One of the things that drives me crazy on occasion is nomenclature. Well, maybe not just nomenclature, it's really the continual changes in the nomenclature, and the time it takes for those changes to ripple through various databases and get reconciled with other kinds of information. And the realization that ...
Do mosquitoes get the mumps? Part V. A general method for finding interesting things in GenBank This is the last in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes and a general method for finding other interesting things. In this last part, I discuss a ...
I suppose I should have expected this. I thought it might be fun to see what the databases had to say about turkeys. So, I queried the NCBI databases, found a taxonomy reference, and started clicking related links to see pictures of the different species. Why? Because it would be ...
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. Human insulin, colored by rainbow. Image from the Molecule World iPad app by Digital World Biology. I wanted to find ...
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 ...
Biological data and databases are ever expanding. This year was no exception as the number of databases tracked by Nucleic Acids Research (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 ...
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 No. This year, the "dead" databases (links no longer valid) outnumber the new ones.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 ...
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 was ...
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 ...
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.
I always look forward to sharing the Nucleic Acids Research (NAR) database issue. This year's blog topic is immunology. The NAR archive lists 31 immunologic databases, but only seven or so are active, and others are not listed in the NAR archive. Read the blog learn more.
This year, I'm a little late with my post on the Nucleic Acids Research (NAR) database issue. While I was procrastinating, a pandemic broke out. So, unsurprisingly, this year's database topic is viruses. The NAR archive lists more than 32 databases related to viruses. Of these, 22 are still operational and five of the databases have information about SARS-CoV-2.
SARS-CoV-2 remains a relevant topic for bio database development. According the the NAR database compendium, and our research, at least 25 SARS-CoV-2 data resources are available to the public. Their Immunoprofiling: How it works specialized topics include immunology, genomics, RNA, proteins, drugs, and SARS-CoV-2 / COVID-19 literature. This post explores the CoV-AbDab database as a resource for studying how antibodies neutralize the virus to protect against serious disease.
It's pretty common these days to pick up an issue of Science or Nature and see people ranting about GenBank (1). Many of the rants are triggered, at least in part, by a wide-spread misunderstanding of what GenBank is and how it works. Perhaps this can be solved through education ...
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 ...
Part I. The back story from the genome record Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank. I. The back story from the genome record II. What do the mumps proteins do ...
Part II. What do mumps proteins do? And how do we find out? This is the second in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes, and a general method for finding interesting things. I. The back story from the genome record II. What do ...
Part III. Serendipity strikes when we Blink In which we find an unexpected result when we Blink while looking at the mumps polymerase. This is the third in a five part series on an unexpected discovery of a paramyxovirus in mosquitoes. And yes, this is where the discovery happens. I ...
Part IV. Assembling the details and making the case for a novel paramyxovirus This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure ...
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 ...
PubMed is an on-line database at the National Center for Biotechnology Information (NCBI) that contains information from scientific literature. Most of the information is related to medical research. To search PubMed, you use a program called Entrez. You go to the NCBI, select PubMed from the menu, type words into ...
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 ...
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 ...
I'm a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases. In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I'm a little skeptical about the blowfly ...
Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let's do a bit of digital biology and see what we can learn. Activity 1. What kinds of animals get the flu? For the past few years we've been worrying ...
or is it just an idea that's ahead of the curve? Last week, I was stunned to discover at least 31 papers in an NCBI Gene database entry that were in the entry for the wrong gene. I wrote about this here, here, here, and here. Now, an oversight like ...
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 ...
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. Sure, those are all cool things to do, but Next Generation DNA ...
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 ...
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 ...
Instead of enjoying a sunny summer day today, or partying with SciBlings in New York, I'm staring out my window watching the rain. Inspiration hit! What about searching for August? Folks, meet the HFQ protein from E. coli. I found this lovely molecule by doing a multi-database search at the ...
A few weeks ago, I wrote about a paper in Science(1) that I read on a connection between a mutation in the dopamine D2 receptor and the genetics of learning. Only, it turned out that when I looked at the gene map... the mutation mapped in a completely different gene ...
In a recent post, I wrote about an article that I read in Science magazine on the genetics of learning. One of things about the article that surprised me quite a bit was a mistake the authors made in placing the polymorphism in the wrong gene. I wrote about that ...
