Bioinformatics:
A potential link between lung cancer and human papilloma virus may make parents even more glad about vaccinating their children with Gardasil®. Not only are the children protected against viruses that commonly cause cervical cancer, they may be protected against some forms of lung cancer as well. The April 25th version of Nature News reports (1) that two viruses, HPV...
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Posted on April 27, 2008 5:50 PM • 10 Comments •
How to compare mutant and normal protein structures.
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Posted on April 26, 2008 1:21 PM • 2 Comments •
One of my favorite web 2.0 technologies is the webinar. When you work at a company and not a University, with constant seminars, it gets a bit harder to hop on a bus and travel across town to learn about new things. Webinars are a good way to fill that gap. I grab my coffee cup, put on my headphones,...
Posted on April 22, 2008 3:36 PM • 2 Comments •
In the class that I'm teaching, we found that several PCR products, amplified from the 16S ribosomal RNA genes from bacterial isolates, contain a mixed base in one or more positions. We picked samples where the mixed bases were located in high quality regions of the sequence (Q >40), and determined that the mixed bases mostly likely come from different...
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Posted on April 17, 2008 8:00 AM • 2 Comments •
Can you solve this puzzle?
Posted on April 11, 2008 8:23 AM • 0 Comments •
Goodbye desktop, we're off to see the web. Both my students and I have been challenged this semester by the diversity of computer platforms, software versions, and unexpected bugs. Naturally, I turned to the world and my readers for help and suggestions. Some readers have suggested we could solve everything by using Linux. Others have convincingly demonstrated that Open Office...
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Posted on April 3, 2008 12:40 PM • 6 Comments •
Is it real or is it April Fools?...
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Posted on April 1, 2008 8:18 AM • 3 Comments •
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA)...
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Posted on March 27, 2008 9:11 AM • 24 Comments •
A video tutorial on molecular structures.
Posted on March 19, 2008 5:37 PM • 1 Comments •
One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies. I've been running into this uncertainty myself lately....
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Posted on March 17, 2008 2:05 PM • 3 Comments •
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...
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Posted on March 13, 2008 6:42 PM • 0 Comments •
It's a Solexa data directory. I've held off on blogging about Next Generation Sequencing here, but now that one of my colleagues has started blogging about it, it seems like a good time to write a little about FinchTalk, our company blog. We've decided that we can serve an educational role for people who are interested in Next Generation DNA...
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Posted on March 13, 2008 12:28 PM • 0 Comments •
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...
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Posted on March 12, 2008 12:50 PM • 35 Comments •
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA...
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Posted on March 11, 2008 12:00 PM • 6 Comments •
The other day, I wrote that I wanted to make things easier for my students by using the kinds of software that they were likely to have on their computers and the kinds that they are likely to see in the business and biotech world when they graduate from college. More than one person told me that I should have...
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Posted on March 11, 2008 8:00 AM • 33 Comments •
The NASA Earth Observing System is an incredible resource for both science and education. One of the amazing things about it is all the different kinds and quantities of data are assembled together into pictures that even grade school kids can immediately comprehend. How do they do it? Each of the EOS satellites delivers a terabyte or more of data...
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Posted on March 10, 2008 9:31 AM • 0 Comments •
Three (or more) operating systems times three (or more) versions of software with bugs unique to one or systems (that I don't have) means too many systems for me to manage teaching. Thank the FSM they're not using Linux, too. (Let me see that would be Ubuntu Linux, RedHat Linux, Debian Linux, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It...
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Posted on March 10, 2008 8:09 AM • 12 Comments •
Here's a fun puzzler for you to figure out. The blast graph is here:...
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Posted on March 7, 2008 12:28 PM • 2 Comments •
Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that...
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Posted on February 26, 2008 10:58 AM • 3 Comments •
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus....
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Posted on February 26, 2008 10:47 AM • 0 Comments •
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes....
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Posted on February 26, 2008 10:19 AM • 0 Comments •
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every...
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Posted on February 26, 2008 10:14 AM • 0 Comments •
I love the way you show me secret things. All I do is type: Select * from name_of_a_table And you share everything with me. Without you, my vision is obscured, and all I see is the display on the page. In fact, this was the push that finally made me decide to learn SQL....
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Posted on February 16, 2008 7:42 PM • 3 Comments •
A quick video introduction to BLAST.
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Posted on February 12, 2008 8:14 AM • 13 Comments •
A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say "no." Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other's expertise. Well, I've changed my mind in one respect. Most biologists need to work with some kind...
