Databases

It's time for the annual blog about the annual Nucleic Acids Research (NAR) database issue. This is the 24th database issue for NAR and the seventh blog for @finchtalk. Like most years I have no idea what I'm going to write about until I start reading the new issue. Something always inspires me. This year's inspiration came from missing data.

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Someone missed the memo. Over the past year, news and presentations by NIH leaders like Philip Bourne have communicated that the proliferation biologically focused databases is unsustainable. However, unlike last year, where the number of databases tracked by Nucleic Acids Research (NAR) dropped by three databases, 2015's net growth ... Read more

When finding a female scientists' data turns into an archeological treasure hunt. A few months ago, I decided it would be interesting to celebrate various scientific contributions by making images of chemical / molecular structures in the Molecule World iPad app and posting them on Twitter  (@MoleculeWorld).  Whenever I can, I like to ... Read more

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  No.  This year, the "dead" databases (links no longer valid) outnumber the new ones.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 ... Read more

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.

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 fun blog posts about pinene, ... Read more

By @finchtalk (Todd Smith)

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 NAR grew from 1512 to 1552. In the leadoff introduction [1] the authors summarize this year’s issue and the status of the NAR index. The 21st issue includes 185 articles with 58 new databases and 123 updates. In the 1552 database repository, 193 had their URLs corrected and 24 were removed because they were deemed obsolete. ... Read more

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 collected, they end up in a database somewhere and the University researchers analyze them and write papers. At least that's my impression so far. It seems to me, that with all kinds of databases out there, on-line, there should be plenty of opportunity for both citizens and student ... Read more

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.


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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 of the drug and get patients the correct dose more quickly. And it seems obvious that a test that would allow doctors to predict your ability to metabolize warfarin, would be a great thing, right?

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