biotechnology
sporte | November 14, 2007This structure is called a "kissing loop" and I find that name just a bit odd, given the source of the structure.
Now, here's the puzzle: Why would I say that the name "kissing loop" is ironic?
sporte | November 13, 2007Congratulations to George Cachianes (who I've written about before), his amazing students from Abraham Lincoln High School, and collaborators at UCSF!
These students, from a public high school no less, placed in the top 6 finalists, along with only one other US team. The other top teams were: Peking University (China), University of Science and Technology (China), University of Paris (France), University of Ljubljana (Slovenia), and UC Berkeley. I'm really impressed that these public high school students managed to beat students from MIT, Stanford, Harvard, Caltech, and Princeton, but…
sporte | October 27, 2007The 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 and sequences: ATAGATAGACGAGTAG, without any supporting information to help them evaluate if the sequence is correct. If DNA sequencing and personalized genetic testing are to become commonplace, the practice of ignoring data quality is (in my opinion) simply unacceptable.
So, for awhile anyway, I'm making a…
sporte | October 26, 2007We 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.
The general process is this:
1. We sort the chromatogram data to identify good data and separate it from bad data. Informatics can help you determine if data is good, and measure how good it is, but it cannot turn bad data into good data. And, there's no point in wasting time with…
grrlscientist | October 24, 2007tags: book review, biotechnology, biomedicine, stem cells, ethics, Cloning: A Beginner's Guide, Aaron Levine
Would you drink milk from a cloned cow?
Should we clone extinct or endangered species?
Are we justified in using stem cells to develop cures?
When will we clone the first human?
Ever since Dolly the sheep was born, questions like these have been part of the public consciousness, and now, cloning is poised to revolutionize medicine, healthcare, and even the food we eat. Regardless of what certain politicians do to slow the progress of scientific research, cloning is here to stay, and…
sporte | October 23, 2007It's hard to teach bioinformatics when schools work so hard to keep us from using computers.
Anecdotes from the past
Back in my days as a full-time instructor, I fought many battles with our IT department. Like many colleges, we had a few centralized computer labs, tightly controlled by IT (aka the IT nazis), where students were supposed to go to do their computing. Instructors also had a centralized computer lab, but over the years, we gained the right to have computers in our offices. Our major battle was whether or not we'd be allowed to use Macs.
There are certainly advantages in…
sporte | October 21, 2007Welcome 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 subject that you can really grasp without getting your fingers dirty. So, this course will include a lot of hands-on work.
My friend and collaborator at Johns Hopkins University has given me data sets from the past three years and we…
sporte | October 16, 2007A 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?
Genome Technology asked J. Craig himself. In the October 2007 issue of GT, JCV estimates that the cost from the first Celera human genome project (guess who?) was about $100 million and that the cost of his most recent genome project was at least $70 million.…
sporte | September 11, 2007Two protein structures from an avian influenza virus are shown below. One form of the protein makes influenza virus resistant to Oseltamivir (Tamiflu®)
Don't worry, these proteins aren't from H5N1, but they do come from a related influenza virus that also infects birds.
technorati tags: molecular models, protein structures, influenza, bioinformatics, Cn3D
One protein structure is from a strain that is sensitive to an anti-viral drug called "Tamiflu®". The other structure is from the same virus, except there's a slight difference. A single base change in the viral RNA changed the codon that…
sporte | September 6, 2007One of my readers asked: Why does genome sequencing cost so much?
My short answer is because it's big.
But I thought it would be fun to give a better answer to this question, especially since I'm sure many of you are wondering the same thing.
Okay, so let's do some math.
Don't worry, this math isn't very complicated and I'll explain where most of the numbers come from.
Estimating costs from salaries
First, we'll take the easy route. My experience with grant budgets has taught me that the greatest cost for any project comes from salaries. If we look at the PLoS paper with Craig Venter's…
sporte | September 5, 2007If 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 SNP?
Never fear, hopefully this post will answer some of those questions.
tags: DNA sequencing, DNA , SNPs, genetic testing
SNP stands for Single Nucleotide Polymorphism. That's a mouthful. It means some people, will have one base at a certain position, in a…
sporte | September 4, 2007
"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 map, then slowly lifted his eyes and coldly surveyed his subject's beaming countenance. "You have an affinity for the ocean," said Holmes, "that you indulged to excess as a reckless youth. An experience as a medic in the military changed your life and gave you a reason to do more than…
sporte | August 27, 2007Some of them work for Bayer.
technorati tags: biotechnology, education, biotechnology education, high school biotechnology
The San Francisco Chronicle has a nice article on a 15 year old education program in Berkeley that serves students from Berkeley High and Life Academy. Over 1500 students have participated in this program, with 862 placed in internships.
I really liked reading about some of the kids who started in the Bayer Biotech partners program and finding out what they're doing now. One of those interviewed started the program in 1992, as a 15 year old. He liked it so much, his…
sporte | August 25, 2007Why the ABRF of course!
I spend a fair amount time every summer giving workshops for college and high-school teachers on genomics and bioinformatics. One of the things that always surprises them, is the amount of lab work that's carried out by people working in shared, or core lab facilities. For example, if I was working at a research university and I wanted to sequence some DNA, maybe several patient samples, or a bacterial genome, I would send the DNA to a core lab and they would send me the sequences. I would analyze the data and write the paper.
I've simplified that process a bit in…
sporte | August 22, 2007I get asked this question often enough and now that's it's come up again, it seems that I might as well answer it once and for all and get it over with.
First, I want to change the question. Of course they don't need to learn programming.
A better question is would it benefit biologists to learn programming?
My flip half-way serious answer is yes, if they want to change careers.
You see, programming is really seductive when you've been a wet-bench biologist. It's like heroin. (At least I suspect it is, I know about programming, I don't have any experience with the other beyond reading…
sporte | August 21, 2007
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 figure out the results.
My results from last week suggested that re-processing chromatogram data (from the ABI 3730) with phred was probably a bad idea, but still, I only had one data point and I really wanted to know if anyone had done a more thorough study and compared larger numbers of chromatograms.
Naturally, someone had.
tags: DNA…
sporte | August 15, 2007Sometimes 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 of fate, I ended up taking a look at the DNA sequences produced by two different base calling programs from the same chromatogram file, from an ABI 3730 DNA sequencing instrument. I thought they would be the same, or at least similar.
tags: DNA…
sporte | August 14, 2007What 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
Sometimes I open up files and do short experiments just because - well, I'm curious. And sometimes I immediately wish I hadn't done that because what I opened looks like a larger can of worms than I really want to see.
These graphs show the quality of each base, in a DNA sequence, on the y axis and the position of…
sporte | August 8, 2007Some maggots have gotten good press lately because of their helpful ability to clean out wounds by consuming dead tissue. Screwworms however; also known as Cochliomyia hominivorax, will never be welcomed in an operating room or anywhere else.
USDA Agricultural Research Service
These are the creatures of nightmares. During part of their lives, they live and travel as flies, and lay their eggs in the wounds of warm-blooded animals. When the eggs hatch, the screwworm maggots feed on the living flesh of the infested animals.
Fortunately, we've learned how to control the screwworm and we…
sporte | August 3, 2007
Many medical conditions today are treated but never cured. Imagine, a child with a genetic disease like juvenile diabetes or hemophilia. This child will be taking expensive medications for their entire lives. In the case of some diseases the cost of the medications might be more than child or their parents can ever hope to earn in their lifetimes, much less spend on a life-saving drug.
This is one of the many reasons why people have placed such great hopes in gene therapy. If a disease results from a defective gene, and we could replace it or supplement it with a functional gene, perhaps we…