Archive for October, 2009
Google to launch online book store in 2010
October 19, 2009A match made in Silicon-Heaven?
October 8, 2009IBM Research jumps into genetic sequencing
October 6, 2009It took 13 years for researchers to catalog all the information in a human genome the first time. Now IBM believes it can do better–somewhat perversely by equipping a newer genetic sequencing method with brakes.
Big Blue is among those who believe electronics technology can be applied to the task of sequencing a person’s genes, thereby bringing genetic testing into the computing era and lowering its cost to something like $100 to $1,000.
IBM is working on prototype DNA-processing electronics that slurps strands of DNA through an extremely small hole called a nanopore, measuring the electrical properties of the chemicals as they go by to determine the genetic information. That technique is used beyond IBM, but what Big Blue researchers have been working on is a way to slow down, an essential step toward improving its precision, said Gustavo Stolovitzky/a>, manager of the IBM Functional Genomics and Systems Biology Group.
IBM Chief Executive Sam Palmisano is scheduled to unveil the project and what the company calls its “DNA transistor” Tuesday in a talk, “IT Innovation in Healthcare,” at the Cleveland Clinic, IBM said.
The ultimate goal for such research is affordable genetic sequencing. “It would allow DNA sequences to be more or less routine,” Stolovitzky said, forecasting that the technology will arrive in five or ten years.
OK, but why should you care?
“It would enable the possibility of going to the doctor with some infection, and the doctor gets the sequence pretty much on spot of the bacteria affecting the patient or the virus is in the blood,” Stolovitzky said.
Or another possibility: knowing patients’ specific genotypes could mean doctors would know if they had a negative reaction to some drug. That could mean some drugs useful that today are banned could become useful to a subset of the population.
IBM isn’t the only one working on this technology. In addition to various academic efforts, start-up 23andMe offers some genetic analysis today.
The genes of animals and plants are encoded in DNA with just four molecular-scale substances–adenine, thymine, guanine, and cytosine. Their particular order governs not only their the formation of humans and other organisms but also the day-to-day biochemistry that keeps us alive.
IBM’s sequencing technique to transcribe this biochemical data has been under way for three years, and it’s easier said than done. The company is in the process of creating a new prototype device updated to reflect what IBM learned from an earlier one that didn’t work as hoped.
“Translocation control we should have in a year’s time more or less,” Stolovitzky said, referring to the ability to ease the DNA through the nanopore one pair at a time.
The distance scales alone make the work difficult. Each DNA base is about 5 or 6 angstroms away from its neighbor–about half a billionth of a meter. By comparison, a human hair is colossal, about a ten-thousandth of a meter in diameter. And the DNA strands slip through a nanopore that’s 2 to 3 billionths of a meter wide.
One problem with the nanopore approach is that it’s hard to distinguish the four substances, called bases, as they slip through the hole. The four bases have overlapping electrical properties, so the more time spent measuring each, the better the accuracy.
Yahoo to shut down Xoopit for Gmail users
October 3, 2009Xoopit, which aggregates media files from users’ Gmail accounts, was acquired by Google rival Yahoo in late July and has since been integrated into the company’s own Web mail service.
Users of Xoopit will have until November 13 to grab any media from Yahoo’s servers, after which it will no longer be available. Doing this is necessary only for users who have deleted the source file from their Gmail account, as Xoopit simply copies over the media, leaving the version on Google’s servers intact. Yahoo will continue to hold on to all users’ data until next February to comply with its 90-day data retention policy, it said.
In Yahoo’s note, the company says one of the main reasons for the shutdown of Gmail compatibility is to enable the team to focus on making a better version of its product for Yahoo Mail, which only began working with the Xoopit service in December. It also said that discontinuing resources into tools designed to improve competing Web mail providers would leave Gmail users with a “lousy experience.”
Along with access to Xoopit, Yahoo is also discontinuing its Firefox add-on and Facebook integration for Gmail.
The browser add-on has let users view attachments and other media in their Gmail accounts as a file explorer–functionality that has since been replaced by some of Google’s Gmail Labs add-ons. Users with the browser add-on installed could also connect with Facebook to see and view status updates from within Gmail, a feature that will also become unavailable.
