bioinformatics
sporte | January 27, 2007Considering that several genomes that have been sequenced in the past decade, it seems amazing in retrospect, that the first complete bacterial genome sequence was only published 12 years ago (1). Now, the Genome database at the NCBI lists 450 complete microbial genomes (procaryotes and archea), 1476 genomes from eucaryotes, 2145 viruses, and genome sequences from 407 phage.
Much of the methodology used for sequencing DNA is designed to confront one big technical hurdle.
That is, we can only determine the sequence of small pieces of DNA at a time. This means that you must break a larger…
sporte | January 25, 2007Note to self: doing live BLAST searches during a lecture is not a good idea.
Would Julia Child make her viewers watch the food bake?
Standing in front of a class and waiting for results to appear, makes me realize how much instructors can learn a lot from watching Julia Child demonstrate cooking. I think if Julia Child taught bioinformatics this is how she would discuss BLAST results with her class:
Afer a BLAST search has been submitted to the NCBI, your results are stored there for 24 hours, and you can get them with the request ID. If you do searches ahead of time and save the…
sporte | January 22, 2007About a week ago, I offered to answer questions about subjects that I've either worked with, studied or taught.
I haven't had many questions yet, but I can certainly answer the ones I've had so far. Today, I'll answer the first question:
How do you sequence a genome?
Before we get into the technical details, there are some other genomic questions that you might like answered.
How much does it cost to sequence a genome?
I remember in 2002, when we were at the O'Reilly bioinformatics conference and we heard Lee Hood challenge the DNA sequencing community to lower the costs of genomic…
sporte | January 21, 2007In 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 would never get done.
Well, okay, technically speaking he didn't ask me for help. But, since I'm a biologist, as soon as I looked at the definition that he chose, from Modern Genetic Analysis (by Griffiths, Lewontin, Miller, and Gelbart), I couldn't help but find something wrong.
The definition from…
sporte | January 12, 2007The 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.
Why not use the Web?
Before going on, I should probably explain, why we use desktop programs, we have so many things available on the web. We do use the web whenever we can. Web services are nice because you can shift the computation burden to someone else's computer. (I think this…
sporte | January 10, 2007I 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 happy about it, though. By this time of the school year, they've caught on that every snowday has a price. And, they will pay that price IN JUNE. Already the last day of school has been postponed until the 25th of June.
Who knows? The kids…
sporte | January 9, 2007There'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 concentrating on the sorts of activities that biotechnology technicians are likely to use on the job. It's fun. It's practical. And I don't have to suffer through any lectures about the Semantic Web.
I'm also getting reminded (although not for…
sporte | January 8, 2007Our 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 in a health-related field, we will focus quite a bit on practical applications.
I posted tonight's topics here since I've been told that some of you might not have access to Blackboard for a couple of days. Feel free to look around the place. ScienceBloggers discuss lots of topics that you might find…
mikethemadbiologist | January 7, 2007How does the entire NIH go offline? I realize it's free, but every so often, it just is inaccessible for hours at a time, particularly on weekends. Don't they know that science never rests...
sporte | January 1, 2007When 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 back to blaming the computer. Never mind that the lab was using home made software that they "inherited from someone" (and apparently didn't test it) the five retracted papers were the fault of the software! Not the scientists who forgot to…
sporte | December 22, 2006Bacteria 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 partly to blame.
In one study, the authors studied the bacterial populations of their volunteers' intestines by compiling a data set of 18,348 DNA sequences for bacterial 16S ribosomal RNA by sampling feces. Wow! That's a lot of ... well, I won't say it, but you know what I mean. In…
mikethemadbiologist | December 15, 2006I was recently at a conference (pdf file) where one speaker (Dr. Thomas O'Brien) suggested 'VRSA hospital insurance' to prevent the spread of vancomycin resistant Staphylococcus aureus outbreaks ('VRSA'). Before I get into the plan, let's talk about VRSA.
VRSA are staphylococci which are not only resistant to vancomycin, which is one of the last effective drugs against methicillin resistant Staphylococcus aureus ('MRSA'), but are also resistant to most (or usually) all other available antibiotics. While tigecycline can be used to treat some infections (skin and abdomindal), it is not used…
sporte | December 7, 2006Five 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, it's the Libyan government that will be killing innocent people.
The clock is ticking.
Some of you might be wondering (I know I was): How exactly is molecular sequence data being used to solve the crime? Why are scientists and science bloggers claiming that the Tripoli six are innocent?
Let's begin by…
sporte | December 1, 2006In 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 many word pairs that once made phrases—;log in, data set, file name, set up, and pick up—;have been condensed into single words, that I've had to start using Google to double-check my editing. Perhaps it's surprising then, that I like "ome," "omics," and even Sydney Brenner's chief phrase-to-hate, "systems biology."
I…
sporte | November 30, 2006The 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 in the session on scientific communication.
The conference will take place Dec. 4th-8th, 2006. Don't worry if you don't have a plane ticket or a place to stay, you're virtually there. How? It's all on-line.
Some of you might be wondering how a virtual conference works.
1…
sporte | October 13, 2006In last week's episode, your assignment was to think of an interesting plant trait and find a description about a gene, related to that trait, by searching PubMed.
Since coming up with an interesting trait might be a challenge for some people, let's think about how to approach this step.
Picking your trait. If you're having a hard time thinking of a trait, it might be helpful think about where plants grow, why we grow plants, and why it might be hard or easy for plants to grow.
Some of the environmental factors that affect plant growth are: climate, soil composition, nutrient…
sporte | October 10, 2006Why 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 discover, for themselves, that certain genes are expressed in some tissues but not in others. My goal here, as part of our NSF-funded project, is to show how students can learn biology by doing science with bioinformatics tools.
If you already know all about ESTs, you might want to jump ahead and read about the activity. If…
sporte | October 5, 2006Many of you might take this for granted, and I know it seems amazing today, but I when first started teaching, our access to scientific literature was pretty limited. I could go to the UW and use Grateful Med to search Medline, but we didn't have anything like it at my college and web browsers, like Mosaic, had yet to be invented. So, when I first started giving workshops for teachers on biotechnology and the world of the web, many were quite surprised to find out about the PubMed database.
Since PubMed is (to me) one of the best resources to ever come along, I think we should explore it a…
sporte | October 1, 2006Welcome to the fourth edition of Bio::Blogs!
This is the carnival where we explore topics at the intersection of computing, biology, and sometimes a bit human behavior.
In this edition, we consider issues with annotation, agonize over standards, explore the question of whether or not it's possible to tame those wild and wooly computational biologists and make them laugh their way into writing programs that other people can use, give the Perl fans something to do while waiting for that program to run, and much, much, more.
Today, we'll begin on the biology side of spectrum and work our way…
sporte | September 27, 2006We went on an excursion last weekend to see the Dead Sea Scrolls at the Pacific Science Center. None of us could resist going downtown to look at written texts over 2000 years old. Uncovered in 1946, by a Bedouin shepherd, the scrolls have had an interesting history over the past 50 years, most of it out of the public eye. Only recently, have a large number of scholars and members of the public been granted access.
We're still kind of amazed that they came to Seattle.
I'm fascinated by archeology, but I was also interested in how DNA analysis is being used to study the scrolls and…