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A note about my last name

The preferred spelling of my last name is VanHoudnos. The V is capitalized, the H is capitalized and there is no space between them. It is pronounced van-HOD-ness.

When my great-grandfather came to Nebraska from Belgium, he changed his last name from Van Houwenhuyse to VanHoudenos. No one in the family quite knows why he made the change, but there it is. My guess is that he wanted to break with the old world, so he adopted what he thought was a more American version of the name. Perhaps he chose to eliminate the space because it was confusing to Americans. I could imagine something like this happening: "Hey Peter, why do you always say your middle name? Wouldn't it be simpler to introduce yourself as Peter Houdenos?"

At some point before my father was born, my grandfather dropped the e from VanHoudenos to become VanHoudnos. No one quite knows why grandpa did that. His brother, for example, did not, so there is a whole branch of our family tree that retains the VanHoudenos spelling. Unfortunately, we never got a chance to ask grandpa why he changed the spelling because he died when my father was young. In any case, my father kept the spelling as VanHoudnos.

In a sense, I could reasonably be referred to as

  • Nathan Van Houwenhuyse, if I were to retain the original Flemish spelling. Note that the V is capitalized because that's just the way Flemish surnames are spelled;
  • Nathan VanHoudenos, if I were to adopt my great-grandfather's Americanized spelling; or
  • Nathan VanHoudnos, which is how I prefer to be known because it is the name my parents chose to give me.

The irregular nature of my last name can cause confusion. I have seen the following alternate spellings in the wild:

  • Nathan Vanhoudnos among those who think its weird to have a capital letter in the middle of your last name;
  • Nathan van Houdnos among those who are familiar with non-Flemish Dutch last names; and
  • Nathan Van Houdnos among those familiar with Flemish last names.

In any case, I prefer Nathan VanHoudnos. It may be irregular, but it is what it is.

Raising money for Nepal

During college, I worked for project Hi-CLIMB to install seismometers throughout Nepal and Tibet. Our goal was to better understand the underlying plate tectonic structure of the region, specifically what was happening as India slowly (over the course of millennia) smashes itself into China. Since Hi-CLIMB's home base was in the Lazimpat neighborhood of Kathmandu, we also devoted a portion of our time to collecting data within the Kathmandu valley itself in order to better understand how the city would be affected by a large earthquake.

The recent 7.8-magnitude earthquake heavily damaged both Kathmandu and the surrounding rural areas. It hurts to see the images of the devastation. Thankfully, my colleagues in Nepal are all safe and accounted for.

I have decided to raise money for World Vision, a Christian relief organization, that has been working in Nepal since 1982. From World Vision's website:

How is World Vision helping?

  • Over 1.1 million people reached through long-term development projects, including earthquake-preparedness trainings that educated over 65,000 people
  • Currently operating 73 projects utilising 205 staff
  • Emergency response teams are already mobilising relief

Through access to its regional warehouses in Nepal and Asia, World Vision has immediate access to necessary supplies, like hygiene kits, cooking kits, mosquito nets, sleeping bags and sleeping mats, buckets and water purification tablets, many of which are already on their way to remote village communities in desperate need of basic supplies.

World Vision will address the immediate needs of children, including establishing Child Friendly Spaces, which provide a safe environment for children to learn, play and emotionally recover from traumatic events.

Staff on the ground have prioritized getting potable water, food, temporary shelter, household supplies, and child protection, education and health programs to affected areas as soon as possible, with the aim of reaching 100,000 people in relief response.

Please keep the people of Nepal in your prayers and consider giving a gift of $50 or more to help them today.

Thank you,

Nathan VanHoudnos

Managing Latex packages manually in Ubuntu 12.04

Ubuntu is great, but making it play nice with latex is a bit of a pain. There are three parts to this:

  1. Ubuntu comes with APT, a really nice package management system that lets you easily install, update, and remove software that has been helpfully packaged by both Canonical and the wider Debian community.
  2. Tex Live, the official release of latex, comes with tlmgr, an equally great package manager for managing the all of the latex packages on CTAN.
  3. Ubuntu's distribution of latex omits tlmgr and forces developers to repackage the latex packages to fit into the APT scheme. (source)

This seems to be why my previous post about fixing moderncv for Ubuntu was so popular. It is not obvious to most users that to fix the

LaTeX Error: File `marvosym.sty' not found.

error, the user has to both (1) find the Ubuntu package that provides marvosym.sty and then (2) install that Ubuntu package along with every other latex package that happens to be bundled with it.

