bioinformatics
sporte | May 21, 2007tags: PubMed, PubMed Central, medical informatics, bioinformatics, finding scientific articles
This three part series covers the problem of finding scientific articles, compares results from a few different methods, and presents instructions for the best method.
A day in the life of an English physician
In April, I had the great fortune to attend (and speak at) a conference on scientific publishing sponsored by the Association of Learned and Professional Society Publishers. One of the first speakers was an English physician who described his trials and a typical ordeal in trying to use the…
sporte | May 18, 2007tags: plants, bioinformatics, sequence analysis, viruses, fungi
Quick synopsis: A type of grass grows in Yellowstone National Park in hot (65° C), unfriendly soil. How the plant manages this feat is a mystery. What we do know, is that the grass can only tolerate high temperatures if it's been infected by a fungus, and the fungus has to be infected by an RNA virus. In the paper describing this discovery, the researchers provided the GenBank accession numbers for the viral sequences. I decided to see if I could find out more about the proteins and what they do. Read part I, part II, and part…
sporte | May 11, 2007Do you want to learn how to use some cool biotechnology and bioinformatics methods in your college or high school class?
If you're on the East coast, the best place to go is the Fralin Biotechnology Conference at Virignia Tech, July 18-21st.
(Yes, it's the same Virgina Tech, and that's why I waited to post this announcement).
There's something for everyone at this conference. For beginners, there's a pre-conference Biotech Boot camp where you can learn to run gels and clone genes. For instructors with more experience, there are great talks, new techniques to test, and plenty of…
sporte | May 10, 2007tags: moose, bioinformatics class, willows, plant genes
PZ's morning post about a bear killing a moose in someone's yard (they do live in Alaska, after all), reminded me that it's time to make an announcement about our upcoming course.
No, no, no! We're not going to kill any moose on the premises. We're going to learn about the moose and its food, not the moose as its food.
But, if you take the course that precedes ours, you might get to see some moose, and you might get to see some bears eating salmon.
The class before ours is entitled "Ecology of South Central Alaska " and they have…
sporte | April 21, 2007If you've ever looked at an evolutionary tree, contemplated phylogeny, cladistics, or the like, you're probably aware that Joe Felsenstein is one of the leaders of the pack.
And you will certainly enjoy, this interview that Blind Scientist has posted.
I wouldn't advise reading the interview to learn about doing phylogenetics, but you will learn a bit about the social anthropology of the field. Felsenstein does a wonderful job of supplying historical context to phylogenetic arguments and filling in the missing details.
A phylogenetic tree is a kind of model or hypothesis that's put forth…
mikethemadbiologist | April 19, 2007One of the things that has been revealed by the VA Tech shooting is that the government keeps a database of prescription drug users. This has bothered some. Glenn Greenwald writes (italics mine):
Let me ask you this question: let's say I come into your office (I'm a mentally competent adult -- at least in our hypothetical) and tell you that I want to take a Schedule II drug (or Schedule III) for Medical Problem X (or even just garden-variety insomnia, depression, or anxiety). You tell me that I shouldn't, that there is a high risk of addiction, that the problem doesn't warrant that…
mikethemadbiologist | March 29, 2007In response to us foul-mouthed evolutionists, Casey Luskin asks, "Yet for all their numbers and name-calling, not a single one has answered Egnor's question: How does [sic] Darwinian mechanisms produce new biological information?" I've never liked the whole "biological information" concept.
As far as I can tell, the creationists started bandying the term about after this George Gilder article in Wired was published:
Just as physicists discovered that the atom was not a massy particle, as Newton believed, but a baffling quantum arena accessible only through mathematics, so too are biologists…
mikethemadbiologist | March 21, 2007In scientific publishing, one of the important things is what is known as the "impact factor" which is the the average number of citations a journal receives over a 2 year period. The impact factor is often used by librarians and researchers to determine which journals to purchase and where to publish. There are some problems with the impact factor, however.
The basic problem is that the impact factor does not consider the importance of the citing article. In other words, the cited paper is far more likely to be looked up by a reader if it is cited in five high profile journal articles (or…
sporte | March 10, 2007It must be spring. Summer course announcements are popping up everywhere and this site is no exception.
Last Friday, I posted an announcement about our summer bioinformatics course in Alaska, June 27-29th.
This week, I have a couple more conferences to announce. Naturally, I'll be at both of them, leading hands-on workshops for college and high school teachers in using the technology.
Today, I want to tell you about the Bio-Link Summer Fellows Workshop, June 4th-8th Berkeley, CA
I became involved with Bio-Link ten years ago when I was running the biotechnology program at Seattle…
sporte | March 9, 2007Registration has opened a bit late this year, but it's always tricky when large programs change hands. The Chautauqua Short Course program for College Teachers is no different. In fact, as far as I know, we may still be waiting for the National Science Foundation to make a final decision on funding.
Still, summer is rapidly approaching and I know many of you are making plans for attending summer workshops and squeezing in a bit of vacation time.
That's why I think you might like to consider learning bioinformatics in Alaska.
Yes. I did write "Alaska."
Anchorage, Alaska.
