Tuesday, April 17, 2018

Singularity: can it go to infinity?

Singularity: can it go to infinity?: 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(link is external).  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.  Read the full blog

Tuesday, March 27, 2018

Docker - can it be contained?

Docker - can it be contained?: 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.”


Thursday, March 22, 2018

Microbiome and Metagenomics Benchtop to Bioinformatics: Technical Approaches to Sequencing, DNA Extractions, and Data Analysis

Microbiome and Metagenomics Benchtop to Bioinformatics: Technical Approaches to Sequencing, DNA Extractions, and Data Analysis: Want to incorporate microbiome and metagnomics research into your lab or teaching? Sign up for the ABRF 2018 microbiome and metagnomics 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.

Wednesday, March 14, 2018

Solving the Bioinformatics Singularity with Containers

Solving the Bioinformatics Singularity with Containers: ​​​​​The technological Singularity is the moment beyond which "technological progress will become incomprehensibly rapid and complicated [1].” Hmmm.  That sounds like bioinformatics. Read more at Digital World Biology.

Tuesday, February 27, 2018

Getting Started with Infrared Photography

Getting Started with Infrared Photography: 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.

Thursday, February 22, 2018

Socializing Social Media

Socializing Social Media From communicating with friends and colleagues, to promoting business, to influencing elections, social media’s impact can be significant ... read more at Digital World Biology

Thursday, February 8, 2018

Displaying peptides on MHC proteins is hard work

Displaying peptides on MHC proteins is hard work 

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)...

Friday, January 19, 2018

Bio Databases 2018: How do they taste?

Bio Databases 2018: How do they taste?

It’s a new year and new edition of Nucleic Acids Research’s (NAR’s) Annual Database issue(link is external). It’s the 25th year for the NAR database series, the eighth for FinchTalk, and the first at the new home for Discovering Biology in a Digital World. 

Saturday, October 28, 2017

Synthetic Biology: Lowering environmental impact

Synthetic Biology: Lowering environmental impact

One of the themes of the recent @synbiobeta #sbbsf17 annual meeting (Oct 4,5 2017) was the impact of synthetic biology on making new things or making old things in new ways. From cement to food, synthetic biology is causing people to rethink the way things are made. One of the most interesting ideas is the notion of using synthetic biology to manufacture materials in a way that's more friendly to the environment.  

Synbiobeta - the future is now.

Synbiobeta - the future is now.