Program of LISC2013 Sydney on October 21st, 2013 published

3rd International Workshop on Linked Science 2013—Supporting  Reproducibility, Scientific Investigations and Experiments (LISC2013)

When: October 21st, 2013
Where: Sydney Masonic Conference & Function Centre, Sydney, Australia
Collocated with the 12th International Semantic Web Conference (ISWC2013).


9.00 – 10.00 Keynote by Carole Goble.

Results may vary: reproducibility, open science and all that jazz.

How could we evaluate research and researchers? Reproducibility underpins the scientific method: at least in principle if not practice. The willing exchange of results and the transparent conduct of research can only be expected up to a point in a competitive environment. Contributions to science are acknowledged, but not if the credit is for data curation or software. From a bioinformatics view point, how far could our results be reproducible before the pain is just too high? Is open science a dangerous, utopian vision or a legitimate, feasible expectation? How do we move bioinformatics from one where results are post-hoc “made reproducible”, to pre-hoc “born reproducible”? And why, in our computational information age, do we communicate results through fragmented, fixed documents rather than cohesive, versioned releases? In this talk, which I gave as a keynote at the 2013 joint conference Intelligent Systems in Molecular Biology / European Conference on Computational Biology, I will explore these questions drawing on 20 years of experience in both the development of technical infrastructure for Life Science and the social infrastructure in which Life Science operates.


10.00-10:30 Paper session I

  • Timo Willemsen, Anton Feenstra and Paul Groth. Building Executable Biological Pathway Models Automatically from BioPAX

10.30 -11.00 break

11.00 – 12.45 Paper session II

  • Guillermo Palma, Maria-Esther Vidal, Louiqa Raschid and Andreas Thor. Exploiting Semantics from Ontologies and Shared Annotations to Find Patterns in Annotated Linked Open Data
  • Cameron Mclean, Mark Gahegan and Fabiana Kubke. Capturing intent and rationale for Linked Science: design patterns as a resource for linked laboratory experiments
  • Jun Zhao, Graham Klyne, Matthew Gamble and Carole Goble. A Checklist-Based Approach for Quality Assessment of Scientific Information

12.45-13.45 Lunch

13.45-15.30 Paper session III

  • Nico Adams, Armin Haller, Alexander Krumpholz and Kerry Taylor. A Semantic Lab Notebook – Report on a Use Case Modelling an Experiment of a Microwave-based Quarantine Method
  • Niels Ockeloen, Antske Fokkens, Serge Ter Braake and Piek Vossen. BiographyNet: Managing Provenance at multiple levels and from different perspectives
  • Michiel Hildebrand, Rinke Hoekstra and Jacco van Ossenbruggen. Using Semantic Web Technologies to Reproduce a Pharmacovigelance Case Study

15.30-16.00 Break

16.00-17.30 Co-writing session: how can linked science techniques solve problems in scientific reproducibility 2+45 minutes

  • 1st 45 minutes: produce reproducibility problem/potential linked science technology matrix in breakout groups
  • 2nd 45 minutes: merging matrices into consensus view and/or paper ideas/blog post