Web 2.0 and social networking for scientists

[Excellent slide deck on various web 2.0 tools available for scientists and researchers, and the impact they are having on research. Thanks to Richard Ackerman for this pointer-BSA]

http://scilib.typepad.com/science_library_pad/2008/12/science-networking-online.html

Many eyes

From the New York Times -- >

Novelties
Lines and Bubbles and Bars, Oh My! New Ways to Sift Data By Anne Eisenberg

PEOPLE share their videos on YouTube and their photos at Flickr. Now they can share more technical types of displays: graphs, charts and other visuals they create to help them analyze data buried in spreadsheets, tables or text.

At an experimental Web site, Many Eyes, (www.many-eyes.com), users can upload the data they want to visualize, then try sophisticated tools to generate interactive displays. These might range from maps of relationships in the New Testament to a display of the comparative frequency of words used in speeches by Senators Hillary Rodham Clinton and Barack Obama.

The site was created by scientists at the Watson Research Center of I.B.M. in Cambridge, Mass., to help people publish and discuss graphics in a group. Those who register at the site can comment on one another's work, perhaps visualizing the same information with different tools and discovering unexpected patterns in the data.

Collaboration like this can be an effective way to spur insight, said Pat Hanrahan, a professor of computer science at Stanford whose research includes scientific visualization. "When analyzing information, no single person knows it all," he said. "When you have a group look at data, you protect against bias. You get more perspectives, and this can lead to more reliable decisions."

The site is the brainchild of Martin Wattenberg and Fernanda B.
Viégas, two I.B.M. researchers at the Cambridge lab. Dr. Wattenberg, a computer scientist and mathematician, says sophisticated visualization tools have historically been the province of professionals in academia, business and government. "We want to bring visualization to a whole new audience," he said — to people who have had relatively few ways to create and discuss such use of data.

"The conversation about the data is as important as the flow of data from the database," he said.

The Many Eyes site, begun in January 2007, offers 16 ways to present data, from stack graphs and bar charts to diagrams that let people map relationships. TreeMaps, showing information in colorful rectangles, are among the popular tools.

Initially, the site offered only analytical tools like graphs for visualizing numerical data. "The interesting thing we noticed was that users kept trying to upload blog posts, and entire books," Dr. Viégas said, so the site added techniques for unstructured text. One tool, called an interleaved tag cloud, lets users compare side by side the relative frequencies of the words in two passages — for instance, President Bush's State of the Union addresses in 2002 and 2003.

Almost all the tools are interactive, allowing users to change parameters, zoom in or out or show more information when the mouse moves over an image, Dr. Wattenberg said.

Users can embed images and links to their visualizations in their Web sites or blogs, just as they can embed YouTube videos. "It's great that people can paste in a YouTube video of cats" on their blogs, Dr.
Viégas said. "So why not a visual that gives you some insight into the sea of data that surrounds us? I might find one thing; someone else, something completely different, and that's where the conversation starts."

Rich Hoeg, a technology manager who lives in New Hope, Minn., and has a blog at econtent.typepad.com, was so taken with the possibilities for group collaboration that he wrote a tutorial on using Many Eyes as part of his series called "NorthStar Nerd Tutorials."

[snip]RSS Feed:

Impact of Citizen Science on academic research

[Good article on the impact of citizen science on academic research.
Cyber-infrastructure will not only impact the way we do science at
universities but with the advent of clouds, grids, SOA, remote
instrumentation and Web 2.0 I believe we are entering a new renaissance era
where amateur scientists can have access to the same tools and techniques
used by professional researchers. Of course these same tools also allow us
to move power hungry laboratory and computer equipment off of our campuses
to more environmentally friendly zero carbon renewable energy sites -
accessible to all. From a posting on Dewayne Hendricks list. BSA]



http://www.nypost.com/seven/08242008/postopinion/postopbooks/crowdsourcing_1
25790.htm



"CROWDSOURCING"

Wired writer Jeff Howe's "Crowdsourcing" thesis is this: the "experts" -
whether they're top-tier physicists or movie-studio heads - don't have a
monopoly on the creation or distribution of information anymore. The crowd,
through technology that's been available for little more than a decade, has
broken that monopoly, transforming everything from entertainment to cancer
research.

.

Howe introduces this change with an amusing story about birdwatchers. Until
the Internet age, it was the experts who decided whether a bird is extinct
or not - and those experts still think they do. A few years ago, the
official scientific birdwatchers decided, after much study, that an extinct
bird in Mexico was actually not extinct.

But the amateur birdwatchers had long beaten them to this discovery with
their own online literature. "The birdwatchers were like, 'That's
interesting, but we did that a few years ago,' " one professional
ornithologist told Howe.

.

Before the 19th century, it was amateurs - often, but not always, from the
aristocracy - who made scientific discoveries, writing to each other to
share knowledge through informal societies like "the Invisible College,"
which later became the Royal Society.

But by the 1800s, universities and their increasingly specialized graduates
were jealous of the competition posed by amateurs, and started to shut them
out - successfully, until recently, when amateurs in fields ranging from
organic chemistry to investigative journalism could once again fairly
compete with the pros.

.

