text:
Online RNA design game garners unexpected interest from nonscientists.
It was a typical lab meeting. The latest RNA synthesis results were in, and they were puzzling. The data indicated deviations from the target fold in unexpected ways despite the fact that all eight designs were highly optimized variants of a previously successful design. It looked like another round of synthesis would be inevitable, and the floor was open for suggestions.
"This is different than the RNAFold prediction, at least using the Turner 1999 parameters." "Yes, the frequency of the MFE in the ensemble doesn't track with what's going on in the leftmost 1x1 loop."
"Could there be an error in the SHAPE analysis?"
"No, position 50 is highly accessible in several similar designs, so it's not a one-time glitch. But that means we have no idea what position 41 is bonding to …"The thing was, I wasn't in lab. I wasn't even talking to scientists. I was playing an online RNA folding game called EteRNA, and my fellow labmates consisted of computer analysts, project managers, stay-at-home moms (and one dad), retirees and home-schooled teenagers from around the world. And none of them had any formal education in biochemistry.
EteRNA is a National Science Foundation-funded joint effort between an RNA lab at Stanford University and a computer science lab at Carnegie Mellon University. It's very slick and well executed; you can dive right into designing RNAs without knowing anything about molecular biology or bioinformatics. It's all about brightly colored dots, wiggling bonds and getting a higher score than your peers, at least at first. Indeed, 95 percent of the players probably are just substituting EteRNA for their nightly round of Sudoku or Bejeweled.
What sets EteRNA apart from other games is the lab portion. Each week, top players create sequences designed to fold into a target shape. They then vote for eight sequences to be synthesized at Stanford and assayed for secondary structure content using the SHAPE primer extension assay (which measures 2'-OH accessibility). Every week, eight lucky players anxiously await the arrival of the experimentally observed secondary structure of their RNA design. When it's not at all what they expected, they become intrigued, hooked and obsessed. Suddenly, they find themselves spending hours each night in intense online discussions with fellow designers, crunching spreadsheets, looking for patterns and bouncing around ideas for the next round.
In short order, players who had never heard of Turner's Rules proved that the underlying energy algorithm acted only on nearest neighbors. They created online charts showing all possible permutations of adjacent base pairs and their free energy contributions as measured by exhaustive in-game enumeration. Shortly thereafter, they discovered that bulges and loops could be stabilized with a dangling purine at the 3' end of a helix and that certain tetraloop sequences got a bonus. Most significantly, they concluded that strategies that worked for the canned puzzles did not work for the actual design challenges.
One might think, given the game's emphasis on points and rankings, that players would hoard their best tricks to themselves – just as the gentleman-scientists of antiquity were loath to publish their most significant findings. But that's not how events have unfolded. Each new insight is posted, analyzed and heatedly discussed in public online forums. Credit for ideas always is duly attributed. Massive design spreadsheets annotated with musings from the top players are freely shared. Most impressively, this cadre of elite players devotes countless hours showing the ropes to newbies so that they, too, can get synthesized and ultimately contribute fresh ideas to the fold – even if it means giving up their own coveted synthesis slots!
How many of us card-carrying scientists honestly can claim to adhere to the same ethos?
There were obstacles, however, to creating this self-sustaining ecosystem. The small, overstretched team of graduate students responsible for day-to-day operations of the game soon found themselves inundated by requests for more detailed explanations of the underlying science. What does free energy mean, anyhow, and why did designs with extremely negative free energies fail to synthesize in the lab? What is a suboptimal fold? Why is RNA only shown in 2-D? Players were getting frustrated and were quickly losing interest.
So I decided to stop being a passive observer. I linked review articles on folding algorithms, some key primary literature and other bioinformatics tools they could use to analyze their designs. I started logging in late at night to field random questions from curious players about anything and everything, from "What's a tetraloop?" to "How can RNAs be used to treat cancer?"
It was like pouring gasoline on a fire.
The resulting flurry of activity in the forums and chat rooms proved something I had suspected all along. Ordinary citizens can read and absorb primary literature; they can formulate hypotheses, test them and analyze data. In other words, ordinary citizens can participate in science! They just need to be introduced to an interesting problem, provided with the right tools, and given access to someone willing to answer their questions. EteRNA already provided two of the three.
