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. 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
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
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
It's well understood in science education that students are more engaged when they work on problems that matter. Right now, Zika virus matters. Zika is a very scary problem that matters a great deal to anyone who might want to start a family and greatly concerns my students. I teach a bioinformatics course where students use computational tools to research biology. Since my students are learning how to use tools that can be applied to this problem, I decided to have them apply their new bioinformatics skills to identify drugs that work against Zika virus. We don't have the lab facilities ... 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.
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
We feel interesting and sometimes painful sensations when capsaicin, from chilis, and the allyl isothiocyantes from wasabi,bind to receptors in our mouths. In this article, we look at the structures that communicate information to the cell. How do they tell the cell that capsaicin or wasabi compounds are bound? Read more