sporte | October 29, 2007One of the greatest shocks when I started working in industry was the realization that the peer-reviewed paper, the most valuable form of currency in the academic world, was valued so little.
In academics, there is a well-established reward system for getting your work published in peer-reviewed journals. Whether or you not get hired, get money to do research, get to keep your job (i.e. get tenure), all depend on depend on your ability to get papers written and accepted by your peers. (Community colleges are an exception to this, there it's your teaching abilities that matter, not your…
sporte | October 28, 2007Metagenomics is a field where people interrogate the living world by isolating and sequencing nucleic acids. Since all living things have DNA, and viruses have either DNA or RNA, we can identify who's around by looking at bits of their genome.
Researchers are using this approach to find the culprit that's killing the honeybees. We're also trying to find out who else shares our bodies, and lives in our skin, in our stomachs, and other places where the sun doesn't shine. Craig Venter used metagenomics when he sailed around the world and sequenced DNA samples from the Sargasso Seas.
In this…
sporte | October 27, 2007The simple fact is this: some DNA sequences are more believable than others.
The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad."
All they see are the base calls and sequences: ATAGATAGACGAGTAG, without any supporting information to help them evaluate if the sequence is correct. If DNA sequencing and personalized genetic testing are to become commonplace, the practice of ignoring data quality is (in my opinion) simply unacceptable.
So, for awhile anyway, I'm making a…
sporte | October 26, 2007We have lots of DNA samples from bacteria that were isolated from dirt. Now it's time to our own metagenomics project and figure out what they are. Our class project is on a much smaller scale than the honeybee metagenomics project that I wrote about yesterday, but we're using many of the same principles.
The general process is this:
1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is good, and measure how good it is, but it cannot turn bad data into good data. And, there's no point in wasting time with…
sporte | October 25, 2007The next time you bite into a crisp juicy apple and the tart juices spill out around your tongue, remember the honeybee. Our fall harvest depends heavily on honeybees carrying pollen from plant to plant. Luscious fruits and vegetables wouldn't grace our table, were it not for the honeybees and other pollinators.
Lately though, the buzz about our furry little helpers hasn't been good. Honeybees have been dying, victims of a new disease called "colony collapse disorder," with the US, alone losing a large number of hives in recent years.
Why?
Researchers have speculated about everything…
sporte | October 24, 2007Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?
This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman. (See see "Sequencing the campus at the Johns Hopkins University" for more background.)
We are going to do a bit of metagenomics by using FinchTV and blastn to identify the soil bacteria that were sampled from different biomes and then use an SQL query that I…
sporte | October 23, 2007The NASA Earth observatory has some amazing photos of the wildfires in California. I've put a small version of one image here, but you should go to the NASA site and see the high resolution images. The fires are horrible but the images are fantastic.
sporte | October 23, 2007It's hard to teach bioinformatics when schools work so hard to keep us from using computers.
Anecdotes from the past
Back in my days as a full-time instructor, I fought many battles with our IT department. Like many colleges, we had a few centralized computer labs, tightly controlled by IT (aka the IT nazis), where students were supposed to go to do their computing. Instructors also had a centralized computer lab, but over the years, we gained the right to have computers in our offices. Our major battle was whether or not we'd be allowed to use Macs.
There are certainly advantages in…
sporte | October 21, 2007Welcome Bio256 students!
This quarter, we're going to do some very cool things. We are going to use bioinformatics resources and tools to investigate some biological questions. My goal, is for you to remember that these resources exist and hopefully, be able to use them when you're out working in the biotech world. I don't believe that bioinformatics is a subject that you can really grasp without getting your fingers dirty. So, this course will include a lot of hands-on work.
My friend and collaborator at Johns Hopkins University has given me data sets from the past three years and we…
sporte | October 17, 2007If like me, you were a little disoriented and confused when you visited Second Life and traveled through orientation island, then you may like this.
The Wired Campus (from The Chronicle for Higher Education) led me to an interesting post from the New Media Consortium and a new place to visit once I get a bit of time to do so.
The NMC has set up a special orientation island for educators. From the photos, this island looks like a unusually clean and artistic rendition of San Francisco, complete with the Golden Gate bridge and a few Bay area landmarks.
Unlike the usual orientation, though,…
sporte | October 16, 2007A few weeks ago, I did some "back-of-the-envelope" calculations to explain to a reader why genome sequencing costs so much.
I estimated that, if JCV's genome were sequenced at the cost advertised by university core laboratories, his genome would cost about $128 million.
That was an estimate, of course. But what did it really cost?