In science, an Italian homemaker with a heretofore unused organic chemistry
degree can put her talents to use after she puts her kids to bed, helping
companies like Procter and Gamble solve problems their own scientists
couldn't solve through a venture called InnoCentive. Participating companies
pay successful problem-solvers tens of thousands of dollars for their
breakthroughs. Video-renter Netflix has a $1 million reward on offer for
anyone who can increase a component of its customer-service software by 10
percent.

Armchair Astronomer - Galaxy Zoo

[Extracts from the Economist magazine article -- BSA]

http://www.economist.com/science/displaystory.cfm?story_id=11614176&fsrc=RSS

An armchair astronomer discovers something very odd

THE task of peering into the cosmos and discovering strange new galaxies sounds like a job for astronomers armed with big and very expensive telescopes. But almost a year ago that all changed when a group of stargazers decided to ask the public to help in a project to explore the northern sky.

The Sloan Digital Sky Survey had been looking in this part of space for 16 years, producing so much information that astronomers assumed they would never get through it. So the public was let loose, to help sort what they had found. The scheme is called the Galaxy Zoo project.

...within a month of the opening, Hanny van Arkel, a physics teacher from the Netherlands, posted a message on the zoo’s forum about some strange blue stuff she had spotted and asked what it might be.

By January the zoo’s professional keepers had started to pay attention to what the teacher had called a voorwerp, the Dutch word for object. Now it is becoming famous.

What this object might be was a complete mystery at first. It was initially thought to be a distant galaxy, says Chris Lintott, an Oxford University astronomer involved in the project. But after further study astronomers realised that there were no stars in it, and so it must be a cloud of gas. But why the gas was so hot (about 15,000ºC) was a mystery, because there seemed to be no stars to heat it up.

The weird blob could become immortalised as Hanny’s Voorwerp, the name given to the object in a paper Dr Lintott and his colleagues are submitting to the Monthly Notices of the Royal Astronomical Society. And towards the end of the year, if the mission to service the Hubble telescope goes as planned, a high-quality image of the voorwerp could emerge.

Earlier projects in distributed computing, such as SETI@home, which searched for extraterrestrial life, have used the power of millions of home computers. But more recently, scientists have begun to realise that distributed human brain power itself can be a useful commodity, as in working out the shape of proteins. Dr Szalay says that the voorwerp episode has shown how immensely valuable the public can be.

When the data were put online Dr Szalay thought it was only a matter of time before someone made a big discovery. “It just happened much faster than we thought.” In the past year 40m classifications of galaxies have been submitted on 1m galactic objects in the Galaxy Zoo. Dr Lintott says that the project has proved that the public en masse is as good as professional astronomers at classifying galaxies.

The next step is to ask people to do more complicated things, such as keeping an eye out for weird objects, which is bound to appeal to armchair astronomers. Hanny’s object had been there for decades, unnoticed in the astronomical archives. The idea now is for the public to explore strange new galaxies; to seek out new voorwerps and to boldly go where no amateur has gone before.

Distributed Computing for Eartquake Monitoring

[Here are too cool distributed computing applications (similar in operation
to SETI@Home.




http://www.dailytech.com/Distributing+Computing+Project+For+Earthquake+Monit
oring+Coming+Soon/article11276.htm

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~_/) ~~

Science
Distributing Computing Project For Earthquake Monitoring Coming Soon Levi Beckerson (Blog) - April 3, 2008 9:23 AM

UC Riverside researcher's earthquake monitoring system via distributed computing will soon be a reality.

Many computer enthusiasts as well as casual users are familiar with the various distributed computing projects such as Folding@home and SETI@home. And if there weren't enough familiarity for PC users, Sony's PlayStation 3 can also run Folding@home and does so very well thanks to its Cell Broadband Engine.
[..]
The magic behind distributed computing is in using all those unused processing cycles where computers lie semi-inert, simply passing time by spinning cooling fans. The various clients utilize unused cycles by crunching numbers for a given project.
[..]

The Quake-Catcher Network will use spare processing power as well as already installed accelerometers in laptops to monitor for seismic activity.

The accelerometers in modern laptops are used to help protect hard disk drives from suffering mechanical failure due to sudden impacts. As they are designed to measure vibration, they are a perfect fit for the Quake-Catcher Network's monitoring system.

Unlike the underground seismic sensors that dot southern California, which,after the data is transferred to one of several universities, takes 15 to 20 seconds to analyze, the network's seismic monitoring would happen in
real-time thanks to the way distributed networking works. The monitoring network could be used as an early warning system to give people in neighboring towns 10 to 15 seconds to prepare for the shock waves.

The data gathered by a dense network of monitoring stations could also be used to map the seismic data from the event, giving scientists a time line as well as information about material density and distance. The gathered
results will be freely available to the public and researchers.
[..]

Join the hunt to feed the world's hungry through broadband Internet

[Another good example of citizen science. Excerpts from NY Times article -- BSA]

http://bits.blogs.nytimes.com/2008/05/14/join-the-hunt-for-super-rice/?ref=technology

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.

.

Researchers Launch Online Protein Folding Game

[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.

http://games.slashdot.org/games/08/05/08/2112208.shtml

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.'"