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Tag: Bench Press

Kinect for Science

(Cross posted to Bench Press)

kinect_heroWe’ve blogged before about applying gaming technology to science, but much of that has been about using games or gaming system chips. A recent Wired magazine article reveals another interesting use case: taking the capabilities of something like Microsoft’s Xbox360 Kinect system and applying it directly to science research!

Apparently, a number of groups have decided to try out the Kinect as a “poor man’s” LIDAR (a tool that can be used to see and measure where things are in three dimensions)/complicated 3D camera setups which are expensive and require sophisticated calibration/post-processing analysis.

Of course, the Kinect is not a panacea: it has much more limited range, requires researchers to build their own analytical software, and the Kinect can’t do high-speed video (yet). But, because of its much lower price, its size, and the availability of drivers because of the active Kinect hacking/DIY community (and the support that even Microsoft is providing for people using Kinect beyond gaming), a number of researchers have decided to embrace the Kinect as a scientific tool.

The article profiles two potential use cases which only begin to scratch the surface of what this technology could be capable of: mapping meltwater lakes that form on top of glaciers (see images below) and studying small body impacts in space.

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But, potentially the most valuable use of Kinect? As the Wired article puts it:

The Kinect’s best asset may be that it inspires students, Tedesco said. Rather than a daunting black box with convoluted cables and arcane software, the Kinect is something that many students are already familiar with.

“This creates a different mindset in students,” he said. “They’re not so scared about using the Kinect, and they can really get involved in learning and basic research.”

“I’m actually on my way to buy two of them right now,” he added.

(Image credit – Kinect) (Image credit – Kinect glacier map)

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Phylo

(Cross posted to Bench Press)

A few years ago, I blogged about an ingenious crowdsourced game called Fold.It. The concept was pretty simple:

    • Use human intuition to help solve complicated three-dimensional protein folding challenges which is oftentimes as effective but significantly faster & cheaper than computational algorithms
    • Pool together lots of human volunteers
    • Turn the whole experience into a game to get more volunteers to spend more time

The result was a nifty little game which contributed findings which have made it, to date, into a number of peer-reviewed publications (see PNAS paper here and Nature Structure & Molecular Biology paper here)!

Well some researchers at McGill University in Canada want to take a page out of this playbook with a game they built called Phylo (HT: MedGadget) to help deal with another challenging issue in bioinformatics: multiple sequence alignment. In a nutshell, to better understand DNA and how it impacts life, we need to see how stretches of DNA line up with one another. Now, computers are extremely good at taking care of this problem for short stretches of DNA and for “roughly” aligning longer stretches of DNA – but its fairly difficult and costly to do it accurately for long stretches using computer algorithms.

People, however, are curiously intuitive about patterns and shapes. So, the researchers turned the multiple sequence alignment problem into a puzzle game they’ve called Phylo (see image below) where the goal is to line up multiple colored blocks. Players tackle the individual puzzles (in a browser or even on their mobile phone) and the researchers aggregate all of this into improved sequence alignments which help them better understand the underlying genetics of disease.

And how has it been doing? According to the McGill University press release:

So far, it has been working very well. Since the game was launched in November 2010, the researchers have received more than 350,000 solutions to alignment sequence problems. “Phylo has contributed to improving our understanding of the regulation of 521 genes involved in a variety of diseases. It also confirms that difficult computational problems can be embedded in a casual game that can easily be played by people without any scientific training,” Waldispuhl said. “What we’re doing here is different from classical citizen science approaches. We aren’t substituting humans for computers or asking them to compete with the machines. They are working together. It’s a synergy of humans and machines that helps to solve one of the most fundamental biological problems.

With the new games and platforms, the researchers are hoping to encourage even more gamers to join the fun and contribute to a better understanding of genetically-based diseases at the same time.

Try it out – I have to admit I’m not especially good with puzzle games, so I haven’t been doing particularly well, but the researchers have done a pretty good job with the design of the game (esp. relative to many other academic-inspired gaming programs that I’ve seen) – and who knows, you might be a key contributor to the next big drug treatment!

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Singapore to Combat Dengue with Social Media

(Cross posted to Bench Press)

Singapore is a fascinating country – despite the lack of what most in the West would recognize as democratic freedom, it consistently ranks well in terms of lack of corruption and high and growing standard of living for its people.

It is also one of the boldest when it comes to instituting policies and reforms: they were the first to implement a congestion tax to help manage traffic. Unlike most countries, Singapore is open to competition and investment from foreigners in strategic areas like telecommunications, power generation, and financial services. Singapore has also been extremely active in attempting to build up its capabilities as a center for life sciences excellence.

