12 October 2015

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In this weeks meeting Charlie started things off with laying out what questions we still had for Oli such as dates for the trip, in what location, and where would we be staying. We also discussed the logistics of the Xsede conference and the likely-hood of needing to fly directly from Iceland to Miami. On a side note, the idea of a Wilderness type program at Earlham was brought up. Our next topic was brought up by Erin, that we might have some issues with the balloon idea but that running the balloon off of a telephone pole might be the better option. Ben detailed what he had found regarding the thermal camera and that will start on a way to map the data and logistics of using it. Nic annotated a page on android dev explaining how processes work and when to use them, as well as possible implementations of old Sheshat code into the FieldDay app. Deeksha went over requirements for the SIGCSE poster. Kristin has been working with the LightBlueBean, figuring out the interface enough to get a test up and running and has been working with Charlie and Nic with the design and implementation of FieldDay app. Tara has been doing work with the sensors and has been working with Mike Deibel on soil fertility and found we might be bale to build an equivalent to a near IR spectroscopy. The Munsel colour test is definitely viable for use with visible light. Eamon started doing work with the front end and getting google maps to geolocate points and the Drop menus are finished and easily useable.

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.

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.

And so they begin…

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September 7th, 2015 marked the beginning of our preparation for our trip to Iceland in the summer of 2016. Four alums to the project, Charlie, Tara, Deeksha, and myself, and four newcomers, Nic, Eamon, Erin, and Ben met in the Hopper lab in the new Center for Science and Technology, excited and eager to get started on the projects for next summer.

There’s lots to be done before we can go off to Iceland next summer. There are a number of projects that the members are working on, a summary is below with the name of the person/s working on them in parentheses:

  • Bird nesting site survey at Skalanes (Erin, Ben)
  • Field Science Android application development (Kristin, Charlie, Nic, Tara)
  • Soil Platform (Tara)
  • Environmental monitoring/sustainable energy (Erin)
  • Visualization Tool (Eamon, Deeksha)
  • Wet Lab work (Nic, Erin, Tara, Deeksha)
  • Data Model (Deeksha, Eamon, Everyone)
  • Archaeology site survey (?)
  • Archaeology species survey (?)