Jennifer Dean: Data Analysis and Downward Dog, May 17, 2018


NOAA Teacher at Sea

Jennifer Dean

Aboard NOAA Ship Pisces

May 12 – May 24th, 2018

Mission: Conduct ROV and multibeam sonar surveys inside and outside six marine protected areas (MPAs) and the Oculina Experimental Closed Area (OECA) to assess the efficacy of this management tool to protect species of the snapper grouper complex and Oculina coral

Geographic Area of Cruise: Continental shelf edge of the South Atlantic Bight between Port Canaveral, FL and Cape Hatteras, NC

Date: May 17th, 2018

Weather Data from the Bridge
Latitude:  23° 29.6290’ N
Longitude: 80° 09.6070’ W
Sea Wave Height: 2-3 feet
Wind Speed:  18.2 knots
Wind Direction: 199.3°
Visibility: 89 nautical miles
Air Temperature: 25.3°C
Sky: Scattered clouds

Science and Technology Log

Software: ArcGIS and Microsoft Access
Data processing may be seen by some to be a less glamorous role compared to ROV operators and their joysticks.  But data management is essential for communicating and validating findings of the ROV dives.  Huge data sets are created on each dive.  24,000 records were created on just 2 dives that needed to be inventoried and processed.

Processing Photos

Stephanie Farrington processing the photo grabs taken every 2 minutes from the dive

Stephanie Farrington, Biological Research Specialist with Harbor Branch Oceanographic Institute at Florida Atlantic University, gave me a crash course on data management that may be better explained through some of the pictures and activities I was involved in below.  Two types of software seemed of particular significance, ArcGIS and Microsoft Access.

 

 

ArcGIS screen

ArcGIS (Geographic Information System) provides layers of information

ArcGIS (Geographic Information System) provides layers of information, anything from land use patterns, topography to local data for an area on water quality or hurricane patterns.  The software allows you to stack this information on top of each other geographically to look for patterns or to make graphic and visual displays of complex data sets.  On May 16th the dive gathered footage at two sites where barges were dropped to the ocean floor in 2014, one at approximately 80 meters and the other at 100 meters.  After seeing that the structure had undergone considerable changes in its integrity, a question arose about the potential impact a hurricane could have made with these barge structures.  The photo above is an example of a layer of information on hurricane travel patterns and how GIS might be used to make predictions on whether this sort of event could have impacted the barge wreck sites integrity.

Access is a Relational Database and is used as an information and storage management tool for larger data sets. It is less prone to errors compared to Excel and better for managing “big data”.  One skill Stephanie demonstrated to me was her code writing abilities that, once written, allow the keyboard and the database to communicate with each other.  As I typed in the key for “new note,” the image below with the heading on the right saying “Site Number” would pop up ready for me to enter information about the type of bottom substrate, the slope and other features of the sample site. Each of these button choices immediately populated the database and created a running record of the dive’s key features.  Microsoft Access is built using SQL and uses VBA script to create macros (repeated, automatic behaviors).

X-Keyboard

Keyboard programmed to automatically communicate information into a database for quick counts and standard methods of habitat classifications

The X-Keyboard was purchased from a company called P.I. Engineering and comes with its own GUI (Graphical User Interface) for programming the individual keys.

In the image below is an example of a portion of one of John Reed’s notes taken during the dive to record times, observations and coral reef communities observed.  Notice that Weather, Salinity, Wind Direction and Depth are all added into the notes as well as discrepancies or issues that arise.  Notes on this page demonstrate a point early in the dive when it became clear the map features between the ROV operator and Stephanie’s screen were off by many meters, this was because an incorrect Geographic Datum (the screen displaying in WGS 1984 but the ROV feed was being sent to the screen in NAD 1983 causing a false skew in the visualized data stream).

The bathymetric data collected by NOAA is available here for anyone to download;
https://maps.ngdc.noaa.gov/viewers/bathymetry/ 

The following links provides more information on the differences between Excel and Access and the advantages and disadvantages.  And additional information on the uses of GIS.
https://www.weather.gov/gis/
https://webgis.wr.usgs.gov/globalgis/tutorials/arcview.htm
https://www.opengatesw.net/ms-access-tutorials/What-Is-Microsoft-Access-Used-For.htm

Personal Log

How many people can say that one of their first yoga experiences happened on the flying bridge on a NOAA ship in an offshore location in the Atlantic?  LT Felicia Drummond, a newly certified yoga instructor, introduced us to Ashtanga yoga philosophy and techniques, and I finally know what the pose downward dog should look like.  Ashtanga yoga philosophy focuses on breathing and balanced movements to build the strength of your core and muscles.

yoga

Forward fold = Uttanansana

Classes held on the ship’s deck like this would certainly tone one’s body and improve your focus. There are standing, sitting and finishing poses.   I considered myself lucky if I didn’t fall on my face or crash into the pillars with anything but a sitting pose.  But it reminded me of the balance needed in life- both in the physical and mental demands we put on ourselves.  Even at sea there is a need to search for these moments of time to quiet our mind.