Dr. Linnea…
sporte | February 21, 2007Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things.
Step right up! Watch original research, as it happens, on the web!
I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants.
Previous parts:
Part I. The research
Part II. An introduction
Today: Part III: An inordinate fondness for hypothetical proteins
After today, we will have:
Part IV: Did we get lost in translation?
(I will add the link after it's posted)
Let's begin
Sigh.
It always happens when I have homework to grade.…
sporte | February 9, 2007I found it in the MeSH database.
Really!
Looking for a quick answer? Don't ask a scientist
It doesn't take long to realize that scientists can spend countless hours debating the meaning of words. Our very own ScienceBlogs is a great example, just look at the many ways we can define (and debate) the meaning of a small, four-letter word like "gene". We also like to qualify our answers with a thousand conditions "usually, it's like this, but...."
This habit can be very frustrating if all you want is a quick concise answer.
On your marks, define that term!
So, many people turn to Google and…
sporte | February 8, 2007"Beware the Jabberwock, my son!
The jaws that bite, the claws that catch!
Beware the Jubjub bird, and shun
The frumious Bandersnatch!"
- from Jabberwocky, by Lewis Carroll
I'm certain that if we ever sequenced DNA from the frumious Bandersnatch it would match hypothetical and putative proteins.
Why?
Because we always (well, almost always) get matches to hypothetical and putative proteins when we do a database search with a protein sequence.
Why?
Because many of the protein sequences in GenBank (at the NCBI) are a result of conceptual translations.
What? !!
A conceptual translation…
sporte | February 7, 2007Yesterday, both Joshua and I wrote about grasses that grow in the unusually hot soil at Yellowstone National Park.
Now, I knew that hot springs bacteria can tolerate high temperatures, but I was really surprised to learn that plants could.
It was even more surprising to learn that this amazing ability was conferred on the plants by an infected fungus. I presented the data yesterday. If the fungus wasn't infected, the plants couldn't tolerate high temperatures. And, not only was the fungus-virus combination important for the grass, it had the unusual ability to confer temperature…
sporte | February 5, 2007How to win the X PRIZE in genomics
In October, 2006, the X PRIZE foundation announced that second X prize would focus on genomics. The first team to successfully sequence 100 human genomes in 10 days will win $10 million dollars.
And I would venture to guess, that the winning team would also win in the IP (intellectual property) game and the genetic testing market since they will gain an unprecedented look at genetic variation.
But when is done really done?
The first trick is defining what it means to be done. My husband says that "a sequencing project is done when the people who are…
sporte | February 2, 2007Vizzini: He didn't fall? Inconceivable!
Inigio: You keep using that word. I do not think it means what you think it means.
- William Goldman, The Princess Bride
Excuse me while I temporarily interrupt the genome sequencing series to define a word.
Artifacts in the classroom
It's disorienting. You learn a word in certain context. You're sure of it's meaning and then you end up in a situation where people use the word in a completely unexpected way and no one else seems bothered by this!
I had this happen once with the word "artifact." I had organized a conference and some workshop…
sporte | February 1, 2007To the ancient Greeks, a chimera was a kind of monster, with the body of a goat, the tail of a dragon, and a lion's head. To geneticists, a chimera can be an animal that's derived from two embryos, such as a transgenic mouse. Or if the organism is a plant, it can be a plant with a graft. We have a chimeric cherry tree in our back yard with branches from Rainier cherries, Bing cherries, and Van cherries. And you should see the chimeras that hang out at evolgen.
Naturally, the DNA cloning and sequencing world has it's chimeras, too. There are two main kinds that I know. Sometimes chimeras…
sporte | January 31, 2007The general steps in genome sequencing were presented in the earlier installments ( there are links at the bottom of the page), but it's worth repeating them again since each of the earlier steps has a bearing on the outcome of those that come later.
These are:
Break the genome into lots of small pieces at random positions.
Determine the sequence of each small piece of DNA.
Use an assembly program to figure out which pieces fit together.
That first step, making a collection of DNA fragments (a library), with breakpoints at random positions is of critical importance to the success of later…
sporte | January 30, 2007"How much do I love you?
I'll tell you no lie.
How deep is the ocean?
How high is the sky?"
- Irving Berlin
The other installments are here:Part I: IntroductionPart II: Sequencing strategiesPart III: Reads and chromatsPart V: checking out the library
We all know that sequencing a genome must be a lot of work. But unlike love, it is something we can measure. In fact, an important part of genome sequencing is estimating just how much work needs to be done. This is especially important if you're the one paying for it or the one writing the grant proposal.
Coverage depth: or why do we…
sporte | January 28, 2007Shotgun sequencing. Sounds like fun.
Speculations on the origin of the phrase
I think that this term came from shotgun cloning. In the early days of gene cloning before cDNA, PCR, or electroporation; molecular biologists would break genomic DNA up into lots of smaller pieces, package DNA in lambda phage, transduce E. coli, and hope for the best. Consistent with the shotgun metaphor, we even used to store our microfuge tubes in plastic bullet boxes that my boss found at the sporting goods store. (Apparently this practice was unique to Minnesota, though. When I moved out west for graduate…