr. Chris Baker’s laboratory).  Alexandre has produced a great overview from the perspective of someone who has just learned the SADI framework from-scratch - hopefully this will be useful to other newcomers to the project!  Everyone is welcome!!!  If you need help/advice just ask…

HOWTO: SADI Taverna plugin snapshots

The latest release of the SADI Taverna plugin is available in Taverna by default, but you can also install pre-release snapshots of the plugin by adding a custom update site.  Here’s how:

  1. From the Advanced menu, choose Updates and plugins.
  2. If you have installed the release version of the SADI plugin, uninstall it by selecting it from the list and clicking the Uninstall button.
  3. Click the Find New Plugins button.
  4. Click the Add update site button.
  5. Type in the Site Name field, type in the Site URL field, and click the OK button.
  6. In the new box, click the check box next to SADI activity plugin $VERSION-SNAPSHOT, and click the Install button.
  7. Restart Taverna.

Taverna will now notify you of updates to the SNAPSHOT version of the plugin.  If you ever want to switch back to the release version, you will have to uninstall the SNAPSHOT version.

SHARE & The Semantic Web - This Time it’s Personal!

Luke’s publication at the 2010 OWLED:

OWL : Experiences and Directions
Seventh International Workshop
San Francisco, California, USA
21-22 June 2010

The slides are available on SlideShare: SHARE & the Semantic Web — This Time it’s Personal.

Manuscript on the SADI Plugin to Taverna

SADI Taverna manuscript  A manuscript about the SADI-Taverna plug-in has been accepted to the Workflow Construction track at ISoLA.  A link to the final pre-proof copy is below.

SADI for Taverna Tutorial

Uploaded to SlideShare:

(Written by David Withers)

OWL as hypothesis — reproducible in silico science

This is a draft of the introduction to my student Soroush Samidian’s Ph.D. thesis:Reproducibility is a cornerstone of Science. To be truly reproducible, an experiment should be explicit and thorough in describing every stage of the analysis, starting with the initial question or hypothesis, continuing on through the methodology by which candidate data were selected and analyzed, and finishing with a fully-documented result, including all provenance information (which resource, which version, when, and why). As modern biology becomes increasingly in silico-based, many of these best practices in reproducibility are being managed with much higher efficiency. The emergence of analytical workflows as first-class referenceable and shareable objects in bioinformatics has led to a high level of precision in describing in silico “materials and methods”, as well as the ability to automate collection of highly detailed provenance information. However, the earlier stages in the scientific process – the posing of the hypothesis and the selection of candidate data – are still largely limited to human cognition; we pose our hypotheses in the form of sentences, and we often select and screen candidate data based on expert knowledge or intuition. This is particularly acute in the interface between clinical sciences and molecular sciences, where clinicians are the ultimate arbiters of patient phenotypic classification, often based entirely on their personal expert opinion, while in contrast molecular association studies depend on deeply understanding these classifications in order to make statistical links between phenotypic traits and molecular traits. (read more…)

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