среда, 14 марта 2012 г.

You don't get it both ways

ERIC Pickles, our own MP, has finally confirmed what many of ushave long suspected: local government costs too much and is beingchoked by red tape. Not that it should come as a surprise; LouiseMcKinlay, leader of Brentwood council, has spoken on numerousoccasions about the importance of taking action to cut waste.Indeed, the Gazette itself has previously reported on how thecouncil has saved hundreds of thousands of pounds in the past yearalone, simply by working smarter.

The Coalition's line is simple.

When there is overlap, local authorities should look at sharingservices and personnel with neighbouring boroughs and other taxpayerfunded organisations. …

Saddam's Former Deputy Hanged in Iraq

BAGHDAD - The former deputy in Saddam Hussein's government was hanged before dawn Tuesday for the killings of 148 Shiites, an official with the prime minister's office said.

Taha Yassin Ramadan, who was Saddam's vice president when the regime was ousted four years ago, was the fourth man to be executed in the killings of 148 Shiites following a 1982 assassination attempt against the former leader in the city of Dujail.

The official, who witnessed the hanging but spoke on condition of anonymity because an official announcement had not been made, said precautions had been taken to prevent a repeat of what happened to Saddam's half brother Barzan Ibrahim, who was decapitated …

Rights group makes Kazakh media appeal

A prominent watchdog group has called on Kazakhstan's government to stop pursuing independent reporters with libel suits.

The Committee to Protect Journalists says six independent news outlets and their reporters were targeted by more than 60 defamation lawsuits last year in the former Soviet Central Asian state.

The group in a statement late Monday cited Kazakh …

Surprise! State can get dibs on `abandoned' mutuals

We had a great bull market for the past decade or so, and theinvestors who bought in at the bottom in 1981 and just held on havesome fabulous profits. Buy and hold was a good strategy for the1980s and a lot of mutual fund holders reaped the profits but decidednot to cash in their shares.

So imagine my surprise when I received a letter from one of mymutual funds, informing me that even though I had been re-investingmy dividends regularly and stashing the quarterly statements in myfile cabinet, I was at risk of losing my entire investment to thestate of Illinois.

That's right. According to Illinois law on abandoned property,any financial account that has not had …

The Cincinnati Reds have won the National League Central division title

CINCINNATI (AP) — The Cincinnati Reds have …

The State of Bioinformatics Kits

A toolkit is what to us, the users? It's that collection of software shortcuts that runs a biological idea through the processor. Familiar bioinformatics toolkits include Bio Java, BioPerl, BioPython, and BioRuby. Their corresponding languages -Java, Perl, Python, and Ruby- know no science. But a kit knows chem- and bio- or any informatic that presents its face. These languages are not language-like. They are stiffthey reveal an odd love of a standard and change, if at all, with lurching and heavy labor. The kit is what the language is not-a route to an answer through code that reduces and conceals the language. The kit is clay to the language's concrete.

There is some unknown relating the language and its kit Emit the name of the language "PHP" close to the screen of one of your more inflammable friends and watch in delight as a derision reaction ignites in fumes and sparks in his brain. But that thing creates the MediaWiki kit which begat Wikipedia, the Wiki that begat a thousand Wikis. Our most correct language, Java, composes Bio Java, but it is barbarous Perl that hacks out BioPerl, the kit that draws the most biologists to our fruitful addiction. Is that because PHP and Perl are, in their hearts, kits?

Claim to Fame

People working in and around open source notice that is frequently accomplished through heroism, preternatural efforts by the few on behalf of the many (or sometimes by and the few). The kit is their claim to fame, their playground and their gallery, their blue sky. They weave with words, pulling the bit-net tighter until it's all under their touch. So for that we thank the near-anonymous in this simple way: Sendu Bala and Chris Fields, of BioPerl, and Yaron Koren, from the Semantic Wiki world.

We are nothing if not disproportionate. We place each leaf in an ontology with care, but then these trees will dot the datascape, far from the massive data mounds. We decipher and notate the genomes but each in our own way, building detailed memorials to the DNA, with no roads between. Connecting all dots is not what we always do. We have created machines that write billions of nucleotides in a day, but will we leave meaning buried beneath? A million scintillants on their dark grids, times the number of phosphorylated flows. That times the number of precious samples and that times the highway, time. We're now like the astronomers with their fourth dimension, measuring genomes in evolution, meta-genomes over seasons, genomes over lifespans. We've hit supernumerary.

Open Source & Ownership

But when you do dig deep in sequence you may find a treasure. A highlight at the recent Advances in Genome Biology and Technology conference (see p. 8) was the talk by a studious Canadian, Marco Marra. Neuroblastoma is a rare cancer, but we all know it because of its frequency in children, the fatalities, and the severity of treatment. Marra and his group wanted the full mutational details of its transcriptome, from cells highly enriched for the tumor initiators, as close to the cold events as you can get But the expectation and the result were a profound mismatch. What they read was a list of changes in sequences with gene names that are only linked to B cell development, not neurons. The story of this disease is completely transformed by this surprise, the medicine will refocus on new therapies, and hopes of different outcomes.