All of that is fine if a kind-hearted developer had the foresight to bundle the latex package you want/need in a convient form for installation with APT. If not, you have two options:

  1. Keep Tex Live under the control of Ubuntu's package management and manually install the Latex packages you need. An easy way to do this is described below.
  2. Break out Tex Live from Ubuntu's package manager and use tlmgr for Latex package management. This gives you MikTex style latex package management for Ubuntu, but you are responsible for keeping Tex Live up to date. See the answers to this Stack Exchange question for details of how to do it.

For now I'm sticking with Option 1. Here is a worked example to install the Latex package outlines for Ubuntu:

  1. Look at the path Latex searches to find packages with 'kpsepath tex' which should give output similar to:
    nathanvan@nathanvan-N61Jq:~$ kpsepath tex | sed -e 's/:/\n:/g'
    .
    :/home/nathanvan/.texmf-config/tex/kpsewhich//
    :/home/nathanvan/.texmf-var/tex/kpsewhich//
    :/home/nathanvan/texmf/tex/kpsewhich//
    :/etc/texmf/tex/kpsewhich//
    :!!/var/lib/texmf/tex/kpsewhich//
    :!!/usr/local/share/texmf/tex/kpsewhich//
    :!!/usr/share/texmf/tex/kpsewhich//
    :!!/usr/share/texmf-texlive/tex/kpsewhich//
    :/home/nathanvan/.texmf-config/tex/generic//
    :/home/nathanvan/.texmf-var/tex/generic//
    :/home/nathanvan/texmf/tex/generic//
    :/etc/texmf/tex/generic//
    :!!/var/lib/texmf/tex/generic//
    :!!/usr/local/share/texmf/tex/generic//
    :!!/usr/share/texmf/tex/generic//
    :!!/usr/share/texmf-texlive/tex/generic//
    :/home/nathanvan/.texmf-config/tex///
    :/home/nathanvan/.texmf-var/tex///
    :/home/nathanvan/texmf/tex///
    :/etc/texmf/tex///
    :!!/var/lib/texmf/tex///
    :!!/usr/local/share/texmf/tex///
    :!!/usr/share/texmf/tex///
    :!!/usr/share/texmf-texlive/tex///
    
  2. Note that the entry on line 21 is '/home/nathanvan/texmf/tex//', which tells latex to search every subdirectory under '/home/nathanvan/texmf/tex' to find packages that haven't been found yet. You'll have something similar for your home directory.
  3. Make a 'texmf/tex/latex' directory under your home directory:
    nathanvan@nathanvan-N61Jq:~$ mkdir -p ~/texmf/tex/latex
    
  4. Find the pacakge you want on CTAN, say outlines, because you read this blog post and want to try it out.
  5. Download the 'the contents of this directory bundled as a zip file', as CTAN likes to say it, and save it to '~/texmf/tex/latex'
  6. Unzip it right there:
    nathanvan@nathanvan-N61Jq:~$ cd texmf/tex/latex
    nathanvan@nathanvan-N61Jq:~/texmf/tex/latex$ ls
    outlines.zip
    nathanvan@nathanvan-N61Jq:~/texmf/tex/latex$ unzip outlines.zip
    Archive: outlines.zip
    creating: outlines/
    inflating: outlines/outlines.pdf
    inflating: outlines/outlines.sty
    inflating: outlines/outlines.tex
    inflating: outlines/README
    nathanvan@nathanvan-N61Jq:~/texmf/tex/latex$ ls
    outlines outlines.zip
    

And then you are done installing the latex package. It works great without any big hassles.

Edit: If the package you were installing contains fonts, this won't quite work. See Steve Kroon's comment below for details of how to fix it.

Edit: Thanks to jon for pointing out the correct directory structure for ~/texmf in the first comment to this answer. For the curious, more details, including why the directory is called texmf, can be found here.

My first citation in a published work

Back in undergrad, I wrote a term paper for May Berenbaum's Insects & People honors seminar. The assignment was to relate something about insects to people's daily lives. At the time, I was finishing up the first course in the year long classical mechanics sequence, so my daily life was physics problem sets. For the first time, I noticed something. There are a lot of insects in mechanics word problems (if a roach is walking on a turntable...; if a bee files in a spiral parametrized by... ). It seems they were always there, but take a class on insects and all of sudden you notice them making cameos. So, that's what I wrote about. It was a fun paper.

Seven years later, this paper makes it into the first chapter of her book: The Earwig's Tail: A Modern Bestiary of Multi-legged Legends.

It's kinda funny; reading it on Google Books. My only complaint is that she misspelled my last name. It's not Van Houdnos; it's VanHoudnos. That's why I didn't know about it; I had never google stalked myself with the alternate spelling of "nathan van houdnos" before. (Update: A bit more detail about my last name.)

