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Discovering Biology in a Digital World

My thoughts on biology, teaching, life, and exploring the living world via the digital one. Only my opinions are represented by these postings, they do not represent the viewpoints of any funding agency or Geospiza, Inc.

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Sandra Porter 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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    Biotechnology:

    The wonders of webinars

    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,...

    How to use Cn3D

    A video tutorial on molecular structures.

    GloFish® really glow!

    GloFish for the cloned "glow in the dark" kitties.

    By request, the glowing cheeseburger LOL cat

    Well, some of you asked for this...

    Korean scientists clone cats that glow in the dark!

    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....

    Irony in RNA: a puzzle

    RNA by any other name would smell as sweet. Or would it?

    The real cost of J. C. Venter's genome

    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?...

    How does a single nucleotide change make influenza virus resistant to a drug?

    Fun with molecular models!

    Why is sequencing a human genome so expensive?

    Adding the costs and doing the math.

    Genetic Variation I: What is a SNP?

    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...

    Watson's genome, Venter's genome, what's the difference?

    "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....

    What happens to graduates of high school biotech programs?

    Some of them work for Bayer.

    Got DNA sequencing problems? Who ya gonna call?

    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...

    Is phred dead? Let's see the data

    Calling all bases, how many are correct?

    Will the real DNA sequence please stand up?

    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...

    What is the truth in DNA sequencing?

    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...

    The X-ray method for pest control

    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...

    Gene therapy with AAV: too risky for a cure?

    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...

    Digital Biology Friday: the answer to last week's puzzle

    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:...

    Summer time and the mosquitoes are biting

    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...

    Careers in biotechnology, part IV: the tip of the informatics iceberg

    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...

    Careers in biotechnology, part II bioinformatics

    Where does bioinformatics fit in the biotech food chain?

    Careers in biotechnology, part I.

    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...

    "A college education is not job training"

    Answers to a commenter who bemoans bioinformatics education.

    Biotechnology Education in Viriginia

    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...

    From Louis Pasteur to "Lab-on-a-chip"

    Blogging from the 2007 NW branch ASM meeting

    Hot plants and viruses, part III: An inordinate fondness for hypothetical proteins

    How do plants grow at 65°C?

    Sequencing a Genome, part VII: Want to win $10 million dollars?

    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...

    Biology as a second language: what is a vector?

    Defining a biology term for scientists in other disciplines.

    Sequencing a Genome, part V: checking out the library

    Send in the clones, but only the random ones.

    Basics: How do you sequence a genome? Part IV. How many reads does it take?

    "How deep is the ocean? How high is the sky?"

    Basics: How do you sequence a genome? part III, reads and chromats

    In which we define reads, chromatograms, and shotgun sequencing.

    Basics: How do you sequence a genome, part II

    Some background on the strategies: mapping vs. shotgun

    Make your own stem cells!

    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...

    Home, home on the range, where the deer and the catteleo play

    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...

    Antibiotics au naturale?

    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....

    Molecular biology in the age of kits

    Do more kits mean more science or more science that's bad?

    Let's watch that again in slow motion, shall we?

    We need lab movies of people doing things wrong.

    Mysterious lab protocols: Film at 11

    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....

    Things that go wrong in the lab

    Like sex education in a religious household, lab technique must sometimes be learned from your friends.

    What's it really like on the "dark side?"

    To some inhabitants of the ivory tower, industry looks like paradise.

    Confessions of an organic gardener, part I.

    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...

    Biotechnology cleans my clothes

    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...

    Digital Biology Friday: Hey, who moved my DNA?

    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...

    Anti-freeze for winter weather

    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...

    Sequencing the campus at the Johns Hopkins University

    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...

    Digital Biology Friday: It's still Friday!

    "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....

    Digital Biology Friday: What was that gene anyway?

    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...

    Digital Biology Friday: Those BLASTed results!

    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,...

    If you build it, will they come?

    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...

    Quantitative measures of DNA sequence quality

    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....

    Hang on, just let me make a quick clone fall

    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....

    Digital Biology Fridays: It begins with a BLAST

    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...

    Am I really related to Cleopatra? Qualitatively measuring DNA sequence quality

    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...

    "It's all about Aunt Millie"

    "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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