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.
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).
e-mail digitalbio at gmail.com
February 26, 2008
Category: Microbiology
Do different kinds of biomes (forest vs. creek) support different kinds of bacteria? Or do we find the same amounts of each genus wherever we look? Those are the questions that we'll answer in this last video. We're going to use pivot tables and count all the genera that live in each biome. Then, we'll make pie graphs so that...
Posted by Sandra Porter at 10:58 AM • 3 Comments •
Category: Microbiology
This is third video in our series on analyzing the DNA sequences that came from bacteria on the JHU campus. In this video, we use a pivot table to count all the different types of bacteria that students found in 2004 and we make a pie graph to visualize the different numbers of each genus....
Posted by Sandra Porter at 10:47 AM • 0 Comments •
Category: Bioinformatics
What do you do after you've used DNA sequencing to identify the bacteria, viruses, or other organisms in the environment? What's the next step? This four part video series covers those next steps. In this part, we learn that a surprisingly large portion of bioinformatics, or any type of informatics is concerned with fixing data entry errors and spelling mistakes....
Posted by Sandra Porter at 10:19 AM • 0 Comments •
Category: Bioinformatics
For the past few years, I've been collaborating with a friend, Dr. Rebecca Pearlman, who teaches introductory biology at the Johns Hopkins University. Her students isolate bacteria from different environments on campus, use PCR to amplify the 16S ribosomal RNA genes, send the samples to the JHU core lab for sequencing, and use blastn to identify what they found. Every...
Posted by Sandra Porter at 10:14 AM • 0 Comments •
February 25, 2008
Category: Science education
When will science lab courses start teaching more of what we do now, and less of what we did twenty years ago?
Posted by Sandra Porter at 2:48 PM • 24 Comments •
February 23, 2008
Category: cubical world
In the cubical world, is the "Gesundheit" the right thing to say?
Posted by Sandra Porter at 12:26 PM • 38 Comments •
February 16, 2008
Category: Bioinformatics
I love the way you show me secret things. All I do is type: Select * from name_of_a_table And you share everything with me. Without you, my vision is obscured, and all I see is the display on the page. In fact, this was the push that finally made me decide to learn SQL....
Posted by Sandra Porter at 7:42 PM • 3 Comments •
February 14, 2008
Category: Miscellany
They could have used the data from my serial killer survey, but no, being scientists or science-related, the ScienceBlogs overseers want to find out for themselves. Plus the chance of winning and iPod is higher than the chance of winning the lottery and you don't even have to buy a ticket. Take the survey, maybe even win. I wonder if...
Posted by Sandra Porter at 1:04 PM • 3 Comments •
Category: Valentine's Day
Believe it or not, this is a DNA kiss....
Posted by Sandra Porter at 9:06 AM • 0 Comments •
February 13, 2008
Category: bioethics
Confused about terms like "autonomy" and "beneficance" and their relationship to biomedical research? The Northwest Association for Biomedical Research (NWABR) is offering a short course at the University of Washington, Feb. 29th and March 1st, on Ethics in Science. Registration details and a description are below....
Posted by Sandra Porter at 9:10 AM • 0 Comments •
February 12, 2008
Category: Microbiology
Getting paid to do it?
Posted by Sandra Porter at 1:39 PM • 2 Comments •
Category: Bioinformatics
A quick video introduction to BLAST.
Posted by Sandra Porter at 8:14 AM • 13 Comments •
February 11, 2008
Category: Computers and software
What could be more fun on a rainy day than a relational database?
Posted by Sandra Porter at 8:54 AM • 8 Comments •
February 10, 2008
Category: Science education
A few weeks ago I attended a education conference at Pacific Science Center entitled, "A Conversation that Can Change the World."...
Posted by Sandra Porter at 12:17 PM • 6 Comments •
February 9, 2008
Category: Computers and software
A long standing debate in my field is whether or not biologists, who work with computers, need to learn how to program. I usually say "no." Let the programmers program, the biologists interpret the results, and let everyone can benefit from each other's expertise. Well, I've changed my mind in one respect. Most biologists need to work with some kind...
Posted by Sandra Porter at 5:55 PM • 21 Comments •
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