Linux in 2013: One *Billion* Dollars!
October 2, 2009It’s a rare day on the Linux blogs when comparisons don’t get made between Windows and our favorite operating system, but when those comparisons take the form of benchmarks, we can’t help but sit up and listen.
Sure enough, following a like comparison earlier this year, the bloggers over at TuxRadar recently put Windows 7, Vista and various versions of Ubuntu through their paces again to see just how they compare.
Bottom line? “There’s nothing in Windows 7 that Linux can’t do, and in most cases, do it better,” the TuxRadar bloggers wrote. “Our machines are quicker and more efficient. Our desktops are more innovative and less static. Our apps are more powerful, cheaper and less partisan, and Linux security has never been better.
“Best of all, we have complete control over the future of Linux, and its success or failure at the hands of Windows 7 is in our hands,” they added.
‘LINUX = Leave It Now Unless Xpert’
The reaction? Scores of comments on the TuxRadar site, covering all bases between the congratulatory and the outraged.
To wit: “I would have never thought I would read something like this in a Linux publication but you did a great job of comparing Windows 7 to Linux,” wrote Anonymous Penguin. “For me I am sticking to XP and Ubuntu, Fedora 11 and AntiX. These run my older hardware the best.”
Then again: “LINUX = Leave It Now Unless Xpert,” wrote another Anonymous Penguin. “WINDOWS = When IN Doubt Order Windows Seven.”
Not to mention: “I’ve seen more fair and balanced comparisons on Fox News,” added Blast Hardcheese.
‘No Linux Option Is Suitable on My Laptop’
The fact that “every current Linux distro fails to make 3-D and WiFi work together” makes it tough to take such benchmarks seriously, Dean noted.
“My problem might well be rooted in fglrx, but it’s entirely irrelevant since neither replacement of the hardware nor change in my use habits are viable options for me,” he said. “The simple fact of the matter is, no Linux option is suitable on my laptop today, and Windows 7 ‘just works,’ including 3-D and WiFi.”
Not only that, but “unlike Windows XP or Vista, it does so out of the box,” he asserted.
‘On the Server’
Linux will almost certainly end up a billion-dollar business “on the SERVER,” Slashdot blogger hairyfeet told LinuxInsider.
“On a server you have experienced admins who prefer a text-heavy CLI interface because it saves on resources that could be better used serving clients,” he explained. “That is why Windows server 2K8 comes with the ability to just run ‘core’ and have only that which you need most.”
That said, however, “I have found even my most Linux-happy server admin friends keep one or more Windows Domain Controllers on the network,” hairyfeet asserted. “Why? Because Linux has yet to come up with a ‘top-to-bottom full stack’ approach that touches AD+Exchange+Sharepoint+GPO for ease of use.”
‘It Is More Complex and More Work’
Linux gurus get “paid more for doing the same job because it is more complex and I would argue more work to get the same functionality from Linux that you get from Windows and the ‘full stack’ approach,” added hairyfeet.
“Hell, I could probably teach my 16-year-old in a month or so enough to admin a basic Windows domain setup,” he explained. “Everything is, set up in an easy to understand and visualize tree hierarchy, and there is even a nice wizard that will walk you through most of the basic tasks.”
The closest approximation in the Linux world is Xandros server, hairyfeet added, and “while it gets a lot of the way towards the Server+Exchange functionality, it isn’t nearly as good at GPO as a Winserver is. And I haven’t seen a ‘Sharepoint killer’ or an ‘Outlook killer’ yet come from the Linux world.”
‘The Better It Does, the Better I Do’
So, “while I have no doubt that pretty much all the web servers will end up firmly in the Linux domain, everything behind the firewall will most likely stay firmly rooted in Windows,” hairyfeet predicted. “Not only because there are still so many mission-critical apps that simply aren’t offered in Linux — from custom apps to CAD and graphics — but admining a Windows Server is just so much easier than doing the same job in the Linux camp.”
Either way, however, there’s no denying that increasing success for Linux means the same for those who work with it.
“I certainly hope Linux continues to do well,” Montreal consultant and Slashdot blogger Gerhard Mack told LinuxInsider. “Linux is my bread and butter, so the better it does, the better I do.”
For Further Details..