Computers and software
sporte | January 16, 2015Pull 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 see…
sporte | May 1, 2011Last 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…
sporte | January 8, 2010These 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 learn more about this and go on a virtual tour in this…
sporte | May 6, 2009We 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
digital caliper
Two levels
flashlight
emergency SOS light
Some of these…
sporte | March 15, 2009"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 as…
sporte | February 4, 2009
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 Jones! Coming from my backpack! Thousands of eyes turned disapprovingly to stare at my red face. Scrambling frantically over people to reach the aisle, I ran out the back of the room and answered the phone.
"Hi, my name is Tim, and I'm looking for a financial advisor in your area...."
What!! Who is this! The…
sporte | November 23, 2008Some people, like Imelda Marcos and our new Dr. Isis, have a thing for fancy shoes.
I go crazy for gadgets.
technorati tags: iphone, DNA, molecules, molecular structure, molecular modeling, Science education
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!
Spreading your fingers…
sporte | November 21, 2008There'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 every…
sporte | November 15, 2008Poor 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 with Google Docs.
TomJoe said that he started using Scribd because he couldn't share things with Google.
I use Google docs quite a bit, but I haven't tried to share any documents with more than a few people, so I took at look…
sporte | November 13, 2008Well, 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 another application to open" problem that I find so frustrating when I want to quickly read (okay, skim) a pdf document that's linked from something on…
sporte | November 10, 2008Worldmapper is a web site with 366 maps of the world. These maps however, are not the kinds of maps you've seen in school, with every country shown by size. These maps are cartograms. It's a bit like seeing a cartoon version of a Thomas Friedman book. These maps present a whole new way of visualizing information about the world.
In a cartogram, the size of each country or geographic region is drawn in proportion to some kind of variable. The variable could be population size, number of people who practice a certain religion, incidence of infant mortality, voting patterns, energy use,…
sporte | September 24, 2008Part IV. Assembling the details and making the case for a novel paramyxovirus
This is the fourth in a five part series on an unexpected discovery of a paramyxovirus in a mosquito. In this part, we take a look at all the evidence we can find and try to figure out how a gene from a virus came to be part of the Aedes aegypti genome.
image from the Public Health Library
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a novel mosquito paramyxovirus
V. A…
sporte | September 21, 2008Part I. The back story from the genome record
Together, these five posts describe the discovery of a novel paramyxovirus in the Aedes aegyptii genome and a new method for finding interesting anomalies in GenBank.
I. The back story from the genome record
II. What do the mumps proteins do? And how do we find out?
III. Serendipity strikes when we Blink.
IV. Assembling the details of the case for a mosquito paramyxovirus
V. A general method for finding interesting things in GenBank
I began this series on mumps intending to write about immunology and how vaccines work to stimulate the immune…
sporte | August 6, 2008This the third part of case study where we see what happens when high school students clone and sequence genomic plant DNA. In this last part, we use the results from an automated comparison program to determine if the students cloned any genes at all and, if so, which genes were cloned. (You can also read part I and part II.)
Did they clone or not clone? That is the question.
But first, we have to answer a different question about which parts of their reads are usable and which parts are not. (A read is the sequence of bases obtained from a chromatogram file.)
How does our data get…
sporte | August 5, 2008This the second part of three part case study where we see what happens when high school students clone and sequence genomic plant DNA. In this part, we do a bit of forensics to see how well their sequencing worked and to see if we can anything that could help them improve their results the next time they sequence.
How well did the sequencing work?
Anyone who sequences DNA needs to be aware of two kinds of problems that afflict their results. We can divide these into two categories: technical and biological.
Technical problems are identified using quality values and the number of bases…
sporte | June 17, 2008In its simplest sense, we imagine that learning occurs through a series of positive and negative rewards. Some actions lead to pleasure, others to pain, and it seems reasonable to expect that people will repeat the actions with pleasurable results and avoid those that ended in pain. Yet, we all know people who aren't deterred by the idea of punishment. We all know people who never seem to learn.
Could there be a physical reason, hidden in their genes?
In December 2007, Science published a study by Klein et. al. (1) where they asked if a specific genotype at a location called "DRD2-TAQ-IA"…
sporte | March 20, 2008Believe 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 or QT.
What do you think?
sporte | March 19, 2008The University of Virginia does.
They survey students every year to find out what they're up to tech-wise. Apparently 99% of their first year students own computers.
And, a large majority of those computers are laptops (3058/3113 or 98%).
And, what's on those laptops? Let's have a drum roll:
60% have Windows VISTA
26% have Mac OS X
12% have Windows XP
and, 2% or less have something else - like Linux.
This is why I really, really, want good web-based applications.
Just for the record, I don't care what operating systems students use. My concern how to help them use those computers to do…
sporte | March 14, 2008I'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 doesn't seem to have the same bugs that appear on Windows. However, I would like things to work for my students. Since I don't want to have to write instructions for every software system on the planet, Google Docs would be my ideal answer, if it…
sporte | March 13, 2008I 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 out that it was harder than they expected.
Lessons learned
Okay, what did we learn?
1. The community is the best thing about Open Source
The Open Office advocates enjoy a challenge and are truly, quite helpful. That was something that adventure…