Publications by Brian Connelly
Creating Colorblind-Friendly Figures
Color is often used to display an extra dimension in plots of scientific data. Unfortunately, everyone does not decode color in exactly the same way. This is especially true for those with color vision deficiency, which affects up to 8 percent of the population in its 2 most common forms. As a result, it has been estimated that the odds of a giv...
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Analyzing Microbial Growth with R
In experimental evolution research, few things are more important than growth. Both the rate of growth and the resulting yield can provide direct insights into a strain or species’ fitness. Whether one strain with a trait of interest can outgrow (and outcompete) another that possesses a variation of that trait often depends primarily on the fit...
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Plotting Microtiter Plate Maps
I recently wrote about my workflow for Analyzing Microbial Growth with R. Perhaps the most important part of that process is the plate map, which describes the different experimental variables and where they occur. In the example case, the plate map described which strain was growing and in which environment for each of the wells used in a 96-wel...
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Creating Reproducible Software Environments with Packrat
Open science has grown tremendously in the past few years. While there’s stilla long way to go, the availability of data, software, and other materials is making it possible to re-use these products to expand upon previous work and apply them to new areas. Through responsible conduct of research (RCR) training, journal requirements, changing in...
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Connecting R to Everything with IFTTT
IFTTT (“if this then that”) is one of my favorite tools. I use it to keep and share articles, turn on my home’s lights at sundown, alert me when certain keywords are mentioned on Twitter/Reddit/etc., and many other things. Recently, the great people at IFTTT announced the Maker Channel, which allows recipes to make and receive web requests....
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R Phone Home: Notifications with pushoverr
There are a lot of times when it would be great if your computer talked to you. pushoverr allows you to send yourself or your group notifications from R. Instead of compulsively checking the status of a running job, you can just have R tell you when it’s done, if it failed, or what the results are. To get started, download a Pushover client for...
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