Posts Tagged ‘MIT’

MIT Team Developing ‘DNA Origami’ Software

April 29th, 2011

A team at MIT are developing software that will allow people to play with DNA. When developed, this program will allow people to construct virtual 2D and 3D models and nanoscale tools, in a strategy that is being called DNA origami.

DNA molecules are highly useful in the development of synthetic photocells and targeted drugs among other things. However, the challenge of making new sequences and building DNA models for specific tasks has always been very difficult.

Enter the MIT team led by biological engineer Mark Bathe, who are continuing the work of Paul Rothemund from CalTech and William Shih’s from the Harvard Medical School. This new software is being developed to make it much easier for researchers to predict 3D shapes when working with given DNA templates.

“They’re sort of building blocks, but it’s even more crude because DNA is just a sequence,” Bathe says. “It’s taking the places you would connect the DNA together and predicting with a computer what it would look like in the final shape. The goal is to really have this be in the inverse, so the designer wants to make a box or a basket or a gear and then the program tries different folding combinations to give you the shape you want.”

Unlike protein modelling and other messy challenges in biology, DNA is relatively clean and obedient and can be dealt with mathematically. Bathe hopes this software will also open up the world of DNA origami to non specialists, saying “Once non-specialists can design arbitrary 3D nanostructures using DNA origami, their imaginations can run free.”

“Designers still have to guess the rules and then based on the shape modify the rules to get closer to the shape,” Bathe says, adding “It’s the Holy Grail to say, ‘I want this,’ and then it happens. We’ve made quite some progress already, so I think in the next half year to a year that should be coming out.”

Source:http://www.geekwithlaptop.com/mit-team-developing-dna-origami-software

MIT software could bring ‘DNA origami’ to the masses

April 28th, 2011

DNA molecules are not merely carriers of information. They are also highly stable and programmable, which is why researchers have been working so feverishly on a design strategy called DNA origami.

And now a team at MIT is developing a program that makes the game playable by more than just a select few.

DNA origami–constructing specific 2D and 3D shapes out of DNA strands–could prove to be a highly effective means of developing nanoscale tools, such as synthetic photocells that perform artificial photosynthesis and highly targeted drugs (think of sending a cancer drug to hunt down a specific tumor).

But it’s still young. Paul Rothemund of CalTech first introduced DNA origami in 2006 (thereby making the cover of Nature and delivering a TED Talk showing tiny DNA smiley faces), and William Shih’s lab at Harvard Medical School was able to up the game from 2D to 3D a few years later.

The result is that today a small number of brilliant and highly specialized minds are bent over a nanoscale game of origami, playing with various sequences to try to build specific shapes for specific tasks. Imagine a room of highly sophisticated gamers playing with building blocks in a world without Tetris; if they had the game, they’d be able to work faster.

This is where the team at MIT, led by biological engineer Mark Bathe, comes in. They’ve developed software that makes it far easier, with a given DNA template, to predict the three-dimensional shape that will result.

“They’re sort of building blocks, but it’s even more crude because DNA is just a sequence,” Bathe says. “It’s taking the places you would connect the DNA together and predicting with a computer what it would look like in the final shape. The goal is to really have this be in the inverse, so the designer wants to make a box or a basket or a gear and then the program tries different folding combinations to give you the shape you want.”

DNA comprises a string of four nucleotide bases called A, T, G, and C, with A binding only with T and G only with C. Rothemund found that he was able to get a long strand of DNA to fold using a viral genome that consisted of 8,000 of these nucleotides to create 2D stars, triangles, and yes, those smiley faces. That one strand served as a scaffold for the rest of the structure, with literally hundreds of shorter strands (only 20 to 40 bases in length) combining with the long strand to hold its desired shape.

Bathe says his software presented a mathematical and computation challenge, but that because DNA is governed by physics in terms of how it bends and twists and folds, DNA origami is very clean and obedient. Proteins, he says, are much messier, making protein-folding far more complex, which is why the game Foldit exists. (Researchers opened the process up to the masses in the hopes that a greater volume of people working on the problem might speed up progress.)

Bathe and his team, who haven’t resorted to a game just yet, provide a primer of their software in the Feb. 25 issue of Nature Methods, and they’re already working on making the program more automated and “unsupervised,” because at this point it’s still largely manual.

