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Whatever happened to Bill Nye the Science Guy?
Category: Humor
We used to love watching him blow stuff up on TV. But things are different now.... GrrlScientist has the movie....
Posted by Sandra Porter at 11:54 AM • 4 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
- A molecule for May
- A vaccine against lung cancer?
- Comparing mutant and wild type structures
- The Personal Genome discussion
- The wonders of webinars
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- Deepak on Workforce shortages in biotechnology, part I. Why is this a problem?
- Jan Miernyk on Would your class like to clone and sequence plant genes?
- Brian M. 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?
- Deepak on Workforce shortages in biotechnology, part I. Why is this a problem?
- Martin Robbins 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?
- Becca on Workforce shortages in biotechnology, part I. Why is this a problem?
- Sigmund on Would your class like to clone and sequence plant genes?
- Christopher Smith on The Genetic Nondiscrimination Act (GINA) is passed by the House
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March 31, 2008
March 29, 2008
What do computer scientists do anway? Inquiring minds want to know.
Category: Science education
Our new Scibling, Jane, is a real life computer scientist. If you've ever wondered what computer scientists really do during the day, Jane will set you straight (I guess they're not playing Nintendo. Darn! Another illusion shattered, just like that.)...
Posted by Sandra Porter at 11:10 AM • 0 Comments •
March 28, 2008
It's bad enough to throw your data away
Category: Microbiology
If you're old enough or you've taken microbiology, there's a chance that sometime in your life you heard of Legionaire's disease. This disease was caused a bacteria that inhabited the air conditioners in a hotel where several veterans held a conference. Naturally, it was the microbiologists who collected samples of the bacteria and figured out what was going on. Now,...
Posted by Sandra Porter at 12:12 AM • 1 Comments •
March 27, 2008
A beginner's guide to making a phylogenetic tree
Category: phylogeny
I made this video (below the fold) to illustrate the steps involved in making a phylogenetic tree. The basic steps are to: Build a data set Align the sequences Make a tree In the class that I'm teaching, we're making these trees in order to compare sequences from our metagenomics experiment with the multiple copies of 16S ribosomal RNA (rRNA)...
Posted by Sandra Porter at 9:11 AM • 22 Comments •
March 20, 2008
Oh internet gurus, what's your advice?
Category: Computers and software
Believe it or not, there is the remote possibility that I may get to have some influence in getting a web application built, that I can use in teaching, that will do something that I want. Unfortunately, I know very little about the relative merits of AJAX/JavaScript vs. Flash vs. a custom C++ plug-in, that does something with WX Windows...
Posted by Sandra Porter at 9:10 AM • 12 Comments •
March 19, 2008
How to use Cn3D
Category: molecular structures
A video tutorial on molecular structures.
Posted by Sandra Porter at 5:37 PM • 1 Comments •
Hey instructors, do you know what kinds of operating systems your students use?
Category: Science education
It's not Linux.
Posted by Sandra Porter at 5:23 PM • 6 Comments •
March 17, 2008
Starting a new biotech program? Teaching a biotech course?
Category: Science education
Bio-Link is accepting applications for this year's National Summer Fellows forum, June 2-6th, in Berkeley, CA. You can get an application at www.bio-link.org I'll be there, doing some kind of bioinformatics workshop. I'll probably be talking about either metagenomics or comparing protein structures and drug resistance, but if you have topic requests, feel free to submit them in the comments....
Posted by Sandra Porter at 6:13 PM • 0 Comments •
DNA sequencing errors hit home
Category: Bioinformatics
One of my colleagues has a two part series on FinchTalk (starting today) that discusses uncertainty in measurement and what that uncertainty means for the present and Next Generation DNA sequencing technologies. I've been running into this uncertainty myself lately....
Posted by Sandra Porter at 2:05 PM • 3 Comments •
March 16, 2008
Wonderful pictures of Gas Works park
Category: Science Art
Things move off of our entry page pretty quick sometimes. If you missed this post from Bioephemera, go take a look. She has great pictures and a fascinating story about one Seattle's favorite places....
Posted by Sandra Porter at 6:20 PM • 2 Comments •
Biologists hunt Washington cougars - and make a video
Category: Cats
Conflicts between predators like cougars and coyotes and human companions like pets and small children are becoming more common as people move into areas that used to be wildlife habitat. The Seattle Times has a great story this morning about biologists in Washington who are studying cougars to learn if cougars and people can coexist. The biologists think most of...
