Thoughts on contemporary life science from a young scientist
I have a kid now, and so do a few people I’ve worked closely with for years. We started talking about sampling bias—not in models, but in life. The neighborhoods we’re raising our kids in, places like Palo Alto and Continue reading
Ever since my time in a crystallography lab, I ve been fascinated by the process of translating raw diffraction patterns into detailed structural models. Back then, we relied on those cool SGI (Silicon Graphics, Inc.) computers—high-performance machines that were the go-to Continue reading
Twenty years ago, my spouse-to-be and I met and became friends. During the pandemic, we got engaged and wanted to create a unique and memorable wedding invitation for our friends and family. Due to a chip shortage, we used both Continue reading
Partner is pregnant, ultrasound looked cool. Had an e-ink dev board collecting dust. So here we are. Pretty simple stuff, the board is an Adafruit MagTag. And all we needed to do was have a progress bar, some graphics, and Continue reading
You’ve all heard of carbon nanotubes. You know, really small tubes made of just carbon atoms; maybe they’re good for moving electrons around. And supposedly carbon nanotubes might play a role in the next type of computers, so-called quantum computers. Continue reading
More and more, as we begin to get a solid grasp on DNA sequencing people are finding the need to understand what makes each type of cell different, or what changes occur before/after the introduction of a therapeutic. Of course, Continue reading
Can we use pipelines developed for human NGS analysis and quickly apply them for viral analysis? With ebolavirus being in the news, it seemed like a good time to try. Just as with a human sequencing project, it s helpful if Continue reading
When it comes to genomics, contemporary bioinformatics follows the dogma of, assemble, detect, and annotate. This over-simplification however, washes over many key features, such as insertions and deletions, which may in fact be pathogenic[1]. High throughput, NGS short read data, and the Continue reading
Over christmas the Genome Reference Consortium gave all of us doing in silico life-science a wonderful present, or maybe it was just a lump of coal. GRCh38, the newest human reference genome assembly, was released to cheers and jeers abound. Of course, Continue reading
Continuing from the previous post[1], dealing with structural effects of variants, we can now abstract one more level up and investigate our sequencing results from a relational pathway model. The Kyoto Encyclopedia of Genes and Genomes (KEGG) has become an Continue reading