My Master Thesis
jmarinas has been developed as part of my master thesis at the University of Genova. I worked on this project with Doc.Paolo Vassallo and Prof.Mauro Fabiano.
A copy of my thesis in Italian can be downloaded ad .pdf (35 Mb).
To know the value and spatial distribution of pollutants or of other variables of ecological interest across an
harbor, or any other similarly complex system, it is common to perform a number of measurements following a matrix sampling strategy (limited
by practical factors like time and cost), or to rely on researcher intuition to do measurements at the assumed most critical points.
Conclusions drawn from the data so gathered are not entirely satisfactory and might even be wrong, the reason laying in the fact
that no guess can safely be made from the measured data about the values of the ecological variables of interest in locations that have
not been included in the sampling set.
It is therefore clear the large improvements that could be obtained by using a robust model capable of predicting the values of ecological variables of interest across the harbor on the basis of basic harbor information like its geometry, pollutant sources locations and so on.
Such a model could be used first to define better sampling strategies, and later for a better understanding of the measured values and for a sounder interpretation of any conclusion based on these values: jmarinas has been developed precisely to serve this purpose.
Furthermore, being a predictive tool, jmarinas find also great use in harbor design.
How jmarinas works?
We have produced the alpha version of a software for managing marinas and small harbors to be used by
scientists and harbor authorities. Our software is able to predict distribution of vulnerability and pollution in the harbur area.
Being a descriptive and predictive tool, jmarinas can be used by scientists to optimize sampling campaign, and by managers and harbor authorities to quickly evaluate anthropic impact of man-made structures and other harbur works.
Our software is written in Java to make it truly portable across many different platforms.
To make jmarinas easy to use even by non experts, we implemented a graphical interface for data input: users load the map of the harbor of interest, and any further data input will be referenced to this map.
The description of the physical environment and of the pollution sources of different nature is done by entering data in a number of "layers", each of them producing a numerical matrix used by the model for the evaluations. The model integrates decision theory, fuzzy logical and ecological concepts.
In the Boundary Layer after having imported the harbor map on the background layer, the User draws the harbor's borders, and inputs intensity and direction of prevalent winds over the harbor area.
In the Internal Sources Layer, the User inputs information about in-harbor waste sources.
In the External Sources Layer the user inputs informations about external sources, that is pollution which come from the outside of the harbor.
In this layer we consider also a function of proximity from the open see, which affects waste concentration.
With the information entered in the Internal Sources Layer and External Sources Layer the software produces four matrices of chemical, dystrophic, sanitary and total pollution values.
jmarinas using a fuzzy variable of intensity, can produce useful results even with limited information about pollution sources.
In the Tortuosity Layer the user describes any pier eventually present in the harbor.
In the last layer, the Bathymetry Layer, a summary description of harbor bathymetry is input through a number of sampling points.
This is used by the model togheter with a thermal stratification function to predict the impact of water friction with the harbor sea bad on pollutant circulation
When it is necessary to have quantitative predictions, the model results can be calibrated using a limited number of sample measurements, producing results that are more reliable than most of the matrix sample campaigns.
Why jmarinas is open source?
As a young marine ecologist, I've never found a similar tool publicly available.
I have developed jmarinas and I'm making it available to the ecologists community hoping that somebody would be interested in joining me in this project so to further develope and test it to make it more and more useful to the people and the environment.
You can download the jmarinas alpha version and experiment with it. Contact me if you have any suggestions or comments or if you are interested in partecipating to the project.