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Posted on February 9, 2008 5:55 PM • 21 Comments •
In which we're reminded that database searches are experiments, too. One of the trickiest things with bioinformatics experiments is repeating them. This challenge isn't related to the validity of the original results, the challenge is that, unless you made your own database and kept it in the same state, the database that you'll be using at a later time, sometimes...
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Posted on December 19, 2007 9:13 AM • 0 Comments •
How do you go about researching a genetic disease? This multi-part series explores how digital resources can be used to learn about Huntingtin's disease. Reposted and updated from the original DigitalBio. A bit of background Alice's Restaurant is a movie with an unforgettable song that mostly revolves around Arlo Guthrie hanging out with his friends. Somewhere in the movie, the...
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Posted on December 18, 2007 9:45 AM • 1 Comments •
Last week I posted an image with two molecules (below the fold), one protein and one nucleic acid, and asked you about the probability of finding similar molecules in different species. You gave me some interesting answers....
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Posted on December 14, 2007 10:33 AM • 4 Comments •
If you like ham and bacon, you might be interested in this. GenomeWeb reports that researchers at the University of Barcelona have developed an assay that tests 46 SNPs and can be used to trace the origin of your pork dinner. According to GenomeWeb, the test identifies both the breed and origin of the animal. The university and the company...
Posted on December 6, 2007 1:00 AM • 2 Comments •
If we suspected a virgin birth, how could we prove it?
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Posted on December 3, 2007 9:00 AM • 13 Comments •
Which read(s): 1. contain either a SNP (a single nucleotide polymorphism) or a position where different members of a multi-gene family have a different base? C 2. doesn't have any DNA? B 3. is a PCR product? A, B, and C. All of three reads were obtained by sequencing PCR products, generated with the same set of primers. The quality...
Posted on November 20, 2007 3:20 PM • 0 Comments •
Kind of like reading tea leaves, but more meaningful.
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Posted on November 19, 2007 10:10 AM • 10 Comments •
You too, can compare chimp and human DNA.
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Posted on November 16, 2007 8:51 AM • 0 Comments •
Can you do it? This is what bioinformatics technicians or data analysts do in diagnostic labs.
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Posted on November 15, 2007 9:09 AM • 4 Comments •
Students at Soldan International High School are participating in an amazing experiment and breaking ground that most science teachers fear to tread. Soldan students, along with hundreds of thousands of other people, are participating in the National Geographic's Genographic Project. Through this project, students send in cheek swabs, DNA is isolated from the cheek cells, and genetic markers are used...
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Posted on November 14, 2007 4:04 PM • 9 Comments •
An evolution activity for the classroom.
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Posted on November 9, 2007 3:47 PM • 0 Comments •
Metagenomics 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...
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Posted on October 28, 2007 2:24 PM • 0 Comments •
Sequencing the dirt: see how it's done
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Posted on October 27, 2007 7:00 PM • 0 Comments •
We 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....
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Posted on October 26, 2007 2:20 PM • 0 Comments •
Dying bees and DNA sequencing
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Posted on October 25, 2007 12:15 PM • 1 Comments •
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt?...
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Posted on October 24, 2007 4:05 PM • 0 Comments •
It's hard to teach bioinformatics when schools work so hard to keep us from using computers....
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Posted on October 23, 2007 2:04 PM • 14 Comments •
Welcome 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...
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Posted on October 21, 2007 4:30 PM • 2 Comments •
A 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?...
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Posted on October 16, 2007 8:06 AM • 8 Comments •
During the past few Fridays (or least here and here), we've been looking at a paper that was published from China with some Β-lactamase sequences that were supposedly from Streptococcus pneumoniae. The amazing thing about these particular sequences is that Β-lactamase has never been seen in S. pneumoniae before, making this a rather significant (and possibly scary) discovery. If it's...
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Posted on September 7, 2007 8:43 AM • 5 Comments •
If you've read any of the many stories lately about Craig Venter or Jim Watson's genome, you've probably seen a "SNP" appear somewhere. (If you haven't read any of the stories, CNN has one here, and my fellow bloggers have posted several here, here, here, here, here, and here.) You may be wondering, and rightly so: just what is a...
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Posted on September 5, 2007 10:35 AM • 4 Comments •
"Come quickly, Watson," said Sherlock Holmes, "I've been asked to review a mysterious sequence, whose importance I'm only now beginning to comprehend." The unidentified stranger handed Holmes a piece of paper inscribed with symbols and said it was a map of unparalleled value....