Posted by Sandra Porter at 11:42 AM • 0 Comments •
March 14, 2008
A Rosetta stone for parents
Category: Humor
It's a good thing my 13 yr old doesn't read my blog. Why? Because I'm on to her. Being a biologist, well, acronyms are my life. And, for a long time, I've been able to interpret some of the lingo that she uses on AIM. Lately, we've certainly been having our little talks about cell phone bills for texting and...
Posted by Sandra Porter at 9:29 PM • 0 Comments •
Exploring Open Office: part II, can we have our pie and eat it too?
Category: Computers and software
I've been writing quite a bit this week about my search for a cross platform spread sheet program that would support pivot tables and make pie graphs correctly. This all started because of a bug that my students encountered in Microsoft Excel, on Windows. I'm not personally motivated to look for something new, since Office 2004 on Mac OS 10.5...
Posted by Sandra Porter at 2:31 PM • 21 Comments •
March 13, 2008
Exploring OpenOffice: what did we learn?, part I
Category: Bioinformatics
I think all of us; me, the students the OO advocates, a thoughtful group of commenters, some instructors; I think many of us learned some things that we didn't anticipate the other day and got some interesting glimpses into the ways that other people view and interact with their computers. Some of the people who participated in the challenge found...
Posted by Sandra Porter at 6:42 PM • 0 Comments •
A Bustard is not just a bird
Category: Bioinformatics
It's a Solexa data directory. I've held off on blogging about Next Generation Sequencing here, but now that one of my colleagues has started blogging about it, it seems like a good time to write a little about FinchTalk, our company blog. We've decided that we can serve an educational role for people who are interested in Next Generation DNA...
Posted by Sandra Porter at 12:28 PM • 0 Comments •
March 12, 2008
The OpenOffice challenge: can you do what needs to be done?
Category: Computers and software
Okay OpenOffice fans, show me what you can do. Earlier this week, I wrote about my challenges with a bug in Microsoft Excel that only appears on Windows computers. Since I use a Mac, I didn't know about the bug when I wrote the assignment and I only found out about it after all but one of my students turned...
Posted by Sandra Porter at 12:50 PM • 35 Comments •
March 11, 2008
Google Maps meets bacterial genomes
Category: Microbiology
I read about this in Bio-IT World and had to go check it out. It's called the Genome Projector and it has to be the coolest genome browser I've ever seen. They have 320 bacterial genomes to play with. Naturally, I chose our friend E. coli. The little red pins in the picture below mark the positions of ribosomal RNA...
Posted by Sandra Porter at 12:00 PM • 6 Comments •
Little monarchs, little monarchs, where are your trees?
Category: Biology (Macroscopic )
Your canopy is disappearing, you're likely to freeze. NASA's Earth Observatory reports that over 1,110 acres of forest were illegally logged, during the past four years, in the Monarch Butterfly Biosphere Reserve in central Mexico. Monarch butterflies travel here from all over the United States and Canada. Images from the Ikonos satellite tell us though, that future migrating butterflies are...
Posted by Sandra Porter at 10:04 AM • 5 Comments •
Linux is amusing, but this is why I teach with Excel
Category: teaching
The other day, I wrote that I wanted to make things easier for my students by using the kinds of software that they were likely to have on their computers and the kinds that they are likely to see in the business and biotech world when they graduate from college. More than one person told me that I should have...
Posted by Sandra Porter at 8:00 AM • 33 Comments •
March 10, 2008
The NASA Earth Observing System and dealing with all that data
Category: Bioinformatics
The NASA Earth Observing System is an incredible resource for both science and education. One of the amazing things about it is all the different kinds and quantities of data are assembled together into pictures that even grade school kids can immediately comprehend. How do they do it? Each of the EOS satellites delivers a terabyte or more of data...
Posted by Sandra Porter at 9:31 AM • 0 Comments •
An unexpected challenge with teaching on-line
Category: teaching
Three (or more) operating systems times three (or more) versions of software with bugs unique to one or systems (that I don't have) means too many systems for me to manage teaching. Thank the FSM they're not using Linux, too. (Let me see that would be Ubuntu Linux, RedHat Linux, Debian Linux, Yellow Dog Linux, Vine, Turbo, Slackware, etc.. It...
Posted by Sandra Porter at 8:09 AM • 12 Comments •
March 9, 2008
The day PZ visited Seattle and became a pirate
Category: Humor
Happy Birthday! Is it PZ Myers or Captain Barbosa in disguise?...
Posted by Sandra Porter at 1:50 PM • 2 Comments •
March 7, 2008
Digital Biology Friday: A microbiology blast puzzler
Category: sequence analysis
Here's a fun puzzler for you to figure out. The blast graph is here:...
Posted by Sandra Porter at 12:28 PM • 2 Comments •
