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Sequencing a Genome, part V: checking out the library
Category: Bioinformatics
Send in the clones, but only the random ones.
Posted by Sandra Porter at 1:02 PM • 2 Comments •
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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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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- Workforce shortages in biotechnology, part I. Why is this a problem?
- Would your class like to clone and sequence plant genes?
- You tell 'em Arnold!
- The Genetic Nondiscrimination Act (GINA) is passed by the House
- The snake rescuer
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- Comparing mutant and wild type structures
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- Sandra Porter on The Genetic Nondiscrimination Act (GINA) is passed by the House
- Josh on The Genetic Nondiscrimination Act (GINA) is passed by the House
- Sandra Porter on A beginner's guide to making a phylogenetic tree
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- Miles on You tell 'em Arnold!
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
- PA on Workforce shortages in biotechnology, part I. Why is this a problem?
- Sandra Porter on Workforce shortages in biotechnology, part I. Why is this a problem?
- PA on Workforce shortages in biotechnology, part I. Why is this a problem?
- TomJoe on Would your class like to clone and sequence plant genes?
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January 31, 2007
January 30, 2007
Basics: How do you sequence a genome? Part IV. How many reads does it take?
Category: Bioinformatics
"How deep is the ocean? How high is the sky?"
Posted by Sandra Porter at 4:49 PM • 2 Comments •
January 29, 2007
Do Science in Las Vegas: Undergraduate Research Opportunities in Environmental Microbiology
Category: Microbiology
Hot springs, salty lakes, arid soil and good science.
Posted by Sandra Porter at 11:39 AM • 1 Comments •
January 28, 2007
Basics: How do you sequence a genome? part III, reads and chromats
Category: Genomics
In which we define reads, chromatograms, and shotgun sequencing.
Posted by Sandra Porter at 8:51 PM • 2 Comments •
January 27, 2007
Basics: How do you sequence a genome, part II
Category: Ask Dr. Science
Some background on the strategies: mapping vs. shotgun
Posted by Sandra Porter at 1:50 PM • 2 Comments •
January 25, 2007
Bioinformatics teaching tip #1: Remember Julia Child!
Category: Bioinformatics
No more live BLAST searches during lectures!
Posted by Sandra Porter at 1:20 PM • 3 Comments •
January 24, 2007
Make your own stem cells!
Category: Biotechnology
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 by Sandra Porter at 1:05 PM • 0 Comments •
January 22, 2007
Basics: How do you sequence a genome?
Category: Genomics
Ask Dr. Science: yes, I do take requests.
Posted by Sandra Porter at 8:59 AM • 7 Comments •
January 21, 2007
What is a gene? My definition is better
Category: Genetics & Molecular Biology
In 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...
Posted by Sandra Porter at 3:44 PM • 7 Comments •
In the movies: fighting flies and lobbing lobsters
Category: Biology (Macroscopic )
And a mutation that makes males flies fight like a girl
Posted by Sandra Porter at 1:41 PM • 0 Comments •
January 19, 2007
Carnivals and fun things to read
Category: Announcements
Imagine yourself curled up and cozy, a glass of wine (or pop) in your hand, a blazing fire, and a wonderfully entertaining book in your hand. Hmmmm. What are you reading? Oh, of course! It's the open laboratory edited by our very own Science Blogger, Bora Zivkovic, who really does seem to (a) Blog Around the Clock. The secrets out,...
Posted by Sandra Porter at 8:32 PM • 0 Comments •
DNA Day is on the way!
Category: Genetics & Molecular Biology
Start writing those essays! You could win cash and a chance to work in a lab!
Posted by Sandra Porter at 4:43 PM • 0 Comments •
January 13, 2007
Ask Dr. Science!
Category: Announcements
or you can try asking me.
Posted by Sandra Porter at 3:07 PM • 10 Comments •
January 12, 2007
Bioinformatics for biotech students: my favorite computer programs
Category: Bioinformatics
The 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....
Posted by Sandra Porter at 1:37 PM • 10 Comments •
January 10, 2007
Snow Day!
Category: Bioinformatics
I 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...
Posted by Sandra Porter at 11:21 PM • 4 Comments •
January 9, 2007
Home, home on the range, where the deer and the catteleo play
Category: Biotechnology
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 by Sandra Porter at 12:28 PM • 3 Comments •
My equipment wish-list for teaching bioinformatics
Category: Bioinformatics
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 college. We're introducing lots of web-based programs, and databases, and...
Posted by Sandra Porter at 12:11 PM • 3 Comments •
January 8, 2007
Welcome Bioinformatics Students!
Category: Bioinformatics
It's the first day of our bioinformatics class.
Posted by Sandra Porter at 6:55 PM • 2 Comments •
January 6, 2007
Doing the right thing isn't always enough
Category: Microbiology
Decan Butler, the Reveres, and Nature have written that verdict is in. The scientific evidence has been shunted aside. The nurses and doctor who traveled to Tripoli on a humanitarian mission have been sentenced to death. There is still a chance, but it seems to be slim....
Posted by Sandra Porter at 11:21 PM • 0 Comments •
Could it be camouflage?
Category: Humor
Are lab-coat wearing researchers just acting like my dog?
Posted by Sandra Porter at 10:04 PM • 1 Comments •
January 5, 2007
Congratulations to Oklahoma City Community College!
Category: Bio-Link
GenomeWeb reports that OKCC and the University of Utah's Genetic Science Learning Center received NIH funds for genomics and bioinformatics education projects, respectively. Congratulations are certainly due to the University of Utah. For a community college, on the other hand, to get NIH funding is very unusual and OKCC should be commended. From GenomeWeb: The NCRR said it will fund...
Posted by Sandra Porter at 1:15 PM • 0 Comments •
January 4, 2007
Making a positive difference: how would you encourage women to major in science, technology, engineering, or math?
Category: women in science
Recruit hotter guys?
Posted by Sandra Porter at 4:48 PM • 7 Comments •
Antibiotic resistance: taking the bypass
Category: Microbiology
The wind storms and heavy rains that hit Seattle recently, demonstrated why a bypass mechanism can be a helpful thing - for both bacteria and motorists. Under the bridge on Mercer, from the Seattle Times...
Posted by Sandra Porter at 8:28 AM • 0 Comments •
January 3, 2007
Tangled Bank #70
Category: Announcements
You can spend all day staring at irreducibly complex patterns in the sand (wow! it's a pattern! Evidence for intelligent design? Or created by random acts of water?). Or, you can do something even more fun and enjoy a treat at Tangled Bank #70. As they say in Spain, Viva La Evolución!...
Posted by Sandra Porter at 12:19 PM • 0 Comments •
Five paths to antibiotic resistance: a quick summary
Category: Microbiology
How do I resist thee? Let me count the ways.
Posted by Sandra Porter at 8:04 AM • 0 Comments •
January 2, 2007
Are antibiotics really only made by bacteria and fungi?
Category: Microbiology
Is it really safe to pierce your tongue?
Posted by Sandra Porter at 9:00 AM • 5 Comments •
January 1, 2007
Favorite stories from 2006
Category: Miscellany
From earwax to smelly things in our refrigerator, your favorites from Digital Biology.
Posted by Sandra Porter at 12:24 PM • 0 Comments •
Did you publish a scientific mistake? Blame the software!
Category: Bioinformatics
When 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...
Posted by Sandra Porter at 8:31 AM • 8 Comments •
