[EA Coast] POGO-SCOR Visiting Fellowship Report

Tue Sep 23 06:26:39 UTC 2008

Dear listers, and Shigalla -

Thanks for your update, the potential for ROMS modelling in the region looks
very good. This is also timely, as I have had the following project in mind,
and Jurgen has encouraged me to send it out via the list ...

I am involved in a climate vulnerability project in the
Rufiji/Mafia/Songo-songo region with WWF, and it involves Dr. Wagner of
UDSM. The study is looking at vulnerability of the coral reef and mangrove
systems to climate change.

What I would like to know is if ROMS can be used to model flow in this
region - the complex set of islands and bathymetry, offshore influence of
the East Africa Coastal Current and plume flow from the Rufiji river. The
area of interest is from Kilwa town in the south to the northern tip of
Mafia island and flow that may enter the basin/island system from the north,
and from the coast out to the main EACC. The main questions of the project
are to what extent clean oceanic water penetrates into the island system and
where/how does this change seasonally, and to what extent is green water
from the plume trapped/recirculated within the basin.

For corals and resistance to bleaching, there is the possibility that turbid
water shields them from light stress thus reduces bleaching, and also that
fresh cool oceanic water shields them from temperature stress Survey data
indicates that the impacts of the 1998 coral bleaching event were minimal on
inner reefs of Songo Songo and mafia, most affected by the river plume, but
outer reefs were very badly bleached and suffered high mortality.

My interest is to get a good picture of currents and mixing in the
archipelago, and the dynamics of oceanic vs. plume water transport at
different times of the year, particularly in the bleaching season of
February-April/May.

What do you think? Is this project modell-able using ROMS? Do we have
sufficient boundary condition data (currents, river flow,
bathymetry/islands, tides, etc)?

Regards,

David Obura

On 22/9/08 22:43, "Shigalla Mahongo" <shigalla at yahoo.co.uk> wrote:

> Dear ALL,
> 
> I would like to share with you part of a  brief report about my POGO-SCOR
> visiting fellowship at Rutgers University in the USA during the months of
> July/August 2008. I hope the report will be useful to you (see below).
> 
> Name of Trainee: Shigalla Mahongo                  Supervisor (Parent
> Institution): Javier Zavala-Garay  Supervisor (Host Institution): Benjamin
> Ngatunga          Dates of Training: 16 July  16 August, 2008  Subject of
> Training: Modelling the dynamics of the Zanzibar Channel, Tanzania
> 1)  Please provide a brief description of activities during the training
> period: First of all, I had to compile and install the Regional Ocean
> Modelling System (ROMS) in my laptop computer so that I could run it anytime
> after returning to Tanzania. Compiling and installing ROMS is a lengthy
> process which includes installation of various sub-programmes. There is an
> upwelling test case in the ROMS tutorial which when run successfully, is a
> confirmation that the model is properly installed. Since ROMS is Unix-based, I
> had to install an interface (Cygwin) for running the model in a windows
> platform. During the process of installation, I realized that the latest
> versions of the various sub-programs do not always work; hence returning to
> lower, stable sub-programmes in some instances.  After completing the process
> of ROMS installation, I had to learn and prepare the forcing files for ROMS
> with an aim of describing the annual cycle of the Zanzibar Channel. These
> included boundary, surface and initial forcing files. The boundary forcing
> file was obtained from the annual cycle of HYCOM with a resolution of 1/12,
> kindly provided by Dr Luis Zamudio (a friend of Dr Zavala-Garay). The surface
> forcing file consisted of 20 years (1985-2004) of monthly meteorological
> observations from Zanzibar (rainfall flux, air temperature, air pressure,
> relative humidity and winds), as well as net short-wave and long-wave
> radiation fluxes from the OPENDAP server of NCEP2. After running the model for
> one year it reaches a steady state describing the annual cycle.  The Zanzibar
> Channel model is actually not the final version, several improvements are
> needed. The model can however still be used as a basic tool to guide us about
> what is needed to better improve the model. There are remaining challenges to
> be able to get a realistic model for the Channel. First, the bathymetry of the
> Channel, especially the southern portion is incomplete (the grid was made
> available by Gabriela Mayorga-Adame). Secondly, the tidal forcing has not yet
> been included because of current lack of data at the boundaries. The only
> available software that could provide such data is the Oregon State Tidal
> Prediction Software (OTPS). However the resolution in Tanzania is actually too
> low to produce a nice forcing for ROMS.  The model was configured to include
> 10 sigma layers in the vertical. The time-step size to solve the 3D momentum
> equation was set to 10 min. The meteorological variables were assumed to be
> uniform over the entire domain, and the model was run for 365 days (1 year) to
> reach a stable state. In my laptop, it took about 23 hours to run the model
> for one year.  
> 2)  What applications of the training received do you envision at your parent
> institution? All the practical training modules that I received in my training
> will be useful in a variety of applications at my parent institution. The
> Zanzibar Channel is an area of interest for research at my institute, but the
> dynamics are poorly known. Scientists working on different fields such as
> fisheries, coral reefs, physical-chemical characteristics etc. are often faced
> with challenges of explaining some of their findings when physical processes
> are involved as causal factors. The model results will therefore assist in
> understanding the driving forces of the oceanic waters both in space and time
> to be able to explain many of the unknowns. The model results will also
> provide an opportunity for scientists to develop a dataset that can be used
> for evaluating the responses of various organisms and habitats to annual
> variability. The dynamical model would as well provide the necessary
> information on determining and predicting the variability of physical
> variables.  The training has also opened up new opportunities in modelling.
> First of all I may participate in the Theiss Research NSF Funded Zanzibar
> Channel Project due to commence next summer. I have also submitted a
> pre-proposal to START (grants in support of one year research related to
> global environmental change in Africa) to carry out a study on ³Modelling the
> dynamics of the Tanzanian coastal waters². Dr Zavala-Garay has agreed to
> provide technical advice if the proposal is eventually approved. I also intend
> to use the START funds to purchase a customized professional workstation
> because ROMS requires an exceptional computing power to perform advanced, CPU
> intensive calculations. Such a computer is currently unavailable at my
> institute (TAFIRI).  There are also plans for continued collaboration with Dr
> Zavala-Garay on modelling the dynamics of the Zanzibar Channel, and we also
> intend to submit one or two manuscripts for publication in the very near
> future (we shall acknowledge POGO-SCOR when we do that). We intend to submit
> the first manuscript in a reputable journal by December 2008. We also intend
> to submit another manuscript on tides using the outputs of the model sometimes
> in 2009. These publications, whose titles have not been firmly decided, will
> be very useful for marine scientists in East Africa as they will provide the
> basic references on the physical processes in the region.  3)  Please provide
> your comments on the Fellowship Programme. The fellowship programme provides
> an excellent opportunity for building capacity in ocean observations for
> scientists from developing countries, I would however, wish to say that the
> fellowship is probably not well known to many scientists in East Africa. One
> way of making the fellowship known (thereby making it much more competitive)
> is to circulate the announcement through such bodies as the regional IOC
> representatives and previous fellowship recipients, and ask them to circulate
> widely. Having benefitted from the fellowship, I will on the other hand, make
> sure that the next announcements are circulated widely in East Africa. As for
> the stipend, it looks adequate depending of course on the cost of
> accommodation. 
> Best regards,
> Mahongo.
> 
> 
> 
> 
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-- 

CORDIO East Africa
9 Kibaki Flats, Kenyatta Public Beach
P.O.BOX 10135 Mombasa 80101, Kenya
Tel: +254-733-851656 (cell)
www.cordioea.org

Chair, IUCN working group on Climate Change and Coral Reefs
Adjunct Senior Lecturer, University of Queensland
Adjunct Senior Scientist, New England Aquarium

Email: dobura@
@cordioea.org  <>  @africaonline.co.ke  <>  @neaq.org 

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