So it shouldn’t surprise me that they are among the first countries to actively utilize social media applications like Facebook and Twitter to help deal with a public health risk like Dengue Fever (from The Jakarta Globe):

The city-state’s National Environment Agency (NEA) plans to roll out … providing information on the latest dengue clusters or areas that have been earmarked as high-risk – on these new media platforms within the next three months … Through Facebook and Twitter, the public will also be able to post feedback or provide tip-offs. For example, if Singaporeans notice an increase in the number of mosquitoes in your neighbourhood or find potential breeding sites, they can alert NEA officers by posting on the agency’s Facebook page or tweeting the NEA account. “We need to put more information out in the public space, so more people can be informed and take action,” said Derek Ho, director of the environmental health department at NEA. “Leveraging on new media channels such as Facebook and Twitter is a good way to do that.”

A refreshing understanding of the uses of social media by a government agency – more interesting than that, though, is the work Singapore’s NEA is doing to build image recognition capabilities into smartphone apps like the NEA’s iPhone app to help field workers (and potentially the public) track and identify mosquitos and mosquito larvae!

The NEA is also in the process of developing a mosquito-recognition program that can identify the species of mosquito from a photograph of its pupae or larvae. With such software, and with the help of a mini microscope that attaches to the camera on a personal digital assistant or cellphone, NEA officers will be able to take photographs of larvae or pupae found in mosquito-breeding sites and instantly find out if they belong to the Aedes species, which spreads dengue … When it is ready, the agency hopes to be able to integrate it with the NEA iPhone application, so that the public or grassroots members conducting checks around the neighbourhood can use the technology as well.
Early identification will allow the NEA to act more swiftly to curb the spread of dengue in potential high-risk zones.

Very cool demonstration of the power of smartphones and of a government that is motivated to try out new technologies to tackle serious problems.

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Grand Challenges

Over at Bench Press, my buddy Anthony posted about the American Association for the Advancement of Science’s collaboration with the White House and Expert Labs to help identify “which scientific and technological challenges should be the focus of policy initiatives in the coming years.” The collaboration is unique in that, to my knowledge, it is the first time (or at least one of the first times) the federal government has used social media/crowdsourcing to help shape science policy.

While my first reaction was “we’re so screwed that the White House is using Twitter/Facebook to figure out our future science policy!?”, I felt it would be fun to participate in my own little way via this blog post (even though the deadline for submission was technically April 15, I’m hoping the non-140-character-limited nature of this blog post carries some weight! :-)).

So, without further ado, here would be my list of ten things (all super-broad and super-idealistic, of course), in no particular order:

  • Enabling medical treatments to be tailored for an individual patient’s history, age, gender, and genetics
  • Safer, more precisely targeted treatments which don’t damage or affect cells they are not supposed to
  • New chemical, physical, or biological processes to more cheaply produce drugs and other chemicals
  • Advanced energy storage capable of at least an order of magnitude better energy density than existing Lithium ion batteries
  • Chemical, physical, or biological methods to capture carbon dioxide and handle the increasing amounts of pollution people are generating
  • An improved understanding of the complex systems which govern our world through new mathematical/computational techniques for approximating NP-complete problems and calculating/understanding non-linear partial differential equations
  • Petaflops-capable supercomputers which cost as much and consume as much energy as a laptop today
  • (Partially inspired by Star Trek) Intelligent natural language processing so that computers can actually understand and translate language
  • (Partially inspired by Star Trek) General-purpose scanning device capable of quickly detecting chemicals, sounds, and forms of radiation as well as performing simple tomography scans (via ultrasound and/or some other form of low-energy radiation scanning)
  • (Partially inspired by Star Trek) Near-light-speed space travel to explore beyond the solar system and allow humans to move beyond near Earth orbit

Picking ten was actually pretty difficult. There are clearly many other important scientific questions to be answered, but these were my ten. What would be on your list?

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2010 Goals

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I don’t usually do the New Year’s resolutions thing. But this year, since I’m now publishing everything  to benjamintseng.com, I think the perceived public scrutiny associated with having a public list of goals for the coming year on my own personal domain name might end up being a good motivator to achieve them.