Today I am reminded of the different ways of knowing.  I have always been a bit of a bookworm, introverted and learning through textbook study.  But learning through experience on this ship is a whole different level in the depth of comprehension. I am immersed in both the history and story-telling of the original discovery of these reefs by watching 1970’s footage of Professor John Reed’s first “Lock-Out” dives within Florida’s Deep-Water Oculina Reefs.  At the same time I am witnessing and participating first-hand in the collection of new data in similar locations.  Although it is sad to see some of the trawling devastation of the past, the regrowth of these areas and the dedication to their protection brings a positive message for me to share with my students.  I am excited to share the video I watched today with them when I return and the story about a Warsaw grouper, Hyporthodus nigritus, that tried to steal calipers during Professor Reed’s coral measurements many years ago.  To read more about some of  Reed’s work click on the hyperlink.

Did You Know?

fireworm

Hermodice carunculate, Bearded Fireworm

Hermodice carunculate, the Bearded Fireworm, bristle out their setae upon touch and those setae act like hypodermic needles to inject a powerful neurotoxin into the offending predator or careless tourist.  The injury can give a sensation that feels like a fire burning for hours.  It reminded me of a fuzzy underwater centipede. This creature was spotted on an ROV dive near a sunken barge at around 100 meters.  Others were clustered along the walls of the barge that were encrusted with oysters and a few purple sea urchins.  Seen in this image next to the Fireworm are hermit crabs.
https://www.scienceandthesea.org/program/201701/fireworm

Fact or Fiction?

NOAA ships never leave port on Fridays.   Check the links below for more information  about marine operations and for Fisheries superstitions.
https://www.omao.noaa.gov/learn/marine-operations/ships
https://nmssanctuaries.blob.core.windows.net/sanctuaries-prod/media/archive/education/voicesofthebay/pdfs/superstitions.pdf

What’s My Story?     Jason White

Jason White at the ROV controls.

Jason White at the ROV controls.

The following section of the blog is dedicated to explaining the story of one crew member on NOAA ship Pisces.

What is your specific title and job description on this mission?  ROV Pilot/Technician.  He assists in keeping the ROV running efficiently and safely.   His job includes taking turns on this mission with Eric Glidden to pilot the ROV and deploy and recovery of the ROV from the ship.

How long have you worked for University of North Carolina? He has worked for University of North Carolina for almost 5 years.

What is your favorite and least favorite part of your job? Troubleshooting computer problems is his least favorite part of the job. His favorite part of the job is getting to work with different scientists from all around the United States and world on different types of scientific projects.

When did you first become interested in this career (oceanography) and why?  He grew up watching the weather channel and surfing in North Carolina.  Dr. Steve Lyons on weather channel and predicting surf inspired his original interest in the study of meteorology/oceanography.

What science classes or other opportunities would you recommend to high school students who are interested in preparing for this sort of career? He said if you are a student interested in the technical aspect of the study of oceanography you should look for a marine technology program at a university or community college.  He uses a lot of math and physics and recommends at the high school level to take a full course load in bothHe also recommends taking any available electronic classes and stay proficient in computers.

What is one of the most interesting places you have visited?  His most interesting trip was in the Philippines where he ate white rice for 2 weeks straight and people were on the back deck of the ship fishing for the very same fish he was collecting video footage on.  He mentioned that the Philippines had the most beautiful coral he had ever seen.

Questions from my Environmental Science Students in Camas, WA 

How heavy is the ROV? With the skid on it, approximately 800 lbs

How tough is it? Moderately –you can run the ROV into things but don’t want to run into a steel ship or you break things.

How expensive is it? If it somehow broke, what would you have to do?  Try and repair it on the ship with spare parts?  A half-million dollars.  Yes.  They have spares for most everything except the high definition video camera and digital stills camera, which cost $27,000 and $32,000 respectively.

How many cameras are on the ROV and how easy is it to maneuver? 5. One main video camera to navigate the ROV, digital still camera, 3 lipstick cameras on the skid to collect samples and see with the manipulator.  If there is no current then the ROV is fairly easy to maneuver but when conditions decrease by, murkiness, current (more than ½ knot)  or terrain is in high relief it becomes more difficult.  Ship wrecks with steel debris are also especially difficult to maneuver around.

What is the ROV like to control, does it respond quickly or is there a lag time from when you control it to when it responds? It instantaneously responds. 