Somehow if you can sift your haystack your way, you don't worry about the needles. It is not just craft but the feel of collective ownership that pushes open source, a deep wish to create extraordinary function that all will use. One current thought is that we may want to wrap a new present, the "Next Generation" toolkit

The Bio* toolkits were born when "single" was the norm: gene, interaction, protein, message, CPU. We will now create the 21st century kit, which will gyre vast hashes about their axes, all ids, terms, and data, cutting, intersecting and jetting off to methods to precisely annotate and detect Or will we? This next one looks less like a standalone codebase than a knitting together of R and BioConductor and Perl perhaps, or the BioLib project's libraries, a kit of kits.

Can we count you in? There is an ebb and a flow in open source, one worker rests, then you want another to feel the brilliance. The apps are there, the languages are there, we wait to wrap our next gift.

[Sidebar]

It is not just craft, but the feel of collective ownership that pushes open source, a deep wish to create function that all will use.

[Author Affiliation]

Brian Osborne is a Principle Investigator at TheBioTeam. He can be reached at briano @bioteam.net.

вторник, 13 марта 2012 г.

In Rafa, Roger meets the Man with The Iron Chin

PARIS (AP) — This time, it felt less like "au revoir" and more like farewell for Roger Federer.

What may have been the great man's last best chance to beat Rafael Nadal at the French Open has come and gone.

And so, some will say, and perhaps not outlandishly, have his best years.

The verdict from France's red clay was merciless, yet again.

As magnificent as Federer is, and he acquitted himself so sublimely at Roland Garros on Sunday that his magnificence must still be described in the present tense, his four lost French finals to Nadal are a blot — well, perhaps more of an inkspot — on the greatest career tennis has seen.

Correction. Make that greatest career seen so far.

Nadal is collecting Grand Slam titles at a pace that, if it continues, could see him eclipse Federer's high water mark of 16.

That, of course, is a lot of "ifs." Judging from his fine play here, Federer could still win yet more majors, with his sights already set on his own personal favorite, Wimbledon, next.

Other ifs are Nadal's knees and assorted joints. They've seized up in the past and, given the pounding he gives them, could always do so again. Plus, Nadal moaned at this tournament about how hard he grinds to stay at the top of tennis, saying the sport he believes should be a "passion" sometimes feels too much "like work."

That is not to say that the No. 1 is anywhere close to even thinking about easing up. But it takes a truly special player to match the gold standard of motivation that Federer has set since he bagged his first major in 2003.

And there's Novak Djokovic to consider, too. Even though Federer ended his 43-match winning streak in the semifinals here, he has muscled his way, permanently one feels, into the Roger-Rafa rivalry. Given his youth, the 24-year-old Serb could be Nadal's next big rival after Federer, who'll hit his 30s this August.

This final, like so many of the previous 24 Rafa-Roger matchups, should have been broadcast with a health warning: Caution, you will be glued to your set.

The 7-5, 7-6 (3), 5-7, 6-1 score didn't capture just how fluctuating and intense this contest was. A Federer backhand drop shot that plopped just wide of the line would have, had it gone in, given him the first set. It felt like a turning point, and it produced the kind of doubt that will become more inevitable with every passing year: Would that ball have landed inside the court during his younger years when Federer was practically unbeatable?

Maybe.

Similar questions were thrown up by his repeatedly wayward forehands. Federer of old perhaps wouldn't have let Nadal off the hook quite so often.

Which is one reason why this felt like Federer's best last chance against Nadal at Roland Garros, a tournament the Swiss has won just once, in 2009, when Nadal had already been sent home to some fishing in Mallorca.

Federer said Sunday he'll be back next year. But he won't be any younger.

Plus, Nadal showed signs of fragility at times during these two weeks in Paris, kicking himself on occasion for not playing to his own high, exacting standards. Federer, on the other hand, didn't lose a set until his impressive victory against Djokovic.

Nadal now has 10 majors.

Federer was 25 years, 173 days when he hit double digits.

Nadal got there 171 days faster.

Not a margin to write home about. But proof, nonetheless, that when Federer looks behind him, there's a looming Spanish shadow.

If Nadal was a boxer, he'd be billed as The Man with the Iron Chin.

Federer chucked the kitchen sink at him on Sunday. Still, he wouldn't go down.

Forehands that zipped off Federer's racket with a "pop," zany-angled backhands that looked to be scudding out of court: Nadal hunted almost everything down like a hound told to "Fetch!"

Often, he not only retrieves seemingly lost balls but somehow manages to whip them back with interest, too. So where one venomous crosscourt winner might suffice against lesser players, Federer needs two, three or more cannon balls to breach the chateau-like defenses of Nadal.

When it comes off, one can only sit back and applaud Federer's tenacity and ability to make such a succession of fine shots. If at first you don't succeed ...

Because he is forced to make plays, Federer had many more winners — 53 to 39 — than Nadal.

But by hurling his artistry back at him, Nadal also forced Federer into mistakes. Federer had twice as many unforced errors, 56 to 27.

In short, Nadal forced Federer to lose beautifully.

"I like to see him running left and right and left and right and see how long he can sustain it, you know?" Federer said. "Mixing it up. That's what I always do, and he does his things ... You know, I think he's happy to be Rafa; I'm happy to be Roger. That's why we like to play each other, maybe."

It's also why we like to watch them.

Appreciate it while it lasts.

___

John Leicester is an international sports columnist for The Associated Press. Write to him at jleicester(at)ap.org or http://twitter.com/johnleicester