So, without further ado:

  • Finish a Rev 1 of Benchside – While I had a wild ride on Xhibitr and learned a ton, I’m hoping Benchside, the  project that I’m currently working on, will end much more successfully. Whereas Xhibitr was an online social network aimed at fashion, Benchside is a software application designed to run on your computer (not the web) which aims to help you change the way you organize the information on your hard drive. While Benchside officially started about half a year after work on Xhibitr went underway, its progress has suffered from a lack of focus on my part. Despite this, I still have strong faith in the team and the project, and I definitely want to see this through. So, by December 31, 2010, I will have a working version (even if its only barely working and cobbled together with voodoo magic and duct tape) of the core Benchside software working on my computer.
  • Read Pawn in Frankincense and Checkmate by Dorothy Dunnett – My girlfriend adores Dorothy Dunnett’s Lymond Chronicles. They were an integral part of her identity growing up, and she continues to re-read them today whenever she has extra time (and no new reading or knitting material :-)). They are also very meaty books full of well-researched 16th century European history and cultural idiosyncrasies. I’ve already read two (Game of Kings and Disorderly Knights – yes, there’s a chess theme in the titles) and despite priding myself in being well-educated, I found them very difficult to follow (I guess that’s why I read comic books?) So why read two more? In addition to my girlfriend wanting me to read them, she’s raved about the conclusion to this series (Checkmate) for years, and given her refined, educated taste in books (although apparently not in men :-)), I can’t help but want to stretch my own reading ability especially if the payoff is as grand as she has made it seem. Consequently, by December 31, 2010, I will have read both Pawn in Frankincense and Checkmate.
  • Meet at least 3 new people per conference I attend – If I have one great weakness, it is that I find it painfully difficult to talk to people I’m not familiar with. On the Myers-Briggs Type Indicator test, I rank extremely “I” (as in introvert). But, given my upcoming job in venture capital and my desire to pursue opportunities which won’t be so forgiving of my extreme shyness, I’m going to set a goal for myself to help break that habit. At every conference/industry event I attend in 2010, I will meet and have meaningful conversation with at least 3 new people.
  • Read at least 1 academic scientific paper per month – I pride myself on being a science person. In fact, with the notable exception of Xhibitr, my portfolio is full of my old scientific “adventures”.  But, as I’ve dug deeper into the technology and business world, I have unfortunately lost touch with that part of my life. Part of the reason that I still blog about science here and over at Bench Press is a desire to stay connected to those under-exercised scientific interests. This year, to help keep that connection going, and also to help me keep pace with the tech-and-science related news and innovations which give me fodder for more blog posts, in 2010, I will read at least 1 academic (as in journal) scientific paper per month.

I’m sure some of the people reading this list will think that my bar for success is set too low. And, maybe they’re right. But, hey, this is the first time I’ve done something like this, and I’m not about to set myself up for public failure :-).

Happy New Year to everyone! And best of luck with those resolutions!

(Image credit)

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2009 in blog

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As I did with 2008 and 2007, a couple of highlights from this blog for the past year:

Happy new year, everybody!
(Image credit)

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Paradigm Shift@Home

I recently made a post on Bench Press about the potential for distributed computing (projects like Folding@Home and SETI@Home which combine the computing power from volunteers over the internet to do supercomputer style calculations) to help any initiative needing extra number-crunching power, as well as steps that the scientific and distributed computing communities can take to help get us there, as well as what I think is a valuable paradigm shift in science that the distributed computing approach represents:

What impresses me the most about projects like Folding@Home and SETI@Home is that they have defined some brilliant new ways to do science:

  • Use the internet – It’s a common theme on Bench Press, but with more and more people having faster and faster access to the internet, the potential for distributed computing becomes greater and greater. As Folding@Home demonstrated, such approaches can produce computing systems as powerful (or potentially more powerful) as leading supercomputer systems at a fraction of the cost.
  • Mobilize the public – We’ve discussed ways for the scientific community to reach out to the public like using social media and creating interactive applications/tools for the public to use, but efforts like Folding@Home illustrate a way to not only reach out to the public but to get them vested in science. In a world where high school science teachers find it difficult to get teens interested in science, initiatives like Folding@Home have created a system where teams of individuals compete on who can contribute the most to the effort! Instead of simply hoping that the public will continue to fund and listen, why not borrow a page from the many existing cancer-walk-a-thons and make it easy for the public to get involved?
  • Leverage new technology – It may not come as a surprise to our readers that a significant amount of the computational power at Folding@Home comes from graphics cards and Playstation 3’s. But, while many “mainstream” supercomputers ignored the new power afforded by these new chip types, Folding@Home developed software so that volunteers could quickly and easily use these powerful chips to boost their Folding@Home scores. The Folding@Home initiative also developed software to take advantage of innovations AMD and Intel included in their chips (new multi-core architectures and special instructions to speed up calculations). Is it any wonder, then, that Sony, NVIDIA, and AMD have all publically announced support for the initiative with their products?

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For more details on distributed computing and some of my thoughts on how the scientific community can better adopt these, check out the post at http://blog.benchside.com/2008/12/distribute-compute/

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