Book Review: Practical Computing For Biologists

Practical Computing for Biologists
Steven H. D. Haddock and Casey W. Dunn
Sinauer, 2010

Practical Computing for Biologists is an ambitious book that primarily aims to demystify many of the problems that most biologists will hit at some point in their research that can be solved with a bit of simple programming. The book does an admirable job of achieving this goal by exposing the reader to a number of freely available programs and techniques for dealing with text files and other data types. Much of the book (Parts 1-4) … Continue Reading

R 2.12.0 and Eclipse with StatET installation

A while back I outlined the setup process for running R under the Eclipse integrated development environment with the help of’s StatET plugin for Eclipse, in Windows 7. This post is an update on that procedure for the newer versions of each of the programs now available.

Specifically, this information pertains to an installation of Eclipse 3.6 (Helios), StatET version 0.9.1.b201011060900E36sw, and R 2.12.0, under Windows 7 64-bit (circa December 2010). The process for making R work within Eclipse has become a bit more … Continue Reading

Sorting out Sweave in Eclipse/StatET

Using Sweave to produce pretty-looking documentation for R is awfully handy. It takes a little tweaking to get set up in Eclipse and StatET though. I followed the information in Jeromy Anglim’s webpage to originally get Sweave set up. The following is my experience getting it working with Eclipse 3.5, StatET 0.9.1.b201011060900E35sw, Sweave Add-on for StatET 0.9.0.b201011060900E35sw, MiKTeK 2.9, and R 2.12.0 i386 on Windows 7 x64 circa November 2010.

I initially wrote a .Rnw file to be run through Sweave and converted to a pdf. I then set up Eclipse to process the .Rnw file using Sweave. I … Continue Reading

Altering Eclipse user name

Using StatET’s code generation templates is handy, but the standard Eclipse variable for ${user} just inserts the currently logged-in user’s account name. If you want a different name to appear when ${user} is called, one method is to alter the eclipse.ini file.

Specifically, add the line = Your full name
at the end of the .ini file.

For instance, my eclipse.ini file looks like this:
-Xmx512m Miller

When I open a new R-script file in Eclipse now, StatET automatically inserts that user name.

You can further alter the generated code in the Eclipse Preferences window. Go to Window>Preferences and you’ll get the following window.

[caption id=”attachment_502″ align=”aligncenter” … Continue Reading

Current temperature conditions at the Marine Science Center

Updated December 2013: The seawater temperature monitoring is no longer functional since I moved away and someone turned off the computer. The data I collected for 2010, 2011, and part of 2012 are available as one csv file: 2010-2012_MSC_temps.csv  The time stamps are all in Eastern Standard Time (UTC-5, no daylight savings time) and the water and air temperatures are in degrees Celsius.

I put together a temporary monitoring system for the seawater temperature and air temperature here at Northeastern University’s Marine Science Center in Nahant, Massachusetts.

The monitoring system is was running using some homebrewed Labview code … Continue Reading

Analyzing gels and western blots with ImageJ

The following information is an updated version of a method for using ImageJ to analyze western blots from a now-deprecated older page.

If you’re looking for a more comprehensive workflow option for your western blot analyses, please visit my tutorial on using Image Studio LiteIS_lite_icon, a free software package from LI-COR Biosciences. The Image Studio Lite software can be downloaded for free from In addition to the functionality described below for ImageJ, Image Studio Lite provides additional … Continue Reading

Printing to pdf with MS Office 2007

For those not aware, if you have Office 2007, Microsoft makes available a free download to enable you to save files as .pdf. SaveAsPDFandXPS.exe is available on the Microsoft site. It is not necessary to buy a copy of Adobe Acrobat, or go searching for any of the many free pdf printing utilities out there, just to output your Word document as a pdf file.

Pictures from Quoddy Head, Maine

Photo gallery from the Three Seas program trip to Lubec Maine. October 2010.

A thermocouple datalogger based on the Arduino platform

Updated with new Arduino code July 8 2012.

It never hurts to collect more data, and I often find myself wanting to record temperatures from a few extra animals. Most (all?) commercial thermocouple dataloggers that will record temperatures from multiple thermocouples cost several hundred or thousands of dollars. I set out to put together a relatively cheap 8-channel thermocouple datalogger based on the open-source Arduino development platform.

My 8-channel thermocouple datalogger. A single type-T thermocouple is plugged in to one of … Continue Reading

Shooting movies with a Canon 40D

This Sourceforge project “EOS Camera Movie Record” provides the ability to record high quality movies from older Canon EOS DSLR’s that have Live View functionality, but lack a movie mode from the factory (40D, 50D, 450D etc). It requires you to be tethered to a PC to record the video via USB cable, and there’s no sound input.

The video is 1024×680 pixels, and is saved as a .avi file. The video capture¬† seems to hover around 21-22 frames per second (confirmed in Matlab + Labview), even though the EOS Camera Movie Record window may report a higher frame … Continue Reading

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