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Comment: Even cooler - the annotation was done on a *real* (Score 1) 71

by TheHornedOne (#46556685) Attached to: Pine Tree Has Largest Genome Ever Sequenced

Genome annotation (finding all the interest features in the sequence) is really computationally intensive, due in large part to the number of separate (often sub-optimally written) algorithms that have to be chained together and interpreted. My team at the iPlant Collaborative worked with the authors of a popular open-source annotation tool called "MAKER" to get it running at scale on the 302 TFLOP Lonestar 4 supercomputer, which in turn was used by the pine team to do in a few hours what used to be 6 months of painstaking bioinformatics. In another month or so, this algorithm will be available via REST API allowing, literally, "Annotation As A Service".

Comment: Disappointing (Score 2) 68

by TheHornedOne (#46550995) Attached to: Mute Witness: Forensic Sketches From Nothing But DNA

It's a nice story, and they provide a MatLab environment to play around with their model, but ultimately I don't believe this work is reproducible given the materials provided. All we're really given is a sandbox to play in where we can adjust model parameters, and so the work should never have been published.

What would convince me? For starters, the ability to take an arbitrary set of values for these SNPs, punch them in, and see the result change. If I put in SNPs from one of the CEU HapMap samples, I would expect to see a vaguely Caucasian face. If the individual is female, I would expect feminized features. Adding to this, I think we need to see more of the source used in the data wrangling. There's quite a bit of "and then this happened" in the methods.

+ - The NSA's next move: silencing university professors?-> 2

Submitted by wabrandsma
wabrandsma (2551008) writes "From the Guardian:

A Johns Hopkins computer science professor blogs on the NSA and is asked to take it down.

A professor in the computer science department at Johns Hopkins, a leading American university, had written a post on his blog, hosted on the university's servers, focused on his area of expertise, which is cryptography. The post was highly critical of the government, specifically the National Security Agency, whose reckless behavior in attacking online security astonished him.

On Monday, he gets a note from the acting dean of the engineering school asking him to take the post down and stop using the NSA logo as clip art in his posts. The email also informs him that if he resists he will need a lawyer.

Why would an academic dean cave under pressure and send the takedown request without careful review, which would have easily discovered, for example, that the classified documents to which the blog post linked were widely available in the public domain?"

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+ - Windows 8.1 Review: New Version, Same Mess

Submitted by snydeq
snydeq (1272828) writes "If you're stuck with Windows 8, the Windows 8.1 upgrade is a no-brainer, but the fundamental flaws remain, writes Woody Leonhard in his in-depth review of the latest version of Windows 8. 'Windows 8.1 follows Windows 8 in typical Microsoft "version 2.0" fashion, changing a bit of eye candy and dangling several worthwhile improvements — but hardly solving the underlying problem. Touch-loving tablet users are still saddled with a touch-hostile Windows desktop, while point-and-clickers who live and breathe the Windows desktop still can't make Metro go away,' Leonhard writes. 'Windows 8.1 also installs the worst privacy-busting feature Windows has ever seen, and it nukes several key Windows 7 features in its headlong pursuit of SkyDrive profits.'"

+ - An Equifax For Security Risk? -> 1

Submitted by chicksdaddy
chicksdaddy (814965) writes "A Boston-area startup, BitSight, has announced what they say is the first objective security risk rating system that can be used to determine how (relatively) hackable your company is.

BitSight wants to serve the same role with security risk as the “Big Three” credit rating agencies (Standard & Poor’s, Moody’s, and Fitch Group) or consumer rating firms like Experian and TransUnion, which evaluate the credit worthiness of individuals. (BitSight even appears to use the same 800-point scale favored by Experian, TransUnion and the other credit rating agencies).

