Computers and software

Pull a spaghetti noodle out of a box of pasta and take a look.  It's long and stiff.  Try to bend it and it breaks.  But fresh pasta is pliable.  It can fold just like cooked noodles. When students first look at an amino acid sequence, a long string of confusing letters, they often think those letters are part of a chain like an uncooked spaghetti noodle.  Stiff and unbending, with one end far from the other. Molecular modeling apps let us demonstrate that proteins are a bit more like fresh pasta. If we apply rainbow colors (Red Orange Yellow Blue Indigo Violet) to a protein chain, we can ... Read more
Last night we went to see "The Agony and the Ecstasy of Steve Jobs" by Mike Daisey. Two hours vanished as we sat riveted and listened to interspersed stories of Apple and Shenzhen. Mike spoke of Apple and computers as a lover, familiar with the details, and knowledgeable in the special language of geeks and engineers. He was hysterically funny. And we all understood. After all, the night at the play was organized as a spring celebration by the Washington Technology Industry Association, a group intimately familiar with the ways of tech. From the music preceeding the show, to Mike's ... Read more
These days, DNA sequencing happens in one of three ways. In the early days of DNA sequencing (like the 80's), labs prepared their own samples, sequenced those samples, and analyzed their results. Some labs still do this. Then, in the 90's, genome centers came along. Genome centers are like giant factories that manufacture sequence data. They have buildings, dedicated staff, and professional bioinformaticians who write programs and work with other factory members to get the data entered, analyzed, and shipped out to the databases. (You can ... Read more
We always enjoy home science experiments and it was fun the other night to learn about a new experiment we could try with our teenage daughter and an iPhone. As it turned out, the joke was on us. My husband is an enthusiastic fan of the iPhone store. Last night, he downloaded this application called "Army Knife." This application has, I kid you not, the following nine items:
  • unit converter - these are always helpful, especially if you travel
  • ultrasonic whistle
  • protractor
  • Heart (beats per minute) counter
  • measuring tape
  • ... Read more

"Digital biology," as I use the phrase, refers to the idea of using digital information for doing biology. This digital information comes from multiple sources such as DNA sequences, protein sequences, DNA hybridization, molecular structures, analytical chemistry, biomarkers, images, GIS, and more. We obtain this information either from experiments or from a wide variety of databases and we work with this information using several kinds of bioinformatics tools.

The reason I'm calling this field "digital biology" and not "bioinformatics" (even though I typically use the terms ... Read more

The auditorium could have been empty as I focused on the slide overhead. Questions formed out the mist, and my heart pounded as I took a deep breath and began to my raise my hand.

"Da da da dah!  Da da da dah, da da da da da da da dah!!" 

Oh, NO!  The theme song from Indiana ... Read more

Some people, like Imelda Marcos and Dr. Isis have a thing for fancy shoes. I go crazy for gadgets.

For my birthday this year, my family bought me a new iPhone! Yeah! So, I've been killing several hours today filling it with cute little iPhone apps. Who knew one little phone could be so much fun? One app, I enjoy, is called Molecules. Molecules lets you download structure files from the Protein Data Bank (PDB) and play with the structures on your phone!

There's no question that the ability to work with information is one that will be required and valued for a long time to come. I think it's imperative for teachers to have students practice this skill whenever an opportunity comes about. The problem for many teachers is finding the time to identify good data sets. MRSA stands for Methicillin-resistant Staphylococcus aureus (MRSA), a serious problem for hospital patients. Six of out seven people who become infected with MRSA, get it from some kind of health-care facility. In 2007, the CDC issued a report claiming that 18,000 people die ... Read more
Poor PZ! Stranded without a working laptop in a strange town! This is the kind of situation that gives me nightmares, so I like to upload presentation materials to the web just in case. Lately, I've been looking at different methods for doing this to see which ones l like the best. A few days ago, I tested this with Scribd. Today, I'm going to see what we can do ... Read more
Well, I had to test Scribd with something. Why not use a document on the Massachusetts Life Sciences Industry? Scribd is sort of like the YouTube of electronic paper. I found Scribd from TomJoe's post about Life on Mars. His PowerPoint talk is really much more interesting than the life science document that I uploaded as a test, but since you're here anyway, you might as well take a look. What does Scribd do? It solves the "waiting for ... Read more

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