Difference between revisions of "Sara Richardson"

Revision as of 13:26, 20 July 2007

About Me

I am a second year UCSD Bioengineering student and a Calit2 Summer Undergraduate Research Scholar working with Jürgen Schulze.

I enjoy the beach, soccer, and my 'spectrum'.

You can usually find me on the 6th floor open space of Atkinson Hall.

I can be contacted at serichardson@ucsd.edu or 858-539-9950.

Project

After the success of the Human Genome Project, J. Craig Venter launched the Sorcerer II Global Ocean Sampling (GOS) Expedition to collect microbes and analyze their DNA sequences. Along with the microbial data, researchers also collected various metadata (location, depth, microbe size, temperature, salinity, pH, DO). This project will create a 3D visulazation of this metadata through the use of visualization technology. The display can then be used by researchers as a visually immersive way to look for particularly interesting data sites or relations between sites, with the ultimate goal of finding microbes with DNA that produce useful proteins.

This is the map of the GOS Expedition, indicating sample points. I am working on the visualization of metadata from the red/yellow points

Progress

Updated: July 20, 10:00

Week 1

Researched available information on GOS/CAMERA and related visualization

Found available GOS Metadata from CAMERA site.

^ - - This Image shows the text-file containing the GOS Metadata - - ^

Drafted initial ideas for visualization with the OssimPlanet software

Met with Paul Gilna to discuss ideas for and focus of the project

Began reading up on C++ programming language

Week 2

Continued reading about C++ programming language

Attended "How to Conduct Research" by Prof. Trey Ideker as a part of the Calit2 Scholars Colloquia Program

Began working on CAMERAVis plug-in for OpenCOVER (Progress noted as CAMERAVis Plug-in:)

CAMERAVis Plug-in: Parsed GOS data file, Converted latitude and longitude to cartesian coordinates

Attended "How to Present Research" by Martha Stacklin

CAMERAVis Plug-in: Rendered data points on a sphere (yay!)

^ - - This image shows the initial display of the globe and the GOS datapoints - - ^

CAMERAVis Plug-in: Wrote code representing variations in temperature/salinity as variations in the sphere's color/shape (values are accurate but opencover does not illustrate this)

Created first draft of "Research Presentation I" Power Point

Week 3

Completed "Research Presentation I" Power Point

Prepared and Presented "Research Presentation I" Speech ("Yellow Stickers")

CAMERAVis Plug-in: Rendered code varying parameters on OpenCover

^ - - This image shows data points with temperature as color and salinity as size - - ^

Lunch with my associate/partner-in-crime

Attended: "Blue Stickers" Presentations

CAMERAVis Plug-in: Coding for Menu Items and Actions

Week 4

Attended: "How to Start a CAVE Plugin (Project)" with Tung-Ju Hsieh

Attended: "Applying to Graduate School" by Professors Bill Hodgkiss and Gert Lankreit

CAMERAVis Plug-in: Completed Menu in Opencover

^ - - This image shows the breakdown of the CAMERAVis menus currently coded - - ^

CAMERAVis Plug-in: Integrated Display of Both Size and Color through Menu (49 combinations currently available)

^ - - This image displays salinity as color and water depth as size, illustrated by the menu check-marks - - ^

CAMERAVis Plug-in: Added 3 Color Parameters (now utilizing over 10 colors)

CAMERAVis Plug-in: Implemented 3 Shape Parameters (280 different displays currently available)

Attended: "Red Stickers" Presentations

CAMERAVis Plug-in: Added Legend to Explain Visualizations w/in OpenCOVER (was displayed on terminal)

^ - - This image shows the legend explaining the displayed parameters - - ^

Links

Camera Portal

PLoS Biology Publication of the GOS

J. Craig Venture Institute (JCVI) GOS

Sorcerer II Expedition

Calit2 Student RI Portal