Genome Technology asked J. Craig himself. In the October 2007 issue of GT, JCV estimates that the cost from the first Celera human genome project (guess who?) was about $100 million and that the cost of his most recent genome project was at least $70 million.…
sporte | October 15, 2007This morning Bora and I both gave talks in Second Life. Since this was a pretty new experience for me, I thought I'd share my thoughts on it.
Ever since the days when I watched cartoons on Saturday mornings, I thought it might be fun to be in one. But when I tried it this morning, truthfully, it was a bit scary. I haven't experienced stage fright like that for quite awhile. Perhaps it was the setting. I was really nervous and I hadn't practiced with Second Life enough to know what to do.
Watching a talk in Second Life
Moving around in my avatar felt awkward. It was strange not to be…
sporte | October 14, 2007I've been reading quite a bit lately about Universities setting up virtual classrooms in Second Life, so when Bertalan Meskó from ScienceRoll invited me to come give a poster, I decided it was time to take the plunge. Besides, I'm going to be teaching an on-line bioinformatics course this spring for Austin Community College, so this seemed like a good time to find out what the fuss is all about.
Tomorrow, Bora Zivkovic (A Blog Around the Clock) and I will be the first ScienceBloggers (that I know of) to give poster presentations in Second Life. Our talk will be at 4 pm GMT, 12 noon EDT, and…
sporte | October 14, 2007October is a month of darkness, mystery, and dread. Only one holiday brings joy in October and even then, October joy is distilled through fear and apprehension. In the early evenings the sun hurries home and once familiar objects loom ominously in the dark. Giant spiders appear out the fog, lurking on webs that span our walkways and doors. Even Mendel's Garden is dark and malevolent when October greys our skies.
genetics, Mendel's garden, blog carnival.
Horror stories for adults
October looks bleaker than usual if you're out of work and not getting paid. If your income matches this…
sporte | September 26, 2007For the record: Chlamydia is NOT a virus.
I am bummed. I like the little MicrobeWorld radio broadcasts, and the video podcasts are even more fun.
But I was perusing the archives and I found this:
I could ignore this if it came from a different source, but MicrobeWorld is produced with funding from the American Society for Microbiology!
Microbiologists are supposed to know the difference between bacteria and viruses. It's part of our training and big part of what we do.
I know, as scientists we're always supposed to follow the mantra of "buyer beware" and "be skeptical of…
sporte | September 25, 2007Biology as a second-language: the immersion method
Language teachers say the best way to learn a language is by total immersion and even better, spending time in the country where it's spoken conversing with native speakers.
See it, hear it, speak it, use it!
Put yourself in a position where you must do these four things to survive (or at least find the restroom) and you will learn more rapidly than by any other method.
Graduate school serves a similar purpose for scientists. You go from an environment where your fellow students and co-workers spend time chatting about TV shows and…
sporte | September 20, 2007The-Scientist recently posted a short piece on science-related blogs and interviewed seven different science bloggers to find out which blogs they recommend.
One puzzling feature about the piece is that all the bloggers they interviewed were male.
Pretty harmless, right?
Sure.
Except, as others have pointed out (here and here), these kind of invisible moments add up.
Here are some of mine:
I rode my bike to work yesterday and happened on a large bill-board with the phrase: "Are you a long-haired, pony-tail-wearing, software geek?" I was stunned. How did they know? When did I become…
sporte | September 19, 2007But I'm certain that you will find some interesting things.
Mendel's Garden will be ready for harvest, here on Sunday, October 7th, and I need your help.
You won't need to stay on the path, but I would like you to submit your best genetics & molecular biology articles by midnight, Friday October 5th.
Either send your articles to me: digitalbio at gmail dot com
or use the handy-dandy submission form.
With your help, Mendel's Garden is certain to bloom with earthly delights.
sporte | September 18, 2007At least this is what I imagine it's like to live with someone who has bipolar disorder. Tonight - Sept. 19th, between 7-8 pm EDT, there will a "blogger's conference with the experts," discussing this very thing.
The transcript will be posted and you can learn more about the event here.
sporte | September 16, 2007Can you tell the difference between the sort of person who would write a programming language and a serial killer?
It's getting close to Halloween so this is a good time to test your powers of detection.
Malevole has a lovely survey that asks if you can tell whether a person is a famous computer scientist or famous for another reason.
I'm interested in whether biologists as a group are able to tell the difference.
If you'd like to play:
1. Go take Malvole's survey first,
2. Then come back here and take mine.
It won't take much time and I'll post the results up in a couple of weeks.