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FM2 Advanced Glider Short Course

Its been a long time since I’ve last updated this blog, primarily due to the rather hectic nature of my recent schedule! Lots of travelling around and working on different things has let this simply slip my mind. I am going to be playing catch over the next few days or so, before I take off on a 3 week research cruise in the North Atlantic!

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 One of the first major events I need to recount I think, was the week long NEXUSS second training event hosted by University of East Anglia (UEA) back in early February. Unlike the previous event in Southampton, this took the form of an official NERC advanced training short course, with other attendees beside the regular NEXUSS cohort.

 First came the travelling down to Norwich - a 7 hour train journey from Glasgow with stops at Edinburgh & Peterborough. I had planned accordingly to entertain myself, printing off a thesis I found a few weeks before published just 4 months prior, by Victoria Hemsley (NOC), detailing a new exciting method of estimating primary productivity using a Seaglider with a PAR (Photosynthetically Active Radiation) sensor fitted. As dull as this might sound, it actually helped pass the time remarkably quickly! Following a short bus from the station to UEA, I was booked into my on campus accommodation before the turn of 10pm, ready for the excitingly early start the next morning.

 Course Breakdown

The first morning consisted of a series of introductions to the other participants & course staff/helpers aswell as being given our breakoff groups for both practical sessions & data analysis/presentations. The next 1 & a half days were then shared between these practical sessions & lectures on glider technicality, piloting & basic sensor payloads (Temperature, Salinity, Oxygen). We were split into 3 groups for the practical sessions. The first I took part in was the glider tank challenge. One of UEAs PhD students had set up a glider in their ballast tank to be neutrally buoyant. She then changed the pitch, roll & centre of buoyancy parameters on the pilots console to alter its position in the tank. It was then our job to attempt to return it to its previously neutrally buoyant position by making as few changes to the 3 parameters as possible.

The second practical session was by far the most interesting/useful. The head glider technician at UEA, took a glider apart from top to bottom in one of the many workshops. This included removing each outer component (wings, rudder, tail), followed by the outer fairing, pressure hull casing & finally the electronics circuit board. He talked us through each of the sections as we removed them, giving us a highly informative & fun 2-hour session. I just felt sorry for him having to put it all back together again over lunch ready for the next group that afternoon!

The third day of the course was focused around learning to use UEAs glider toolbox, which is used as the first stage of processing for data from a glider mission. Each team of 4 chose a separate sample data set provided to us, went through the different steps of utilizing the toolbox & then carried out various different analyses, including generating maps of the gliders tracks and hydrological plots. This was in preparation for a short group presentation we were expected to give on the final day of the course.

Between this & the presentation, we had several more lectures, talks from guest speakers & also a trip down to the Lowestoft CEFAS office. The lectures covered the wide range of other sensors that have now been integrated/being developed for gliders around the UK such as fluorescence (chlorophyll & turbidity measurement), microstructure (mixed layer turbulence), tuned echosounders (zooplankton/kill detection) & Ph/CO2. We were blessed with guest speakers from autonaut (surface vehicle), MARS fleet (slocum glider) & Kongsberg (Seaglider manufacturer), which culminated in a group display of all the equipment in the lobby. During our trip to CEFAS, we got to take a good look at the UEA Waveglider & speak with its lead technician, as well as interesting talks on why we need UK sustainable seas, other autonomous vehicles found in the UK & how satellites can help us further understand global/regional patterns in the ocean. In the evening we attended a course meal organised by the staff running the course.

Each team gave their presentation on the final morning and given the serious lack of time we had been given, everyone did a stellar job. The afternoon saw us try and solve some glider pilot “what if?” scenarios & complete the end of course feedback.  I then took a long and arduous trip back to Oban, arriving back in the early hours of the morning. This week was by far better than the previous NEXUSS training week and lends me hope for the future. It will also greatly benefit my PhD, as I now know definitively of the many ways in which gliders are used to their full capabilities.

[jasonlsalt-blog]

FM1 NEXUSS Module

     Back in December, it was time to attend the first of 3 core training modules put together by NEXUSS, my project funders. This involved an almighty long trip down south to Southampton, the NEXUSS base and location of the National Oceanography Centre (NOC). 