I'm pretty excited about this. I'll have to see if she'll send me a signed copy. :)

UPDATE 5/9/2011
This essay in the American Entomologist is actually my first citation in a published work. It's from Spring 2003, so it beats the book by several years. (Of course, the essay is the relevant part of the book; it's not like I have two citations or anything.)

Is my bounce rate due to my HIT display?

My HITS have a rather high bounce rate. Between 40-50% of the Turkers who preview my HIT, choose not to accept it. I previously posted a histogram of the screen widths that I observed from workers who had accepted at least one HIT. That is very clearly a biased sample; it could be that only workers with screens large enough to comfortably display my HIT choose to accept it. I was curious to see if there was another population of Turkers that chose not to accept my HIT because their screens were too small.

I made the necessary modifications to my webapp and then generated the following graph:

Histogram split by worker acceptance

Screen resolution observed for Experiment 15

You'll notice that there isn't much of a practical difference between the workers who accept the HIT and those that do not. This makes me feel a little better. I'm not worried that my bounce rate is due to a display artifact. It does make me wonder though, is my bounce rate typical?

General Purpose AMT webapp based on web2py

I wrote in my previous post about some scripts I developed to make interacting with Amazon Mechanical Turk a bit easier from the command line. I didn't talk much about the web2py + Google AppEngine piece that actually serves the ExternalQuestion HITS. I realized after talking to another PhD student that people might be interested in a way to host general purpose HITS for free. My web2py application does that.

Getting it running is pretty simple. Sign up for an AppEngine account, install their SDK, install web2py into the SDK, and copy my application (really a directory) into your web2py installation. Use the development webserver included with the SDK to test that your installation is sane. Push it to google to make sure your account is working right. Once you have it running on appspot, install the Amazon Command line tools, install my wrapper scripts to make them behave better, and run the test experiment on the sandbox to verify that AMT + GAE + web2py are talking nicely in the clouds.

Once that's done, defining your own rubrics for HITS is pretty easy:

  1. Define a new controller to handle your custom rubrics. Example: grade6.py to hold grade6_test2_problem35_version1
  2. Copy the provided method template and modify it to handle a given rubricCode. The template builds a SQLFORM.factory to present the questions to Turkers and then validate the form input. Once the form is accepted, the method processes the result (scores it) and forwards it to a generic method to write it to the GAE datastore and sends it back to AMT. Example: def grade6_test2_problem35_version1() ....
  3. Copy the provided view template and modify it to ask the question you want for a given rubric code. The template extends a view class that knows how to display an informed consent in preview mode and track whenever a Turker clicks on a form element. It uses standard web2py tricks to protect you against injection and give you form validation for free. Example: grade6_test2_problem35_version1.html
  4. Prep the HITS by using my scripts to cross the rubricCode with the image (or whatever) you want to display. Run it on the sandbox and test it out. Promote the experiment and run it on production when you are ready.

Okay. Well maybe the setup doesn't look easy, but a complete definition of a HIT is just over 125 lines of code including comments. That's not really that bad. It's a heck-of-a-lot easier than trying to put an ExternalQuestion together from scratch. If the internet is interested, I'll clean up the application code (read: remove the parts pertinent to my research and IRB restrictions) and post it on GitHub. Leave a comment or send me mail if you are interested.

A better way to interact with AMT from the command line

Amazon Mechanical Turk is a useful thing. Interacting with it can be a giant pain.

My "standard" approach is to use web2py running on top of Google AppEngine to serve ExternalQuestion HITs. This allows me to have quite a bit of control over the Turker's experience and collect useful data like when they click on each button in the webapp. Although my current project doesn't use this click history, a related, later project will. It also let's me do fun things like use a bit of JavaScript to figure out the distribution of screen widths across workers so that I can optimize their viewing experience.

Width histogram

Anything under 700 pixels is fair game.

But that's not what this post is about. I'd like to eventually use boto to build the control of AMT directly in to the webapp itself. For now, I'm using the command line interface that Amazon provides. The CLT is an ugly hack that implements the Java API in a bunch of shell scripts. I have written my own wrapper around their scripts that enforces a certain amount of sanity. You can get the scripts over on gitHub.

There isn't really any documentation beyond the scripts themselves. The idea is that you create an amt-script directory where the new-and-improved scripts live. Under that directory, you create several exp# directories that hold the info that you need for experiments. Even ones are for production runs. Odd ones are for sandbox runs. Once you get a sandbox run working you run buildGoLiveExp.sh and it makes a copy from the staged experiment to a new go-live experiment. It's a bit of a hack at the moment, but it works for me. I like it because it gives me an audit trail for each thing I run on AMT. Feel free to use them yourself. (Or use them as inspiration for something better that you can write yourself!)