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Computational Honeycombs Drip with Data
Stephanie Dutchen
Posted February 16, 2010

Video of green and red hexagons in a honeycomb formation. Each hexagon represents a gene that shifts color from red to green based on experiemtn data.

Each hexagon in this shifting honeycomb represents a gene. A computer program called GATE makes these movies by reading the data from an experiment and grouping genes that turn on (red) and off (green) at similar times. Credit: Ma'ayan Laboratory, Mount Sinai School of Medicine
Each hexagon in this shifting honeycomb represents a gene. A computer program called GATE makes these movies by reading the data from an experiment and grouping genes that turn on (red) and off (green) at similar times. Credit: Ma'ayan Laboratory, Mount Sinai School of Medicine

No, it's not Christmas in a beehive. Instead, each hexagon in this shifting honeycomb represents a gene. A computer program called GATE makes these movies by reading the data from an experiment and grouping genes that turn on (red) and off (green) at similar times.

Mount Sinai Medical Center computational biologist Avi Ma'ayan and two members of his lab designed GATE—short for Grid Analysis of Time-Series Expression—to map how genes or other variables change over time.

Making Sense of Data

While cool research tools like genome sequencers and mass spectrometers let biologists track molecules and their interactions in unprecedented detail, they also generate reams of data that are hard to make sense of.

That's where computers—more specifically, computer scientists—come in. They create databases to house and organize all the information, and they write software to analyze it. Now they've built GATE to help biologists visualize and interact with their data.

GATE transforms information about genes, proteins, molecules or other variables into movies that show what happened during an experiment. When biologists click on any part of the honeycomb, GATE connects them to databases with more information about what they're watching. The researchers can then explore new questions and come up with hypotheses to test.

GATE to Date

So far, researchers have used GATE to explore a variety of questions. One lab group that collaborates with Ma'ayan probed information they'd collected from embryonic stem cells to learn more about how these "blank slate" cells start to transform into the specialized cell types that make up the human body.

"This could help in understanding how to make tissue for regenerative medicine," says Ma'ayan.

Other labs have looked at how genes are expressed in plants and bacteria. And one team in Canada used GATE to see how different organisms evolve together in ecological systems collected from the Pacific Ocean.

"Users of GATE are very diverse and find new ways to use it for things we did not think of," says Ma'ayan.

Bridging Disciplines

GATE also points to a larger trend: team science.

GATE emerged when biologists joined forces with mathematicians and computer scientists to tackle the problem of data visualization. Ma'ayan predicts that computer scientists, mathematicians and engineers will continue play an increasingly important role in every stage of biological research.

Learn about related research

This page last reviewed on April 22, 2011