     I left Oban on the train at 12 noon on Sunday 11th. Upon arriving at Glasgow International airport later that evening, I checked my luggage in, had a spot of food at one of the pubs in the departures lounge and then after checking the information board... found out my flight to Southampton had been cancelled! Great! 

    After being rerouted to Birmingham and then to Southampton by coach, I eventually arrived at the airport at about 2am. As the trains were no longer running I decided to give Uber taxi’s a go for first time. I was not disappointed! There was a driver with me in minutes.  

     Following a not so decent nights sleep at the Travel lodge that I had been put up in by NEXUSS, I decided to walk to the location of the first days activities: Boldrewood Campus via the Southampton common. In the final stretch, I got soaked due to a sporadic downpour. 

The 4 days of training were broken down into 3 consecutive sessions:

Day 1  & 2 - Designing an Air Launched Ocean Drifter

   The loose idea for these 2 days is in the title. However, as a collective cohort of NEXUSS students (11 of us) we only merely progressed to the stage of having a very vague concept design for 2 different type of drifters. It felt a little bit like we were just given a very brief introduction and then left to our own devices for 1 and a half days. I think the thing that complicated the task was that it was not made clear to us for what purpose we were designing a drifter for: general use or specifically for the Grand Challenge (Locating a mock oil spill in Ardmucknish Bay, September 2017). The main argument that split the group almost in half (with regards to the GC) was whether we wanted to:

1) use the drifter(s) to locate the spill (fluorescien dye) by using fluorometers and having no drogue (drag device below the surface of the water). The idea here being to use the wind to disperse the drifters in a mesh network across the bay and identify a change if concentration, then following the gradient back to the source of the spill.

2) simply using the drifters to calculate the particle trajectories (with a drogue) so that if we located some of the dye within the bay (using a different platform/piece of equipment), we would be able to backtrack using a validated hydrodynamic model to the source. 

We did however manage to generate a reasonable detailed hull and internal electronics design which you can see below:

Day 3 - Electrical Integration of Sensors onto Platforms

    I really enjoyed today. It started off really simple, going over the basics of what data is in computers (binary) and how ASCII is coded and the various syntax we needed. It progressed onto exploring RS232 Serial connections, how to make a connector (through soldering), how to successfully connect two ends of a cable and communicate and transfer information using a terminal.         We also viewed our messages electrical signal using oscilloscopes, discussed issues regarding battery life for sensors and the importance of having an interface specification document when setting up/fitting a new sensor to a platform. 

Day 4 - Mission design & Mechanical Integration of Sensors onto Platforms

    The morning session consisted of an overview of how to plan a mission using autonomous platforms. We were given details of the various types of sensors (Electrochemical, Wet chemical & Optical) and platforms (ROVS, AutoSubs, Surface Vehicles & Gliders) available, all with different specifications, power consumption, shapes, sizes and many other statistics and then set on a mock mission plan in teams of 3 (for simplicity's sake) with very few limitations. The mission aim was to detect a CO2 leak from a subsurface carbon storage site.  We were then talked through the ETI CCS-MMV CO2 leak monitoring project that had recently been undertaken at NOC. 

    The final afternoon session dealt with the engineering process in place at NOC to successfully integrate a new sensor into a platform. This was broken down into 4 stages: 1/ Pre-integration (Science requirements, Mission planning, Storage and recovery of Sensor Data, risk assessment & Risk Mitigation), 2/ Physical integration (Cabling, fixing brackets, housing & testing), 3/ Ground Truthing & Calibration & 4/ (After mission) Collection and processing of Final Data. We were then talked through a case study of the successful integration of a nutrient analyzer into a Seaglider to show the nitrate draw-down from surface waters that occurs during a spring phytoplankton bloom. 

 Final thoughts

    Overall I enjoyed meeting the rest of the NEXUSS cohort this week, as I couldn’t go to the induction week in September, but some of the sessions fell a bit short of my expectations. Having traveled a rather long way (over 500 miles) and losing a week of time I could use for other PhD work, I was expecting to learn more than I did.

