Difference between revisions of "Sara Richardson"

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== Sara Richardson ==
+
== About Me ==
 
I am a second year UCSD Bioengineering student and a Calit2 Summer Undergraduate Research Scholar working with [http://www.calit2.net/~jschulze/ Jürgen Schulze].
 
I am a second year UCSD Bioengineering student and a Calit2 Summer Undergraduate Research Scholar working with [http://www.calit2.net/~jschulze/ Jürgen Schulze].
  
−
I can be contacted at serichardson@ucsd.edu or 858-539-9950.
+
I enjoy the beach, soccer, and my 'spectrum'.
  
 +
[[Image:SaraBeach.jpg]]
 +
 +
 +
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 ==
 
== 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.
 
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.
  
−
[[Image:GOSmap.jpg]]
+
[[Image:GOSmap.jpg]]  
  
 +
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 ==
 
== Progress ==
−
Updated: June 26, 11:30
+
Updated: August 31, 10:15
  
 
=== Week 1 ===
 
=== Week 1 ===
 
Researched available information on GOS/CAMERA and related visualization
 
Researched available information on GOS/CAMERA and related visualization
  
−
Drafted initial ideas for visualization on the OSSIMplant software
+
Found available GOS Metadata from CAMERA site.
 +
 
 +
[[Image:MetadataTF.png]]
 +
 
 +
^ - - 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
 
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!)
 +
 +
[[Image:WhiteDataPoints.png]]
 +
 +
^ - - 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
 +
 +
[[Image:TempColorSalSizeGlobe.png]]
 +
 +
^ - - 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
 +
 +
[[Image:MenuScreenshot.png]]
 +
 +
^ - - 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)
 +
 +
[[Image:MenuCornersScreenshot.png]]
 +
 +
^ - - 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)
 +
 +
[[Image:LegendScreenshot.png]]
 +
 +
^ - - 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
 +
 +
[[Image:ToolTipScreenshot.png]]
 +
 +
^ - - 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
 +
 +
[[Image:HudScreenshot.png]]
 +
 +
^ - - 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
 +
 +
[[Image:YesPotiScreenshot.png]] [[Image:NoPotiScreenshot.png]]
 +
 +
^ - - 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!)
 +
 +
[[Image:TexturedEarthScreenshot.png]]
 +
 +
^ - - 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.
 +
 +
[[Image:SimilarValuesScreenshot.png]]
 +
 +
^ - - 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
 +
 +
[[Image:StatisticsScreenshot.png]]
 +
 +
^ - - 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
 +
 +
[[Image:GOS1Screenshot.png]] [[Image:GOS2Screenshot.png]] [[Image:GOS3Screenshot.png]] [[Image:GOS4Screenshot.png]]
 +
 +
^ - - 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
 +
 +
[[Image:GalapagosBigScreenshot.png]] [[Image:GalapagosScaledScreenshot.png]]
 +
 +
^ - - (L) Sites are in a big, indistinguishable clump vs. (R) when closer, spheres separate to defined sites- - ^
 +
 +
 +
=== Week 9 ===
 +
CAMERAVis Plug-in: Fixed location tool-tip size to adjust when moving/scaling so it stays visible yet unobtrusive on C-Wall
 +
 +
Attended: "Non-Engineering Career Paths" with Alexandra Hubenko-Baker
 +
 +
CAMERAVis Plug-in: CAMERAVis in the CAVE! - Globe needs work to be rendered, config file needs some values, but otherwise it ran well.
 +
 +
CAMERAVis Plug-in: Wrote a 'User-Guide' for the plug-in at [[CAMERA Meta-Data Visualization]].
 +
 +
CAMERAVis Plug-in: Added pictures to the User-Guide
 +
 +
Attended: "Red Stickers" Presentations
 +
 +
CAMERAVis Plug-in: Changed certain variables to config values to aid with transitions between environments
 +
 +
Presented CAMERAVis Plug-in to Paul Gilna (CAMERA Director) and Tom DeFanti
 +
 +
CAMERAVis Plug-in: Changed C-Wall viewing options so that center of globe stays in place
 +
 +
Attended: UCSD Staff Picnic Volleyball Tournament
 +
 +
 +
=== Week 10 ===
 +
CAMERAVis Plug-in: Cleaned up, reorganized, and commented code in the cpp and header files
 +
 +
Attended: "Purple Stickers" Presentations
 +
 +
CAMERAVis Plug-in: Added additional options for the location tool-tip display, upon suggestion from P Gilna
 +
 +
[[Image: NewToolTipScreenshot.png]]
 +
 +
^ - - This shows the location tip menu and all of the available options for display - - ^
 +
 +
Calit2 Poster: Sketched some poster layouts to try, Wrote textual components for poster
 +
 +
Calit2 Poster: Took screenshots with enlarged text for poster readability
 +
 +
Calit2 Poster: Finished Poster using power point (30"x36" portrait). All black and white text with color pictures (brightened)
 +
 +
Attended: "Green Stickers" Presentations
 +
 +
CAMERAVis Plug-in: Changed HUDs (info window, legend, stats window) to Matrix Transforms from CameraNodes and made adjustments to resize and position them
 +
 +
CAMERAVis Plug-in: Made the HUDs moveable
 +
 +
Presented plug-in to Eric Allen, a biologist from SDSU to get his input and guidance for possible publication
  