“Designers still have to guess the rules and then based on the shape modify the rules to get closer to the shape,” Bathe says. “It’s the Holy Grail to say, ‘I want this,’ and then it happens. We’ve made quite some progress already, so I think in the next half year to a year that should be coming out.”

Ever the optimist, Bathe was quoted in the MIT news release saying, “Once nonspecialists can design arbitrary 3D nanostructures using DNA origami, their imaginations can run free.” Ever the realist, I had to ask whether such an achievement might also be risky in the wrong hands. For Bathe, this is the conundrum we face in light of most advancements; the potential for progress, he hopes, far outweighs the risks.

Source:http://news.cnet.com/8301-27083_3-20057983-247.html

Software package aids motor recovery in stroke patients

April 5th, 2011

Researchers at Ulster University’s School of Computing and Information Engineering and School of Health Science designed the virtual environment games to simulate daily activities such as washing and dressing.

The software package, called myGames, can be used alone with a webcam or in conjunction with a robotic arm designed by Myomo, a US company spun out from the Massachusetts Institute of Technology (MIT).

‘The goal we had was to design something that was usable by people in their own home, much like the [Nintendo] Wii and the [Microsoft] Kinect,’ said Dr Michael McNeill of Ulster.

‘What we found when we looked at a lot of these commercial games is that the pace and design are not suitable for something as unique as motor-function rehab, so we stripped down the problem and looked intensely at the principles of game design, in particular feedback and challenge,’ he added.

Performing basic repetitive movements has been clinically proven to promote motor recovery in stroke patients and the current project aims to build on this. For patients with particularly severe disability, Myomo’s mPower 1000 robotic arm can be used with myGames.

The device has sensors that sit on the skin’s surface and detect even a very faint muscle signal. When a person with a weak or partially paralysed arm tries to move, and a muscle signal fires in the arm, the robotics in the device engage to assist in completing the desired movement.

‘If you have a really severe deficit you tend to be disenfranchised. It’s all very well the physiotherapist saying: “reach for that ball or put that cup over there”, but it can be difficult to get any feeling of accomplishment, so the robotic brace and the games are designed to give powerful assistance to that,’ said McNeill.

Source:http://www.theengineer.co.uk/sectors/medical-and-healthcare/news/software-package-aids-motor-recovery-in-stroke-patients/1008143.article

Team competes in NASA, MIT software challenge

October 23rd, 2010

A group of students skipped the homecoming pep rally in favor of strategizing their next move on what looks like a primitive computer game.

The students weren’t playing, however.

A Friendswood High School computer science team is designing software that will program small satellites on the International Space Station.

Friendswood will compete against 23 schools from across the country in the HelioSPHERES challenge, a part of NASA and the Massachusetts Institute of Technology’s Zero-Robotics program that aims to inspire future scientists and engineers.

Synchronized Position Hold, Engage and Reorient Experimental Satellites, or SPHERES, are three volleyball-sized satellites in the space station’s cabin that test advanced spacecraft maneuvers, including autonomous rendezvous and docking, NASA spokesman Michael Curie said.

The competition challenges students to program the satellites to find a solar panel that has detached from the space station, retrieve and deliver the panel to the station and determine a strategy to disrupt an opponent, Friendswood senior Noah Kessler said.

“You can make a program that will repel other teams’ satellites away from the panel,” Kessler said. “That’s one of the things we have to figure out, whether we’re going to be more offensive or not.”

Teams will compete in elimination rounds using online simulations and ground-based testing at MIT.

Software created by the top 10 winners will be sent to the space station, where an astronaut will program the satellites to run the students’ tests.

Friendswood is the only high school from Texas that NASA and MIT selected for the challenge.

Designing the software is similar to playing a game, Friendswood senior Ryan Ham said.

Ham’s dad, Kenneth Ham, has been an astronaut since 1998, and in May served as commander of the Space Shuttle Atlantis flight to the space station.

“We’re trying to find a way to program so we don’t lose,” Ryan Ham said. “We have to plan the best way to find the panel and anticipate how an opponent might try to distract us.”

Students will submit their program by the end of October for the competition’s first round.

Teams that progress to the final round will travel in December to MIT to watch the programs run from the space station.

David Goeken, a NASA mentor to the Friendswood team, works at the Johnson Space Center writing software for the space station and flight controllers.

Goeken developed some of the math models the students are using to propel their satellites in the program.