    Saying this, the whole third day was highly informative (even if it started a little but too simple for me), as was the final session on day 4. However. the former was far better structured and the final session at times felt like every slide was filled with walls of text. It reminded me of first year undergrad cell biology lectures at Liverpool. Well the next module is in early February and is about glider data processing, so might be a bit more relevant to my PhD! 

[jasonlsalt-blog]

Efficient note storing and searching! - OneNote 2016

   I decided after a rather insightful induction session at UHI in October that I didn’t want to carry on storing all of my notes in physical folders or ring binders! Its just not very efficient. However, I am already really well suited to note-taking in a notebook or scrap paper, whatever may be at hand while you’re on the receiving end of an information dump. While I’m aware that recording sessions such as this and going back over it at a slower pace also works, I believe the process to be way more time consuming! OneNote has allowed me to continue in my old ways of physical note-taking, while embracing the new cyber age and highly reliable cloud storage offered by Microsoft. In terms of carrying out my PhD, I am finding it to be a highly valuable resource. 

 Why OneNote?

1/ Keeping things far more organised

Another note taking software out there that you may be aware of is Evernote. While Evernote is less fiddly to set up, it is inferior in its organisational capabilities. Evernote (Free version) allows for an unlimited supply of notes to be stored within it, but each notebook can’t have any subheadings/subsections (not yet anyway). 

OneNote 2016 allows you to break each Notebook you create into Sections. You can choose which type of section you want: a grouped section (which can have further subsections) or a normal section. You can also create grouped sections within other grouped sections, similar to how a directory/folder system on your computer works. You can then create note pages with the information on whatever specific topic you are creating content for within each subsection (for grouped sections) or normal section. 

2/ Make use of your handwritten notes 

One of the main reasons I shifted to OneNote is so that I can take my notes by hand during a seminar, workshop, meeting or general learning session as I normally would. You can then take a picture of the page of notes you have written and insert these images onto a note page in order using the OneNote mobile office app (If you have both your phone and computer synced with your One-drive account). You can then add a short line of typed text underneath detailing the keywords/content in the image uploaded, so that you can search for it later.

3/ Superb information searching ability

The purpose of putting keywords under each image of handwritten notes is so that you can quickly search for them. The search bar in both the mobile and desktop versions allow you to search for a key string of information. This will then by default search through every notebook, Section, subsection and individual note pages and list the instances that it occurs. The Desktop version will also allow you to choose exactly what level you want to search, which makes things even easier. 

  The one thing that sold it to me though is just what text it will read when searching. I had took pictures of some textbook pages with important figures on while carrying out my revision of Biological Oceanography theory and put these in my notes. I noticed during one search I conducted, it brought up a result for Text within the image that I had inserted. This is fantastic! It took me by surprise and has many many applications for future note storage. 

4/ Neat and functional looking design

Finally, I must make a point of how easy on the eye the interface is. In the Desktop version, each different section/subsection is colour coded (which you can edit with a choice of 16 different shades).The toolbar options features just about everything in that you might need to edit your notes including: image cropping, free drawing lines and shapes of various colours & thickness, converting handwritten maths expressions to text, inserting hyperlinks to documents, opening spreadsheets, inserting tables, recording videos, adding ruled lines, language proofing and much much more.

On top of this, you can also share a notebook share notebooks with others via email, link etc and password protect sections that you want to limit access to for certain individuals. 

 In summary, the possibilities and uses that arise from using OneNote are endless in an organisational capacity for any form of information that you want to be easy and quick to access, without the bulk of large numbers of folders and files taking up shelf space!

[jasonlsalt-blog]

Getting back into things

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   So this is just going to be a short update before I head into an extended period of study, but I felt the need to post an update due to the importance of this “transitional phase” of my current progress.

   My week back from UHI conference consisted of catching up on many many emails, going back over the findings of my Poster and arranging a Supervisory meeting to get a plan together for moving forward running up until Christmas. 

   I took the best part of a week setting myself to be far more organised going forward with this project, using the resourcefulness of OneNote 2016 and Trello to my advantage. I never even considered using either of these before attending the UHI post grad induction back in September. They are now both going to play a major role in research or general project I undertake for the foreseeable future. I will do two separate posts giving more info on these over the coming weeks. 

