[Another good example of citizen science. Excerpts from NY Times article -- BSA]
Join the Hunt for Super-Rice
There is no quick fix to the world food crisis, but a project getting underway Wednesday could make a difference in the long run. Rice
A team of researchers at the University of Washington are putting a genomics project on the World Community Grid in the computational search for strains of rice that have traits like higher yields, disease resistance and a wider range of nutrients.
The purpose is to hasten the pace of modern rice genetics, which since the 1960s has delivered a series of new strains, starting with higher-yielding semidwarf varieties, a breakthrough that was hailed as the Green Revolution.
But the demand — all those mouths to feed — keeps rising. Rice is the main staple food for more than half the world’s population. In Asia alone, more than two billion people get up to 70 percent of their dietary energy from rice.
The World Community Grid, begun in 2004, gives selected humanitarian scientific projects access to massive computing resources. It taps the unused computing cycles of nearly one million computers around the world — much like SETI@home, the best-known distributed computing effort, which claims it has harnessed more than 3 million PCs in the search for extraterrestrial life.
The World Community Grid places a small piece of software on your PC that taps your unused computing cycles and combines them with others to create a virtual supercomputer. Its equivalent computing power would make it the world’s third-largest supercomputer, according to I.B.M., which has donated the hardware, software and technical expertise for the project.
The grid will run a three-dimensional modeling program created by the computational biologists at the University of Washington to study the structures of the proteins that make up the building blocks of rice. Understanding the structures provides clues to their functions, interactions between the molecular parts and how certain desired traits are expressed.
About Citizizen Science
This blog is a summary of various news items and pointers on how scientific research is being transformed by new web 2.0 tools, web services and Service Oriented Architectures (SOA). Not only will this transform science through the development of cyber-infrastructure and eSceince but it will enable greater participation by students and the general public in the scientific process in the analysis of data and control of instruments
Thursday, May 22, 2008
Friday, May 9, 2008
[Another great example of the potential of Citizen Science. Extracts from Slashdot and original article--BSA
Researchers Launch Online Protein Folding Game http://www.hhmi.org/news/foldit20080508.html
Multiplayer online gaming brings to mind fabulously successful titles, such as “World of Warcraft” and “Ultima.” On May 8, Howard Hughes Medical Institute (HHMI) researchers at the University of Washington are bringing the arcane world of protein folding to the online gaming arena with the launch of “Foldit,” a free game in which players around the world compete to design proteins. The real world benefit: Scientists will test proteins designed by the game's players to see if they make viable candidate compounds for new drugs.
Users can access the game via the web at www.fold.it
The development of the online game is a natural extension of HHMI investigator David Baker's quest to understand how proteins - the building blocks of cells — fold into unique three-dimensional shapes. Over the past decade, Baker and his colleagues have made steady progress in developing computer algorithms to predict how a linear string of amino acids will fold into a given protein's characteristic shape. A detailed understanding of a protein's structure can offer scientists a wealth of information — revealing intricacies about the protein's biological function and suggesting new ideas for drug design.
Predicting the shapes that natural proteins will take is one of the preeminent challenges in biology, and modeling even a small protein requires making trillions of calculations. Over the last three years, volunteers around the globe — now numbering about 200,000— have donated their computer down-time to performing those calculations in a distributed network called Rosetta@home. The computing logic behind the network is an algorithm called Rosetta that uses the Monte Carlo technique to find the best “fit” for all of the parts of a given protein.
But as the Rosetta volunteers watched their computers blindly trying to work out a solution by methodically testing every possible combination and shape to find the best fit, they began to think that a little human intervention might speed things up. “People were writing in, saying, `Hey! The computer is doing silly things! It would be great if we could help guide it,'” remembers Baker, who is based at the University of Washington (UW) where he developed the Rosetta algorithm and network.
Baker didn't know how he could make that happen until about 18 months ago, when he went hiking on Mt. Rainier with his neighbor David Salesin, a University of Washington computer scientist who also runs a research laboratory at nearby Adobe Systems. Baker and Salesin began discussing ways to make Rosetta more interactive. With the inherent fun of competition, Salesin thought a multiplayer online game was the way to go. By the time they got back to the car, they had settled on that idea. Salesin provided Baker with the names of three colleagues, led by UW computer scientist Zoran Popović, who could help Baker create the game.
Over the next several months, Popović, and his students Adrien Treuille and Seth Cooper, created the program, and the team tested it in small venues. One match between teams from the University of California and the University of Illinois aroused unexpected fervor and cheering among spectators. “30 or 40 people participated,” says Baker. “The competition was very intense.”
“Foldit” takes players through a series of practice levels designed to teach the basics of protein folding, before turning them loose on real proteins from nature. “Our main goal was to make sure that anyone could do it, even if they didn't know what biochemistry or protein folding was,” says Popović. At the moment, the game only uses proteins whose three-dimensional structures have been solved by researchers. But, says Popović, “soon we'll be introducing puzzles for which we don't know the solution.”
Baker has high hopes that the game will speed up the sometimes tedious business of structure prediction. But the part of the game that excites him most is scheduled to debut this fall, when gamers will be able to design all-new proteins. Novel proteins could find use in any number of applications, from pharmaceuticals to industrial chemicals, to pollution clean up. With the ability for any person with a computer and an internet hookup to start building proteins, Baker thinks the pace of discovery could skyrocket. “My dream is that a 12-year-old in Indonesia will turn out to be a prodigy, and build a cure for HIV,” he says.
writes "Tired of justifying your gaming addiction? Now you can really help accomplish something while you play... thanks to Howard Hughes Medical Institute researcher David Baker at the University of Washington." In collaboration with others, Baker has designed a game, called "Foldit," with a practical outcome: players manipulate on-screen images of protein chains and attempt to predict their folding patterns. From the article: "'Our main goal was to make sure that anyone could do it, even if they didn't know what biochemistry or protein folding was,' says [co-creator Zoran] Popovic. At the moment, the game only uses proteins whose three-dimensional structures have been solved by researchers. But, says Popovic, 'soon we'll be introducing puzzles for which we don't know the solution.'"