Marylee Murphy and Jon Weinberg
The project will be aimed at creating a tool to assist in Professor Sonya Skoog's research on migrations of Ostracoda in the Arctic Ocean.
The first step in creating the tool will be to map the bathymetry (or depth contours) of the Arctic Ocean. The University of Hawaii has a publicly available and widely used Generic Mapping Tool (GMT) available on their website. Using this program and information from a publicly available world ocean database, the basemap will be created on which the rest of the project will build.
Next, the data that has been collected from cores in the Arctic Ocean will be plotted on the base map. Since the core data represents Ostracoda presences over time, first a number of maps representing the time intervals and Ostracoda occurences will be plotted. These maps will then be animated and the times between the known periods will be estimated to achieve smooth animation. Since there are 47 species of Ostracoda, the user will be able to choose which species they would like to view to eliminate clutter on the map.
If the above step finds that there are migrations of the Ostracoda, the next step will be to attempt to determine a cause for these migrations. A number of environmental factors will be investigated, most notabale temperature changes, currents, water masses, and any other variables that seem apropriate to include. These variables will be mapped and overlain on the basemap and the ostracod migrations and may also be colored and animated to show the passage of time. At this point the user will be able to choose which species to look at and which variables to observe. At this point a mathematical relationship may be looked for to compare the Ostracoda patterns to the variables.
Once the model is built, it will be possible to investigate any number of scientific questions. Are any species of ostracod native to certain water depths? What is the preferred temperature for which species? Are there definite migrations of the Ostracod populations? How does temperature affect the migrations? How does the water current affect the migration? Are all or any of these variables correlated with the migrations? Did different species migrate with respect to different variables? If a correlation can be established between the patterns and variables, it would be possible to make assumptions about arctic conditions millions of years ago.
The main programming language that will be utilized in this project will be Java. The Generic Mapping to will be the base software for this project that will be used to create any mapping portions of the project. The animation will most likely be a combination of maps created using GMT and Java programming to create smooth animation. The user interface will also be programmed in Java. Though GMT is written in C, there will be alterations that will be necessary to make to it that will be programmed in Java. Through this project java visualization, animation, creating user-friendly user interfaces, working with algorithms that can handle large data sets well to aid in creating smoothly animated images, and general data manipulation techniques will be explored.
There are many parts of this project that are poised to create significant challenges. The entire project is going to be done in a Linux environment which is not fully operational at this writing. Installing GMT and a suitable Java Development Environment on the Linux machine could also pose problems. The main obstacle in this project will probably turn out to be facilitating the cooperation between the Java programs and the GMT. A main Java program will probably run the whole project, and it will have to invoke shell scripts and output post script files that were created by GMT.