Sara Richardson
Contents |
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: August 16, 17:00
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
Attended: "Yellow Stickers" Presentations
Presented: "Research Presentation I" research update
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 - - ^
Week 5
Out Monday and Tuesday with illness
CAMERAVis Plug-in: Began working on intersection interactions
Attended: "GroZi Presentation with Professor Serge Belongie
CAMERAVis Plug-in: Tooltip working, displays location of data point moused over
^ - - This image shows the Location ToolTip Displayed as You Mouse-Over a Data Point - - ^
Week 6
CAMERAVis Plug-in: Began working on a Hud to display all available data for a certain data point
Attended: "Green Stickers" Presentations
CAMERAVis Plug-in: Completed MetaData Hud, displayed when a data point is clicked
CAMERAVis Plug-in: Changed Legend to a Hud, takes up less space than as a menu and stays visible
^ - - This image shows the Metadata (bottom) and Legend (top) Huds - - ^
CAMERAVis Plug-in: Changed ToolTip to display location name and value of variables being displayed
CAMERAVis Plug-in: Completed Poti for Display Size and Display Color menus to adjust range of values shown
^ - - Adjusted with Poti (left) vs. Without Poti (right), differences between points are more defined, ToolTip shows values of parameters displayed - - ^
Attended: "Entrepreneurship" with Dr. Paul Kedrosky
Week 7
Worked on "Research Presentation II" PowerPoint
Attended: SIGGRAPH Presentations - "Rage to Know", "Rhyme of Tang Dynasty", "Bibigi", "Imago", "Performing Arts for the Future Mobile Generation", "Dynamic Spaces", "AutoCosm", and "Takashi's Season"
CAMERAVis Plug-in: Changed plain blue Globe to a Textured Earth (yay!)
^ - - Shows textured earth and all available options/features - - ^
CAMERAVis Plug-in: Wrote code for future use in 'Calculating Statistics'
CAMERAVis Plug-in: Added a "Similar Values" feature. Select a data point, parameter, and range. Matches are colored, non-matches are white.
^ - - Shows points within 3 degrees (range) of the temperature
(parameter) of the selected point in red, others in white- - ^
Presented: "Research Presentation II" research update
Attended: "Yellow Stickers" Presentations
Week 8
Attended: "CRCA and Calit2 Visualization Spaces Tour"
CAMERAVis Plug-in: Added 'Statistics' feature to select multiple spheres and display min/max/ave and commonalities
^ - - Selected points highlighted in red, statistics window in upper right - - ^
Received data for 142 additional GOS sites: siteID, location, latitude, longitude, date, time
CAMERAVis Plug-in: Placed new data sites on globe
^ - - Shows the location of all 196 sites in the GOS dataset, displayed around the globe - - ^
Attended: "Blue Stickers" Presentations
CAMERAVis Plug-in: Adjusted Scaling - as scene is zoomed in on, points become smaller relative to globe but stay same size on screen
^ - - (L) Sites are in a big, indistinguishable clump vs. (R) when closer, spheres separate to defined sites- - ^
Links
PLoS Biology Publication of the GOS