“I can’t tell them what to do,” Goeken said. “I can only shepherd them in the right direction. They’ve come up with some good ideas on their own.”

The enticement of winning another computer science competition is driving the students, Kessler said.

Friendswood has won the University Interscholastic League class 4A state championship in computer science for the past two years.

Competitions show students there’s more to a career in designing software than sitting in a room coding all day, Friendswood computer science teacher Annette Walter said.

The school’s proximity to the Johnson Space Center and access to aerospace computer programmers as mentors doesn’t hurt either, she said.

“These competitions teach students those essential social skills of how to work in teams in real-life situations,” Walter said. “This is what they will encounter in college and beyond.”

Source:http://galvestondailynews.com/story.lasso?ewcd=b4fb586ccdd9ea45

Dentsu partners Nihon Unisys, MIT on comms project

September 26th, 2010

Dentsu Inc announced Friday its collaboration with Nihon Unisys and the Media Lab in a project aimed at creating a “context-reading communication computer”.

The aim of this project is to create a database of the shared common background knowledge and senses what we humans use when we converse with others, and then, by using this database in a computer system, create a computer that can understand implicit meanings and nuances of language in the same way as humans, and use the appropriate knowledge and words at the appropriate time.

The project will be driven not only by special researchers and laboratories, but also through the user participation model of crowdsourcing, which will enable the database to be created by involving the general public who will have fun as they take part.

The project is divided into two sections: the building of a database of common sense (the “input project”), and communication that utilizes this database (the “output project”).

As a first step, activity programs inviting the public to participate were uploaded to the project website (URL: http://www.omcs.jp) on Friday. In the input project, an association game called “Play a Quiz Game with Nadya” will be used to gather common sense from the players. The output project will feature the “Poi bot” robot character which can imitate a person’s conversation by learning his/her distinctive communication style and way of thinking.

Dentsu and Nihon Unisys are collaborating with the MIT Media Lab, where Professor Emeritus Marvin Minsky, one of the world’s leading authorities on artificial intelligence, has made fundamental contributions to the fields of robotics and computer-aided learning technologies. At the Lab, they are working with Henry Lieberman, head of the Software Agents Research Group, whose research focuses on developing software that utilizes common-sense reasoning.

Through this project’s diverse research activities, Dentsu is seeking a solution that will contribute to the realization of enhanced customer-oriented services, namely a next-generation client-consumer marketing communication model employing artificial intelligence that has common sense.

Nihon Unisys is pursuing an interface that will provide a next-level experience to consumers at both online shopping sites and bricks-and-mortar stores.

Source:http://tellycafe.com/general-news/3481-dentsu-partners-nihon-unisys-mit-on-comms-project.html

The MIT roots of Google’s new software

August 20th, 2010

Google’s App Inventor, which lets people with no previous programming experience build applications for mobile phones, draws on decades of MIT research.

In July, Google released a trial version of new software, called the Google App Inventor, intended to let people with no previous programming experience design applications for phones that use Google’s Android operating system. The software has provoked much commentary in the technology press, and Google has been trumpeting it as a way to give people direct control of their own phones. But App Inventor is the latest outgrowth of a tradition of MIT research that dates back at least 40 years.
The App Inventor project was led by Hal Abelson, the Class of 1922 Professor of Computer Science and Engineering, who spent a sabbatical year at Google as a visiting professor. Instead of having to write traditional computer code, users of App Inventor can create programs by snapping together virtual, color-coded instruction “blocks.” For instance, to add a button to an application, the user would drag the button block into App Inventor’s workspace window and determine the button’s visual properties by selecting from pull-down menus. Then, to determine what the button will do, the user would snap a block that defines a function — like emitting a noise, or making a phone call, or changing the screen’s background color — into the button block.

The App Inventor blocks are based on the MIT master’s thesis of Ricarose Roque, for which she built a general version of a programming interface that Eric Klopfer, the director of MIT’s Teacher Education Program, had developed for a simulation program called StarLogo. StarLogo, in turn, began as the PhD thesis of Mitchel Resnick, who heads MIT’s Media Arts and Sciences Program, and whose graduate advisors were Abelson and Seymour Papert, a pioneer of educational computing.
Papert, who came to MIT in 1963, is most famous for inventing Logo, a simple computer language designed to introduce young children to the principles of programming. Initially, programs written in Logo would guide a robot with a pen attached to its undercarriage — a “turtle” — across a sheet of paper, executing a drawing. In the late 1960s, when Abelson was a graduate student at MIT, he helped Papert begin testing the system in Boston-area schools.

