PAG Presentation on CEDE and microbial profiling with cpn60

On Tuesday Jan 17th at 5pm local (San Diego) Matt will be presenting a talk at the Plant & Animal Genome conference on microbial profiling using cpn60 and CEDE. Thanks to Genome Prairie for sponsoring attendance at PAG. 

Location - Sunset room in Meeting House @ Town and Country in San Diego

You mean people use a phylogenetic marker other than 16S rRNA? 

Yes some people use cpn60 (and rpoB) instead and they aren't all crazy. Matt may be but that's a story for another time.

The talk will provide some context for why choosing cpn60 may be advantageous. 

In the talk Matt will also be presenting CEDE (Collaborative Exploratory Data Environment). CEDE is a project than enables end-point collaboration at distance. It is a multi-user and multi-touch environment where a team of researchers / collaborators / Ag producers / clinicians / public can interact in real time to analyze microbiome data. 

Please see the following URLs for a demo video on CEDE.

English sub-titles

French sub-titles 

Miles Buchwaldt is awarded prestigious scholarship

SaskCanola has awarded Miles with a award for his graduate studies. 

The Dr. Roger Rimmer Award for Excellence in Graduate Research is a $18,000 / year (renewable up to 2 years) award that is targeted to a deserving University of Saskatchewan M.Sc. or Ph.D. student where their thesis is positioned to address development or utilization of canola.

Congratulations Miles!!!

2 Seminars - Tuesday Nov. 25, 2014

We are very geeked to be able to host longtime colleague Dr. Mark Wilkinson from the Technical University of Madrid as he delivers 2 seminars on Tuesday Nov. 25th 2014.

10:30am Tuesday, Nov. 25th in Meeting room #2 at the National Research Council of Canada 110 Gymnasium Place

It ain't over 'till it's over:  polyadenylation of messages in Rice Blast Fungus

RNA-binding proteins are critical in the regulation of gene expression at the post-transcriptional level.   Mark will present the results of his recent RNAseq analysis of the "polyadenylome" of Magnaporthe oryzae, and of a deletion mutant - rbp35 - that exhibits dramatically reduced pathogenicity.  RBP35 is a component of the polyadenylation complex, but is not essential for viability of the fungus.  We show that RBP35 is a gene-specific regulator of polyadenylation, and in particular affects the process of alternative polyadenylation site selection.  

3:30pm Tuesday, Nov. 25th, 2014 in Agriculture 5C61

A little semantics goes a long way, but a lot goes a long long way

Projections suggest that the delay between scientific discovery, and the dissemination and implementation of the knowledge embodied in that discovery, will soon vanish. At that point, all data and knowledge resulting from an investigation will be instantly interpreted and disseminated, influencing other researcher's experiments, and their results, immediately and transparently. This clearly requires that research results be of extremely high quality and reliability, and that research processes – from hypothesis to publication – become tightly integrated into the Web. Though the technologies necessary to achieve this kind of “Web Science” do not yet exist, our recently-published studies of automated in silico investigation demonstrate that we are enticingly close, and a path toward next-generation Web Science is now clear. 
     Scientific research has been largely unaffected by modern Web technologies. From hypothesis generation through experimentation to the publication of results, scientists continue to manually integrate data-sets, assemble analytical pipelines, and publish manuscripts that can cannot be understood by machines. This is despite voluminous evidence that (a) researchers cannot keep-up with the literature, (b) high-throughput studies are increasingly non-reproducible due to errors in integration, execution, or lack of methodological documentation, and (c) peer review is failing to detect these mistakes, thus global scientific knowledge is being contaminated with factual errors.  Our research programme is targeted at providing an end-to-end in silico research platform that takes advantage of modern Semantic Web technologies to improve accuracy and reproducibility. Experiments are designed, executed, published, and re-used entirely within the Web. The hypotheses behind experiments are explicit; the experiments are self-describing; analytical pipelines automatically utilize globally distributed expertise to ensure accuracy; and results are fully annotated, facilitating rigorous peer-review.  The Web, to date, has only cosmetically changed the research process.  Our vision for Web-embedded science re-defines scientific methodology by fully integrating it with a global network of knowledge and expertise on the Semantic Web. 


Dr. Mark Wilkinson is the BBVA Foundation Chair of Biological Informatics and Isaac Peral Distinguished Researcher at the Center for Plant Biotechnology and Genomics, Technical University of Madrid, and Adjunct Professor of Medical Genetics, University of British Columbia. His research over the past decade has focused on the problem of enabling bio/medical researchers to accurately and reproducibly execute their own "big data" manipulation and analysis. Much of this work has involved the application of “semantics” to both scientific data and the analytical services that operate on them. He was founder of the BioMoby Semantic Web Service interoperability framework which, at its peak, included more than 1600 bioinformatics data-sources and tools.  More recently he created SADI - a set of design practices that enhance interoperability between semantic Web services - and SHARE, a novel query resolver that combines a workflow engine with a logical reasoner to dynamically generate, and execute, a data retrieval and analysis workflow in response to questions posed by the user. His work on supporting multi-lingual end-user query construction in SHARE won first prize for “Best Demonstration of Semantic Technology” at the Semantic Web Applications and Tools for Life Sciences 2010 meeting in Berlin. He is on the Editorial Board of the Journal of Biomedical Semantics, and is an invited expert for the W3C’s Semantic Web in Health Care and Life Sciences Interest Group



Seminar - Tuesday Sept. 9, 2014 - Thorv rm 124

We are grateful to Amanda Murdoch who has said she is willing to present a seminar on her recent work with Eyetracking while she visit's Saskatoon. 

Amanda is a recent graduate from a MMath in Computational Math program at UWaterloo, prior to which she completed a BMath in Statistics, also in Waterloo. During the Masters program, she conducted research studying the way people look at statistical graphics. In particular, she worked on creating graphics with some interesting structure, and using eye tracking hardware to record where people look when they make decisions about some classic plots.

Tracking Eye Movement when Viewing Statistical Graphics

Eye tracking has been used in a variety of studies in the past, in recording where people look when they view art, documents, websites, faces, and more. One area where not much study has been done is on statistical graphics or data visualizations. A preliminary study has now been conducted, using a Tobii brand eye tracking device and human participants to generate data on where people are really looking when they view plots. Three types of plots have been used, each with an associated simple question for the participant. Participant's responses to the questions were recorded as well as the data output from the tracker. Results from this study show that people use different approaches for answering the same questions. The current work has led to many more questions about further work that may be done in this area.