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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.

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

Submitted by Esther Schindler
Esther Schindler 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?

Submission + - Beijing Says That 400 Million Chinese Cannot Speak Mandarin (bbc.co.uk)

Submitted by dryriver
dryriver 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.
Hardware

Submission + - Cheaper, more powerful alternative to FPGAs (technologyreview.com) 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."
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."

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