I had the good fortune on Thursday to hear a fascinating talk on deep transcriptome analysis by Chris Mason, Assistant Professor, at the Institute for Computational Biomedicine at Cornell University. Several intriguing observations were presented during the talk. I'll present the key points first and then discuss the data. These ...
This October (9-11, 2019), I attended the 3rd NIBLSE conference entitled: "Integration of Bioinformatics into Life Science Education: Roadmap for the Future." It was held at " Hot Shops" in Omaha Nebraska, a space for artists to work, sell, and meet.
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 ...
Bacteria can cause other epidemics, why not obesity? Is there a relationship between our body weight and our bacterial inhabitants? Two reports in Nature (1, 2) suggest that bacterial populations differ between people who are obese and people who not, and that the bacterial inhabitants of their guts, may be ...
A friend of mine; serial entrepreneur, and former president of Genetic Systems; Joe Ashley, told me once that starting a business is an unnatural act. Now that I've done it, I agree. Even with my multiple back-up plans, possible grants, and part-time activities, my stomach still hurts and my mind ...
We had a great discussion in the comments yesterday after I published my NJ trees from some of the flu sequences. If I list all the wonderful pieces of advice that readers shared, I wouldn't have any time to do the searches, but there are a few that I want ...
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 ...
How did the human genome ever get finished if every one of the three billion bases had to be reviewed by human eyes? In the early days of the human genome project, laboratory personnel routinely scanned printed copies of chromatograms, editing and reviewing all DNA sequences by eye. For more ...
The general steps in genome sequencing were presented in the earlier installments ( there are links at the bottom of the page), but it's worth repeating them again since each of the earlier steps has a bearing on the outcome of those that come later. These are: Break the genome ...
To the ancient Greeks, a chimera was a kind of monster, with the body of a goat, the tail of a dragon, and a lion's head. To geneticists, a chimera can be an animal that's derived from two embryos, such as a transgenic mouse. Or if the organism is a ...
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 ...
Have you ever wondered how people actually go about sequencing a genome? If they're sequencing a chicken genome, do they raise chickens in the lab and get DNA from the eggs? Does the DNA sequence come out in one piece? Why is there so much talk about computers? What are ...
A few years ago, the General Biology students at the Johns Hopkins University began to interrogate the unseen world. During this semester-long project, they study the ecosystems of the Homewood campus, and engage in novel research by exploring the microbial ecosystems in different sections of the campus. Biology lab students ...
"Eew!" Is how high performance computing (HPC) admins react to Docker, according to Dr. Vanessa Saurus when she described the motivation for developing Singularity [1] at the Cyverse Container Camp. Like Docker, Singularity allows one to package programs and their dependencies in ways that they can be run as virtual ...
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 ...
The technological Singularity is the moment beyond which "technological progress will become incomprehensibly rapid and complicated [1].” Hmmm. That sounds like bioinformatics.
Surviving the Singularity requires reducing complexity. This was the topic of a recent three-day Cyverse Container Camp hosted at the University of Arizona, Tucson AZ. I attended the ...
In its simplest sense, we imagine that learning occurs through a series of positive and negative rewards. Some actions lead to pleasure, others to pain, and it seems reasonable to expect that people will repeat the actions with pleasurable results and avoid those that ended in pain. Yet, we all ...
I got my copy of " A short guide to the human genome" by Stewart Scherer today from Cold Spring Harbor Laboratory Press (2008, ISBN 978-087969791-4). Usually, I would wait until after I've read a book to write a review, but this book doesn't require that kind of study. As ...
Computers, biological data (molecular sequences, structures, and other data), websites, and databases are integral to modern research. Innovations like precision, or personalized medicine, expect a certain level of patient participation, and our future food and environmental sustainability will require that society can access a multitude of computer-based resources. Thus, higher ...
In part I, I wrote about my first semester of teaching on-line and talked about our challenges with technology. Blackboard had a database corruption event during finals week and I had all kinds of struggles with the Windows version of Microsoft Excel. Mike wrote and asked if I thought students ...
