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Tag Archives: tools

Playing with sequence data

I’ve been playing with sequence data a lot recently. It’s been so long since I have done any real work with this stuff that I’ve fallen behind in my knowledge of the tools for analyzing the data. 

I hope to post a couple of things here after I have been working on as a sort of tutorial on how to use ClustalX as an alignment tool that (I think) can even build phylogenetic trees from homology data.

 
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Posted by on March 5, 2014 in Uncategorized

 

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Another Semester Ends .. A quick note

Suddenly, the end of every semester rushes in surprising me with how little time is left to finish the material I wanted to cover. As with any semester, I could have used more time. Despite reaching the end of my syllabi, I could easily have used another week or more to fully cover that material for each class.

But done is done. All in all, I’d call it a good semester.

But what’s next?

My next semester brings a return of Microbiology, where I will again try to sit material from the front end of the course in order to have more time to cover immunology at the end.

I will also be teaching Ecology. This will be a first time for me doing this class, so I expect it to be interesting. My ideal is a discussion-based class where we do a bunch of reading, maybe watch a film or two and then talk through the big ideas. Because I expect us to spend a good amount of time talking about evolution, we will be reading Jerry Coyne’s Why Evolution is True, and follow his blog for some spontaneous talk about evolution and related topics (like cats).

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HHMI’s Earth Viewer complements readings from Shubbin’s Your Inner Fish

In the meantime, I’ve been invited to speak on the use of technology in the classroom- featuring my use of the iPad to present an interactive handbook, apps that go along with course material, games (and/ or gamification) as learning tools and other online resources like HHMI, NobelPrize.org or iTunes Course Manager.

I look forward to the opportunity to find out what others are doing in this area and maybe even find collaborators to help put together even better materials.

 
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Posted by on December 13, 2013 in Uncategorized

 

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Felling a tree at 100 degrees F is insane…

but relying on a homemade surveying device and distant memories of trigonometry might take this over the edge.

Last year something has come through Kansas killing a ton of pine trees. Our problem is that one of these is pretty close to the house and the dead branches have begun to droop so low that they scrape the car when we drive under it. That’s a problem by itself, but then there’s the fact that the branches have become so brittle that I really worry about it toppling over onto us, our cars or the house.

With that in mind I decided that it had to come down. The strategy was to tackle the problem head-on first thing in the morning. I started by removing all the lower branches (I would have kept going, but I could feel the sway of the tree and I kept thinking…’brittle.’ So, I didn’t finish off the top.

Oh, right – I forgot to mention that a couple weeks ago someone broke into our garage/shop and stole my chainsaw, so this whole process is being undertaken with just an axe and bow – saw.

Once the lower branches were off, it was decision time. The last tree I took down I took off the branches and then the top of the tree before chopping down the trunk. It was a pretty scary process, because high in the tree I cut the top and despite all my efforts, the top came down in a way that hit both me and the ladder I was on pretty hard. This time around, I was remembering that clearly while deciding on my next step.

My solution was that I needed to get a good measurement of how tall the tree was to know if it was even safe to bring it down all in one piece or if I just needed to face the prospect of knocking myself off the tree or otherwise hurting myself. But how to measure this?

That’s where high school trig came to mind.

The tangent of an angle equals the opposite over the adjacent sides. So, if I could measure the angle to the top of the tree from any point a known distance away, then I could compute the opposite side (the height of the tree).

How do you measure angles? With a protractor – damn, I don’t have one…. but I can make one!!

Then I need to be able to sight my angle…how about using a straw as a sight?!? And from where on the tree am I measuring the height? I wanted to use a laser pointer, but that didn’t work, so I just sighted that as well.

Here’s the device I used in the hands of my helper:

The reading:

The answer:

tan 25 = tree height / 726″

tree height = about 9.5 yards

I worked for about three hours with a lot of breaks in the shade, but I’m still not finished. I hope it’s safe until tomorrow morning when it’s cool again.

 
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Posted by on July 18, 2012 in Personal Life

 

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