The company recently secured a $24 million Series A funding round (http://www.bitsighttech.com/news/press/060513-bitsight-technologies-secures-24-million-series-A-financing) after emerging from NSF-sponsored research by co-founders Stephen Boyer and Nagarjuna Venna. (http://blogs.wsj.com/venturecapital/2013/06/05/youth-and-age-mix-at-bitsight/)

BitSight Partner SecurityRating, announced on Tuesday, is a cloud based service that offers realtime ratings of organizations’ security risk based on what it calls “externally visible network behavior." In the consumer credit space, that might be new lines of credit, or a late payment to an existing lender. In security risk, it could be the presence of stolen data on a cyber criminal group’s “drop site” – a likely indicator of compromise. Systems attached to corporate domains that participate in a botnet or distributed denial of service attack (DDoS) could also bring an organization’s risk rating down."

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+ - How to Turn Your Pile of Code into an Open Source Project

Submitted by Esther Schindler
Esther Schindler (16185) writes "You’ve written some code, you think it would be useful to the world, and you’d like to give back to the open source world. But how do you do it? Andy Lester provides a checksheet for developers for how to release an open source project and get it noticed. For instance: Before you release the project to the wild, write some documentation, create a mailing list, create an issue tracker, and so on. You think he's missing anything?"

+ - Beijing Says That 400 Million Chinese Cannot Speak Mandarin->

Submitted by dryriver
dryriver (1010635) writes "China's Education Ministry says that about 400 million people — or 30% of the population — cannot speak the country's national language. Of the 70% of the population who can speak Mandarin, many do not do it well enough, a ministry spokeswoman told Xinhua news agency on Thursday. The admission from officials came as the government launched another push for linguistic unity in China. China is home to thousands of dialects and several minority languages. These include Cantonese and Hokkien, which enjoy strong regional support. Mandarin — formally called Putonghua in China, meaning "common tongue" — is one of the most widely-spoken languages in the world. The Education Ministry spokeswoman said the push would be focusing on the countryside and areas with ethnic minorities. For decades, the ruling Communist Party has promoted Mandarin in an attempt to unite the most populous nation in the world. But government efforts have been hampered by the sheer size of the country and a lack of investment in education, particularly the rural areas, says the BBC's Martin Patience in Beijing."
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Hardware

+ - Cheaper, more powerful alternative to FPGAs-> 2

Submitted by
holy_calamity
holy_calamity writes "Technology Review takes a look at a competitor to FPGAs claimed to be significantly faster and cheaper. Startup Tabula recently picked up another $108m in funding and says their chips make it economic to ship products with reconfigurable hardware, enabling novel upgrade strategies that include hardware as well as software."
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Businesses

+ - Cisco Killed A Wi-Fi Enabled Flip-> 1

Submitted by
jfruhlinger
jfruhlinger writes "When Cisco killed the Flip earlier this week, a lot of tech commentators reacted with sadness. The video camera line might have seemed a bit out of date in the world of video-enabled smartphones, but they were much loved devices. And now word is filtering out that Flip had a Wi-Fi-enabled Flip camera, which may have had live Internet broadcasting capabilities, ready to be released at the moment when the decision to shut down the division was made."
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Games

The Psychology of Achievement In Playing Games 80

Posted by Soulskill
from the no-you-don't-get-points-for-reading-this dept.
A post on Pixel Poppers looks at the psychological underpinnings of the types of challenges offered by different game genres, and the effect those challenges have on determining which players find the games entertaining. Quoting: "To progress in an action game, the player has to improve, which is by no means guaranteed — but to progress in an RPG, the characters have to improve, which is inevitable. ... It turns out there are two different ways people respond to challenges. Some people see them as opportunities to perform — to demonstrate their talent or intellect. Others see them as opportunities to master — to improve their skill or knowledge. Say you take a person with a performance orientation ('Paul') and a person with a mastery orientation ('Matt'). Give them each an easy puzzle, and they will both do well. Paul will complete it quickly and smile proudly at how well he performed. Matt will complete it quickly and be satisfied that he has mastered the skill involved. Now give them each a difficult puzzle. Paul will jump in gamely, but it will soon become clear he cannot overcome it as impressively as he did the last one. The opportunity to show off has disappeared, and Paul will lose interest and give up. Matt, on the other hand, when stymied, will push harder. His early failure means there's still something to be learned here, and he will persevere until he does so and solves the puzzle."

Logic is a systematic method of coming to the wrong conclusion with confidence.

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