To be fair, EteRNA is a research project about crowdsourcing to optimize RNA folding algorithms. It was not envisioned as an outreach project, judging by the lack of educators on staff and the lengths taken to shield players from the details of the underlying science. And while such measures were necessary to appeal to casual players, the need to provide detailed explanations to sustain the interest of the most talented players initially was overlooked. This has been addressed as of late, as players now are being allowed to participate actively in improving the game itself. There even is a planned series of Q&A sessions with actual RNA researchers.
Perhaps the real problem is that we are all guilty of systematically underestimating the public's appetite to be meaningfully engaged in science. Consider that millions of gamers donate CPU time to distributed computing projects like Folding@home despite the pinch of electricity bills. Some actually purchase separate computers solely to contribute more CPU cycles to research they find fascinating. How many of them would jump at an opportunity to participate actively in that science, to have it be more than just a pretty screensaver?
This experience really has forced me to think hard about how we, as scientists, go about fulfilling our mandates to be involved in public outreach. Should we really pat ourselves on the back when we open our lab doors to straight-A high school students from dual-doctorate households or ambitious premeds looking to buff their resumes? And when we dazzle little kids with explosions and freezing flowers in liquid nitrogen – is that education or just entertainment? Is this really what the NSF has in mind when they ask us to detail our broad impacts to society?
Meanwhile, out in cyberspace, stay-at-home moms and college dropouts have arrived at their own, home-grown scientific method for creating RNA designs that work – despite being invisible to traditional venues of science education. Maybe, someday, one of these gamers will consider a career in science. Whether or not that occurs, the NSF – and the public that funds it – has gotten a fantastic return on this investment.
More from the current issue


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subset: commoncrawl


text:
Best Buy is confident that its latest policy change will kill "showrooming" in its stores for good.
Starting on March 3, the retailer will price match all local retail competitors, along with 19 "major online competitors" in all product categories, whenever a customer asks for it, the company announced.
"There is no doubt that this new policy ends showrooming for Best Buy customers," company spokesman Matt Furman told Bloomberg.
Back during the holiday rush, Best Buy announced a temporary price-matching initiative. This is its permanent version.
Showrooming, the practice of looking at items in a physical store then going online to make the actual purchase, has been a big worry for consumer electronics stores. Customers showroom electronics items more than any other category, according to data from comScore.
Chris Morran at the Consumerist obtained an internal document from Best Buy that announces the change and has more details. Here's what it says:
Starting March 3, 2013 Best Buy will price match the current pre-tax price for new, identical, immediately available products from local retail competitors and select designated major online retailers at the time of purchase only. (No subsequent price matching of competitors is allowed)
If Best Buy lowers a price on a product (online or in-store) we will allow price-matching up to 15 days following the original purchase. This applies to all customers including Reward Zone Premier Silver members. Please note: After a transition period for Reward Zone Premier Silver members through April 18, 2013, the 15 day period of the Price Match policy goes into effect (post-purchase – Best Buy only).
There has also been one major change to Best Buy's return policy.
The "Return and Exchange" period is being cut in half to 15 days from its previous length of 30 days. All returns will still require a receipt and I.D., plus Reward Zone Premier Silver members will retain their 60-day return eligibility.
Here is the full list of big online competitors that are included in the price-matching guarantee:
- Amazon.com
- Apple.com
- Bhphotovideo.com
- Buy.com
- Crutchfield.com
- Dell.com
- Frys.com
- hhgregg.com
- HP.com
- HomeDepot.com
- Lowes.com
- Newegg.com
- OfficeDepot.com
- OfficeMax.com
- Sears.com
- Staples.com
- Target.com
- TigerDirect.com
- Walmart.com


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Meeting Notes 2012 01 17
HOWTO run a meeting.[edit]
Pick a moderator, and a note-taker. The note-taker should:
- write notes in this page, put them back up online when they're done,
- edit the Current Consensus Items if anything is decided to be up for consensus next week (stuff raised for consensus this week should be publicised for a final decision next week)
- edit the Consensus Items History if anything was consensed or failed to consense this week.
