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?

GTEx is throwing away 90% of their data

http://liorpachter.wordpress.com/2013/10/21/gtex/

Ubuntu System Halted Won't Power Off

When you shutdown from Ubuntu, the system freezes, system hangs and does not power off.

Try this:

$ gksu gedit /etc/default/grub

GRUB_CMDLINE_LINUX="acpi=force pci=noacpi apm=power_off"

$ sudo update-grub

Or try disabling ACPI in the computer's BIOS.

Change Login Screen Wallpaper with Ubuntu Tweak

Ubuntu Tweak > Tweaks > Login Settings

Click the "Unlock" button at the top, pick a picture and voila!

Free audiobooks

Free audiobooks

http://librivox.org/

http://www.gutenberg.org/wiki/Gutenberg:The_Audio_Books_Project

God In My Everything

God In My Everything

Ken Shigematsu shows that spiritual formation is more than just solitude and contemplative reflections. Spiritual formation happens in the everyday, in each and every moment of life. For those caught up in the busyness of work, family, and church, it often feels like time with God is just another thing on a crowded 'to-do' list. Ken explains how the time-tested spiritual practice of the 'rule of life' can help bring busy people into a closer relationship with God. He shows how a personal rule of life can fit almost any vocation or life situation. In God in My Everything, you will discover how to create and practice a life-giving, sustainable rhythm in the midst of your demanding life. If you long for a deeper spirituality but often feel that the busyness of life makes a close relationship with God challenging---and, at times, seemingly impossible---this book is for you


http://www.goodreads.com/book/show/17133254-god-in-my-everything

The Double Helix : A Personal Account of the Discovery of the Structure of DNA

The Double Helix : A Personal Account of the Discovery of the Structure of DNA is an autobiographical account of the discovery of the double helixstructure of DNA written by James D. Watson and published in 1968. It was and remains a controversial account.

http://en.wikipedia.org/wiki/The_Double_Helix

Rap video by 7 graders
http://www.genomeweb.com/node/1296296 

E.C. Manning Provincial Park

Lightning Lake, Flash Lake, Strike Lake, Thunder lake

http://canadianveggie.wordpress.com/2011/08/11/greater-vancouver-hike-lightning-lakes-chain/

Surrogate variable analysis

http://www.bioconductor.org/packages/2.12/bioc/vignettes/sva/inst/doc/sva.pdf

The sva package contains functions for removing batch e ects and other unwanted variation
in high-throughput experiments. Speci cally, the sva package contains functions for identifying and building surrogate variables for high-dimensional data sets. Surrogate variables
are covariates constructed directly from high-dimensional data (like gene expression/RNA
sequencing/methylation/brain imaging data) that can be used in subsequent analyses to
adjust for unknown, unmodeled, or latent sources of noise.

Genes In Life .org

http://www.genesinlife.org/

Genes in Life is a place to learn about all the ways genetics is a part of your life. On this site you will learn how genetics affects you and your family, why you should talk to your healthcare providers about genetics, how to get involved in genetics research, and much more!