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Book Excerpt: 'The Passage'
Justin Cronin's best-selling book "The Passage" takes place in a post-apocalyptic future. A U.S. government experiment in prolonging life goes horribly wrong, letting loose twelve vampires, or "virals" on the world. A hundred years later, there are a handful of human survivors, and their only hope is a little girl who was also part of the experiment. "The Passage" was inspired by Justin Cronin's nine year old daughter who helped her dad write the book, excerpted below.
Note: There's language in the excerpt that some may find offensive.
Related: How was vampire imagery used to demonize Mormons?
Wolgast had been to the Compound only once, the previous summer, to meet with Colonel Sykes. Not a job interview, exactly; it had been made clear to Wolgast that the assignment was his if he wanted it. A pair of soldiers drove him in a van with blacked out windows, but Wolgast could tell they were taking him west from Denver, into the mountains. The drive took six hours, and by the time they pulled into the Compound, he'd actually managed to fall asleep. He stepped from the van into the bright sunshine of a summer afternoon. He stretched and looked around. From the topography, he'd have guessed he was somewhere around Telluride. It could have been further north. The air felt thin and clean in his lungs; he felt the dull throb of a high-altitude headache at the top of his skull.
He was met in the parking lot by a civilian, a compact man dressed in jeans and a khaki shirt rolled at the sleeves, a pair of old-fashioned aviators perched on his wide, faintly bulbous nose. This was Richards.
"Hope the ride wasn't too bad," Richards said as they shook hands. Up close Wolgast saw that Richards' cheeks were pockmarked with old acne scars. "We're pretty high up here. If you're not used to it, you'll want to take it easy."
Richards escorted Wolgast across the parking area to a building he called the Chalet, which was exactly what it sounded like: a large Tudor structure, three stories tall, with the exposed timbers of an old-fashioned sportsman's lodge. The mountains had once been full of these places, Wolgast knew, hulking relics from an era before time-share condos and modern resorts. The building faced an open lawn, and beyond, at a hundred yards or so, a cluster of more workaday structures: cinderblock barracks, a half-dozen military inflatables, a low-slung building that resembled a roadside motel. Military vehicles, Humvees and smaller jeeps and five ton trucks, were moving up and down the drive; in the center of the lawn, a group of men with broad chests and trim haircuts, naked to the waist, were sunning themselves on lawn chairs.
Stepping into the Chalet, Wolgast had the disorienting sensation of peeking behind a movie set; the place had been gutted to the studs, its original architecture replaced by the neutral textures of a modern office building: gray carpeting, institutional lighting, acoustic tile drop ceilings. He might have been in a dentist's office, or the high-rise off the freeway where he met his accountant once a year to do his taxes. They stopped at the front desk, where Richards asked him to turn over his handheld and his weapon, which he passed to the guard, a kid in cammos, who tagged them. There was an elevator, but Richards walked past it and led Wolgast down a narrow hallway to a heavy metal door that opened on a flight of stairs. They ascended to the second floor, and made their way down another non-descript hallway to Sykes' office.
Sykes rose from behind his desk as they entered: a tall, well-built man in uniform, his chest spangled with the various bars and little bits of color that Wolgast had never understood. His office was neat as a pin, its arrangement of objects, right down to the framed photos on his desk, giving the impression of having been placed for maximum efficiency. Resting in the center of the desk was a single manila folder, fat with folded paper. Wolgast knew it was almost certainly his personnel file, or some version of it.
They shook hands and Sykes offered him coffee, which Wolgast accepted. He wasn't drowsy but the caffeine, he knew, would help the headache.
"Sorry about the bullshit with the van," Sykes said, and waved him to a chair. "That's just how we do things."
A soldier brought in the coffee, a plastic carafe and two china cups on a tray. Richards remained standing behind Sykes' desk, his back to the broad windows that looked out on the woodlands that ringed the Compound. Sykes explained what he wanted Wolgast to do. It was all quite straight forward, he said, and by now Wolgast knew the basics. The Army needed between ten and twenty death-row inmates to serve in the third-stage trials of an experimental drug therapy, codenamed Project Noah. In exchange for their consent, these men would have their sentences commuted to life without parole. It would be Wolgast's job to obtain the signatures of these men, nothing more. Everything had been legally vetted, but because the project was a matter of national security, all of these men would be declared legally dead. Thereafter, they would spend the rest of their lives in the care of the federal penal system, a white-collar prison camp, under assumed identities. The men would be chosen based upon a number of factors, but all would be men between the ages of twenty and thirty-five with no living first-degree relatives. Wolgast would report directly to Sykes; he'd have no other contact, though he'd remain, technically, in the employment of the Bureau.