- tell firstname.lastname@example.com and email@example.com if there are new members.
Moderator should:
- make sure everyone gets a chance to speak
- speak minimally themselves
- keep the meeting moving! you're in charge of summarising the consensus, and/or suggesting things that need to be done!
- get the membership binders and ensure they are returned to the black desk
The 196th Meeting of Noisebridge
Note-taker: User:Malaclyps
Moderator: User:snail
Introduction and Names[edit]
- What Noisebridge is about: "Noisebridge is a 501c3 nonprofit that provides a space for creation, collaboration, and learning about technology and creative projects. Noisebridge provides space, power tools, and infrastructure to help the public learn new skills and create cool things. Noisebridge continues to exist through and depends entirely on membership fees and donations. Our code of conduct is 'Be excellent to each other'."
- Round of introductions: What's your name, what do you do, and if you are new, how did you hear about Noisebridge? Start with the moderator and go left.
- A brief primer on consensus process: We agree and so should you! Only paid-up members can block consensus.
SuperQ -- moderating
Robert Rayc
Elijah -- works with noiserep
Mike technowanderer not quartermaster
Short Announcements[edit]
Elijah -- this is Noiserep, new location! Two new machines under construction, two more to come. Wednesday 6PM to whenever!
I'm Michel, sorry but I'm French. Social scientist from Paris, I know Philip ?? worked on hackerspace in Paris. Visiting scholar in Berkeley, working on Max Weber! Very interested in experiment that is Noisebridge. My project would be to make a book or something that I could write on Noisebridge, so I would like to do some interviews.
Rayc is planning to build some more shelves for the electronics shelf
Tony is looking for content for the zine before midnight! He shows off the cover.
Carl a couple of elevator men came to repair the elevator. They said, don't mess with the buttons.
SuperQ is working some more on the lights. If you have questions mail email@example.com
New or Stale Events[edit]
Machine learning is moving to Thursday
Sunday we had inaugural Android usability hacking event. We had ten people, good discussion, fine times, fine times.
Financial Report[edit]
Funds in bank: $20429.85
Noisetor balance: $3789.54 -- colo has been paid for thru Feb 7th. Additional 4 months of colo service in the balance.
Membership Binder[edit]
- Read off any names from the binder for the past month. Write a check on every open application.
- Anyone up for joining this week (ie have four checks by their name + have two sponsors) should introduce themselves then leave the area in search of gifts (traditionally beer and a lime) for the rest of the group. The rest of the meeting should consense on whether they may join.
Consensus items[edit]
- Matching funds for Noisetor donations should go to Noisetor. (Proposed by Tom)
- Now that Noisetor has undergone a trial period of operation, Noisebridge should extend the authorization of the Noisetor project for another six months. (Proposed by MCT, Andy, Leif)
Discussion Items[edit]
- drama* Elijah vouches for Robert. Moderation breaks. A discussion forms on the sidelines and the meeting continues.
- Using approval voting for the Board election (Proposed Leif)
- Proposed language for two consensus items next week:
- Noisebridge should use the approval voting process for Board elections.
- In the case of a tie between Noisebridge board candidates, we have a lottery among the tied persons.
- Proposed language for two consensus items next week:
- Discuss adopting the Policy Wonks' suggestion for membership expiry, for consensus next week.
- Discuss adopting the Policy Wonks' suggestion for members going on hiatus, for consensus next week.
- Discuss adopting the Policy Wonks' suggested clarification of the membership application process, for consensus next week.
- Discuss adopting the Policy Wonks' suggestions for how to be a Noisebridge member, for consensus next week.
Motivations for the change are to reduce process for members who become unresponsive, and to discourage using hiatus for members who are experiencing temporary financial difficulty. Will discuss methods for dealing with the latter. Memberships would expire sooner. Members will be responsible for keeping the tresurer informed about thier contact info.
We need someone to run the election.
