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.

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

getting the images was the hardest part

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 [1]. Another report suggests there are over 77,000 employers [2]. 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

Last fall, Dr. Thomas Tubon and I presented a Bio-Link webinar on Genome Engineering with CRISPR-Cas9. Since my part will be to help our audience understand the basics of this system, I prepared a short tutorial with Molecule World . Enjoy!

A Quick CRISPR Tutorial

Go to the Digital World Biology CRISPR Structure Collection . Download the second item in the list, 5F9R, by clicking the link in the Download structure column. Identify the three components of the CRISPR - Cas system: The Cas9 protein, the ... Read more

For many years, many of you have been using our popular BLAST for beginners tutorial and the BLASTing through the kingdom of life activity. We decided with the recent updates to the NCBI BLAST pages that it was a good time to update the tutorial and some of the sequences as well. In the tutorial, we've added images that represent the current web pages at the NCBI. For our data set of sequences, we made a couple of the sequences longer, to remove the ambiguity in determining which sequence matches the query best.

Of course, this meant that we also needed to update the answer key. ... Read more

Scale, proportion, and quantity belong to one of the cross cutting concepts in the next generation science standards (NGSS). According to Volume 2 of the NGSS, "in engineering, no structure could be conceived much less constructed without the engineer's precise sense of scale." The authors go on to note that scale and proportion are best understood using the scientific practice of working with models. Read more

April 25th (4/25) is national DNA day. Digital World Biology ™ celebrates by sharing some of our favorite DNA structures. We created these photos with Molecule World ™ Molecule World is a tools for exploring molecular and chemical structures on an iPhone or iPad.

Read more