Week of 11 October 2015

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Lots of little things this week. I upgraded my laptop to El Capitan so I could install the latest and greatest Android development toolchain, worked on the latest to/from Oli email, discussed soil probes and measuring glaciers with a group of you, considered balloons for aerial imagery and Internet service, listened to Jay Roberts of the CIL pitch me on adding a “wilderness” like component to our work in Iceland, and worked with Sally Southard in Alumni/Development on identifying likely places to apply for funding.

A Higher Elevation

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In dealing with tScreen Shot 2015-10-10 at 10.52.53 AMhe issue of improving internet at Skalanes I did some research into the topography between the Skalanes lodge and the ferry station where the internet antenna is. I used google earth to draw a line from the ferry station to the lodge. It turns out that the are some mountains over 2,000ft in between which could be a large Screen Shot 2015-10-12 at 3.08.31 PMobstacle in the implementation of a balloon. Although the signal ‘curves’ it still seems like it would be hard to make the internet here more reliable this way. The screenshot on the left shows the topographic 3D map from the ferry station, looking down the fiord towards Skalanes.

Next I looked for the telephone wire running to Skalanes which, I believe, is in the google earth image on the right.
A few more things about arctic terns:

average mass is 100g

105.63 F mean body temperature according to Body Temperatures of Antarctic Birds Carl R. Eklund (1942)

Screen Shot 2015-10-12 at 3.13.12 PM
Birds: Winged and Feathered Animals by Suzanne Slade and Kristin West

SIGCSE 2016

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I’ve been looking at the poster submission for SIGCSE 2016. SIGCSE(Special Interest Group for Computer Science Education) is a conference that as the name indicates,cares about CS education and pedagogy. Since we’ve recently had some experience in writing about computer science education because of the paper,it makes sense to submit a poster to SIGCSE. I’ve been bringing together all the bits and pieces of usable material for this project,with the primary source of data being the XSEDE paper and related bits. We already have a plethora of prose,both used and unused,about CS pedagogy and our take on it, the task now at hand is compiling them into an existing poster. There’s now a folder in Drive for SIGCSE,and it’s where I’ve been putting all relevant material.

The poster deadline is in 9 days,so the clock is ticking on this one….

 

Progress Report 10/4-10

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During this week, I actually got to use the thermal camera! It’s super cool to just look at the thermal output from things I would never have imagined was detectable. This includes tracking footprints from the thermal signature left by our feet, the heat given off by the switch panels in CST, tracking living things such as squirrels and people, and trying to identify factors that effect the thermal signature of humans. Thick clothing seems to obfuscate heat, making other places seem to give off more heat. For example when my friend was without a coat, their face registered as 87 degrees F (on the surface) and torso around 82 F, whereas with a coat, torso was practically indistinguishable from ambient temperature (Ok maybe +10, but my point being that coats reduced heat output. I forgot to record this data precisely.), and their head warmed up to 92 +-2 degrees Fahrenheit. I’m still unclear on which birds exactly we will study, and will probably leave that decision to the ecologists in Iceland and perhaps Erin (if she has a preference). Once we know that, it might be possible to more accurately model the birds with maybe a local animal with similar insulative properties and heat output, but that remains to be seen…

 

In the mean time, I’ve tried to track squirrels with only a thermal camera and my success was very limited. The first problem was that it is hard to find a fixed focus at which the squirrel appears sharp. This might be fixed with the balloon-tether idea which would yield a fixed height from the ground and thus static focal range. However most pressing was the battery life on the camera. I had trouble getting 5 minutes out of the device. If this is standard, we might need to design a new battery, and if it’s a result of slow degradation of the battery, maybe we should purchase a new one. Next week I’ll be sure to post pics of us looking for small animals and how well that works!

Progress Report 9/27-10/3

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Apparently Erin and Charlie are talking to the Maintenance Dept. here at Earlham College about using their thermal camera. This would be an ideal solution, because it removes a huge amount of reinventing of the wheel. It would possibly take decades to get to the level of refinement found in a real thermal camera. In the mean time, I’m mostly waiting on info from the ecologists in Iceland who will tell us which birds we can actually study in Skalines. Until we have an idea of what birds to study, I’m not sure what kind of progress I can really make.

Progress Report 9/20-26

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In this week I explored more options for thermal imaging. None of these seemed particularly promising, many of these are either expensive, inaccurate, slow, or the range is limited. So far the thermal sensor options seem to be a “pick any two” of the following options: range, accuracy, cost. Unfortunately, because picking up the thermal signature of a small animal at a sizeable range requires a significant amount of all three, there’s either going to need to be a massive engineering breakthrough on my part, or a massive budget. The same problems persist for other parts of the camera, for example, the optics. Focusing long wave IR requires exotic materials which cost an enormous amount of money to procure individually or manufacture.

 

My conclusion is that thermal imaging is a field with an extremely high barrier to entry. I doubt that I have the skills or expertise to surmount the difficulties I’ve touched on, and I hope that another solution will present itself.

Spectra and Soil

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This week I met with Mike Deibel regarding soil fertility measurements. One of the primary accepted ways to measure soil fertility is the combustion method. We don’t want to do that. Other alternatives are spectroscopy of the soil directly (requires infrared electromagnetic range) or of a soil solution after a reaction (can be done in the visible light range, but requires reagents and possibly a flow-injection system). For the munsell color test, a visible-range spectrometer that uses fiber optic cables to transmit signal could be used.

