And so, we landed!

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Today marks our fist day here in Iceland.

Events started in a bit of a disarray with the airlines misplacing some important biology items and Charlie attempting new fashion trends,

but nevertheless after collecting our things from the baggage claim we soon found the members of our group who had arrived ahead of the main party. 

Dan was our fearless leader of the day and we organised into groups to get some errands done such as getting an emergency SIM card, going grocery shopping, and getting dry ice. At this point everyone was feeling the effects of tiredness, jet lag, and the every present brightness special to Iceland.

The day was far from over though, for our first real taste of Icelandic scenery the group went off to Þingvellir, a national shrine and home of the first parliament in existence, that lies directly next to the Almannagjá canyon which is made by the separation of the north American and European tectonic plates.
In such a short time, we have already been met by so much beauty here in the land of fire, ice, and trolls, we are all excited for what the next couple of weeks have in store for us.

I’m leaving on a jet plane

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All my bags are packed, I’m ready to go!

We’re just about ready for departure. Three of us leave this afternoon for flights out of Chicago, and the rest of the crew departs early tomorrow morning: Earlham –> IND/DAY –> JFK (7 hour layover) –> KEF –> Reykjavik!

It’s been a very busy 1.5 weeks, but, ready or not, we will all be in Iceland in less than 48 hours. We can anticipate cloudy weather in the 40s and 50s. We’re looking forward to experiencing another place, expanding our horizons (culturally, scientifically, emotionally), eating fermented shark, implementing our algorithms and devices, going back to Skalanes, to run in Iceland, seeing birds (especially Puffins), geocaching, standing on a glacier (and possibly sledding down it), climbing a volcano or two, lounging in a hot spring, and trying to learn some of the language.

Our gear is packed.

Our daily plans have been formulated.

Our devices are primed and charged.

Our sense of adventure is fully present.

Our Spotify playlist has been populated. What more do we need?

See you in Iceland!

Hey, DNA!

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Our biology and soil team has begun a practice run of the sampling, DNA extraction, and MinION sequencing protocols so that we are prepared and familiar with the process before we get to Iceland. We started by collecting soil samples from various places around Earlham campus: The Heart, the Japanese garden by Stout, the horse barn, the rain garden by the Wellness Center, and a popular social gathering place back campus. We used Maria, one of our elevation platforms, to record the coordinates of each sample site, and as a placeholder for the soil temperature readings we will take in Iceland. We put the samples on ice to preserve the living organisms within, since we are trying to identify what kind of biotic activity takes place and varies at each site, both here at Earlham and eventually in Iceland on Sólheimajökull. Back at the lab, we extracted the DNA.

Much pipette fun was had by all!

We also ran a gel electrophoresis and a Nano Drop to test the quality of the DNA. The former told us how long the strands were, and the latter told us how many nanograms per microliter of DNA we had in our samples. Both yielded positive results, meaning we have a good quality and quantity of DNA to put through the MinION.

DNA on the gel tray

We had some technical difficulties at first with this new tech, but we made it work eventually and are now working on setting up the nanopore. We are almost ready to sequence the DNA and find out what microorganisms are living all around us! We had a great win the other day with QGIS. Though we had a rocky start, we were finally able to georeference our first map! Enthusiastic cheers echoed through the Turing room, and we all celebrated with a trip to Dairy Queen.

Laser Beams and Drones

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Over the last few days, we have been making good progress with our LiDAR endeavors. Neil and Charlie have been working on weight-efficient methods to attach the LiDAR to our drone, Kia. The initial prototype was too heavy, and a test run over-heated Kia’s battery. It turns out that we can cover one of Kia’s sensors without catastrophe, which will allow us to attach the LiDAR to Kia underneath said sensor without needing extra material like a platform for the LiDAR to sit on.

It will be useful for us to sync up the LiDAR data with GPS data from Kia. Fortunately, both the LiDAR and Kia transmit time-data. Unfortunately, that data is not easily accessible, much less synchronizable. Kellan and Nic have been working on methods to extract this data so we can sync up and get going. They have also been working on installing software and writing code for analyzing point clouds (3-D depictions of LiDAR readings).

I have been familiarizing myself with the tools and methods used for analyzing point clouds. Once we have gathered our LiDAR data, how do we extract meaning from any of it? First we will need to reduce noise, which can be done by using statistical analysis to detect outlier points (laser reflects off of a piece of airborne dust, for instance). Since we will be looking for particular kinds of things (archaeological ruins, bird nests, etc.), we will then need to have methods for detecting particular features. For example, the foundation of a structure will likely have near-straight lines. If we have a tool that will highlight all near-straight lines, we can search for archaeological ruins more efficiently. There are many object-detection techniques, all of which involve very clever math. If we’re lucky, any noise-filtering and object-detection algorithms that we may need are already out there. If not, enough work has been done in this field that synthesizing existing methods will (hopefully) be doable.

 

We are currently searching for a renegade tablet that seems to have wandered off. I can’t imagine it can run very fast or far, so we should come across it soon if it doesn’t get tired and come home by itself.

Biology and Pockets

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Lately we’ve been trying to figure out how to track the movement of the Sólheimajökull glacier to determine where to take samples of the soil, which we are then going to extract microbe DNA and thenot sequence that DNA with the MinION  (as seen previously in the blog post wherein Emi was being very excited about her new gadget.) Moving away from the maps, we’ve passed the location torch to Dan and Ai Lena and georeferencing software, QGIS, as I found through several hours of soul crushingly fruitless work to get our three maps to the same scale that the analog method was not the best route. However with that issue off my plate, I am freed to work on honing my soil sampling, protocol following, and biology learning skills. So yesterday, for example, Dan, Cait, and I worked on practicing our pipetting so today we can gather soils from around campus to do a practice run of our DNA extraction kit and presumably the sequencing kit as well. I also learned that bacteria and archaea are different, also that I have a pocket that combines three pockets in one.

