bioinformatics
sporte | July 23, 2007Last week I found a bug in the new NCBI BLAST interface.
Of course, I reported it to the NCBI help desk so it will probably get fixed sometime soon. But it occurred to me, especially after seeing people joke about whether computer science is really a science or not, that it might surprise people to learn how much of the scientific method goes into testing software and doing digital biology.
tags: blast, software testing, scientific method, science education
What happens when the scientific method isn't used?
I wrote earlier in January about applying scientific principles from the wet…
sporte | July 18, 2007If you missed reading some of the comments on yesterday's post, I highly recommend that you go back and catch up.
I especially want you all to pay close attention to the comments from Deepak and Keith Robison. Like me, they work in industry and not in an ivory tower. Unlike me, they actually work in the biotech industry, while I work with people who slave away building the picks and shovels (picture a Greta Garbo sigh, for dramatic effect).
Their words ring true to me and match the kinds of things that I've seen and experienced. If you're interested in bioinformatics as a career or how…
sporte | July 17, 2007I had an enlightening experience recently, after I wrote some bioinformatics activities, under contract, for a community college. At the end of the project, the person at the college asked me if the activities were anything like the things that a "bioinformatics technician" would do on the job.
tags: biotechnology careers, biotechnology, career+descriptions,bioinformatics
Well no, I said, and added that I'd never heard of a bioinformatics technician before and I really didn't know what they would do. I thought that the people most likely to use our activities on-the-job would be research…
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 13, 2007Although, I didn't believe it when I first saw it. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my eyes.
Yet here is parallel DNA, with both strands oriented in the same direction, right here on your monitor. And the commenters were correct.
tags: DNA structure, DNA , molecular structure, biochemistry
The image that I posted a couple of days ago was made from part of this same structure. In that image, I hid the rest of the bases to make it easier to see why this structure is so strange.
Here are two images that show the landmarks a…
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 10, 2007Okay, all of you biochemists and molecular biology types. I have a puzzle for you that I found by accident during a lecture. Yes, I was the one lecturing and the notes will be posted soon.
In the meantime, here's your puzzle: What's unusual about this pair of bases?
tags: DNA structure, DNA , molecular structure, biochemistry
(Those of you who attended our Chautauqua course - I know you probably know the answer - but don't answer, okay?)
sporte | July 9, 2007It was only a couple of weeks ago but it seems like years. I had spent a month learning how to use most of the features on my shiny new phone and we were in Alaska using Google maps to find our way around Fairbanks.
My thumbs were getting sore, but so what? I could a give a slide show on my phone, I could read my Gmail messages, and we could find a friend's house in the Google map satellite view and amaze our older relatives with the thrill of technology.
I'm not even a materialistic, gadgety sort of person, but I was in love.
And now, well, maybe you guessed it.
tags: chromatograms,…
sporte | June 22, 2007What happens when a biologist tries to talk with the IT group? Needless to say, they don't speak the same language.
Reposted from the archives.
Imagine this. You've been sequencing DNA for a few years now, perhaps ESTs, or something else, and storing files on your local network. Your system administrator makes backup files for you and all is well.
But one day you learn about interesting results that other people are getting by assembling sequence data themselves and you decide to try it, too.
Watch out! You are about to descend into bioinformatics hell.
Soon you learn that the assembly…
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 | June 20, 2007Quoth Dr. Stemwedel, from Adventures in Science and Ethics.
In the case of Universities and four-yr colleges, I completely agree. If you're looking for job training, go to a community college.
This post is in response to one of the comments from the other day. This commenter expressed frustration at having a completed a bioinformatics training program that left him/her with a certificate but without the right skills to find a job.
tags: bioinformatics, education
He/she suggested that "the government must select candidates for teaching from industry"
This post is my answer.
In the U.S.,…
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 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 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, 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 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, 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 structuresIf 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 what this…
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.…