NIR spec focuses on the infrared region of the electromagnetic spectrum. Building a NIR spectrometer is tricky because a lot of things absorb infrared wavelengths and because I would have to build some sort of detector that scans through individual wavelengths very precisely. This isn’t impossible, but it isn’t trivial – so I’m still looking into it. There are a large number of DIY spectrophotometers projects out there but few of them dip very far into the IR range, precisely because it is so difficult.

There is a nice DIY solution for flow-injection analysis (a stream of reagent is merged with a stream of sample and the mixture is analyzed). [3D printed syringe pump] [Nitrate quantification]

For the munsell color test, things are a lot simpler because we only need to deal with the visible light range. Reverse-engineering a visible light spectrometer like this one is not at all an unreasonable thing to do.

Birds, Balloons, Bluetooth!

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The following is a summary of our meeting on October 6, 2015.

Deeksha has been working on a ‘master table’ of sensor and ambiance data from both Iceland trips and Nicaragua. She is now working on grooming it to be internally consistent before we push it up to the field science SQL server. Kristin observed that even data without an associated metagenomic sample is worth curating in the SQL table.

Charlie, Kristin and Nic have met to discuss the field science app and have started working together on improving it. Kristin has updated the main page of the app and improved its aesthetic design and has come up with the name, ‘Field Day’, for the app. ‘Field Day’ was received very well by everyone at the meeting. The ambiance platform is moving away from Yocopuce and towards Arduino. Four LightBlue beans have been ordered.

Each of the soil platforms are coming along well in the prototyping phase. The field sensor will use bluetooth – possibly a LightBlue bean or a bluetooth shield. I (Tara) am planning to use the Arduino UNO as it is a very sturdy and well-documented board.

Erin has been communicating with Bernard about bird life in Iceland and has obtained a list of species nesting around Skalanes. She is looking into nesting times so we have a better idea of which birds will be nesting in the time frame of our visit. Ben and Erin have been vetting the Fluke IR camera for use in mapping bird life (there isn’t a lot of documentation on this usage because it is relatively uncommon, but there are many reasons to believe it will work very well). They plan to test it out on squirrels and birds around Earlham. They are also looking into the possibility of using balloons for the bird nest survey. Charlie pointed out that a balloon with a tether could provide a relatively easy way to survey an area form a constant elevation.

Another possible use for balloons is setting up an internet connection for Skalanes. We need to know how high a balloon with a wifi antenna would need to be for the signal to clear the mountains in between the station providing signal and Skalanes. Erin will be looking for the point of maximum elevation between Skalanes and the station on google Earth in order to answer this question.

 

Untitled drawing

Eamon is working on a set of tools for data visualization downstream of the data curation Deeksha is working on. Charlie observed that, in the field, a visualization tool that allows us to check the coverage of our sampling would be extremely useful. If we missed a section of our site, we would rather know about it while it’s still an option to go back and gather more data. Charlie is envisioning an interface that prompts the user for the geographical area they want to look at and the sampling day(s). The program could return sampling data plotted by geocode on a map of the sampling site. This would allow us to check our coverage. A tool like this would be invaluable for use in the field. It could also be evolved further for visualizing the data after we return including genomic post-processing data such as 16s sequencer output.

The Bean arrives!

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Last week, the bean arrived! We got four beans in the mail, which came with a ‘Maker Kit.’ The Maker Kit really just contained some headers, a buzzer, and your basic accessories. I was able to connect to all four of the Beans through my computer and my phone! It’s pretty cool that you can connect and upload code right from your phone. The ‘Bean Loader’ computer application integrates with Arduino really well. You write the code in the Arduino IDE, and just send it to the Bean through the Bean Loader. I followed this guide OSX Starting Guide to get started using the bean with my laptop. This is the guide I followed for iOS Guide for setting it up on my iPhone.

Unlike most Arduino board, the Bean has no headers already soldered in. We don’t want to solder right away. We still need to make a prototype and test that it works. So, what I did was set up a little prototyping configuration using a breadboard and some wires. You can see it below — it’s a light sensor. The LED on the Bean gets brighter as it detects more light and dimmer as it detects less light. I was able to get this running with the Bean Example Projects page.

IMG_0408

I’ve been looking through different websites like MakerShed, SparkFun, and Adafruit for different ambiance type sensors. There are many options to choose from, that have a wide range in prices. What sensors to get, we should probably decide as a group. Also, the Bean has a built-in Temperature sensor that we need to test, and perhaps we could cross that off the list of sensors to buy.

Another week, another $7USD

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Managed to frustrate Facilities trying to sort who owned the TIC, etc. It’s now in our possession for the duration. List management related to Skalanes and the various projects there; we have a GDrive document now with questions/answers for/from Oli at Skalanes. Talked to Erin about how to do an elevation transect from the house at Skalanes to the roof of the gangplank tower at the ferry terminal to see if a ballon might be practical for doing line-of-sight between the two. Sent email to SallyS in A/D about funding sources, also considering how to approach the Dean, etc. about their recent policy change of not supporting graduating seniors. Started to re-learn Android development, how often are these people going to change their minds…

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