By the numbers…

With apologies to Harper’s:

23 days in Iceland  (plus 50 days of somewhat intense preparation)
1,300 km traveled by bus
170 km traveled by ferry
23.9 hours of daylight per day (on average while we were there)

125,026 geocoded sensor data records (ambiance, gas, soil, and water)
70 geocoded water and soil samples
60 2ml tubes of extracted DNA

317 giga base pairs of sequencer output (estimated for now)
3,900 lines of source code (Java/Android + Arduino + Perl + Python + SQL)
8,004 pictures and movies (worth keeping, significantly less;  destroyed to protect the innocent, a few…)
65 songs on our playlist

Time Lapses Across Iceland

Time lapses offer a unique view of events that occur on a scale of hours or days. Chronologically below are a few time lapses we took while in Iceland.

Leaving Earlham


Grundarfjörður


Skálanes:


Extracting DNA at the University of Akureyri

Eldfell: a True Story by Willie Wallance

During our trip we visited the Eldfell Volcano, located on an island just off the southern coast of Iceland. This story describes our trip from the perspective of Willie Wallance, a geology student, for whom this visit was more than special.

“The crisp sea air biting at my face with each gust, I stood on the deck of the ferry, staring at the horizon. It would not be long until we reached our destination of Heimaey—an Island just thirty minutes off the coast of Iceland. It was there that in 1973 the inhabitants had to stop the flow of lava from Eldfell, which threatened to destroy their town and livelihood. I and the others in our group were going to climb this active volcano, and take some samples for testing.

Heimaey grew closer until we were finally able to disembark, perhaps a little greener in hue than before we left. Our next objective would be to climb to the summit with the equipment. Tristan was already miles ahead of the rest of the group as we headed to the base of Eldfell. Long legs aside, even he was slightly put off when the earth began to sigh, but we were not deterred. Still we pressed on, determined to reach the top of the volcano which had once caused the evacuation of the entire island.

After struggling through the arduous climb, I hopelessly looked around to enjoy the view that I felt I had earned and take some pictures. A clinging mist filled the air and obstructed the view of my surroundings. The only thing that I thought I would have after leaving Eldfell was a cold from the thick mist—if only I was so lucky.

The sighing had been but a warning. A thunderous roar ripped through the sky, and the earth began to quake, bringing us to our knees. Stumbling to my feet, I began to feel the ground shifting below me, and soon I could see a rift forming just below the feet of Elena and Ivan. With all my might I pushed them, and just in time. A huge sulfurous blast of air erupted from the fissure, making me jump back just a bit too close to the cliff and lose my balance, but I was lucky. Ivan thrust his hand out toward me, and I grasped at it. I thought that I might not be able to reach it, but luck was on my side—so I thought.

The unstable stone gave way and crumbled beneath my feet, and I fell. Ivan did all that he could to hold on to me as Elena helped to try to pull us up. My world began to go into slow motion as I looked upon the horror on everyone’s faces when I slipped and slid down the rocky cliff face. As I fell, I tried my best to stop my descent by grabbing onto any rocky outcroppings I could see, causing my hands to get lacerated from the jagged basalt, but all of the rocks were loose and would break off when they came under my full weight; until, finally I did find a sturdy enough protrusion, but my stop was too abrupt; the momentum I had built up brought my head smashing into the side of Eldfell. My mouth was filled with hot blood, which soon began to trickle onto my cheek and chin through the hole in my face. I held on to the rock with everything that I could, but I had become so woozy.

I couldn’t have been there for more than ten minutes when I heard Charlie shouting something I couldn’t quite make out. I blinked and he was by my side. Through my delirium, I was able to make out that he was trying to tell me that I would be fine as he and Ivan pulled my cheek back together and covered it as best as they could, preparing for the trek back down to the town at the base of the volcano. Elena was nowhere to be seen. After providing Charlie and Ivan with all of her sanitized and organized first aid supplies, she had went up Eldfell to collect the samples necessary for the research—she was the only one brave enough to continue up a volcano that was falling apart.

Just as Elena came back down from the top, the volcano began to spew ash into the sky. The dark cloud loomed overhead, and the air began to get thick, making breathing all the harder for me. I blacked out and awoke some time later in the hospital. I’m told that Tristan, with his amazing running prowess, was able to carry me down the mountain twenty minutes faster than everyone else, and if Charlie and the gang had not been there with their fast responses and running, I would be dead. But, who would believe that?”

—– Willie Wallance

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At the Arctic Circle

On Wednesday July 17th we took a break from the lab and headed north. Our final destination was a small island called Grímsey around 60 km away from Akureyri. The only obstacle was an open ocean. Grímsey was the priority among the list of the places we wanted to visit because of the Arctic Circle running through the middle of the island. Another fascinating thing (which we learned once we arrived) is that Grímsey shifts towards north 14 meters per year which is 4.1 cm per day.

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Our day started at 7am when we left the hostel and headed to the bus station where we took a bus to Dalvík. There, we boarded a ferry for the ride to Grímsey. The trip lasted about 3 hours and some of our group members did not handle the open sea very well. Charlie pointed out that he learned how to say “I need to puke” in 8 different languages. For me, it was a great place to connect, think, and at the same time enjoy looking at the immense and beautiful ocean.

Three hours later we were on “terra firma” eating amazing local delicacies. Afterwards we started walking towards the Arctic Circle. You know that you are on a small island when the airport runway is half of the island’s length and the number of inhabitants is 86.

Once we were above the Arctic Circle, we took a few soil samples and soon after that we headed to the iconic bridge separating the Arctic and Northern Temperate Zones.