Diy bookscanner project - Danny
End of Meeting[edit]
- PGP Key Signing could happen now, check the list to see who wants in on the action.
- Put back the membership binder in the black desk.
- Save the meeting notes to the wiki.
- Send a copy of the meeting notes to the discussion list.
- Copy the Meeting Notes Template for next week's agenda and update the main wiki page's link to it.
- Enjoy a cocktail with your fellow hacker or robot.


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On Wednesday night, more than 160 female contestants descended upon Hollywood to begin their quest to become the first female American Idol in five years. But before they can take on the boys, the girls must duke it out amongst themselves and it wasn't going to be easy – or pretty. With more females than males earning tickets to Hollywood, the cuts would have to be deeper in order to winnow down the pool of American Idol contestants. This meant added pressure on the girls.
But let us not forget that such intense eliminations are also a burden on our poor American Idol judges. Mariah Carey was obviously feeling under-appreciated when she lamented, "Nobody understands what we endure." Thankfully, she managed to muster up the courage to make it through the day. Perhaps in an effort to make herself feel better, Mariah arrived the next day practically dripping with diamonds. So, while we may not understand what Mariah endures, we certainly understand why she endures it.
Some American Idol contestants went home on the first day and never got the chance to see Mariah glitter – not to be confused with never getting the chance to see Mariah's "Glitter," which is something we should all pray for. Those who missed the former opportunity included early favorite Mariah Pulice, whose struggle with anorexia pulled at many heartstrings during her Chicago audition. Of course, pulled heart strings can't compare to the anguish endured by her sister, who seemed to be in constant tears throughout her Mariah's short Idol career. Also joining Mariah and her soggy sister, was Megan Miller. Viewers might remember that Megan was the contestant on crutches who broke out of the hospital right before surgery to audition. Thank goodness Miss Baton Rouge's decision to do so didn't cause any permanent damage, otherwise her walk of shame in Hollywood (sans crutches) would have been that much more painful.
On Day Two, the 76 remaining girls were divided into 19 groups but for possibly the first time in American Idol history, the judging went on without Randy Jackson. According to host Ryan Seacrest, Randy was busy in the studio. Guessing that viewers might doubt this implausible story, American Idol accompanied the claim with what appeared to be images of Randy actually in a studio. (Apparently the Obama Administration strategists are now consulting for American Idol.)
Regardless of where Mr. Jackson was, it was an unfortunate time to go MIA since he missed the opportunity to see Candice Glover perform with her group, "The Swagettes," and while the group's other members, Melinda Ademi, Denise Jackson, and Kamaria Ousley, were all good enough to advance, Candice Glover was to "The Swagettes," what Beyonce was to "Destiny's Child."
Enough said.
While "The Swagettes's" success was not a total surprise, there were other groups whose success was not expected. Take "The Misfits," for example. "The Misfits," included Kez Ban, so right off the bat, you know that the group couldn't have been more aptly named unless they dropped the "s." Kez's eccentric personality and inability to focus on anything other than food and "California Dreamin'," pushed the entire group, including Massachusetts's own Angela Miller, to the brink. (I am mentioning Angela not only because she's talented and happens to live in the town right next to mine, but more importantly because one of her friends, who accompanied Angela to her audition in New York, happens to be our local barista. Which is to say, he has unrivaled power and influence over my life.)
Anyway, back to "The Misfits." Despite being pushed to the brink of disaster, the members of the group all maintained a relatively positive attitude and managed, against all odds, to deliver a strong performance, earning each of them another opportunity to make it to the American Idol live shows.
Even more shocking was when all of the members of, "The Dramatics," made it through to the solo performances. These girls set out to prove that anything boys can do, girls can do better; including forgetting their lyrics. But for some reason, Nicki Minaj loved them, especially Janel Stinney, who didn't even attempt to remember the words but just hummed her way through her solo portion. Neither Keith Urban nor Randy enjoyed the performance but Nicki exercised her unexplainable sway over the panel and got her way again. Rooting for the underdogs and outcasts, like Papa Peachez and Kez Ban, is one thing but this isn't the first time Nicki has rewarded an entire group after they completely botched their performance.
