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Thomson Reuters Web of Science is still using OCR text recognition for new citations?

A co-author emailed me the other day to point out that somehow my name had been misspelled in the Web of Science citation database on our recent paper in Ecological Applications.

The Web of Science listing has my first name listed as “Luice”, which judging by the name of this here website, isn’t how you spell my first name. Thomson Reuters managed to replace the “k” in my name with an “ic”. That looks suspiciously like an optical character recognition (OCR) error , which you might have run into if you’ve ever scanned in an old document and … Continue Reading

Arduino code for MS5803 pressure sensors

I have recently been developing a library for the Measurement Specialties MS5803 line of digital pressure sensors. These sensors are available in several different pressure ranges from 1 to 30 bar, they are submersible if installed in a proper housing, they communicate via I2C or SPI, and they cost around US$35. It’s fairly straightforward to interface the MS5803 with a microcontroller like the Arduino that can also communicate via the I2C or SPI protocols. They are a surface-mount style chip, meant to solder onto a 1.27mm pitch SOIC-8 layout (like the green board I used in the picture below).

[caption … 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

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.


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

ImageJ StartupMacros

Before I lose this file again: StartupMacros.txt This is a text file, based on the original StartupMacros.txt file that came with ImageJ, that can be dropped in the ImageJ/macros folder that is created when you install ImageJ. Start up ImageJ, and if this macro doesn’t automatically run, go to Plugins>Macros>Startup Macros to load it. It installs a few more drawing tools on the ImageJ toolbar and creates some keyboard shortcuts for the following tools:

  • Line tool – press ‘l’
  • Brush tool – press ‘b’
  • Eraser tool – press ‘e’
  • Wand tool – press ‘w’

I either found or created some code … Continue Reading

Adventures in kludgy software – Diving PAM edition

As a general rule, expensive pieces of lab equipment must come with software of questionable quality. In this case, I just want the raw data off a $20,000 submersible DIVING-PAM fluorometer, which can be used for measuring the photosynthetic yield of algae and plants out in the field, away from a computer. But downloading the data requires a mini-odyssey through some needlessly confusing software that comes with the unit.

To start with, the packaged instruction manual for our DIVING-PAM still references a DOS-era utility for downloading the data, because the (brand new, delivered in 2012) instruction manual was printed in 1998. … Continue Reading