Follow Slashdot blog updates by subscribing to our blog RSS feed


Forgot your password?
Slashdot Deals: Deal of the Day - 6 month subscription of Pandora One at 46% off. ×

Submission + - International challenge to computationally interpret protein function (

Shipud writes: We live in the post-genomic era, when DNA sequence data is growing exponentially. However, for most of the genes that we identify, we have no idea of their biological functions. They are like words in a foreign language, waiting to be deciphered. The Critical Assessment of Function Annotation, or CAFA, is a new community-wide experiment to assess the performance of the multitude of computational methods developed by research groups worldwide to help channel the flood of data from genome research to deduce the function of proteins.

Thirty research groups participated in the first CAFA, presenting a total of 54 algorithms. The results are published in an article in Nature Methods. The researchers participated in blind-test experiments in which they predicted the function of protein sequences for which the functions are already known but haven't yet been made publicly available. Independent assessors then judged their performance. The challenge organizers explain that: 'The accurate annotation of protein function is key to understanding life at the molecular level and has great biochemical and pharmaceutical implications, explain the study authors; however, with its inherent difficulty and expense, experimental characterization of function cannot scale up to accommodate the vast amount of sequence data already available.The computational annotation of protein function has therefore emerged as a problem at the forefront of computational and molecular biology.'

Submission + - APA: Free Research Violates Gov't Transparency Rul (

An anonymous reader writes: There's been a years-long debate going on over whether or not federally funded research should be accessible to the public. A few years back, the NIH started requiring that any of the research it funds be put in the free and open PubMed database one year after publication (still granting research journals one year to keep the research locked up). The Obama administration has been looking to expand that to all federally funded research. However journal publishers are notably upset about this, as they've been able to charge huge prices for subscriptions to their journals (on top of charging researchers to publish their work — and keeping the copyright — and getting free peer review labor) and they're afraid that their free ride may be ending. The latest attempt to stop this is to claim that requiring free access to federally funded research violates Obama's pledge for transparent government. Yes, making research accessible to more people is supposed to violate transparency rules. As you might expect, the reasoning behind this doesn't make much sense, and is debunked at that link.

Submission + - Android Leaves Iphone Behind (

adeft writes: Daily Tech's thoughts on why the Android OS has left the Iphone behind and some logical points as to how it can be remedied.

Submission + - Google Android Outsells Apple iPhone (

gollum123 writes: Smartphones based on Google’s Android mobile operating system have outsold Apple’s iPhone in the U.S. during the first quarter of 2010, according to a report by research firm The NPD Group. The data places Android, with 28 percent of the smartphone market, in second place behind RIM’s Blackberry smartphone market share of 36 percent. Apple now sits in third place with 21 percent. NPD points to a Verizon buy-one-get-one-free promotion for all of its smartphones as a major factor in the first quarter numbers. Verizon saw strong sales for the Motorola Droid and Droid Eris Android phones, as well as the Blackberry Curve, thanks to its promotional offer. Verizon launched a $100 million marketing campaign for the Droid when it hit the market in November 2009, which likely attributed to strong sales in the first quarter as well.

Comment Re:U.S. Air Force Sergeant, Not U.S. Army (Score 4, Insightful) 311

I agree with your point, but I have an issue with with this:

Can you fly a F15? How about a F22? Can you even fly a Cessna? Then what makes you qualified to even judge these pilots?

Wall street "quants" have changed the financial game without knowing finance. Many pro sports scouts were never good enough to play professionally, but are the best in the world at judging talent that they don't have. There are a billion examples that your opinion that only a pilot can judge a pilot is dead wrong. Most people trot out this type of argument when they want to forcefully shut down an argument that they are going to lose, so it has a "smell" of weakness when used.

BTW, if your reasoning was solid, then who would decide the best course of treatment for patient with severe brain injuries? Would we have to ask the few gorillas that know sign language how to treat gorillas? Would children decide what gets taught in school?

Comment Re:Can't be affecting all users (Score 0) 449

For what it's worth, does a forum post from January with a total of five people reporting a problem really deserve to be on Slashdot? Oh wait, it's anti-MS. Nevermind.

The argument that Slashdot is simply anti-MS is getting a bit old fashioned. I won't deny it, but come on, if the defragmentation utility does not play nice with the system restore utility, then clearly something is wrong.

Now I'm sure most Windows users on Slashdot don't really much care for the defragmentation utility, because why should a filesystem even fragment in the first place? That's stupid. And so they turn it off. But most people, like regular folk, they probably would want it on (because they've probably heard (wrongly) it provides them with more space), and so their restore utility won't work.

So the bug may not be 'extraordinary', but it is stupid. Is what.

Comment Thoughts about thoughts about flash (Score 1) 944

Steve Jobs has made his case against flash on the iPad. It's interesting, and I kept reminding myself about the presence of the well known reality distortion field that permeates his being.

As a programmer, and person, I hate reality distortion fields. This blog post is meant as an exercise in building skills to see through it.

First, the post was not just Steve, sitting in his office, jotting down a few notes. He's thought about it, long and hard, carefully avoiding certain areas that might cost him points, while pushing the strengths of his position. Lots of my stuff here is off the cuff, and might qualify as a jot... his definitely is not something quick and dirty.

First, there is "open", as Steve said. Just how do you send code to someone who owns an iPad? It appears to this observer that the way is definitely not open, but only goes through the Apple toll both. Open ports like USB would be nice too.

The there is the "full web"... Flash sucks because it's a layer between the web and the browser. It's a shim at best. However, it's the best shim out there for most cases. Allowing flash, with some disclaimers would be far better than denying the use of this shim.

Then there is security. If you can't protect your iPad from bugs in Flash, you certainly can't protect it from any other rogue applications either. It's just a matter of time before the holes start showing up. Steve - read up on Capability Based Security.

