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  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.
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 .”
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
The technological Singularity is the moment beyond which "technological progress will become incomprehensibly rapid and complicated .” 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 ... Read more
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.
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
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
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.
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
A lot of our colleagues are interested in bioinformatics and data science. While it is clear that bioinformatics is important, even essential, in modern biology research, there is the question about the levels of programming and computer skills needed for different jobs. I'm not going to answer that question here. Instead I'm going to focus on one end of the problem, that is, how is a bioinformatician similar to a data scientist? I'll illustrate the kinds of skills that are needed for this role by sharing my recent experience of how we moved the Discovering Biology in a Digital World (DWB ... Read more
A simple web search says biotech is really big. One estimate indicates that the industry will have $400 billion in sales in 2017 with growth to over $775 billion by 2024 . Another report suggests there are over 77,000 employers . That’s big, but is it real, and what you can do with this information?
At Biotech-Careers.org we're interested in helping students and graduates of biotech programs at community and four-year colleges learn about the multitude of opportunities available in the biotech industry. To be helpful we ... Read more