A few weeks in, lots to do

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Unfortunately, we haven’t been keeping an overall summary each week, but that’s going to change now, from this week on.

In our meeting on September 28th, members came with a lot of progress and new information. Charlie and I had received an email from Oli (our contact at Skalanes in Iceland) with answers for our questions about specific projects. Oli is very interested in the Bird Nest Site Survey and the Sustainable energy project to power the ranch. He sent a link and information for the nearest weather station to Skalanes in Iceland to retrieve averages for different types of weather (wind, solar, etc.). We are giving this project thought as we progress, but no members are focusing on it as their one project right now.

Erin and Ben are the two members focusing on the Bird Nest Site Survey. Erin has been in contact with Bernard, a Scottish student that we met last time in Iceland, who has given her lot of information on all different types of birds in Skalanes. Erin is trying to research the exact nesting times for all of the birds at Skalanes, and which birds will be nesting when we go next summer. A question that needs to be answered is: what birds do we care about surveying? Only the endangered ones? Erin and Ben have also acquired the thermal camera and will begin testing it out. Oli noted that he is very into using a drone for the surveying, so as to avoid trampling through the bird’s nesting areas.

Oli also told us that the Archaeological Site projects will have to be on the back burner for now, because their license with the site has expired. We are going to ask him if we can do something that won’t involve actually being in the sites or digging up the sites to identify more sites. We’ve considered and research Archaeology Site Survey Techniques (Geophysical Surveying) and some of the options are Ground Penetrating Radar, Magnetometers, Electrical Resistance and Conductivity).

While at Skalanes last summer, we noticed that the internet was extremely slow and unreliable. Oli noted in his last message that the internet has gotten even worse. Nic mentioned using a balloon for internet. This may work. Google has been doing this for a little while, trying to give ‘Loon for All,’ where they are trying to give internet to areas that do not have it, under a project called Project Loon (Project Loon).

The soil platform/s is almost ready for prototype. Tara has decided that using the old soil platform in a better built casing, and Bluetooth is the option for the in-the-field platform. There are also three other platforms that are being researched that will be considered and used ‘on-the-bench’. They are the organic matter content, pH, and Munsell color. The organic matter content sensor is almost ready for prototype. Tara has come up with an idea that uses lasers and photoreceptors. A tube of soil will be placed in a stand, a laser will start at one end (top or bottom) and scan the the tube with a photoreceptor collecting light values on the other side of the tube. Organic matter in soil floats, so once the photoreceptor has a light value much lower than and previous value, then the organic matter has started. The photoreceptor should record that value until the organic matter has stopped, meaning the value is high again (a lot of light is going through). Tara has found some information on using Arduino with pH and will most likely follow those people’s tutorials. More information and research is still to be done about the Munsell color sensor.

The Field Science Android application is finally in the position to be worked on.Gitlab is all setup with our old repositories and we have all been able to pull from them. Our old code, Seshat, has been archived and is not allowed to be edited. This will force us to begin work on a new project, which Kristin has already created the shell for and pushed to the Gitlab repository. Nic, Kristin, and Charlie will decide a time to meet to discuss where to begin on the application, and what code to save from the old app.

The Ambiance platform has gotten some thought as well. We are no longer going to use Yoctopuce devices. They are more expensive than something like Arduino, do not work well with Bluetooth (which is something we desperately desire) and we have all agreed having similar types of sensors for each platform would be nice. More research is being done about which board and sensors to use.

Eamon has been able to extract the rows and columns from all of our CSV files and import them into a postgres database. He has been working with Flask for the Data Visualization project. There has been some debate on what is the correct language to use — php vs. javascript. Which one scales better? Eamon is waiting on more information from us about what exactly we want it to do. Some characteristics that we already know we want the data viz to have are: the ability to easily use it the night after sampling, and make sure we covered all the spots in the area that we wanted to cover, start out simple connect it to our project first, uses a static data model that we all decide on. Next week, the Data Viz will be the focus of our meeting after we briefly discuss the progress of the other projects.

Deeksha has been doing some work on the data model. She’s looked at our old data dictionary file and all of the CSVs from our different trips (Iceland 2013, Iceland 2014, and Nicaragua 2014) which are in wildly different formats and has figured out the exact data model with used for each of those trips and the differences between those models. She is using a database modeling tool to map out what we want the database to look like — primary keys, different tables, etc. and will then put them into postgres to have them all in the same place and format.

