Discovering Biology in a Digital World

Welcome to the new home of Discovering Biology in a Digital World.
Posts from ScienceBlogs, 2006 to 2017, can be found in the archive.

Molecule in Space
Singularity: the point at which a function takes an infinite value.

"Eew!" Is how high performance computing (HPC) admins react to Docker, according to Dr. Vanessa Saurus when she described the motivation for developing Singularity [1] at the Cyverse Container Camp . Like Docker, Singularity allows one to package programs and their dependencies in ways that they can be run as virtual instances with low overhead. Singularity improves on Docker to make it possible to run containers in HPC environments such as super computers.

Why another ... Read more

Container on a train

Containerization technologies like Docker are designed to solve challenges associated with installing and running complex software such as bioinformatics pipelines and web servers. Docker will change the world ... maybe. While clearly powerful and enabling, the magic of Docker can also be an overpromise. To understand why, you need to understand the “ The Law of Leaky Abstractions .” Read more

Stefan Green zip-lines though a volcano

Want to incorporate microbiome and metagenomics research into your lab or teaching? Sign up for the ABRF 2018 microbiome and metagenomics workshop. It may not teach you to zip-line through fire, but you will learn how to generate and manage a fire hose worth of data from microbiome projects. Read more

Celebrate DNA Day 2018 by making science art with molecular models of DNA. Read more

Infrared Cacti
​​​​​Saguaro National Park - Tucson AZ

The technological Singularity is the moment beyond which "technological progress will become incomprehensibly rapid and complicated [1].” Hmmm. That sounds like bioinformatics.

Surviving the Singularity requires reducing complexity. This was the topic of a recent three-day Cyverse Container Camp hosted at the University of Arizona, Tucson AZ. I attended the camp as part of Digital World Biology's effort to design ... Read more

Infrared of Ballard Locks entrance

Infrared (IR) photography creates pictures in a whole new light. When I first experimented with infrared in the late 70's early 80's it was with black and white infrared film using a dark red Wratten 89b IR filter. It was okay, but not great. Digital cameras change that by opening the experience to easy experimentation to explore color and black and white.

Read more
Social media platforms
Social media platforms

From communicating with friends and colleagues, to promoting business, to influencing elections, social media’s impact can be significant. Once you’ve decided to use social media, you need to pick platforms and measure your effectiveness. This can be daunting. What are the must-haves and what are the nice-to-haves? Do you have to have a Facebook page, a LinkedIn page, a Pinterest page, and your own website? What about Twitter, blogging, Instagram, and Snapchat? The simple answer to these questions is - it depends. It depends on your goals. What do you want to ... Read more

MHC-I with antigen from Molecule World

Lately I’ve been thinking about immunology, and not just because it is flu season, it is because Digital World Biology (DWB) is collaborating with Shoreline Community College to design a five-week bioinformatics course that will be component of their one year immuno-biotechnology certificate (1).

An aspect of the course will cover the ways in which industry studies and utilizes components of the immune system from vaccines to making antibodies to measuring T-Cell Receptor (TCRs) repertoires as biomarkers. In the classes, bioinformatics methods will be used to to reinforce ... Read more

BioDatabases 2018

It’s a new year and new edition of Nucleic Acids Research’s (NAR’s) Annual Database issue. NAR’s database now catalogs 1737 molecular biology databases, up 75 from last year. Of the new databases, FlavorDB is a favorite. Read more

A few years ago, when the iPhone first came out, I fell in love with an app called "Molecules." It was easy to use, the images were lovely, and I thought manipulating molecules by touch could help solve some of the problems my students had with using Cn3D.

I was all set to switch.

But I couldn't. When it came to teaching, I needed features that Molecules just didn't have.

To make a long story short, we had an SBIR grant from National Science Foundation and the good fortune to work with Molecules' developer and another brilliant engineer to make a new app called " ... Read more