Biological Ontologies

http://www.berkeleybop.org/ontologies

The BBOP, located at the Lawrence Berkeley National Labs, is a diverse group of scientific researchers and software engineers dedicated to developing tools and applying computational technologies to solve biological problems. Members of the group contribute to a number of projects, including the Gene Ontology, OBO Foundry, the Phenotypic Quality Ontology, modENCODE, and the Generic Model Organism Database Project.

http://www.ontobee.org/ 

Ontobee: A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs by generating RDF/XML source code for Semantic Web applications, and providing a well-structured HTML web page for user-friendly visualization in a web browser. Ontobee is the default linked data server for most OBO Foundry and OBO Library ontologies.  

http://ehcache.org/

Ehcache: Java's Most Widely-Used Cache

Ehcache is an open source, standards-based cache for boosting performance, offloading your database, and simplifying scalability. It's the most widely-used Java-based cache because it's robust, proven, and full-featured. Ehcache scales from in-process, with one or more nodes, all the way to mixed in-process/out-of-process configurations with terabyte-sized caches.

Teaching the art of guessing

http://blogs.nature.com/thescepticalchymist/2013/08/teaching-the-art-of-guessing.html

Estimation of chemical quantities is, in my opinion, one of the most important skills a chemist can have. It is also one that my students are simultaneously skeptical of — why not just use a search engine to find the ‘real’ value or crunch numbers to 8 decimal places in your calculator — and intimidated by (I probably don’t help by telling this story about Fermi).

I emphasize the need to gather a tool kit of anchor points (key chemical values) and maps (relationships between quantities) and provide examples. Here is the handout (pdf)

Slides and Video: Metrics that Matter with Chris Geoghegan

http://www.net2van.com/2013/09/slides-and-video-metrics-that-matter-with-chris-geoghegan/

Chris has bad news. Most of the time you spend looking at your analytics is probably in vain. There is too much data that tells you too little information. You thought analytics was all about using information to make better decisions, but it isn’t working. How do you go beyond just giving yourself a nice pat on the back with how many visitors you got last month?