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If you remember from earlier, we threw our frisbee from Eurasia to the North American plate when we were at the bridge between two continents. As is now our tradition, we threw the disk from the Arctic to the Northern Temperate Zone.

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One person from our group introduced us to a very interesting “modern global game” called Geocaching) which is the open GPS cache hunt game. The idea is to search for hidden items in a multitude of places around the globe. Our friend collected the online hints about the location of the caches on Grímsey, we found one near the bridge that marks the border of the Arctic Circle. This cache was a little metal water resistant tube with the list of the names of the people who previously found the cache. We wrote our names on the small folded piece of paper, placed it back to the tube and then put it back in its original hiding place. You can go to these coordinates – N 66° 32.689 W 018° 01.267 – and check it for yourself.

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Vatnshellir Lava Cave

On July 6th we visited the Vatnshellir lava tube located in western Iceland on the Snæfellsnes peninsula. It is believed that this cave was created in an eruption between 6,000 and 8,000 years ago. The cave holds unique formations generated by the lava cooling. While 34m underground (with a rapid temperature drop to 6C) we collected five ground samples and one water sample from a pond in the cave’s floor. We discovered that in most of the cases the cave walls were covered with bacteria, unique to Iceland. For that reason, we spread out our sampling within the different depths from the entrance to analyze how the bacterial life progressed and changed from the deepest point of the cave to the entrance.

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The cave contained many mysteries: an unknown organism that we discovered in a crack in the ground (in Tristan’s opinion it is just human trash), the skeleton of an arctic fox trapped in the cave for hundreds of years, and the huge rectangular rock that is believed to be the meeting table for the trolls that gather there every 100 years.

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Our guide was impressed with the scientific interest our group showed by asking questions and our willingness to learn more about the formation of the cave which she said is so untypical for tourists. We wrapped up this adventurous trip by spending a minute inside of the cave in complete darkness, listening to the sounds of the cave and being absorbed in the darkness.

Lab Day

In the last 17 days we have collected numerous water and soil samples from variety of different and very interesting sites. We have been carrying them with us as we traveled around Iceland until today because, finally, we have arrived at the laboratory where we can extract the DNA from the water and soil samples. The laboratory is at the University of Akureyri which is about a 15 minute walk from the hostel where we are staying.

This morning we took all of our samples and the DNA extraction tools and headed to the lab. The Geology students, all nine of them, and their instructor Dr. Kathleen Affholter joined us. The lab technician at the university did an amazing job of preparing everything our group had requested, we recently learned that he is from Ohio. The world is truly becoming a smaller and a smaller place to live.

The first thing we did today was a crash course in pipetting. Some of the students had never used them before. A lack of material led us to be creative: we generated an innovative tool for pipetting practice. At the same time, we made a Google document with a table of different values in microliters and opened it on our Nexus7s. The unit of measure used for setting up reactions is the microliter (µl). One microliter is one millionth (10-6) of a liter. So: 1 L = 1,000,000 µl, and 1 ml = 1,000 µl.  The students then practiced pipetting directly onto the glass surface of the Nexus 7′s

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We had three groups of students extracting the DNA from water, each group had 3 water samples to take care of. Group names were Russian Team, Viking Alpha and Kitties. We finished around 17:00 and checked one sample for the quantity of the DNA. It looked very promising, what is even more important is that everyone had fun doing the actual science. Tomorrow we are going to the Arctic Circle (Grímsey Island) and then on Thursday and Friday we will be back in the lab extracting the DNA from our soil samples.
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Our Workflow

We were tasked with creating reliable tools for scientists to use in the field, it’s an open objective and a lot of code no matter how you approach it. Full on development started a few months ago, here’s what we’ve got

The App, Frontend

Over the last few months we’ve been constructing a series of tools which collects geocoded data from a variety of sensors. The primary app is Seshat on Android. Normally Seshat is plugged into a set of sensors which stream values and stores them. When needed manual samples can be taken, effectively making the device a clipboard for geocoded data. The saved data on the device and can be sent over an HTTP POST to a server running a CGI script.

The Server, Backend

In our case our server software is running on a late 2012 13″ MacBook Air. The server receives files from Seshat’s HTTP POST as well as hosting all our code and miscellaneous files. It has been the most “on” device in our arsenal. It also has a Postgres database on it which we dump our sensor and sample readings in.

Code, File, and Task Management

Code

All the code for the visualization software, the server, and the app are maintained in a Git repository. We used Git mainly because the CVS we had wasn’t working up to our liking. The branching and merging features in the end worked really well for a team of our size.

Files

Most files that we need access to on the go are stored in a Git repository and accessed through an open source alternative to Dropbox called Sparkleshare. We choose SparkleShare over Google Drive and Dropbox because we can utilize it without an internet connection. All we have to do is run git daemon and we can get all our documents so long as

Tasks

With so much to do how can we keep track of it? We looked into Asana and Remember the Milk but found them to be lacking for the scope of all the projects we had. Instead we setup a Google Drive spreadsheet with columns describing the task’s activity, progress, assignee, priority/due date, and comments. This worked out really well for us in the end. We could even meet remotely and go through the active tasks we had checking them and incrementing their progress collaboratively.

Visualization

Sorry Excell this problem space is too much for you to handle. While all our data (so far comprising of more than 50,000 rows) is on a Postgres instance, we’re displaying and showing this data with either Gnuplot or R. We’re using these because they are highly automatic and customizable. Note: Visualization is the least mature portion of the workflow at the time of writing. There should be a post coming soon on what we’ve been doing with it.