For those of you who may have been wondering where I've been, these past few weeks have seen me grading final projects, writing a chapter on analyzing Next Gen DNA sequencing data for the Current Protocols series, and flying back and forth between Seattle and various meetings elsewhere in the ...
The EMBL graduate students have organized an ingenious conference titled: Life Sciences - Shaping the Future. Learn about Omics and Systems Biology from speakers like Leroy Hood, Stuart Kim, and Ronald Krause (and more). Explore options for career development, and learn how you can join the Web 2.0 science revolution ...
Modified from the original post. Playing around with molecular structures is one of the more entertaining activities that you can do with digital biology. I've become totally entranced with molecular structures, both because they're a fascinating art form and because every structure has its own story. I learned this because ...
One of my hobbies lately has been to get either RNA seq or microarray data from GEO and do quick analyses. Not only is this fun, I can find good examples to use for teaching biology. One of these fun examples comes from some Arabidopsis data. In this experiment, some ...
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 ...
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 ...
I was pretty impressed to find the swine flu genome sequences, from the cases in California and Texas, already for viewing at the NCBI. You can get them and work them, too. It's pretty easy. Tomorrow, we'll align sequences and make trees. Activity 3: Getting the swine flu sequence data ...
tags: 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 ...
tags: 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 ...
tags: 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 ...
tags: 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 ...
I 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 ...
I'm a big of learning from data. There are many things we can learn about swine flu and other kinds of flu by using public databases. In digital biology activity 1, we learned about the kinds of creatures that can get flu. Personally, I'm a little skeptical about the blowfly ...
It 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 ...
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. You may be wondering, and rightly so: just what is a SNP? Never fear, hopefully this post will answer some of those questions. SNP stands for Single ...
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 ...
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 ...
Genome sequences from California and Texas isolates of the H1N1 swine flu are already available for exploration at the NCBI. Let's do a bit of digital biology and see what we can learn. Activity 1. What kinds of animals get the flu? For the past few years we've been worrying ...
Why is an eye, an eye and a nose, a nose? Why do different cells create different kinds of tissues when all the cells in a single organism start out with the same set of instructions (aka DNA)? Head, Shoulders, Knees, and Toes is a learning activity that helps students ...
HealthMap is a great site that could be an excellent resource when teaching a biology, microbiology, or health class. Not to mention, I can picture people using it before they travel somewhere or even just for fun. I learned about HealthMap awhile ago from Mike the Mad Biologist, but I ...
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 ...
Grasses at Yellowstone National Park are able to grow temperatures (65°; C) that would toast most living things. Step right up! Watch original research, as it happens, on the web! I'm going to use bioinformatics to see if I can find that answer to the puzzle of heat-tolerant plants. Previous ...
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. It was even more surprising to learn that this amazing ...
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 ...
Have you ever wondered how to view and annotate molecular structures? At least digital versions? It's surprisingly easy and lots of fun. Here's a movie I made that demonstrates how you can use Cn3D, a free structure-viewing program from the NCBI. Luckily, Cn3D behaves almost the same way on both ...
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 ...
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 ...
These days, DNA sequencing happens in one of three ways. In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this. Then, in the 90's, genome centers came along. Genome centers are like giant ...
In my last post, I wrote about insulin and interesting features of the insulin structure. Some of the things I learned were really surprising. For example, I was surprised to learn how similar pig and human insulin are. I hadn't considered this before, but this made me wonder about the ...
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 ...
Since DNA diagnostics companies seem to be sprouting like mushrooms after the rain, it seemed like a good time to talk about how DNA testing companies decipher meaning from the tests they perform. Last week, I wrote about interpreting DNA sequence traces and the kind of work that a data ...
Immuno-bioinformatics is a fast growing subdiscipline of immuno-biotechnology. New technologies like immune-profiling and targeted cancer therapies are leading to job growth and demands for new skills and knowledge in biomanufacturing, quality systems, informatics, and cancer biology.
or is it just an idea that's ahead of the curve? Last week, I was stunned to discover at least 31 papers in an NCBI Gene database entry that were in the entry for the wrong gene. I wrote about this here, here, here, and here. Now, an oversight like ...
If you've read the previous posts on this topic, here and here, you're probably aware by now that I have this weird ( okay, maybe fanatical) obsession with data. Or at least, with knowing if my data are right so I can get on with life, do the analysis and ...
Bio::Blogs#2 is been out for a few days but it's certainly not out of interesting ideas and things to read. There is some interesting stuff about Brisbane. Queensland looks like a lovely place and much different than my mental images of Australia. Sorry, but when I picture Australia, I get ...
Although, 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 ...
Although, I certainly didn't believe it. Truly in nature, it can be described as nonpareil. With all the years that I've heard (or taught) that all DNA is antiparallel, it was hard to believe my own eyes when I saw this structure. Yet here is, on the screen, parallel DNA ...
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 ...
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 ...
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 ...
Would you like to have some fun playing with chromatograms and helping our class identify bacteria in the dirt? This quarter, my bioinformatics class, at Shoreline Community College, will be working with chromatograms that were obtained by students at Johns Hopkins University, and graciously made available by Dr. Rebecca Pearlman ...
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 ...
DNA sequence traces are often used in cases where: We want to identify the source of the nucleic acid. We want to detect drug-resistant variants of human immune deficiency virus. We want to know which base is located at which position, especially where we might be able to diagnose a ...
I 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 ...
The next time you bite into a crisp juicy apple and the tart juices spill out around your tongue, remember the honeybee. Our fall harvest depends heavily on honeybees carrying pollen from plant to plant. Luscious fruits and vegetables wouldn't grace our table, were it not for the honeybees and ...
The simple fact is this: some DNA sequences are more believable than others. The problem is, that many students and researchers never see any of the metrics that we use for evaluating whether a sequence is "good" and whether a sequence is "bad." All they see are the base calls ...
Hey students: if you are looking for a summer internship in marine metagenomics and you can get your application together before June 16th, Jonathan Eisen posted information about an open position on his blog. It also looks like he's looking for post-docs (see the side bar on the right of ...
What tells us that this new form of H1N1 is swine flu and not regular old human flu or avian flu? If we had a lab, we might use antibodies, but when you're a digital biologist, you use a computer. Activity 4. Picking influenza sequences and comparing them with phylogenetic ...
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 ...
For many years, I've been perfectly content to work with small numbers of things. Working with one gene or one protein is great. Even small groups of genes are okay. I'm fine with alternatively spliced genes with multiple transcripts, or multiple polymorphisms, or genes in multi-gene families, or groups of ...