LightBlue Bean for Ambiance <3

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After our meeting last Monday, we have decided to step away from Yoctopuce devices for any platform, but specifically the ambiance platform. Although, the Yoctopuce devices are nice, and have the ‘plug and play’ option, they are expensive and complex (in terms of debugging) compared to other options.

We are moving to Arduino-like design for the Ambiance platform. After some research, I found a device called the LightBlue Bean (see below). The LightBlue Bean is a very small device that is configured entirely through Bluetooth Low Energy. You can even upload code on the go with an Android or IPhone application, which is exactly what we need. The Bean has the same chipset as an Arduino, and even has a built in Temperature sensor. A key characteristic of the LightBlue Bean is the on-board battery. In the past, we’ve struggled with our sensor platforms drawing too much energy from our Nexii. We would have to pack extra charged battery packs, which would take up space in the limited space we have for our day. When you’re climbing a volcano or a glacier, it’s ideal to carry the least amount of weight as possible.

We’ve ordered about 4 of the LightBlue Beans and they should get here sometime this week. Once they arrive, we’ll play with them and attach sensors to see how well they work. Can’t wait to play with them!

Week of 20 September 2015

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Kristin and I wrote a long email to Oli @ Skalanes with a bunch of answers and questions for him, his reply arrived this morning. Spoke with Tara about soil sampling protocols and parameters, Erin about infrared imaging for the nest sites and scaling aerial imagery, and Deeksha and Eamon about data models and data conversion. We also talked about where all the various older sets are that need to be harvested and brought into the central data store on the field science machine.

Skalanes Nesting Birds

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After receiving Bernard Lundie’s information, I was able to make headway in nesting birds. He sent me a complete document that lists the birds he know that have nested around Skalanes including waterfowl, grouse, waders and passerines. Eider (waterfowl) and Arctic Terns seemed to be most common in terms of nesting. There is an extensive list, so know narrowing down a specific research question involving the survey of nesting birds will be key, because there are so many species. Do we look just more extensively at nesting arctic terns or do we just survey nest totals in the area, disregarding species. I also spoke with Earlham’s ornithologist, Wendy Tori and she sent me several papers on arctic terns. We talked a little bit about methods but she has never done anything quite like this. The final challenge this week has been getting the thermo camera. Still an issue that might take some more time.

Joys of Reconciliation

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I’ve mainly spent time working on identifying the specific differences in the formats of data we’ve used for the last two years.There are some differences between Iceland 2014 data and Nicaragua 2015 data,and even more significant differences between Iceland 2013 data and the rest of what we’ve collected.To be able to start putting together the pieces of what we have and effectively cleaning them up,we need to locate and tag everything we can find,which is what I’ve been upto.

I now have a master table of sorts of Iceland 2014 data and Nicaragua 2015 data,so I know what/where we need to add/modify so as to have a consistent pattern in our data.

I’ve been working on what additional functionalities we want our data model to accommodate before we go back,and how to fit in the pieces of whatever we do have into the data model we decide is best this year.


Web Development done Python-style

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Over the past couple weeks I’ve been looking into lightweight frameworks for doing web development. I’ve been experimenting with Flask, which is amazingly simple.

I did some python/bash scripting to manipulate data left over from Iceland, and cleaned it up so it would all fit into one database schema. This should be updated later to comply with some kind of standard we all decide on.

I’m beginning to like the idea of developing our data interfacing software under an api-based model of programming. I think it is beneficial to decouple the database from the front end. I’m considering developing a restful api that returns data in a JSON format that can be interpreted and displayed on screen by some kind of JavaScript-based web app. This may also give us the flexibility to later integrate data into Android or desktop apps as well.

One of the big tasks yet to do is to figure out how to send the data between the client application and the database server. Does anyone have any ideas as to how to do that?

Lasers! (And also other sensors)

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Scanning optical organic matter sensor

Organic content can be measured in a variety of ways. The most accurate tests involve measuring the amount of combustable carbon-based matter in a sample by putting it in a chemical oven. In a test like the one pictured below, soil is allowed to sit undisturbed in a falcon tube for a period of time in which the available organic matter floats to the top.