"Do I have to pick them?" Wolgast asked.
Sykes shook his head. "That's our job. You'll get your orders from me. All you have to do is get their consent. Once they're signed on, the Army will take it from there. They'll be moved to the nearest federal lock-up, then we'll transport them here."
Wolgast thought a moment. "Colonel, I have to ask--"
"What we're doing?" He seemed, at that moment, to permit himself an almost human-looking smile.
Wolgast nodded. "I understand I can't be very specific. But I'm going to be asking them to sign over their whole lives. I have to tell them something."
Sykes exchanged a look with Richards, who shrugged. "I'll leave you now," Richards said, and nodded at Wolgast. "Agent."
When Richards had left, Sykes leaned back in his chair. "I'm not a biochemist, agent. You'll have to be satisfied with the layman's version. Here's the background, at least the part I can tell you. About ten years ago, the CDC got a call from a doctor in La Paz. He had four patients, all Americans, who had come down with what looked like Hantavirus – high fever, vomiting, muscle pain, headache, hypoxemia. The four of them had been part of an eco-tour, deep in the jungle. They claimed that they were part of a group of fourteen but had gotten separated from the others and had been wandering in the jungle for weeks. It was sheer luck that they'd stumbled onto a remote trading post run by a bunch of Franciscan friars, who arranged their transport to La Paz. Now, Hanta isn't the common cold, but it's not exactly rare, either, so none of this would have been more than a blip on the CDC's radar if not for one thing. All of them were terminal cancer patients. The tour was organized by an organization called 'Last Wish.' You've heard of them?"
Wolgast nodded. "I thought they just took people skydiving, things like that."
"That's what I thought, too. But apparently not. Of the four, one had an inoperable brain tumor, two had acute lymphocytic leukemia, and the fourth had ovarian cancer. And every single one of them became well. Not just the Hanta, or whatever it was. No cancer. Not a trace."
Wolgast felt lost. "I don't get it."
Sykes sipped his coffee. "Well, neither did anyone at the CDC. But something had happened, some interaction between their immune systems and something, most likely viral, that they'd been exposed to in the jungle. Something they ate? The water they drank? No one could figure it out. They couldn't even say exactly where they'd been." He leaned forward over his desk. "Do you know what the thymus gland is?"
Wolgast shook his head.
Sykes pointed at his chest, just above the breastbone. "Little thing in here, between the sternum and the trachea, about the size of an acorn. In most people, it's atrophied completely by puberty, and you could go your whole life not knowing you had one, unless it was diseased. Nobody really knows what it does, or at least they didn't, until they ran scans on these four patients. The thymus had somehow turned itself back on. More than back on: it had enlarged to three times its usual size. It looked like a malignancy but it wasn't. And their immune systems had gone into overdrive. A hugely accelerated rate of cellular regeneration. And there were other benefits. Remember these were cancer patients, all over fifty. It was like they were teenagers again. Smell, hearing, vision, skin tone, lung volume, physical strength and endurance, even sexual function. One of the men actually grew back a full head of hair."
"A virus did this?'
Sykes nodded. "Like I said, this is the layman's version. But I've got people downstairs who think that's exactly what happened. Some of them have degrees in subjects I can't even spell. They talk to me like I'm a child, and they're not wrong."
"What happened to them? The four patients."
Sykes leaned back in his chair, his face darkening a little.
Excerpted from The Passage by Justin Cronin Copyright © 2010 by Justin Cronin. Excerpted by permission of Ballantine Group, a division of Random House, Inc. All rights reserved. No part of this excerpt may be reproduced or reprinted without permission in writing from the publisher.
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A Little Shakespearean Nerdery
Hello all. Long time, no blog. In case you're interested, and I can't imagine that most of you are, here's my final project for my summer Shakespeare class. The paper is lengthy, but it comes with killer tunes. I suggest … Continue reading
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Armour: NFL haunted by past sins with another lawsuit
Even with all its power and success, the NFL can't escape the sins of its past.
A group of retired players sued the NFL on Tuesday, claiming the league gave them powerful pain killers and anti-inflammatories to keep them on the field, never warning them about the long-term dangers to their health. This as the NFL is still trying to persuade a federal judge to accept a $765 million settlement with another group of former players, who claimed the league hid or ignored the devastating effects of concussions and other head trauma.
"It does seem to reflect a trend, for a period of time, of recklessness on the part of the NFL," said Stanford law professor Bill Gould, the former chair of the National Labor Relations Board. "This litigation, if the complaint is accurate, would reflect very much the same kind of reckless or cavalier attitude toward player safety that seemed to be present the concussion lawsuit."