Battery life - good point. Hardware acceleration is good. It would be nice if I could replace the battery at some point as well.

Then there is Touch - If you don't allow cross compatibility, how are others going to figure out how to deal with touch? You'll always be a special case, and never mainstream.

Conclusion - Steve is good at distorting reality, but it's a near field effect with limited range.

Comment Re:I smell EVIL (Score 1) 174

Not to mention that HTC has been one of the only companies to stick with WinMo through it's recent years of decline through lack of development by MS.

They were also one of, or perhaps the most successful WinMo handset developer when it was going strong too.

Microsoft has a lot of interest in supporting HTC against Apple, even if HTC do continue to create Android handsets.

Comment Re:Pr0n! (Score 1) 280

[...] every time a 3 year old is found playing some porn app, the parent is going to be pissed at Apple.

Such parents should go f*ck themselves instead of blaming a piece of hardware for their failure at parenting.

Comment No bias there ... (Score 1) 216


Is this data comprehensive?


Many of those one-off requests may coincide with our own content policies, so when the numbers get small enough, they don’t necessarily reflect anything about the level of censorship in that country. Similarly, if a governmental agency used a web form to demand removal of content, we generally have no way of including those reports in our statistics.

Do you ever remove content that violates local law without a court order or government demand?

Yes. The statistics we report here do not include content removals that we regularly process every day across our products for violation of our content policies (for example, we do not permit hate speech in Blogger and other similar products) in response to user complaints. In many cases, those removals result in the takedown of material that violates local law, independent of any government demand or court order seeking such removal.

So basically, if the country agrees with Googles version of censorship, its okay ... but if it disagrees with Googles censorship, its not okay ...

I fail to see why exactly I'm supposed to be excited to trade one companies censorship for a countries censorship. In the end, the result will be the same, someone is still deciding who gets to see what, and that someone isn't me, so it doesn't matter who, what, when, where, or why ... Google is just as guilty of censoring as anyone else, by their own admission.

I'm rather happy to have certain things censored by Google. Censorship is not 'bad' just because. If you buy into this and think Google is good for it, you've just been manipulated by Google and a fair amount of your own ignorance. Good job, you're not officially a tool of the man.

Comment Re:Note the lack of mentioning all the other taxes (Score 1) 507

I'm confused. How can someone in Washington, with no presence in California, being taxed by California and responsible to California law, vote on that assembly you assert exists? The issue is interstate commerce where you'd be held to the laws of a location where you have absolutely zero legal presence. That's taxation without representation.
United States

Submission + - White House Plans Open Access for Research

Hugh Pickens writes: "Currently, the National Institutes of Health require that research funded by its grants be made available to the public online at no charge within 12 months of publication. Now the Office of Science and Technology Policy in the Executive Office of the President is launching a “Public Access Policy Forum” to determine whether this policy should be extended to other science agencies and, if so, how it should be implemented. "The NIH model has a variety of features that can be evaluated, and there are other ways to offer the public enhanced access to peer-reviewed scholarly publications," OSTP says in the request for information. "The best models may [be] influenced by agency mission, the culture and rate of scientific development of the discipline, funding to develop archival capabilities, and research funding mechanisms." The OSTP will conduct an interactive, online discussion that will focus on three major questions: Should this policy be extended to other science agencies and, if so, how it should be implemented? In what format should the data be submitted in order to make it easy to search and retrieve information? What are the best mechanisms to ensure compliance? "It's very encouraging to see the Obama Administration focus on ensuring public access to the results of taxpayer-funded research as a key way to maximize our collective investment in science," says Heather Joseph, executive director of the Scholarly Publishing and Academic Resources Coalition"

Comment Stand Out (Score 0) 186

My advice would be to set yourself apart as much as possible. There are just so many conferences out there, and so much competition for the scarce training budget funding, you need to do something to make yours stand out. Maybe you need to think about a niche market or a more targeted audience. If you pick a broad topic like "Java", you will be up against the big boys with the reputation and history to back it up.

I personally view my coveted conference as the time to get caught up on the "cutting edge". See what the newest research and development is. More importantly, to meet peers in my field and exchange battle notes. My advice: stand out and make it worth it to me.

Comment Re:That's totally wrong. (Score 1) 219

First off, most leaders of the left wing imagine a future where scarcity is the norm, largely because they see the consumption of natural resources by the West as unethical in a larger world view. In their eyes, Americans already have "too much" and therefor should have to make due with less. This faux-conservatism, coupled with the right wing's stupid devotion to "free trade", is the underlying cause of this current economic crisis.

America's economy isn't screwed up due to "free trade" nor due to leftarded concerns over consumption. It is a recession. If you haven't noticed in the history of our country we have been in and out of dozens of these. The economy goes up sometimes and down others, it always has, it always will. Yes, manufacturing will die off more and more. This isn't a problem, we are just becoming more and more of a service based economy.

Globalization doesn't mean that one nation will win and the other will lose, assuming that it does means you are making the same economic mistake that people have made since the days of Adam Smith, namely believing trade to be a zero sum game. If I buy a $30 table from China, it doesn't mean the Chinese economy gains $30 while the US economy loses $30, it means I gain a table I value more than my $30 dollars while the Chinese table maker gains $30 which they value more than their table. Both of us have gained something more valuable to us. The $30 wasn't lost value. Money is just a token of value, it isn't the inherent source of it. Money is just an easy way to exchange value for goods and services. It also isn't like the Chinese table maker will eat the $30, they will likely use it to buy stuff (labor, supplies, investments, etc.) and at some point there will be something the US makes that will be exchanged, and even if there isn't something every country is best at, comparative advantage will eventually work it's way in over time.

A failure will not appear until a unit has passed final inspection.