Do you have to have training to be able to operate it? It is on the job training however there are a few ROV specific training schools around the country.

Labelled image of ROV

A labeled diagram of an ROV

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23 responses to “Jennifer Dean: Data Analysis and Downward Dog, May 17, 2018

  1. In HUGS we studied about GIS, and we found that it can help find correlations, in an area, but the ArcGIS seemed to find predictions, so I was wondering if you found any correlations. Also how is that you first time doing yoga??!?!?!?

    • Well it can do both- just a way to stack and visualize data. As far as yoga- i learned you don’t eat a huge meal (see future post of the plates of food I have been eating), go up at 1pm in the hot sun, before your stomach is completely sea worthy and try to do yoga…i only lasted about 20-30 minutes – but I like the concept and will try it again when I am not on a ship.

  2. Is the nerotoxin injected by the Hermodice carunculate deadly to young children or smaller organisms? Does the toxin cause any lasting damage to the brain tissues, or is the injury much like bee or wasp venom, where there is little lasting effect in larger organisms. Finally, is the neurotoxin injected by the Hermodice caruncaulate acidic or alkali? (or is not classified under either group)

  3. How much data is needed for excel to not be on par with access? Would you recommend us using access instead of excel for recording our data for our magnet projects? Also, do you prefer to learn from textbooks or learning on board with hands on learning? With the bearded fireworm, is it able to kill someone from the toxin it releases or does it just cause lots of pain?

  4. Is the neurotoxin released by the Bearded Fireworm a defense mechanism or is it how it hunts down prey?

  5. Wow! A yoga lesson on a boat! That seems… fun? Anyways, you’ve been on the boat for a while and I was wondering if staying on the boat has taken a toll on you physically. And what are the “vibes” on the boat? Is it chill or chaotic with people doing their jobs? And do you ever find yourself gazing into the ocean? I went on a cruise a while back and I found myself looking out into the ocean a lot.

  6. What are the differences between the ArcGIS software program and other similar softwares. What was the reason this software specifically was used instead of other softwares? How accurate the model created by this software?

    • ArcGIS is for geography and already has huge data sets and maps online and available- it is current and i don’t think there is much in the way of other competitive software. NOw Excel- vs. Access- that just has to do with the quantity of files- over thousands, Excel, apparently can become cumbersone. THe models are extremely accurate with today’s technology and GPS systems…if you are talking about the multibeam…it is amazing as well that is layered onto the ArcView…and last night Todd got it down to where he could tell there were “bushes” which I think after seeing the ROV video- were the sea pens. That’s pretty good for something so small at 250 meters.

  7. What does SQL and VBA mean when you were referring to the Microsoft Access? Was this software made specifically for these types of projects or for something else?

  8. Seems as if there’s always things that you do on the boat that I’ve never thought you would do! First a game of Cornhole and now Yoga? I definitely didn’t expect that you could do that on the boat. It’s a good thing, though, as it is good to take a break from always working and do things that you don’t usually do. As you mentioned at the beginning of this post, “24,000 records were created on just 2 dives that needed to be inventoried and processed”. What did you mean by “records”? How and where are the “records” recorded? How big is each “record”?

  9. After being on a ship for almost a week, are there any obvious effects or changes that you are experiencing especially in the ability to maintain balance?

  10. Yoga is hard for taller people in the first place- I can’t imagine how hard it would be to keep your balance on a swaying boat AND doing yoga.

  11. It’s cool to see that you can do many different fun activities like yoga and cornhole, especially on a boat in the sea.

  12. Why would it be important to study the structural integrity of the barges that were dropped to the ocean floor?

  13. Is the X-Keyboard easy to use? If not, while you have been using it has it gotten progressively easier to use?

  14. Does more of the data analysis happen using arcGIS or Microsoft Access?
    Yoga on a boat? Why not! I can imagine that not toppling over would indeed be very difficult.
    Yikes, that fire worm does not sound friendly. Sad, because it looks pretty.

  15. Wow! Yoga on a boat seems pretty difficult to do because of the instability of the boat! Do you think you’re going to continue to do yoga now after the boat?

  16. I noticed you mentioned the damage a hurricane could do with the barge structures. Did you see or notice any damage from hurricanes? If so, what kind of damage, was it directly to the corals, or the habitat and environment in general?

  17. Also, the yoga sounds like a lot of fun. I’ve been wanting to try it, but just haven’t had the time. Definitely something on my to do list!

  18. Not sure I have a good question but I have made several connections to my life. 1.) The specialized keyboard reminds me of the pointless emoji keyboard made by Tom Scott and 2.) when collecting data from ANSYS Academic (a CFD simulator use in simulating airfoils) it returned over 4,000 pages of data for a 30 second animation! We had to use some special tools to crunch it.

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