[EA Coast] POGO-SCOR Visiting Fellowship Report
klwiza at notes.cc.sunysb.edu
klwiza at notes.cc.sunysb.edu
Tue Sep 23 13:33:45 UTC 2008
David,
With all the capabilities of ROMS or any other model your questions would
be best answered by doing field work. Getting to understand the physics of
the estuary from observations is essential. Then you can use the model to
refine the hydrodynamics. I have two students using ROMS to study similar
issues in Long Island Sound (New York), bearing in mind we have much more
observations than one could ever get from Rufiji basin, we still find
ourselves wishing for more field data!
Kamazima Lwiza
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|David Obura <dobura at cordioea.org> |
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|<east.african.coast at theissresearch.org> |
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|09/23/2008 08:31 AM |
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|Re: [EA Coast] POGO-SCOR Visiting Fellowship Report |
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|east.african.coast-bounces at theissresearch.org |
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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 “
Modelling the dynamics of the Tanzanian coastal waters”. 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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