sporte | June 19, 2007Know your biology!
I get asked often about the type of bioinformatics training that students should get and whether it should be a special course or not.
And I answer that I think teaching bioinformatics in the absence of biology is like teaching Microsoft Word in the absence of writing.
There isn't much point.
tags: bioinformatics, education
So I was happy, to discover from BioInform, that I'm not the only one who thinks this way.
To quote Lincoln Stein:
I hope to see bioinformatics becoming a tool like molecular biology that everybody uses, and that the software we're developing now…
sporte | June 4, 2007Do course evaluations have to be a popularity contest? Or can they be useful tools for improving a class?
tags: teaching, student evaluations
A few days ago, evolgen lamented that his students weren't giving him useful information on their end-of-course evaluations.
I'm not surprised.
When I first started teaching, I was a given a copy of the standard-teacher-evaluation-form-that-everyone-used.
The questions read something like this, with ratings between always and never:
1. Does your instructor show up on time? (to what? coffee dates?)
2. Does your instructor dress appropriately…
sporte | June 3, 2007Nodal point is hosting the eleventh issue of Bio::blogs with two special editions. The first special edition, at Bioinformatics Zen covers tips and tricks for bioinformatics. The second special edition is on personalized medicine and can be downloaded from here.
Eye on DNA is hosting Gene Genie, a collection of posts about genetics and genes.
And, wait, wait, there's more! The Daily Transcript has a virtual garden carnival, it's the Mendel's Garden #15 Summer Reading Edition.
With all that good stuff to read, how can you possibly go out in the sun?
sporte | June 1, 2007How does grass grow in the extremely hot soils of Yellowstone National Park? Could a protein from a virus help plants handle global warming? Okay, that second sentence is wild speculation, but we will try to find the answer to our mystery by aligning our protein sequence to a sequence from a related structure.
tags: plants, bioinformatics, sequence analysis, viruses, fungi, global warming,
Read part I, part II, part III, part IV, and part V, to see how we got here.
This week, in our last installment, we will seek the answers in a related structure.
Last week, I found that my…
sporte | May 31, 2007I want my genome sequenced, too!
Apparently, it's become a popular thing to get your genome sequenced. Craig Venter was the first. Jim Watson's genome (of Project Jim) was ceremonially released this morning (courtesy of 454), and now George Chuch, Larry King, cosmologist Stephen Hawking, Google co-founder Larry Page, Microsoft co-founder Paul Allen and former junk-bond trader Michael Milken want theirs done, too (1).
Two articles from different GenomeWeb releases made a strange combination this morning when I turned on my computer. In one release, GW mentioned that NHGRI (the National…
sporte | May 30, 2007I never thought that writing a blog would provide such a wonderful chance to learn from the community. In these past few days, I have learned so much from readers about finding and accessing information. Now, I want to share their knowledge with those of you who might not be checking the comments sections of my posts. I'm sure you, too, will be thankful for their contribution.
The first set of great suggestions is here
and next, the real information experts, the librarians chime in and demonstrate why they are the experts on finding information.
Be sure to read all the way to the bottom…
sporte | May 29, 2007It was a quiet day at the Seattle FolkLife Festival.
But there were signs that PZ might be lurking about.
At least a few people seemed to think so.
Did they think this guy was PZ in disguise?
sporte | May 29, 2007The first research assignment for our Alaska NSF Chautauqua course has been posted. Your task is to find a wound-inducible plant gene, learn something about it, and post a description in the comment section. We've already had one excellent answer, but I know there are at least 54 wound-inducible genes, so I expect to see more.
Once we get our genes in order (and possibly before), we'll talk more about designing an experiment for detecting gene expression.
In the meantime, I have some pre-course reading assignments to help you prepare.
tags: plants, Alaska, NSF Chautauqua courses,…
sporte | May 28, 2007Is the case for open access truly "open and shut"?
Will open access impede science by limiting genetic studies with families?
tags: genetics, genetic privacy, bioethics, open access
Microsoft's brave new world
The April ALPSP conference began with songs for the open access choir. Microsoft's Lee Dirks painted visions of a utopian future where everything will be open, labs shall be judged by the worthiness of their databases, and even scientists will learn to share.
According to Dirks, "Open access to scientific content, specifically data, will become the norm."
Since I've had a few data…
sporte | May 27, 2007An introduction to our Alaskan NSF Chautauqua course and a pre-course assignment.
I don't know how well this will work, but I thought it might be interesting this year to experiment with blogging about our course and sharing some of our experiences with the rest of the world. Here's your chance readers, if you'd like to do some of the assignments, you are very welcome to follow along and give it a try.
tags: plants, Alaska, NSF Chautauqua courses, bioinformatics, sequence analysis, evolution, wound inducible genes, moose
I'm not likely to get all the assignments or course info posted on-…
sporte | May 25, 2007for our overly enthusiastic comment filter. Thankfully, a reader alerted me to the problem.
I've gone through the spam bucket and you should see them now. My, answers though, may take a little more time.
sporte | May 25, 2007tags: plants, bioinformatics, sequence analysis, viruses, fungi
How does grass grow in the extremely hot soils of Yellowstone National Park? The quest continues.
Read part I, part II, part III, and part IV to see how we got here.
And read onward to see where will we go.
In our last episode, I discovered a new tab in the protein database (well, new to me anyway).
Related structures
If you select this tab, you get a list of protein sequences that are similar, by blastp, to the amino sequences in protein structures.
Naturally, I clicked the tab, and then the Links link, to see…
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, 2007Okay, gossip really isn't my thing and I'm not going to make a habit of it, but I'm really kind of surprised by this. Tech crunch (as I learned from Deepak and Eye on DNA) has a post on 23 and me that is quite bothersome.
Apparently, one of the Google founders has invested in a company that specializes in personal genomics. All kinds of accusations of nepotism are flying in the Tech Crunch comments section.
So what if Sergey Brin (co-founder of Google) and Anne Wojcicki (one of the co-founders of 23 and me) are married. Don't you think Brin has proved himself capable of making good…
sporte | May 23, 2007tags: math, math for biologists
Keith Robison from Omics! Omics! and that fellow Evolgen, with a curious fixation on manatees, have been reminiscing about their college math requirements and speculating on which math courses biologists should take.
They've raised some interesting questions that, I think, make a good meme.
If you answer the questions, let me know, and I will add your link at the bottom of the page.
Here are the questions:
Are you a biologist, if so what kind?
What math did you take in college?
What math do you use?
What math do you wish you'd studied?
How do you…
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: evolution, science education, Alliance for Science
A few months ago, I wrote about a contest, sponsored by the Alliance for Science, in celebration of Darwin Day. High school students were asked to write an essay on the topic: "Why would you want your doctor to have studied evolution?"
The winners have been announced and you can read their essays.
Congratulations winners, teachers, and all participants!
sporte | May 21, 2007tags: moon, lunar geology, NASA, astronomy, computer games, learning through computer games
NASA researchers are learning how to design video games and they're looking for high school students to help. They want students between the ages of 13-18 to play an online computer game about lunar geology and they want high school teachers to help recruit the students.
What's in it for the students?
Players are guided through Selene by the director of the Center for Educational Technologies, Chuck Wood, an internationally known lunar geologist who writes a monthly column on the moon for Sky and…
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…