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Physical ocean modelling: Testing international waters

By Alice McGrath, SAEON MSc Student
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SAEON MSc student Alice McGraph visited Brest in France to learn more about the nature and limitations of physical ocean models

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Towards the end of her trip Alice had the opportunity to participate in the Brest 2016 International Maritime Festival.

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Alice volunteered at the UBO Marine Science exhibition, where she presented global sea temperature, salinity and chlorophyll on the "PufferSphere", a spherical projector similar to SAEON's Magic Planet

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During the festival, Alice sailed with physical oceanographer Dr Claude Roy on his yacht and got up close to some magnificent boats

As part of her co-badged MSc degree (University of Cape Town and University of Western Brittany located in Brest, France), Alice McGrath visited Brest for a month to meet and work with the collaborating group of physical oceanographers - Dr Claude Roy, Dr Steven Herbette and PhD candidate Natalie Ragoasha - at Institut Universitaire Européen de la Mer's Laboratory of Physical Oceanography and Space (LOPS).

The aim of the trip was to learn more about the nature and limitations of physical ocean models and in particular the ROMS configuration being used in her MSc dissertation.

The trip also gave her the opportunity to travel to the French Research Institute for Exploration of the Sea (Ifremer) in Sete for a week, funded by L'Institut de recherche pour le développement (IRD), to meet with Dr Christophe Lett, who specialises in mathematical and computer modelling, and work on setting up experiments and simulations in the lagrangian transport programme Ichthyop.

The objective of Alice's multi-disciplinary MSc thesis (a collaborative study between SAEON, the Department of Agriculture, Forestry and Fisheries, University of Cape Town (UCT), University of Western Brittany and LOPS) is two-fold:

  • To examine how spatial variability in spawning and nursery areas influences the transport and retention of sardine in the Southern Benguela region, as investigated by Miller et al., 2006. A particle-tracking individual-based model (IBM) is coupled with two regional 3-D hydrodynamic ocean models, one older, lower resolution model, PLUME, similar to that used by Miller, and the newer higher resolution ROMS model. Keeping all other aspects of the study consistent with Miller et al. (2006) will allow researchers to determine how and to what degree increasing the spatial and temporal resolution of the regional ocean model affects the transport and retention of sardine eggs and larvae in the southern Benguela region.
  • To extend the domain to include the East Coast spawning and recruitment areas to better represent the hypothesised spawning strategy of sardine in South African waters.
  • Alice reports on her experiences:

    The trip was very worthwhile and enabled me to meet and establish a scientific relationship with the people that I will be working with over the next year. It also allowed me to experience an institution set-up in another country, and develop my skill set and practices that I have already gained, and will continue to develop, at UCT.

    Whilst in France my focus was on the principles of ocean modelling and using ROMS (the setup and its limitations). I mainly used materials from previous short courses to refresh my memory on the topic. I also used this time to thoroughly understand the work done by previous IBM studies, such as Miller et al., 2007.

    In the first week of my trip, I presented my Honours project results and my MSc plans to members of LOPS. I was quite nervous but it ended up going really well and I got some good questions at the end.

    I had a number of very worthwhile meetings with Dr Claude Roy, Dr Steven Herbette, Dr Gildas Cambon and Natalie Ragoasha. We discussed the significant SST bias in the output I had been given in May and I have been advised to wait for the next configuration to be run, which will fix the bias. These meetings were useful and made sure everyone is on the same page.

    I spent a very productive week in Sete with Dr Christophe Lett at Ifremer in terms of progress and working with R and Ichthyop. With guidance from Dr Lett, I ran test simulations in Ichthyop with a small amount of particles and adapted the post processing R Scripts. These are now running well and will be used to analyse the results from the final run.

    I returned to Cape Town with a list of papers to read from Claude, and an eagerness to get some results as soon as possible. Most importantly, I returned with a greatly improved understanding of physical modelling, its limitations and the chaotic nature of the region. Despite the delay caused by the model bias, it feels as if I have gained some momentum and I have a better idea of what I need to do moving forward, especially in terms of Ichthyop and R programming.

    Towards the end of my trip I had the opportunity to participate in the Brest 2016 International Maritime Festival. For this popular event all types of sailing boats from around the world meet in Brest every four years for a celebration. The festival was an impressive set up, with food stalls, live music and amazing firework displays.

    I volunteered at the UBO Marine Science exhibition at the festival, where I presented and explained global sea temperature, salinity and chlorophyll on the "PufferSphere", a spherical projector similar to SAEON's Magic Planet.

    During the festival I also had the chance to sail with Dr Claude Roy on his beautiful yacht. It was great to see Brest from the water, and we got up close to some magnificent boats – a real highlight of my trip!

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    Miller et al., 2006. Modelling the effects of physical-biological interactions and spatial variability in spawning and nursery areas on transport and retention of sardine Sardinops sagax eggs and larvae in the southern Benguela ecosystem. Journal of Marine Systems, Volume 61: 3-4, July 2006, Pages 212-229

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