I am currently focusing my workload between these 3 areas:

1) Literature Review

   This is something I really need to get stuck into. Especially as I hardly did any reading/ researching in my first month, due to the Poster deadline. Seeing as I have never actually done a formal literature review of anywhere near this scale before (as I never did a Masters), I felt the need to start simple and get myself a systematic approach set up. Somewhere later down the line I will hopefully start to generate some ideas I want to investigate and pursue for this PhD.

2) Continuation of Poster work

   This will include learning detailed glider operations, how the flight model works, the relationship between the HD coefficients and following what I stated in the final words of the conclusions paragraph on my UHI Poster. For this I’ll need to learn how to use shell scripts in Linux. 

3) Biological and Physical Oceanography Theory 

   Coming from a Zoological background, I am seriously struggling with some general concepts, in particular concerning physical properties of Ocean. I am using a combination of my own undergrad notes and 2 textbooks: Biolgical Oceanography: An Introduction (Lalli & Parsons) & An Introduction to The Physical and Biological Oceanography of Shelf Seas (Simpson & Sharples). 

I also have a trip to Southampton in a few weeks for the first NEXUSS core training module to look forward to, rounding off a couple of busy coming months. 

[jasonlsalt-blog]

An unusually stressful first month

   So, after a rather stressful move from North Wales up to Oban, Scotland over 2 trips during September (2016), I came cycled into SAMS (Scottish Association for Marine Science) bright and early for a 9.30am induction on the first Monday in October. Following the usual pleasantries and detailing of the structure of the PhD process, free soup and sandwiches, I was whisked away to a quick meeting with my Director of Studies: Professor Keith Davidson. 

   After being shown to my desk, I had my general IT induction, followed by a Linux crash course with another of my supervisors: Dr Stefan Gary. After installing some of the key programs I needed for processing and analyzing Sea glider data, I was left to play for a few days with an existing data set from a previous glider mission from 2015 after running it through the processing software: “The Basestation”.  

   Then came the objective of my first month: Put together a poster for the UHI (University of Highlands and Islands) research conference (7-9 Nov), and not just an overview of my project. Stefan set me a challenge: to use a Piloting toolbox he had acquired from University of Washington to investigate the impact of the variation in hydrodynamic coefficients on the processing of the raw glider data. No mean feat. It’s safe to say I got thrown well and truly into the deep ocean almost immediately after starting this PhD. My aim? Not to drown.

   So I had to learn how to use MATLAB and Ferret and FAST, if I was going to be able to get some actual fresh analysis done. Over the next 3 weeks, following the mental breakdowns, computer crashes, full reinstall of MATLAB and countless late nights, I managed to get all of my data analysis completed and all of the figures too.  

   There was just one problem! I needed the poster printed before I left SAMS on Friday 4th! I had less than 4 hours to try and make sense of it all, correct a couple of the graphs, write up the results and discussion and finally format it all! Que the most stressful 4 hours of my life for quite some time, leaving me with a terrible headache on the way home. I DID however, get it printed in time, even after submitting it for printing as an A4 PDF instead of an A0. Nothing comes easy when you’re under pressure. So I picked the poster up from Comms and headed home to clear my head.

I have uploaded an image of the poster above. For a PDF version, click here. I appreciate the sheer brightness would scare many aware from reading it, but I wanted to experiment with something a little bit different this time. Its far from perfect and the final words of the conclusions barely make literal sense, that’s what rushing right up until the deadline does to your work. This first month is not how I envisioned my PhD to start. I was looking for a fresh start, after 2 years away from academia. I was coming into a new field, an area of science I had only briefly touched on in my undergrad degree with a limited memory of the basic chemistry and physics that the interdisciplinary nature of this project would require. 

   Now that I am back from the UHI conference, I felt like starting again, fresh almost, taking a major step back from the chaos that has ensued before this. One of my first steps was to make this blog. A way of me reflecting on my progress and to also convey my ideas to others. In future posts, I will provide information on key updates and developments as the project continues.