 
== Links ==
 
== Links ==
 +
[[CAMERA Meta-Data Visualization]]: User Guide
 +
 
[http://camera.calit2.net/index.php Camera Portal]
 
[http://camera.calit2.net/index.php Camera Portal]
  
 
[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0050077 PLoS Biology Publication of the GOS]
 
[http://biology.plosjournals.org/perlserv/?request=get-document&doi=10.1371%2Fjournal.pbio.0050077 PLoS Biology Publication of the GOS]
  
−
[http://www.jcvi.org/research/gos/ J. Craig Venture Institute (JCVI)]
+
[http://www.jcvi.org/research/gos/ J. Craig Venture Institute (JCVI) GOS]
 +
 
 +
[http://www.sorcerer2expedition.org/version1/HTML/main.htm Sorcerer II Expedition]
 +
 
 +
[http://ri.calit2.net/student/ Calit2 Student RI Portal]

Latest revision as of 15:50, 14 November 2007

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'.

SaraBeach.jpg


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.

GOSmap.jpg

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 31, 10:15

Week 1

Researched available information on GOS/CAMERA and related visualization

Found available GOS Metadata from CAMERA site.

MetadataTF.png

^ - - 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!)

WhiteDataPoints.png

^ - - 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

TempColorSalSizeGlobe.png

^ - - 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

MenuScreenshot.png

^ - - 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)

MenuCornersScreenshot.png

^ - - 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)

LegendScreenshot.png

^ - - 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

ToolTipScreenshot.png

^ - - 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

HudScreenshot.png

^ - - 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

YesPotiScreenshot.png NoPotiScreenshot.png

^ - - 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!)

TexturedEarthScreenshot.png

^ - - 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.

SimilarValuesScreenshot.png

^ - - 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

StatisticsScreenshot.png

^ - - 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

GOS1Screenshot.png GOS2Screenshot.png GOS3Screenshot.png GOS4Screenshot.png

^ - - 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

GalapagosBigScreenshot.png GalapagosScaledScreenshot.png

^ - - (L) Sites are in a big, indistinguishable clump vs. (R) when closer, spheres separate to defined sites- - ^


Week 9

CAMERAVis Plug-in: Fixed location tool-tip size to adjust when moving/scaling so it stays visible yet unobtrusive on C-Wall

Attended: "Non-Engineering Career Paths" with Alexandra Hubenko-Baker

CAMERAVis Plug-in: CAMERAVis in the CAVE! - Globe needs work to be rendered, config file needs some values, but otherwise it ran well.

CAMERAVis Plug-in: Wrote a 'User-Guide' for the plug-in at CAMERA Meta-Data Visualization.

CAMERAVis Plug-in: Added pictures to the User-Guide

Attended: "Red Stickers" Presentations

CAMERAVis Plug-in: Changed certain variables to config values to aid with transitions between environments

Presented CAMERAVis Plug-in to Paul Gilna (CAMERA Director) and Tom DeFanti

CAMERAVis Plug-in: Changed C-Wall viewing options so that center of globe stays in place

Attended: UCSD Staff Picnic Volleyball Tournament


Week 10

CAMERAVis Plug-in: Cleaned up, reorganized, and commented code in the cpp and header files

Attended: "Purple Stickers" Presentations

CAMERAVis Plug-in: Added additional options for the location tool-tip display, upon suggestion from P Gilna

NewToolTipScreenshot.png

^ - - This shows the location tip menu and all of the available options for display - - ^

Calit2 Poster: Sketched some poster layouts to try, Wrote textual components for poster

Calit2 Poster: Took screenshots with enlarged text for poster readability

Calit2 Poster: Finished Poster using power point (30"x36" portrait). All black and white text with color pictures (brightened)

Attended: "Green Stickers" Presentations

CAMERAVis Plug-in: Changed HUDs (info window, legend, stats window) to Matrix Transforms from CameraNodes and made adjustments to resize and position them

CAMERAVis Plug-in: Made the HUDs moveable

Presented plug-in to Eric Allen, a biologist from SDSU to get his input and guidance for possible publication

Links

CAMERA Meta-Data Visualization: User Guide

Camera Portal

PLoS Biology Publication of the GOS

J. Craig Venture Institute (JCVI) GOS

Sorcerer II Expedition

Calit2 Student RI Portal

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