Taking the LiDAR out for a spin

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We took the LiDAR out for a spin on Friday. We had a beautiful (read: high tech) rig that consisted of Neil driving, Kellan holding the LiDAR out the sunroof, and Nic spread out across that back seat with the drone (Kia), laptop, and router, collecting data from the LiDAR. We re-learned that Kia doesn’t like having a lot of metal around, so our plan to collect GPS data was challenged, more on why GPS data is important below.

This is us trying to get a good GPS signal on Kia, not us actually driving with Kia sitting on the roof…
Note: Kia is the drone not that we are in a KIA car

 

 

After a lot of indoors practice with the LiDAR, we determined that the best way to set up Kia when in Iceland is to have a balanced rig with weight evenly distributed to the sides. The elements that we have to consider are the LiDAR, a wifi transmitter as well as battery packs for both. Neil and Charlie are working on getting these built in a reliable prototype.

 

Our ultimate goal is to create point clouds from the LiDAR data based on GPS coordinates. During our test run on Friday we collected data but are still mapping this data based on time instead of GPS. Our plans for Monday are to pull the GPS data from our Friday test run from the Kia and align the GPS/telemetry data with the LiDAR data in a point cloud. This will allow us to correctly map the data in a point cloud. We can’t map the LiDAR data using time because the LiDAR spins faster than our time readings and time is linear and our flight most likely won’t be linear. If we were to create the point cloud using time, we would have a straight line where the data would be stretched out and repeated.

The next generation of next generation sequencers has arrived!

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We have received, from Oxford Nanopore, the MinION. (Min-ION, not one-eyed yellow minions, get it straight.) This device promises whole-genome sequencing of microbes, viruses and archaea from soil samples we will collect at the Solheimajokull glacier. This device is extremely small and portable, and one sequencing run can be done on a laptop in 6-8 hours. One flow cell can run up to 12 samples at a time, and while the samples are being sequenced, internet access will allow simultaneous queries of a database that will determine what species were in our sample. Thus, in REAL TIME, we can identify the composition of the soil microbiome. This is a drastic improvement over prior methods, which involved sending 16s rRNA samples to a company and waiting for 2-3 weeks for results. 

What kind of science are we doing with this device?

We will be collecting soil samples at the Solheimajokull glacier (near the town of Vik in Iceland). We want to obtain samples that have been “out of the freezer” i.e. not covered by the glacier for a specific number of years – 10, 20, 50, 75, 100, 150, 200, etc. We will compare the microbial populations present in these different soil samples and look at the type of soil and flora growing in these different locations. This will teach us how the land “recovers” once it is freed from a glacier.

This device will help us do this analysis on site and give us the data almost immediately. It’s really new, cool and exciting. We’re looking forward to learning about soil succession with the use of this device!

 

Blogger: Emi (Biology Professor and MinION hand modeler)

Driving, of a sort

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This is the first of a couple of short clips from the GoPro dashboard cam that we used in 2016 (we plan to again this year). The wheat-to-chaff ratio is pretty low, but the kernels you do find tend to be gems. In this clip we are driving down to the red sand beach on the West coast of Iceland. It’s near the end of a long day of driving from Akureyri, Nic is at the wheel with “support” from Erin, Deeksha, and the Talking Heads.

Catching-up

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In some sense the amount of activity going on is inversely proportional to the posts we’re making here to document it… Here’s a quick summary of what we’ve been working on since my last post:

o LiDAR – We have new unit which is much more capable. We built a test-rig in Hopper to simulate having it on Kia, we’re just starting to collect data. Nic and Kellan are working on the algorithms/workflow to analyze it. Charlie is working on mounting it on Kia.
o Image processing – Kellan and Nic are working on a workflow for extracting features from the images. Charlie built a map (headed to QGIS) with marked known POIs on the Skalanes peninsula to use as part of the training data.
o Glacier forefield sampling – Tara and Charlie are developing a sampling plan and 16S RRNA workflow for processing the soil samples.
o Benchmarks for registering multi-modal data collected by sensors on the RPA.
o Discovered Siggi’s yoghurt.
o Kristin and Charlie are working on Field Day, mostly on the BLE plumbing.
o Checklist App – More news to follow.
o Gail and Charlie have done lots of logistics and planning.
o Emi is working on the avian surveys and the MinION workflow for processing glacier forefield soil samples
o New ambiance platform (single chip) is designed, construction to follow.

More regular updates to follow, we’re all psyched.

Where are we?

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I learned this week the breadth of coordinate systems that are used to geolocate a “point” on the surface of the earth. A very nice archeological survey was done of the Skalanes peninsula about 10 years ago (as near as I can tell, it is in Icelandic). The locations of the features they catalog are given in eastings and northings from a point that I have not found documented yet. It appears to be UTM but when you use 28 W, the UTM grid zone for eastern Iceland you get kind-of-sort-of close, say within a couple of Km, but nowhere no exact. The survey team used a differential GPS, if we can obtain a copy of their database we should be able to figure-out how to convert from their coordinate system.

In other news Gail and I have finished making the hostel, ferry, and car reservations. Next up is exploring bulk airfare.

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