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Posted on September 4, 2007 12:42 PM • 11 Comments •
I began this series last week with a question about a DNA sequence that was published and reported to be one the first beta-lactamases to be found in Streptococcus pneumoniae. Mike has a great post about one of problems with this paper. I think the data themselves are awfully suspicious....
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Posted on August 24, 2007 6:44 PM • 4 Comments •
Calling all bases, how many are correct?
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Posted on August 21, 2007 8:25 AM • 6 Comments •
Second opinions on bioinformatics careers and programming.
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Posted on August 20, 2007 2:28 PM • 4 Comments •
Developing "biological intuition" through case studies
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Posted on August 17, 2007 1:53 PM • 0 Comments •
Sometimes asking a question can be a mistake. Especially when your question leads to more questions and having to question things that you didn't want to question, and pretty soon you begin to regret ever opening the file and looking at the data and asking the question in the first place. Sigh. Take a deep breath. Yesterday through a twist...
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Posted on August 15, 2007 7:50 PM • 8 Comments •
Yes, you can! Really, I thought this was going to be more challenging, but the nice folks at the NCBI have made a special personal genomics FTP site. You can also get Craig Venter's genome, and maybe even do some comparative genomics and see if one has a few deletions. After all, don't you want you find out who's is...
Posted on August 15, 2007 8:00 AM • 0 Comments •
What do you do when base-callers disagree? Okay DNA sequencing community, I want your help with this one. One of these sequences was called by phred and the other by the ABI KB base calling program. Which one should I believe? tags: DNA sequencing, DNA , base-calling programs...
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Posted on August 14, 2007 1:16 PM • 10 Comments •
Is an academics a dead-end if you're a programmer?
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Posted on August 6, 2007 8:44 AM • 11 Comments •
I don't usually blog about work for wide variety of reasons. But, last week, since I wanted to write about bioinformatics software companies, I broke with tradition and wrote about Geospiza as an example. Naturally, I got some feedback about this. Some people liked it, but one of the most opinionated people said that I had given the software engineering...
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Posted on July 31, 2007 11:07 AM • 6 Comments •
What happens when authors play by different rules?
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Posted on July 28, 2007 3:49 PM • 15 Comments •
What do people do in bioinformatics software companies?
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Posted on July 24, 2007 9:00 AM • 9 Comments •
Software testing and the scientific method.
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Posted on July 23, 2007 3:46 PM • 0 Comments •
If 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...
Posted on July 18, 2007 9:00 AM • 0 Comments •
Where does bioinformatics fit in the biotech food chain?
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Posted on July 17, 2007 8:00 AM • 31 Comments •
Some things I like, some were surprises.
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Posted on July 16, 2007 12:13 PM • 19 Comments •
This DNA is nonpareil.
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Posted on July 13, 2007 9:18 AM • 3 Comments •
BLAST has gotten harder.
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Posted on July 12, 2007 1:39 PM • 4 Comments •
It's a pair of bases, but something's not quite right.
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Posted on July 10, 2007 8:54 PM • 4 Comments •
Viewing chromatogram trace files on iPhone.
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Posted on July 9, 2007 12:12 PM • 3 Comments •
What happens when a biologist tries to talk to the IT group?
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Posted on June 22, 2007 7:00 AM • 8 Comments •
The best PCR animations on the web
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Posted on June 21, 2007 4:00 PM • 8 Comments •
Answers to a commenter who bemoans bioinformatics education.
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Posted on June 20, 2007 1:35 PM • 8 Comments •
Know 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...
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Posted on June 19, 2007 1:41 PM • 14 Comments •
Could a protein from a virus help plants handle global warming?
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Posted on June 1, 2007 9:15 AM • 0 Comments •
Suggestions from librarians and scientists.
Posted on May 30, 2007 1:19 PM • 1 Comments •
Assigned readings on BLAST and phylogenetics.
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Posted on May 29, 2007 9:19 AM • 0 Comments •
An 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...
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Posted on May 27, 2007 10:34 AM • 13 Comments •
Through the Related Structures tab and what I found there.
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Posted on May 25, 2007 9:00 AM • 2 Comments •
One last experiment with PubMed (for now).
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Posted on May 24, 2007 2:34 PM • 2 Comments •
Instructions for using my new favorite method.
