Biotechnology:
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 •
A video tutorial on molecular structures.
Posted on March 19, 2008 5:37 PM • 1 Comments •
GloFish for the cloned "glow in the dark" kitties.
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Posted on December 13, 2007 10:00 AM • 9 Comments •
Well, some of you asked for this...
Posted on December 12, 2007 11:40 PM • 5 Comments •
This is a-mewsing. (Photo Credit: Gyeongsang National University) When Genetic Savings and Clone shut their doors it looked like wishful cat owners were going to be out of luck and short of kittens....
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Posted on December 12, 2007 9:01 PM • 21 Comments •
RNA by any other name would smell as sweet. Or would it?
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Posted on November 14, 2007 9:13 AM • 3 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 •
Fun with molecular models!
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Posted on September 11, 2007 11:46 AM • 3 Comments •
Adding the costs and doing the math.
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Posted on September 6, 2007 12:16 PM • 13 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 •
Some of them work for Bayer.
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Posted on August 27, 2007 2:09 PM • 1 Comments •
Why 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...
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Posted on August 25, 2007 5:30 PM • 0 Comments •
Calling all bases, how many are correct?
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Posted on August 21, 2007 8:25 AM • 6 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 •
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 •
Some 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...
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Posted on August 8, 2007 2:53 PM • 0 Comments •
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...
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Posted on August 3, 2007 4:23 PM • 8 Comments •
Last Friday, we had another in the series of weird DNA structures. (You can see the first here). I asked the audience to identify the unusual feature in this molecule. Here's the first picture: tags: DNA structure, DNA , molecular structure, biochemistry Here's the answer:...
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Posted on August 3, 2007 10:19 AM • 4 Comments •
What do malaria, sleeping sickness, yellow fever, and dengue virus have in common? Sure, they're all tropical diseases, but there's something else. All of these diseases have some kind of insect vector. image from the Public Health Library tags: tropical disease, yellow fever, sleeping sickness, insect control, malaria...
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Posted on August 2, 2007 9:27 AM • 3 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 •
Where does bioinformatics fit in the biotech food chain?
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Posted on July 17, 2007 8:00 AM • 31 Comments •
What do people in biotechnology do on the job? What can students do with a science degree once they've finished college? Some answers can be found at the "Life Sciences Central web site. Created by the Workforce Development Council of Seattle-King County, this is a wonderful resource for anyone who's considering biotechnology for a potential career. My favorite part of...
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Posted on July 11, 2007 8:32 AM • 4 Comments •
Answers to a commenter who bemoans bioinformatics education.
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Posted on June 20, 2007 1:35 PM • 8 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 •
Blogging from the 2007 NW branch ASM meeting
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Posted on March 12, 2007 2:29 PM • 1 Comments •
How do plants grow at 65°C?
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Posted on February 21, 2007 6:19 AM • 2 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 •
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 •
Tired of waiting for congress and you don't want to move to California or out of the US? Attila Csordas shows us in a few photographs how to isolate placental stem cells at home. His series brings back memories. My very first paid technician job in college involved visiting the maternity ward, collecting placentas, and starting primary cell cultures from...
Posted on January 24, 2007 1:05 PM • 0 Comments •
It's true. Chimeras are out and walking among us. These aren't quite the chimeras that RPM is obsessed with, but they're certainly bothersome to some. From Genome Technology Online, we have a report that James Derr, at Texas A&M College of Veterinary Medicine, wants to sequence the genome from a real buffalo, but those buffalo are hard to find. To...
Posted on January 9, 2007 12:28 PM • 3 Comments •
What's the difference between a synthetic drug and an antibiotic? Sometimes there's no difference at all. Let's take a look at chloramphenicol and couple of pencillins....
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Posted on November 29, 2006 8:00 AM • 1 Comments •
Do more kits mean more science or more science that's bad?
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Posted on November 8, 2006 1:53 PM • 14 Comments •
We need lab movies of people doing things wrong.
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Posted on November 6, 2006 9:04 AM • 3 Comments •
You've probably heard about enterprising researchers attaching cameras to dolphins, dogs, and other animals, in order to learn how things look from the critter-point of view. Now, some enterprising lab rats have added a new twist to this technique....
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Posted on November 4, 2006 7:22 PM • 4 Comments •
Like sex education in a religious household, lab technique must sometimes be learned from your friends.
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Posted on November 1, 2006 8:00 AM • 7 Comments •
To some inhabitants of the ivory tower, industry looks like paradise.
