Why publish and be so damned hard to find?

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Chris Parr from Times Higher Education Interviewed Prof Carole Goble at JISC Digifest. You can read and listen to Carole’s views on the lack of transparency about academic research methods by clicking on the links below.

“Outdated practices and lack of simplicity result in ‘unfindable’ work, Carole Goble tells Jisc Digital Festival”

JISC Digifest Keynote

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Carole Goble gave a thought provoking keynote presentation at the JISC Digital Festival where she talked about www.researchobject.org. It was great to see that the TARDIS (Time and Relative Dimensions in Scholarship) analogy was picked up by Chris Parr from Times Higher Education. You can find the talk live on the JISC website here.

Example of Encoding an RO using RDF-a

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rdf-a example screenshot

As an example of encoding a Research Object using RDF-a is now available to the community, see the “Parameter Optimization of an Ecological Niche Modeling Workflow”. The page represents a Research Object representing the optimizations made on the AUC output parameter of the ENM workflow using Support Vector Machines (SVM). The optimizations are performed using genetic algorithms and have been represented with the Research Object Optimization Ontology.



Our Workshop on “What Bioinformaticians need to know about digital publishing beyond the PDF2″ has been accepted for ISMB2014

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Following our very successful workshop on “What Bioinformaticians need to know about digital publishing beyond the PDF” last year in ISMB 2013 (see our blog post), we are thrilled to announce that our workshop series will be continued in ISMB2014, Boston, USA (tentative dates July 13, 14 or 15). This year, we will join force with BioMed Central, to expand our discussion on new ways of digital publishing by a new topic, i.e., new ways of peer review and their impact on bioinformatics. The workshop is organized by the managing board of Research Object, representatives of ISA community, and participation of BioMed Central and their journals Biology Direct and GigaScience. The workshop web site will be announced shortly! Mark your date, and join us in Boston!

The Launch of Research Object Creator Tool (Give it a try!)

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ro creator example screenshot

 Research Object Creator Tool is a very lightweight RO creation tool built by Daniel Garijo of UPM. The tool takes as input a LaTeX file and extracts its title and abstract to create an annotated page in RDF-a. It also produces a structure of the contents to reference, so users only have to fill in (and annotate if you want) the resources to point to. A sample can be seen in the image to the left and more details can be found in Daniel’s blog page.

Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome

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Wf4Ever member Daniel Garijo of UPM published an article, titled “Quantifying Reproducibility in Computational Biology: The Case of the Tuberculosis Drugome” in the world-leading Computational Biology journal PLOS ONE, with researchers from 5 other institutions. The article quantifies the cost of reproducing computational research in computational biology by using an exemplar experiment from one of the co-author’s own research group. The article provides useful insights and guidelines for improving reproducibility.

10th International Conference on Preservation of Digital Objects

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Screen Shot Research Object Digital Library Demo

Half day tutorial: From Preserving Data to Preserving Research: Curation of Process and Context at iPres 2013. The video presented at the tutorial shows the process of building a research object from the music research experiment, with the purpose of sharing and preserving the experiment and its context, in order to facilitate its reusability, reproducibility and better understanding.