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Posted on May 23, 2007 10:06 AM • 14 Comments •
We do an informatics experiment with PubMed to compare different search techniques.
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Posted on May 22, 2007 9:01 AM • 10 Comments •
The trials of an English physician.
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Posted on May 21, 2007 8:38 AM • 2 Comments •
How does grass grow in the hot, inhospitable soils of Yellowstone National Park?
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Posted on May 18, 2007 8:43 AM • 0 Comments •
Do 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...
Posted on May 11, 2007 10:05 AM • 0 Comments •
tags: 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...
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Posted on May 10, 2007 5:34 PM • 3 Comments •
If 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....
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Posted on April 21, 2007 2:54 PM • 3 Comments •
It 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...
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Posted on March 10, 2007 9:00 AM • 0 Comments •
Registration 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...
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Posted on March 9, 2007 11:55 AM • 0 Comments •
How do plants grow at 65°C?
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Posted on February 21, 2007 6:19 AM • 2 Comments •
The best place for biology words.
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Posted on February 9, 2007 11:58 AM • 3 Comments •
"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....
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Posted on February 8, 2007 3:17 PM • 1 Comments •
Yesterday, 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....
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Posted on February 7, 2007 1:36 PM • 0 Comments •
How 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...
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Posted on February 5, 2007 9:00 AM • 2 Comments •
Defining a biology term for scientists in other disciplines.
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Posted on February 2, 2007 2:23 PM • 6 Comments •
Chimeras invade the sequencing lab!
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Posted on February 1, 2007 6:01 PM • 0 Comments •
Send in the clones, but only the random ones.
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Posted on January 31, 2007 1:02 PM • 2 Comments •
"How deep is the ocean? How high is the sky?"
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Posted on January 30, 2007 4:49 PM • 2 Comments •
In which we define reads, chromatograms, and shotgun sequencing.
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Posted on January 28, 2007 8:51 PM • 2 Comments •
Some background on the strategies: mapping vs. shotgun
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Posted on January 27, 2007 1:50 PM • 2 Comments •
No more live BLAST searches during lectures!
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Posted on January 25, 2007 1:20 PM • 3 Comments •
Ask Dr. Science: yes, I do take requests.
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Posted on January 22, 2007 8:59 AM • 7 Comments •
In the effort to help us define a few basic concepts, PZ started out by giving us a nice simple definition of a gene, but as he, rightly noted: I tell you right now that if I asked a half dozen different biologists to help me out with this, they'd rip into it and add a thousand qualifiers, and it...
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Posted on January 21, 2007 3:44 PM • 7 Comments •
The bioinformatics classes that I teach use web services and web sites as much as possible, but I still find that it's helpful to have programs on our classroom computers. Here is a list of my favorite desktop programs for those of you who might want to add some bioinformatics activities to your biology courses....
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Posted on January 12, 2007 1:37 PM • 10 Comments •
I was frantically getting ready for class when I happened to glance out the window. What did I see? Big fluffy white flakes rapidly falling from above. You can't say we weren't warned. The newspapers have been predicting snow since Monday. It's just, well, unusual. And Seattle is never prepared to deal with it. Even the kids aren't looking too...
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Posted on January 10, 2007 11:21 PM • 4 Comments •
There's nothing like the first day of class to make you appreciate the difference between the equipment you end up using at schools and the equipment that you get to use on the job. For the month of January, I'm teaching a night class in bioinformatics at a local community college. We're introducing lots of web-based programs, and databases, and...
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Posted on January 9, 2007 12:11 PM • 3 Comments •
It's the first day of our bioinformatics class.
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Posted on January 8, 2007 6:55 PM • 2 Comments •
When computers first entered the mainstream, it was common to hear them getting blamed for everything. Did you miss a bank statement? that darned computer! Miss a phone call? - again the computer! The latest issue of Science had a new twist on this old story. Now, instead of a researcher failing to take responsibility for doing sloppy science, we're...
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Posted on January 1, 2007 8:31 AM • 8 Comments •
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants?...
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Posted on December 22, 2006 8:00 AM • 0 Comments •
Who infected the children with HIV: Using the data to solve the puzzle.
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Posted on December 7, 2006 6:33 PM • 2 Comments •
A quick guide for the omically challenged.
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Posted on December 1, 2006 1:35 PM •
I am a microbiologist and molecular biologist turned tenured biotech faculty turned bioinformatics scientist turned entrepreneur. My passion is developing instructional materials for 21st century biology (Geospiza Education).
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