BLAST 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 ...
A couple of years ago, I answered a reader's question about the cost of genome sequencing. One of my readers had asked why the cost of sequencing a human genome was so high. At that time, I used some of the prices advertised by core labs on the web and ...
A lot of our colleagues are interested in bioinformatics and data science. While it is clear that bioinformatics is important, even essential, in modern biology research, there is the question about the levels of programming and computer skills needed for different jobs. I'm not going to answer that question here ...
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 ...
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 ...
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 ...
Five Bulgarian nurses and a Palestinian doctor ( dubbed the Tripoli six) may be executed soon by the Libyan government for the crime of deliberately infecting over 400 children with HIV. If they did infect the children, this would be a horrendous crime. If they did not infect the children ...
I'm sure everyone else thinks the big news today is the announcement by the Washington State Health department requiring hospitals to report MRSA cases to the state. I think the cool news is their on-line database. We'll get to that a bit later. What is MRSA? MRSA stands for methicillin-resistant ...
A few weeks ago, I wrote about a paper in Science(1) that I read on a connection between a mutation in the dopamine D2 receptor and the genetics of learning. Only, it turned out that when I looked at the gene map... the mutation mapped in a completely different gene ...
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 ...
In which I present a quick guide for the omically challenged and a defense of 'arth and "ome." Other SciBloggers have shared their thoughts on the use of ome here and here. Sometimes I get frustrated too, with the way language is abused and tweaked by those around me. So ...
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 ...
By 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: Because of these changes ...
I just love this title! It's nerdy and cute, all at the same time. I read about this in www.researchblogging.org and had to check out the paper and blog write up from The Beagle Project (BTW: some of you may be interested in knowing that The Beagle Project is not ...
Pull a spaghetti noodle out of a box of pasta and take a look. It's long and stiff. Try to bend it and it breaks. But fresh pasta is pliable. It can fold just like cooked noodles. When students first look at an amino acid sequence, a long string of ...
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 ...
If 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 ...
The 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 ...
When can a really bad virus be used to do something good? When we can use it to learn. The human immunodeficiency virus, cause of AIDS, scourge of countries, and recent focus of ScienceBlogs; like humans, evolves. As one of my fellow ScienceBloggers noted, few biological systems demonstrate evolution as ...
Let the experiment begin. We're experimenting with HIV in this series. And yes, you can try this at home! If you want to see where we've been and get an idea where we're going, here are the links. Part I. Meet HIV and learn how we're going to use it ...
In which we see the results and come to our own conclusions. If you want to let other people tell you what's right and what's wrong, they will surely do so. Turn on the TV and hordes of happy actors bounce around, only too happy to help you purchase the ...
Did HIV become resistant to Atazanavir because of a genetic change? Was that genetic change inherited? Did HIV evolve? Can we explain why genetic changes at specific sites might help HIV escape the effects of the drug? Let's find out. All of the sequences in the image below (except for ...
In which we identify unknown human proteins. Yesterday, I wrote about using the BLOSUM 62 matrix to calculate a score for matches between two proteins. Those scores give us a good start on understanding how blastp determines whether two sequences are matching by chance or because they're more likely to ...
In which we search for Elvis, using blastp, and find out how old we would have to be to see Elvis in a Las Vegas club. Introduction Once you're acquainted with proteins, amino acids, and the kinds of bonds that hold proteins together, we can talk about using this information ...
Want to learn more about Parkinson's disease? See why a single nucleotide mutation messes up the function of a protein? I have a short activity that uses Cn3D (a molecular viewing program from the NCBI) to look at a protein that seems to be involved in a rare form of ...
" 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. Holmes gazed thoughtfully at the ...
Our goal for this course (BioSci256) is to introduce you to some of the tools and databases that are widely-used in bioinformatics and give you lots of hands-on practice in using these tools to look at some questions in biology. Since many of you are either studying biotechnology or working ...
"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. Why? Because we ...
What 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 ...
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 ...
