In the zone

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Almost all of my free cycles are thinking about Iceland now, my grading is (almost) done and now I can focus a bit more on this. May Term started on Wednesday, we’re spending the mornings working/meeting together in the lab and the afternoons concentrating on our own bits. We submitted three posters to the XSEDE conference, one based on Field Day, one on UAS + LiDAR + DNG and machine learning, and one on Mothur (the software we use to process 16S rRNA sequencer output). Nic and I have a plan for the first round of testing with the UAS, unfortunately using it in the building is difficult because of all the EMI. Kristin is cruising along with Field Day, we are very close to uploaded data to the database (using the new schema) and should be ready to start Field Day Fridays this week. Erin is chugging along on the GIS, she is creating base layers by georeferencing Google Map images for Heimaey, the two glaciers, and Skalanes. Lots of list management and lab sorting this week, this is our chance to align our waterfowl for the run-up to June 23.


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After a week or so of tinkering we have a new version of the database schema that supports Field Day and the visualization stack. Here is the fancy entity relationship diagram for it:


Field Day will load trip, site, and sector information from Postgres (config option) and cache them on the tablet. Deeksha is committed to moving the data from Iceland13 & 14 and Nicaragua14 into this new structure.

Our credit card looks like one of Dali’s clocks…

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Kristin booked our tickets (yes!), and I ordered high precision barometric pressure sensors (to be used for altimeters), Adafruit Feathers to use as the micro-controllers for the ambiance/orienteering and soil (field and bench) platforms. This model has BLE and a battery charging circuit. I built a simple rig for the NIR sensor and scissor table, this is one of the bench soil platforms.

The next thing I would like to wrestle is reconciling the data stream that comes through the sensors into the database. Given that we’ll be collecting readings from multiple sensor platforms at each spot we need a way to aggregate those. This mirrors what happens with 911 incident data, in that case it’s the call number that binds all the different responses (fire, EMS, etc.) to an incident together.

Lots to do, 58 days to do it in…

Let’s design some stuff

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Tara and I designed and prototyped a couple of bench and field devices recently. We have a first pass at a Falcon tube turner, a soil microbe quantifier and a soil temperature and humidity probe.

The Falcon tube turner is designed to be used on a bench to mix soil samples as part of the pH, etc. protocols. Currently it’s based on Lego components, if that basic design works we can easily fabricate a couple robust enough for our needs.

Tara has an idea to quantify the amount of soil microbes by measuring their CO2 respiration. We have data for this from 16S extractions done at one of archeology sites at Skalanes, we can re-sample there and compare the two methods. Pictured below is our first pass at a device for doing this.


The soil temperature and humidity probe is a combination of a stainless steel soil coring tool with the two probes built-in to the end of the tube, see below (kind-of).


I’ve been working on reconciling the data model with the implications that Kristin brought when we worked-through the sensor <-> Arduino <-> BLE <-> Android <-> data model. Stay-tuned for the details.

This is getting really interesting

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o On the archeology front, Rannveig found this article about the possibility of a new Viking site being excavated in Newfoundland. They must have stopped along the way from Scandinavia, and Skalanes seems like a nice place for that. Who knows what we’ll find.

o Nic has made some progress with LIDAR, although the gear is proving to be a bit delicate. We’ll probably order a second unit to work with. Here is an early image taken during today’s meeting. The unit is on the round table, on Nic’s screen is the developing point-cloud of the room and contents. If you look very closely you can see people on couches (/very/ closely…)


o We need to sort a magnetometer before long, hopefully Patrick can loan us one.

o On the logistics front we need to make plane reservations fairly soon. All the lodging and transportation is sorted modulo the ferry to Grimsey, we’ll just wing that early in the morning of the day we travel.

o I started working with our Yocto altimeter recently, we’ll use this as part of the kit that provides more accurate x, y, and z geo-coordinates than consumer grade GPS chipsets alone do.

o Kristin and I worked through most of the details of the interface between FieldDay and the Arduino based sensor platforms. Here is a schematic of it, off to the left is the Postgres database where FieldDay pushes readings in CSV form.


o I think it’s time we started the Iceland16 playlist, it looks like Spotify is currently the most popular platform for doing so.