I would like to use a combination of a laser and a photometer to make a scanning optical device that moves upward from the bottom of the tube. An arduino would log the values of intensity of the light that permeates the tube. The intensity would be reduced for the section of the range that is obstructed by organic matter (or mineral matter at the bottom). I will write software to measure the length of this band and then calculate the volume from this value (thickness*pi*r^2). This method would be faster and more consistent than measuring each band individually by eye.

Screen Shot 2015-09-28 at 10.08.55 AM


Electrical Conductivity & PH Sensing Platform

This platform will also be designed for bench top use because soil samples need significant time to stabilize before accurate readings can be collected. I am focusing on sensors that connect via BNC because they seem to be the cheapest option for arduino interfacing.

The PH interface will be based on this implementation from Sparky’s Widgets (a great all around resource for electrode sensing applications).



I will try to build this interface for the pH probe first and then see how easy it is to modify to read EC. Sparky’s Widgets offers an integrated solution for purchase, but I would like to reengineer it myself if possible.

Temperature and Moisture Field Sensor

This is the only sensor platform I am designing for field use. Right now I am thinking I will design the temperature portion of the sensor to be used right after the soil core sample is taken. I am planning to use infrared sensing in the resulting ~10cm hole to measure soil temp. There are a lot of options out there for infrared sensing – here is a sparkfun sensor I am looking into. I need to get an idea of what precision is necessary for this application.

For moisture I am planning to use a very robust sensor from Adafruit that has been used by students in the past. Building the circuit for this sensor might be a good place to start since I have models to work off of.


NPK and Munsell Color Optical Sensor

A lot of soil nutrient tests involve chemical reactions leading to color changes. I am interesting in using RGB sensors to find a precise value for the color of a solution so I can determine it’s nutrient density. Munsell color test is the official color metric for soil research. I am now researching ways to use RGB LEDs and photosensor to test color of an object. A sensor capable of detecting color could be used for both bench-top NPK tests and Munsell color testing.


App dev thoughts

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Im slowly coming to the conclusion that the android platform is a tinkerer’s dream and that there are hardly any restrictions to get in your way (iOS I’m looking at you). I’ve spent the week continuing to learn the ways of java and android studio but have started to shift my thoughts to how to implement and set up the new $FIELDSCIENCE app. Through exploring the source code and the app itself I know the general nature of what is needed (i.e., ambiance, temp, notepad, etc) in the app and brain storming on new ways to implement them as well as taking note on the things I like from the original app. Things feel like they are starting to get rolling!

Yoctopuce and Bluetooth

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I’ve been doing some research on Yoctopuce and using Bluetooth to communicate with devices, as opposed to USB communication. I could not find any information on using yocto devices with bluetooth. The only official available options are Wifi, USB or Ethernet. This is saddening. Our Yocto ambiance platform is really top-notch, but we need to get rid of cables. They are just not practical. They unplug randomly and we will lose a lot of data in that time. Bluetooth is the only practical option.

I’ve been looking into Arduino sensors on Sparkfun.com and Adafruit to see if we can get the same functionality (and precision) that we can with Yocto devices.

Gitlab, and archiving!

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FINALLY, we have a stable Git environment. On hopper (cluster.earlham.edu) I’ve set-up something called Gitlab. Gitlab is an open source git repo hosting environment. For those of you that are familiar with Github, Gitlab is like a self-hosted version of that. I chose Gitlab because it’s private (in Github, you have to pay for a premium membership to have private repositories) and it’s cleaner and has better access control than just doing it through a user’s directory on the machine.

You can see the Gitlab setup here – Earlham Gitlab. There’s a group called field-science where we are going to host all our code. I’ve already created projects for our Android work. The old android code is now in the archive-android project. This means that it is read-only! Yay! Starting fresh for Android $FIELDSCIENCE app. There’s a new project called FieldScience that we will use for the new app, which I’ve already created the shell for in Android Studio and pushed it to the Gitlab. Yay for cleaning and organization.

On Gitlab, we will store the visualization code, the database code, the arduino/sensor code. All the code! This makes it a lot easier when trying to find stuff later (our old Arduino code is all over the place).

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