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Databases

Category archives for Databases

Bio Databases 2015

Something interesting happened in 2014. The total number of databases that Nucleic Acids Research (NAR) tracks dropped by three databases! What happened?  Did people quit making databases?  No.  This year, the “dead” databases (links no longer valid) outnumber the new ones. To celebrate Digital World Biology’s release of Molecule World I’ll discuss some of the new structure databases…

Sometimes when you go digging through the databases, you find unexpected things. When I was researching the previous posts on insulin structure and insulin evolution, I found something curious indeed.                     I wanted to find out how many different organisms made insulin, so I used a database…

On pinene and inhibiting enzymes. People of a certain age may remember a series of really funny commercials featuring Euell Gibbons and his famous question about whether you’ve ever eaten a pine tree.  “Some parts are edible” said Euell. Perhaps some parts are, but other pine tree products aren’t so nourishing.  Crystallography365, aka @Crystal_in_city  had a couple of…

Bio Databases 2014

By @finchtalk (Todd Smith) In 2014 and beyond Finchtalk will be contributing to Digitalbio’s blog at this site. We kick off 2014 with Finchtalk’s traditional post on the annual database issue from Nucleic Acids Research (NAR). Biological data and databases are ever expanding. This year was no exception as the number of databases tracked by…

Is there a place for citizen scientists in the world of digital biology? Many of the citizen science projects that I’ve been reading about have a common structure. There’s a University lab at the top, outreach educators in the middle, and a group of citizens out in the field collecting data. After the data are…

You might think the coolest thing about the Next Generation DNA Sequencing technologies is that we can use them to sequence long-dead mammoths, entire populations of microbes, or bits of bone from Neanderthals. But you would be wrong.

Warfarin, a commonly used anti-clotting drug, sold under the brand name of Coumadin, has a been a poster child for the promise of pharmacogenomics and personalized medicine. The excitement has come from the idea that knowing a patient’s genotype, in this case for the VKORC1 and CYP2C9 genes, would allow physicians to tailor the dose…

Last night, the phone rang at 9:22 pm. I quickly glanced at the caller ID. Hmmm. Why is the Seattle School district calling us at this time of night? Apparently the swine flu has come to Seattle and the school district thought we should know. Those messages are helpful if you’re a parent, but they…

What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu? If we had a lab, we might use antibodies, but when you’re a digital biologist, you use a computer. Activity 4. Picking influenza sequences and comparing them with phylogenetic trees

I was pretty impressed to find the swine flu genome sequences, from the cases in California and Texas, already for viewing at the NCBI. You can get them and work them, too. It’s pretty easy. Tomorrow, we’ll align sequences and make trees. Activity 3: Getting the swine flu sequence data