In other news: in addition to winning a Grammy for Best New Album on Sunday, Gotye managed to also earn the distinct honor of single-handedly bringing about the demise of the most groups on Wednesday night with his song, "Somebody That I Used to Know."
Why so many groups of females would choose to sing a song that is far better suited for a male-female duet is perplexing but not as perplexing as the sheer number of contestants who managed to forget the lyrics to one of the most overplayed songs on the radio. Shira Gavrielov was but one of the contestants to mangle the song, but unlike the others, Shira was not about to go down without a fight. After her group, "Handsome Women," received their verdict and left the stage, Shira returned to ask the judges to explain why they sent her home. This was a golden opportunity for Nicki to tell off a contestant who truly deserved it - the entire viewing audience held their collective breath waiting for Nicki to open up a can of, "Oh No You Didn't" on Shira. Instead all the judges seemed to empathize with the audacious contestant and wasted everyone's time by actually trying to convince her that her performance was dreadful.
Ugh, these judges simply do not understand what we viewers endure – and we don't have Mariah Carey's comfort diamonds.
On Thursday, the girls will deliver their solo performances and try to live up to the premature hype about being stronger than the boys. The Top 40 contestants will also be revealed...supposedly. But you never can trust that Ryan Seacrest.


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I have $U$ and $V$ independent uniform on $[0,1]$ random variables I have to compute $\mathbb{E}(U | UV)$. Is there a specific trick to do this?
The basic way I know leads me find a function, $f$, such that for any measurable function, $g$, I have: $\mathbb{E}(g(UV)*U) = \mathbb{E}(g(UV)*f(UV))$ , which gives me:
$\displaystyle \int_0^1 \int_0^1 g(xy)*x*dx*dy = \int_0^1 \int_0^1g(xy)*f(xy)*dx*dy$
but then I have no way to proceed and identity $f$... any ideas?
edit : I tagged it as homework but it's actual an exercise from a previous exam I am trying to do.


text:
Active members of XtGem's forum are already aware of this functionality, but I have decided to repost it here for convenience.
First off, register an account on the chosen advertiser's site, then include one of these codes, changing site_id (and zone, in case of mojiva, publisher_id and adspace_id in case of smaato) with your provided account id. You can find these parameters either somewhere on their site while logged in or extract them from one of their provided integration codes (PHP/ASP/etc).
<xt:ad type="admob" site="site_id" />
<xt:ad type="adsense" site="site_id" slotname="slotname" />
<xt:ad type="buzzcity" site="site_id" />
<xt:ad type="inmobi" site="site_id" /> (or type="mkhoj")
<xt:ad type="mojiva" site="site_id" zone="zone" />
<xt:ad type="smaato" site="publisher_id" zone="adspace_id" />
<xt:ad type="admoda" site="site_id" />
<xt:ad type="adultmoda" site="site_id" />
<xt:ad type="webmoblink" site="site_id" />
<xt:ad type="decktrade" site="site_id" />
<xt:ad type="hitcross" uid="site_id" />
<xt:ad type="adiquity" site="site_id" />
<xt:ad type="mobgold" site="site_id" />
You can include as many ad service codes as you want on your site, max one per network and free ads will be returned after the first non-free ad is returned from the service.
So for example if you have these codes:
<xt:ad type="admob" site="site_id" /> <xt:ad type="buzzcity" site="site_id" /> <xt:ad type="admob" site="site_id" />
If admob doesn't return an ad, nothing will be displayed in the first code instance and buzzcity code will be executed. If admob does return an ad, buzzcity will not be executed. Second admob instance will not be executed either way, as it's a duplicate call.
It is also very important to note that you might not see ads on your site at all. This is not XtGem's bug! Either your site has not been accepted by the ad network (you can usually check your site's status on ad network's site) or they do not have any ad inventory with targeting matching your country/browser. Despite that, your site visitors might still be seeing ads. It's best to check ad network's site for stats and see if ads are being delivered.
Samsher has compiled a nice summary of various ad networks on his site here.
If in doubt, try asking for help in the forums.