From Logo to Lego
“You really have to try hard to get into the mindset of that time, because a computer in those days was something that cost several million dollars,” Abelson says. “And the idea that you would take the most advanced computing research equipment around anywhere, and you would let fifth graders … start playing with it, it was just mind boggling. For the first 10 years of that, people just thought we were nuts.”

But that changed in the 1980s, Abelson says, when personal computers started invading elementary- and secondary-school classrooms. Many of today’s software-company executives first learned the principles of programming from a later version of Logo, in which a virtual turtle executed drawings on a computer screen.

Resnick’s PhD thesis was an extension of Logo called StarLogo, which enabled the interaction of hundreds or even thousands of turtles in complex simulated environments. “I was particularly interested in issues around emergent phenomena and decentralized systems,” Resnick says. “How do bird flocks work? How do the individual actions of individual birds lead to the behavior of a flock? Or how do ant colonies work? Or how do traffic jams form? Or how do market economies work, where there’s lots of individual buyers and sellers, but you get these larger-scale patterns that develop? I was interested in helping people understand how large-scale patterns arise from lots of local interactions. That’s always been a very difficult thing for people to understand. So the idea was to try to provide a way for people to play with those ideas by giving very simple rules to lots of individual objects.”

After graduating, Resnick became a professor in the MIT Media Lab, where he began developing a Logo-like system that would allow children to program robots built from Lego bricks with electromechanically activated moving parts. The project ultimately resulted in Lego’s Mindstorms kits. But along the way, an undergraduate named Andy Begel, who’s now at Microsoft Research, developed a graphical programming language — a precursor to the App Inventor’s programming blocks — as a way to let kids program their Lego robots more intuitively.

Crosstalk
Begel’s system influenced the software for Mindstorms, and Resnick and Klopfer have continued to expand on its central ideas, for two different projects. Klopfer’s is a 3-D adaptation of StarLogo called StarLogo TNG, which can be used to build video games, among other things. Resnick’s is Scratch, a successful educational system, launched in 2007, that allows children to design their own interactive stories and games for the Web. “We’ve been able to stay in touch about what’s going on, and we’re now having a chance to revisit what we were doing and making version two of both of our projects,” Klopfer says. “We made some different design decisions along the way, and I think that was really great as research projects, because we can really learn from each other’s successes and failures.”

For her master’s thesis, Roque decoupled Klopfer’s programming blocks from StarLogo, so that they could be reused in other software systems — and indeed, they were the basis for the App Inventor programming interface. And because Scratch is so popular — hundreds of thousands of registered users have used it create more than a million projects — members of Resnick’s group have been consulting with Google about how to build an online community around the system.

But beyond using actual code that was developed at MIT, Abelson says, the Google App Builder project was also motivated by the same philosophy that drove Papert’s “nutty” experiments in the 1960s. “It strikes me that most of the people who are teaching introductory programming have gotten out of step with the reality of how kids experience computing,” Abelson says. “It’s not about sitting at a desktop computer. It’s about these incredibly powerful computers that you now carry around with you that can do location-aware things, and they can find your friends, and they can make phone calls and do other stuff. App Inventor, as an educational program, is about giving young people who are trying to learn about computing power over the real computing that they’re using in their lives.”

Source:http://stockmarketsreview.com/pressrelease/2010/08/20/the-mit-roots-of-google%E2%80%99s-new-software/

The MIT roots of Google’s new software

August 19th, 2010

Google released a trial version of new software, called the Google App Inventor, intended to let people with no previous programming experience design applications for phones that use Google’s Android operating system. The software has provoked much commentary in the technology press, and Google has been trumpeting it as a way to give people direct control of their own phones. But App Inventor is the latest outgrowth of a tradition of MIT research that dates back at least 40 years.

The App Inventor project was led by Hal Abelson, the Class of 1922 Professor of Computer Science and Engineering, who spent a sabbatical year at Google as a visiting professor. Instead of having to write traditional computer code, users of App Inventor can create programs by snapping together virtual, color-coded instruction “blocks.” For instance, to add a button to an application, the user would drag the button block into App Inventor’s workspace window and determine the button’s visual properties by selecting from pull-down menus. Then, to determine what the button will do, the user would snap a block that defines a function — like emitting a noise, or making a phone call, or changing the screen’s background color — into the button block.