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Posted on October 9, 2006 9:18 AM • 0 Comments •
The Ask a Science Blogger question of the week asks if organic foods are really worth the hype. I'm afraid my answer can't fit into one blog post. Let me start by telling you about my garden. This year my garden has been a home to local wildlife, but during the years that I do garden, I have a semi-organic...
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Posted on September 12, 2006 7:30 AM • 4 Comments •
One of the commenters on a previous post, pointed out that proteases have pretty diverse structures, even though they also share a common function. What else could I do? I had to take a look. I found structures for chymotrypsin (from a cow) and subtilisin (from a soil bacteria, Bacillus lentus) and used Cn3D to see how they compare (below...
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Posted on August 9, 2006 12:50 PM • 3 Comments •
Last week, we decided to compare a human mitochondrial DNA sequence with the mitochondrial sequences of our cousins, the apes, and find out how similar these sequences really are. The answer is: really, really, similar. And you can see that, in the BLAST graph, below the fold. A quick glance shows that the ape with the most similar mitochondrial sequence...
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Posted on August 4, 2006 1:39 PM • 3 Comments •
It seems kind of funny to be thinking of anti-freeze at the moment, with heat waves blanketing the U.S., but all this hot weather makes me miss winter. And so I decided it was time to re-post this from the original DigitalBio. Winter is coming soon, my bike ride to work was pretty chilly, and it seems like a good...
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Posted on August 4, 2006 11:38 AM • 5 Comments •
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 gather environmental samples from different campus ecosystems, isolate DNA, amplify...
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Posted on July 24, 2006 9:20 PM • 0 Comments •
"Hey Rocky, watch me pull a rabbit out of my hat!" I realized that I should add just a bit more information to last answer on gene identification, so here it is. After the last installment, Diego commented: but still you do not know exactly what part of your DNA sequence is matching to the annotated protein....
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Posted on July 21, 2006 7:26 PM • 1 Comments •
Welcome back! If you've just joined us, we're in the middle of a quest to find the identity of an unknown nucleotide sequence. To summarize our results so far, we used this sequence to do a blastn search of GenBank, using all the default settings at the NCBI. You can see the beginning of the project here. And we had...
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Posted on July 21, 2006 4:19 PM • 3 Comments •
Last week, we embarked on an adventure with BLAST. BLAST, short for Basic Alignment Search Tool, is a collection of programs, written by scientists at the NCBI (1) that are used to compare sequences of proteins or nucleic acids. BLAST is used in multiple ways, but last week my challenge to you, dear readers, was to a pick a sequence,...
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Posted on July 14, 2006 11:35 AM • 3 Comments •
Many regions in the United States, and the world for that matter, are seeking to entice biotech companies to relocate. As Lorraine Ruff and David Gabrilska describe in their Genetic Engineering News Article, "Metrics for Economic Development," the exhibitors at meetings like BIO work hard to: ".. entice founders and CEOs with a wide spectrum of inducements: institutional and technological...
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Posted on July 12, 2006 11:40 AM • 0 Comments •
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 background, see the post on qualitative measures of DNA quality....
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Posted on July 10, 2006 3:00 PM • 0 Comments •
I mean phone call. Because, if I thought he remembered me, I would call and say "thank you." Because of the time I spent in his lab, I know that cloning started long before Dolly. The first vertebrate animal was cloned over 50 years ago. And it wasn't a sheep....
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Posted on July 8, 2006 9:09 PM • 3 Comments •
My colleagues have come up will all kinds of interesting bloggy things to use as an excuse for Friday celebrations. Adventures in Ethics and Science has Friday Sprog Blogging for cute stories about her kids. A Blog Around the Clock considers Friday's the perfect day to write about weird sex. Pharyngula salutes the spineless with Friday Cephalopods. Good Math, Bad...
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Posted on July 7, 2006 9:00 AM • 2 Comments •
What do genetic testing and genealogy have in common? The easy answer is that they're both used by people who are trying to find out who they are, in more ways than one. Another answer is that both tests can involve DNA sequence data. And that leads us to another question. If the sequence of my mitochondrial DNA is only...
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Posted on July 5, 2006 7:00 AM • 2 Comments •
"It's all about saving Aunt Millie"
Bob Swanson
Co-Founder, Genentech
More blogging from Bio-Link
These next two posts salute instructors who teach in community college and high school biotechnology programs.
Confronted with the daily routines of doing lab work, or keeping up with latest genotyping techniques or chromatography tools, some of us might forget that there's more to biotechnology than just the science.
There are others who will
never forget.
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Posted on June 10, 2006 2:31 PM • 6 Comments •
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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