Combining Docker & R for Reproducible Research

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Interesting preprint posted to arxiv by Carl Boettiger from UC Santa Cruz, describing an example of an increasing trend to use Docker to package up investigations as reproducible research: Carl Boettiger, An introduction to Docker for reproducible research, with examples from the R environment

Example of Encoding an RO using RDF-a

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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… Read more »

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… Read more »

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

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 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… Read more »

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… Read more »

10th International Conference on Preservation of Digital Objects

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  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… Read more »

Launch of W3C Research Object for Scholarly Communication Community Group

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April 2013. To promote the openness and establishment of Researhc Object community, Wf4Ever team members launched a W3C community group, titled Research Object for Scholarly Communication. Since its launch in April, more than 80 participants from a wide variety of background have joined the group.