Make your R figures legible in Powerpoint/Keynote presentations

Having just returned from the SICB 2014 meetings, the appearance of many people’s Powerpoint figures is fresh on my mind. The sheer number of tiny figure labels (tick marks, axis titles, legend text etc) is disappointing. If we want to point fingers, MATLAB users are clearly the worst offenders because of the microscopic default label sizes in that program, but there are plenty of illegible R and matplotlib figures out there as well. Excel is obviously its own special class of terrible, but we will speak of it no more. The default settings in most of these programs … Continue Reading

Seastar wasting syndrome

2013 is turning out to be a bad year for seastars (starfish) along the west coast of North America. As documented by this UC Santa Cruz monitoring webpage, a wasting disease of unknown origin (possibly caused by bacteria or a virus) is causing seastars of several species to fall apart. The map provided by the monitoring group shows all of the places where affected seastars have been found. Seastars on the seashore and below the surface are being found with the disease.

I happened upon a Pisaster ochraceus in the mid-intertidal zone at Hopkins Marine Station today … Continue Reading

Measuring respiration rates

Here’s what the last month of my life was like.

This video shows the process of measuring limpet respiration using a fluorescence-based oxygen measuring system and a custom-built 15-well respiration chamber. The water bath maintains the desired temperature, and the user’s only job is to sit there and move the fiber optic probe to each well and take a reading for ~10 seconds. This goes on for two hours, and then you get to clean up, weigh all the animals, and move on with your life

The littorine snail in that kid’s knee

This news story about a seashore snail found living in a child’s knee wound has been making the rounds lately.

Apparently 4-year old Paul Franklin from Southern California was camping at a beach in central California near Morro Bay, when he fell and hurt his knee (Orange County Register). For several weeks afterwards, the wound refused to heal fully, despite the use of … Continue Reading

The dangers of overexposing western blots

Nigel
It’s like, how much more black could this be? And the answer is none. None more black.

Nigel Tufnel, lead guitarist of Spinal Tap.

 

None more black (or none more white) is a real concern when you’re talking about imaging western blots. If you only want to verify the presence of a protein, you can stop reading here, because even an overexposed image will tell you that there is some protein present in your sample. But an overexposed image of a western blot is essentially useless when you’re … Continue Reading

Stupid water bath tricks

As part of the downward spiral into increasingly esoteric subjects that is currently happening on this site, I now present some info on making a water bath do things. Simple things, but things nonetheless.

An old Cole-Parmer Digital Polystat water bath.

An old Cole-Parmer Digital Polystat water bath.

 

As part of an ongoing project in the lab, it became necessary to start carrying out simple temperature ramps with a water bath. For instance, we’ll start from a temperature of 15°C and go to a target temperature of 35°C at a … Continue Reading

O2 conversion

The molar volume of an ideal gas is ~22.4 liters per mole (we’ll  consider O2 to be an ideal gas for these purposes, and 22.4 is an approximation that varies with temperature, it’s 22.414 at 0C). Convert from 22.4 liters to milliliters ( = 22400 ml per mol). So if you have 1 milliliter of an ideal gas, there is 1 ml / 22400 ml per mol = 0.00004464 mol of that gas, which is 44.64 µmol of the gas. Thus, if you have a volume of a gas in ml, you can calculate the µmols of that gas simply … Continue Reading

Removing security features from a pdf

Whoops, I totally made my own pdf and accidentally included a bunch of security features, so now I can’t use my highlighter or type notes on the document. It sure would be handy to take off those security features that I put there myself when I made the pdf, myself.

With a full copy of Adobe Acrobat and the associated Acrobat Distiller software, the process is as follows:

1. Open the secured pdf in Acrobat.

2. Go to File>Export>Postscript>Postscript and save a .ps version of the pdf file.

3. Open the .ps postscript file in a text editor (WordPad on Windows works fine).

4. Use … Continue Reading

More tide prediction with R

Edit: There is now a full-fledged R package, rtide, to accomplish the same basic task of generating time series of tide predictions that is outlined here. See this more recent post for information.

In the previous post I outlined how to query the XTide software with R and parse the results into a handy-dandy data frame. The biggest hurdle with that method is getting XTide up and running on your computer. The code outlined here works entirely within R, so you don’t need XTide installed on your computer. The trade-off is that it provides substantially … Continue Reading

Interfacing XTide and R

Edit: There is now a full-fledged R package, rtide, to accomplish the same basic task of generating time series of tide predictions that is outlined here. See this more recent post for information.

XTide is an open-source program that predicts tide heights and current speeds for hundreds of tide and current stations around the United States. It can be used to produce tide predictions in the past and future for a site at your chosen interval (down to the minute), as well as producing sunrise and sunset times, moon phases, and times when the tide level … Continue Reading

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