I’ve updated the RGD dashboard widget for the Mac. Nothing very significant has changed other than it now runs the most recent search tools on RGD rather than the older ones. I’m updating the download on the Apple site so it should be accessible from there too.
addthis_url = ‘http%3A%2F%2Ftwigger.hmgc.mcw.edu%2Findex.php%2F2009%2F10%2F21%2Fupdated-rgd-dashboard-widget%2F’;
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As part of our grant with the National Center for Biomedical Ontology we are producing a number of educational videos/screencasts to help introduce ontologies to the broader scientific community. The basic idea behind these videos is that ontologies are really powerful but most of our wet lab colleagues are put off by the complexity and [...]
We are funded as part of the Gene Ontology consortium and participate in GO’s Reference Genome project with RGD’s work in this area being spearheaded by Stan Laulederkind. The consortium recently published a paper describing this project and its work annotating genes across a wide variety of species.
The Gene Ontology’s Reference Genome Project: a unified [...]
We have been doing some work using Amazon’s cloud computing infrastructure (EC2, S3) as a platform for compute-intensive analyses that would normally require the purchase of a local cluster. Tailored to proteomics analysis of mass spec data, this work was recently published in the Journal of Proteomics Research.
Low cost, scalable proteomics data analysis using Amazon’s [...]
We just got news earlier this week that our paper describing ViPDAC, a cloud computing analysis environment for proteomics analysis, was accepted for publication in the Journal of Proteome Research.
Here’s the link to the abstract and preprint version at J. Proteome Research.
Some coverage picked up from the MCW press release:
http://www.azonano.com/news.asp?newsID=10855
http://www.physorg.com/news158583793.html
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It looks like I’ll get a chance to talk about our work with the National Center for Biomedical Ontology (NCBO) at the upcoming 3rd International BioCurator meeting in Berlin. Our abstract was selected as one of the talks in the ‘Standards and Controlled Vocabularies and Ontologies’ session. Here’s a link to the full schedule: http://projects.eml.org/sdbv/events/BiocurationMeeting/schedule.html
This [...]
This is the lab website for the group of Dr Simon Twigger at the Medical College of Wisconsin. Here are our buzzword bingo entries: bioinformatics, proteomics, cloud computing, ruby on rails, ontologies, genomics, data mining, amazon web services, git, agile development, SNPs, genome databases, CTSA, clinical and translational science, biomedical informatics, Flash, screencasts, videos, scivee.
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RGD’s latest publication has just come out in the January edition of Nucleic Acids Research. Entitled ‘Variation, ontologies and pathways’ the article describes the new features introduced on the Rat Genome Database over the past year including pathway diagrams, updates to the Genome browser, new physiological portals and more.
addthis_url = [...]
As part of Nature’s general feature on the challenges of dealing with Big Data in modern scientific research there was an article published covering Biocuration and its associated challenges. Coming in part from the various Biocurator and International Biocurator meetings originally started from a grant awarded to Sue Rhee and Simon Twigger, this paper outlines [...]
I created a quick video tour of RGD’s SNPlotyper tool demonstrating how to use SNPlotyper to visualize and compare SNPs between sets of inbred rat strains. In this screencast I show how to configure the tool to select a region of chromosome 1 between 120Mb and 130Mb and then view SNP genotypes for F344 and [...]
