[EA Coast] POGO-SCOR Visiting Fellowship Report

Tue Sep 23 06:39:38 UTC 2008

Dear Shigalla Mahongo,

Congratulations to both you and Dr Zavala-Garay for the excellent work
completed during your fellowship. IMS, TAFIRI, and IOC are in the final
stages of approval for a ReCoMaP project in Tanzania. This will continue
to build capacity in the small scale coastal hydrodynamic modelling, and
apply the outputs for decision making in shoreline change management in
Zanzibar. I am sure IMS and TAFIRI can soon inform the mailing list of
the planned modelling activities of the ReCoMaP project.

Kind regards,

Stefano

________________________________

From: east.african.coast-bounces at theissresearch.org
[mailto:east.african.coast-bounces at theissresearch.org] On Behalf Of
Shigalla Mahongo
Sent: 22 September 2008 10:43 PM
To: east.african.coast at theissresearch.org
Subject: [EA Coast] POGO-SCOR Visiting Fellowship Report

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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