Sara E. Richardson

serichardson@ucsd.edu

Calit2 Summer Undergraduate Research Scholarship Program

Advisor: Jurgen Schulze

Ivl.calit2.net/wiki

CAMERA is an online data repository for marine microbial metagenomic data. This metagenomic data is accompanied by environmental metadata associated with the sample collection. The dataset used in this project is the Global Ocean Sampling (GOS) dataset, collected by the J. Craig Venter Institute’s Sorcerer II Expedition. The GOS dataset consists of over 150 sample sites (and growing) gathered during a circumnavigation of the globe, including about fifty sites with published metadata: location, lat/long, date, time, salinity, temperature, chlorophyll density, size fraction, water and sample depth, habitat, geographic location, and country.

Metadata from the CAMERA database is accessed through a text file or spreadsheet. Researchers use this metadata to compare different sites and ultimately find correlations between environmental conditions (metadata) and microbial ecology (genes/proteins). However, the multitude of metadata available is often difficult to interpret, compare, and analyze in this textual format.Displaying metadata visually illustrates data to researchers more efficiently than in text. This project uses a virtual reality software framework to display the geospatial metadata of the GOS dataset in a 3D environment on a globe at the location corresponding to the metadata’s associated sample site.

(above) White points represent sample sites with with complete metadata published and can be manipulated to show different metadata values; Gray points contain only location name, lat/long, date, and time. (above center) CAMERAVis Menu, containing interactive options available for the plug-in

In this project I created a software plug-in ‘CAMERAVis’ for COVISE that reads metadata text files and displays the sample sites on NASA’s ‘The Blue Marble.’ CAMERAVis includes versatile display options and interactive analytical tools. The plug-in runs on Linux machines and can be viewed on a desktop (2D), the C-Wall (stereo 4’x8’ screen), and the StarCAVE (stereo 4 wall display w/ 12 screens, 12 computers, 24 projectors).

Incorporating a direct link between the results of a BLAST search and this plug-in will expedite research analysis of the specifically searched gene sequence. Additions of other/future CAMERA datasets into this plug-in will expand its use.

Background

Problem

Solution

Future

Information Display: Legend, Information Window, and Location Tip

Interactive Analysis and Comparison: Statistics and Similar Values

Shows the average, max, min, and commmonalities for selected points (Highlighted with halos)

Statistics

Similar Values

Differentiates, by color, data points of the same parameter category (right: country is USA) or within range of the parameter value (left: salinity is 32.3 +/- 2.50 ppt) as that of the last selected data point

Data Point Manipulation: Size, Color, and Shape Display

Size

Small parameter values displayed smaller/shorter; Large parameter values displayed larger/taller (s/t/ch/sf/wd/sd)

Color by Category

Color by Value

Small parameter values displayed as a lighter shade of a given color; Large parameter values displayed in full color (s/t/ch/sf/wd/sd)

Each category is assigned a different color; Data points are displayed with the color associated with that category (h/gl/c/sf)

Shape

Each category is assigned a different shape; Data points are displayed as the shape falling into that category (h/gl/sf)

s - salinity, t - temperature, ch - chlorophyll, wd - water depth, sd - sample depth, sf - size fraction, h - habitat type, gl - geographic location, c - country

Appears next to the sample site when a point is hovered over

Displays: - Location name - Values of parameters displayed in point manipulation - Values of parameters selected in the ‘Location Tip’ menu

Legend

Explains what the current size, color, and shape visualizations represent, with functionality to show/hide the Legend

InfoWindowContains all metadata available for the last “clicked” sample site, with functionality to show/hide the Info Window

Location Tip