web resources
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 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 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 | 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 8, 2007Bertalan Meskó shares his strategies for keeping up and gives instructions so you can do the same.
He shows how you can save your favorite PubMed searches and have NCBI send you e-mails about new papers. He describes some third party PubMed tools that make pretty graphs. Last, he discusses RSS readers, Connotea, and BioWizard. It's all very helpful and nicely described.
sporte | September 3, 2007The Capitol Hill Seattle blog has a great set of lunar eclipse photos on flickr.
sporte | August 25, 2007Why the ABRF of course!
I spend a fair amount time every summer giving workshops for college and high-school teachers on genomics and bioinformatics. One of the things that always surprises them, is the amount of lab work that's carried out by people working in shared, or core lab facilities. For example, if I was working at a research university and I wanted to sequence some DNA, maybe several patient samples, or a bacterial genome, I would send the DNA to a core lab and they would send me the sequences. I would analyze the data and write the paper.
I've simplified that process a bit in…
sporte | August 21, 2007or maybe seminars on parade?
They're calling them PubCasts, but I don't think I'll be watching them in a pub.
Seriously, SciVee is kind of cute, and has lots of potential down the road, and even has a few unintentional moments of humor right now, but....
It's a bit distracting. I can't watch these without imagining that the speakers are standing on tiptoe, desperately trying to peak their heads above the large bits of text that appear mysteriously on the screen and can't be removed.
Considering the technical glitch, it's just a bit ironic that many of the movies are from the PLoS journal…
sporte | July 30, 2007Amateur astronomers unite! The pros want your help!
image from Astronomy Picture of the Day, Credit: NASA, ESA, A. Aloisi (STScI / ESA), Hubble Heritage (STScI / AURA) - ESA/Hubble Collaboration
I learned about this from the Washington Science Teachers Assocation.
Galaxy Zoo and the Sloan Digital Sky Survey are looking for your help in sorting out different galaxies. It's a cool opportunity for anyone to go where few non-astronomers have gone before and help do real science at the same time.
What does this involve?
Go to the Galaxy Zoo, peruse their tutorial, and learn how to pick…
sporte | July 16, 2007BLAST is a collection of programs that are used to compare sequences (DNA, RNA, or protein) to larger collections of sequences that are stored in databases. I've used BLAST as a teaching tool for many years, partly because it's become a standard tool for biological work and partly because it's very good at illustrating evolutionary relationships on a molecular level.
A few months ago, the NCBI changed the web interface for doing BLAST searches at their site. I wrote earlier about changes that I made to our animated tutorial in response to the new BLAST. Now, I want to mention some of the…
sporte | July 12, 2007By now, many of you have probably seen the the new BLAST web interface at the NCBI. There are many good things that I can say about it, but there are a few others that caught me by surprise during my last couple of classes.
tags: blast, BLAST tutorial, science education
Because of these changes, and because I'm giving a workshop for teachers on BLAST at the Fralin Biotechnology Conference in Blacksburg, VA, next week, it seemed like a good time to update our animated BLAST tutorial at Geospiza Education and save myself some trouble.
I originally created the BLAST for beginners tutorial to…
sporte | July 11, 2007What do people in biotechnology do on the job?
What can students do with a science degree once they've finished college? Some answers can be found at the "Life Sciences Central web site. Created by the Workforce Development Council of Seattle-King County, this is a wonderful resource for anyone who's considering biotechnology for a potential career.
My favorite part of the site is the series of short video interviews from people in the biotech industry, describing what they do on the job and how they got there.
tags: biotechnology careers, biotechnology, career+descriptions
Ten interviews…
sporte | June 21, 2007If we asked any biologist to pick the five most important techniques in biology, that list would certainly include PCR.
PCR stands for Polymerase Chain Reaction. It's used everywhere. We use it to amplify DNA for cloning, we use it for diagnostic tests, for DNA sequencing, for identifying pathogens, for identifying our long-lost relatives (and sometimes parents), and in forensics. If there's a technique that involves DNA, PCR is probably involved somewhere, too.
Since PCR is such an important technique, and we're going to be using PCR in our course, it's worth checking out a few…
sporte | May 24, 2007tags: PubMed, PubMed Central, medical informatics, bioinformatics, finding scientific articles
I meant for this to be a three part series, but in part II, I learned that one more experiment had to be done. I had to know if the articles I found in PubMed Central were the same articles that I found in PubMed.
Part I and part III cover the background and my favorite method. Now, we're going to find out if my favorite method is really enough.
In other words, I had this kind of problem (shown in the diagram) and I just had to know which case was correct:
The method:
To test this, I did a…
sporte | May 23, 2007tags: PubMed, PubMed Central, medical informatics, bioinformatics, finding scientific articles
This is the third, and last part in a three part series on finding free scientific papers. You can read the first part here: Part I: A day in the life of an English physician and the second part, where I compare different methods, here.
Today, I will show you how to use my new favorite method.
How to find free scientific publications
1. Go to the NCBI.
2. Choose the link to PubMed. (It's in the top blue bar, under the DNA icon)
3. Click the Limits tab (circled below).
4. Click the box…
sporte | May 22, 2007tags: PubMed, PubMed Central, medical informatics, bioinformatics, finding scientific articles
This is the second part in a three part series on finding free scientific papers. You can read the first part here: Part I: A day in the life of an English physician
Today, we do an experiment with PubMed and PubMed Central to determine the best way to search for free articles.
The biggest problem that our doctor friend, from part I, faced, wasn't that he couldn't find the information he wanted. His problem was that he found too much information. And, most of what he found, he couldn't get at.…
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 | 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 | January 21, 2007I read about this in Science and immediately had to check it out. Instant gratification on the internet is such a wonderful thing!
The Ed Kravitz lab has made movies of fights and even put them on the web for your viewing pleasure.
You can see the following fly fights that might suit your fancy:
Fighting flies
Male Drosophila melanogaster aggression (with music)
Female Drosophila melanogaster aggression page
Or if you prefer battling sea life, you can watch the lobsters duke it out. Now I know why the lobsters in the grocery store tank always have rubber bands around their claws.
Lobbing…