The App Inventor blocks are based on the MIT master’s thesis of Ricarose Roque, for which she built a general version of a programming interface that Eric Klopfer, the director of MIT’s Teacher Education Program, had developed for a simulation program called StarLogo. StarLogo, in turn, began as the PhD thesis of Mitchel Resnick, who heads MIT’s Media Arts and Sciences Program, and whose graduate advisors were Abelson and Seymour Papert, a pioneer of educational computing.

Papert, who came to MIT in 1963, is most famous for inventing Logo, a simple computer language designed to introduce young children to the principles of programming. Initially, programs written in Logo would guide a robot with a pen attached to its undercarriage — a “turtle” — across a sheet of paper, executing a drawing. In the late 1960s, when Abelson was a graduate student at MIT, he helped Papert begin testing the system in Boston-area schools.

From Logo to Lego

“You really have to try hard to get into the mindset of that time, because a computer in those days was something that cost several million dollars,” Abelson says. “And the idea that you would take the most advanced computing research equipment around anywhere, and you would let fifth graders … start playing with it, it was just mind boggling. For the first 10 years of that, people just thought we were nuts.”

But that changed in the 1980s, Abelson says, when personal computers started invading elementary- and secondary-school classrooms. Many of today’s software-company executives first learned the principles of programming from a later version of Logo, in which a virtual turtle executed drawings on a computer screen.

Resnick’s PhD thesis was an extension of Logo called StarLogo, which enabled the interaction of hundreds or even thousands of turtles in complex simulated environments. “I was particularly interested in issues around emergent phenomena and decentralized systems,” Resnick says. “How do bird flocks work? How do the individual actions of individual birds lead to the behavior of a flock? Or how do ant colonies work? Or how do traffic jams form? Or how do market economies work, where there’s lots of individual buyers and sellers, but you get these larger-scale patterns that develop? I was interested in helping people understand how large-scale patterns arise from lots of local interactions. That’s always been a very difficult thing for people to understand. So the idea was to try to provide a way for people to play with those ideas by giving very simple rules to lots of individual objects.”

After graduating, Resnick became a professor in the MIT Media Lab, where he began developing a Logo-like system that would allow children to program robots built from Lego bricks with electromechanically activated moving parts. The project ultimately resulted in Lego’s Mindstorms kits. But along the way, an undergraduate named Andy Begel, who’s now at Microsoft Research, developed a graphical programming language — a precursor to the App Inventor’s programming blocks — as a way to let kids program their Lego robots more intuitively.

Crosstalk

Begel’s system influenced the software for Mindstorms, and Resnick and Klopfer have continued to expand on its central ideas, for two different projects. Klopfer’s is a 3-D adaptation of StarLogo called StarLogo TNG, which can be used to build video games, among other things. Resnick’s is Scratch, a successful educational system, launched in 2007, that allows children to design their own interactive stories and games for the Web. “We’ve been able to stay in touch about what’s going on, and we’re now having a chance to revisit what we were doing and making version two of both of our projects,” Klopfer says. “We made some different design decisions along the way, and I think that was really great as research projects, because we can really learn from each other’s successes and failures.”

For her master’s thesis, Roque decoupled Klopfer’s programming blocks from StarLogo, so that they could be reused in other software systems — and indeed, they were the basis for the App Inventor programming interface. And because Scratch is so popular — hundreds of thousands of registered users have used it create more than a million projects — members of Resnick’s group have been consulting with Google about how to build an online community around the system.

But beyond using actual code that was developed at MIT, Abelson says, the Google App Builder project was also motivated by the same philosophy that drove Papert’s “nutty” experiments in the 1960s. “It strikes me that most of the people who are teaching introductory programming have gotten out of step with the reality of how kids experience computing,” Abelson says. “It’s not about sitting at a desktop computer. It’s about these incredibly powerful computers that you now carry around with you that can do location-aware things, and they can find your friends, and they can make phone calls and do other stuff. App Inventor, as an educational program, is about giving young people who are trying to learn about computing power over the real computing that they’re using in their lives.”

Source:http://web.mit.edu/newsoffice/2010/android-abelson-0819.html

Get Adobe Flash playerPlugin by wpburn.com wordpress themes