There’s only 28 thousand days…

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Actually it’s only about 80 days until we leave but Alicia Keys’ song is stuck in my head after hearing it this morning when we were working in the lab. I do know the answer to her second question, Iceland.

Eamon and Deeksha are making progress on the data, data model, and viz tool. We are going to create a function that measures the distance between two lat,lon pairs to make annotating the site information easier and to provide a hook for the bounding-box interface.  We wire-framed the viz tool UI, Eamon is going to construct a message to Patrick about open map tiles that we can cache on our devices.

Erin is chugging along with QGIS, we owe Patrick an adult beverage for suggesting that we use it. Nic recently discovered that there is a plug-in for it that supports LIDAR generated point-clouds in a layer (as a layer?).

I ran into Kelly Gaither (chair of XSEDE16) at IU on Friday, she strongly encouraged us to produce a poster for XSEDE16 on the UAS + LIDAR + machine learning package. She thinks it’s quite unique. Unfortunately she did remember me from the conference last summer when I hid under the table during the awards ceremony.

Next up for me is working on the high resolution Z platform and the soil temperature platform. I would like to work on Field Day too.

I love the details…

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The past week has been .23 zillion small things. A few travel related, a few data, and a lot of sensor platforms. The UAS and LIDAR gear is in-house, so far Nic has made the LIDAR spin (he said it was “working”…) and the UAS has charged batteries. I’ve been meeting with Anna and Katie looking at measuring the voltage potential generated by the pH testers. Anna and I worked-through the software architecture for connecting Arduino-based sensors to FieldDay via BlueTooth. There is some data aggregation to be done on the Arduino, and we should probably look at George’s libraries.

Tara and I built a rig out of Lego for spinning 50ML Falcon tubes, if the basic principle works we can fab it out of “real” materials. That was so much easier than the last thing she asked me for, a suction filtration device on the Sunday after Christmas in Leon, Nicaragua.

I worked with Deeksha and Eamon on the data organization, cleanup, visualization, etc. It’s moving along albeit a tad slowly.

The Lilly map sale is today, I’m going to see what I can find for topos of the Wayne county area that we can use for testing the orienteering gear. Kristin and I were interviewed by Mark Brim about how we collaborate, that was fun.

Mid-February through Mid-March, 2016

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I really have to do this more regularly. Over the past month we have:

o Worked with Nic and others to figure-out that we will start with the DJI Phantom 3 Advanced as our UAS platform, and the RPLIDAR unit as a likely candidate for the LIDAR component. Both of these are in-house as of yesterday.

o Sorted funding for this year’s trip. Since we will be doing a combination of science and developing the field studies program we are drawing from a variety of funding sources. Stay tuned for our bake sale announcements 😉

o Developed the in-country calendar, started on the pre-trip calendar.

o Sorted all the in-country travel and lodging. This was no small feat, Kristin spent about 2 weeks working on all the details including determining the cargo volume and payload for an appropriate vehicle.

o Worked with Deeksha and Eamon on organizing, labeling, and curating our field data sets from Iceland2013, Iceland2014 and Nicaragua2014.

I am hoping to wade into Arduino <-> BLE <-> Android next, and then work with Nic on the UAS/LIDAR rig. The temperature probe, ambiance with altitude, and visualization interface should follow soon after.

Mid-January to mid-February, 2016

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After being distracted during the break by a downstream software project (Mothur, 16S analysis tool) I have spent most of my time organizing the pieces, making lists, thinking about the Icelandic Field Studies program, and looking for money. We have sent proposals to the Natural Science Summer Research fund, the Dean, and the office of sponsored research (Institutional Advancement). Our “Sanity Check” email will be sent soon. I setup Anna and Katie with the tools and materials to work on the soil pH sensor platform.

We’re in irregular contact with Oli, hopefully some of the loose ends associated with our work at Skalanes will be addressed. The biggest question is which projects will we pursue there.

Next is developing the pre-departure calendar with Kristin, working on list management (Kanbanchi), and ultimately getting back to the BLE Android interface.

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