And it's the one thing that could bring ruin to the NFL.
"We're seeing a change in attitude about the costs that it's fair to impose on players for playing professional (sports)," said David Orentlicher, a lawyer and physician who is co-director of the Hall Center for Law and Health at Indiana University's Robert H. McKinney School of Law.
"It's not uncommon these days to hear parents say, 'My kid's not playing football.' So I think that's the larger question. Is this going to snowball in a way that people are going to start turning their attention to other sports?"
Because the latest lawsuit is in its early stages, it's too soon to say what its prospects for success are or how costly it could be to the NFL. The league hasn't seen the lawsuit yet, spokesman Greg Aiello said, and its attorneys haven't had an opportunity to review it.
There are the horror stories told by the eight plaintiffs, three of whom were Super Bowl champions with the 1985 Chicago Bears: Hall of Fame defensive end Richard Dent, Jim McMahon and Keith Van Horne. And there are enough similarities to claims made in the concussion lawsuit to warrant a closer look.
The eight players– attorneys have asked for class-action status, saying more than 500 former players are involved – paint a picture of a league that "recklessly and negligently created and maintained a culture of drug misuse, substituting players' health for profit."
Team doctors and trainers "were handing out drugs like it was Halloween candy," attorney Steve Silverman said, "to mask these injuries to get these guys out on the field, to their detriment." The list of narcotics, anti-inflammatories and local anesthetics reads like a pharmacy -- Toradol, Percocet, Vicodin, Ambien, Prednisone, Lidocaine – and the eight players estimate they were given "hundreds, if not thousands" of injections and pills over the years.
Not once were they warned about the potential dangers.
Jeremy Newberry, who played center for the three teams from 1998 to 2008, said he would get a shot of Toradol, an anti-inflammatory that can cause bleeding and renal failure, before a game, then get multiple injections of pain killers during the game. Afterward, he'd take Vicodin and Ambien. He now has Stage-3 renal failure.
McMahon, Dent and J.D. Hill, a wide receiver for the Buffalo Bills and Detroit Lions in the 1970s, all said they became addicted to painkillers. Hill's addiction got so bad it left him homeless, and he was in and out of treatment centers for more than 20 years before he finally got clean.
But it wasn't just the drugs. The players say there was a general disregard for their health. McMahon only learned two or three years ago that he'd broken his neck during his career. Van Horne, an offensive tackle, said he played an entire season on a broken leg. Not only was he not told for five years, he was "fed a constant diet of pills to deal with the pain."
"This is a lose-lose situation for the NFL," Gould said. "Just the focus of attention on this general subject of player safety and the reckless abandon that's associated with NFL play, it can do them no good."
This won't be as easy a case as the concussion lawsuit. Yes, the dangers of drugs were clearer and known earlier than that of concussions. But there is something about a person's diminishing memory — their very being — that engenders sympathy like nothing else.
There's also the notion that players should have known better with such a violent game. Sure, NFL players are going to have aches and pains. That comes with being an athlete. But the days of these guys being seen as bionic gladiators died with Junior Seau.
These are men with families and futures, and their lives shouldn't be cut short in the name of entertainment.
Follow Nancy Armour on Twitter @nrarmour.


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Tech stocks: The new safe havens?February 6, 2014: 1:27 PM ET
The opinions expressed in this commentary are solely those of Paul R. La Monica. Other than Time Warner, the parent of CNNMoney, Abbott Laboratories and AbbVie, La Monica does not own positions in any individual stocks.
Even though stocks are enjoying a nice little rally today, green on the screen has been the exception rather than the rule in 2014. The Dow is still down about 6% so far this year.
But as my colleague Stephen Gandel from Fortune pointed out Wednesday, tech stocks have held up better during the recent tumult. The Nasdaq is down just 3%. CNNMoney's new Tech 30 index has also outperformed the broader market. It's off by only 2.7%.
It may seem a bit odd that tech stocks are not getting crushed more than the overall market. After all, the Nasdaq was the top index in 2013. It surged 38%, compared with a 26% gain for the Dow and 30% pop for the S&P 500.
Related: Investors should stop freaking out
Still, it makes sense that techs are now safe havens. Or at least some of them. Why? Earnings. Plain and simple.
Look at the stocks that are actually up sharply this year. You'll notice that many of them are tech companies that have reported solid results.
Juniper Networks (JNPR) and F5 Networks (FFIV), two competitors to Cisco (CSCO), are the fourth and fifth top gainers in the S&P 500 this year. Each stock is up more than 15% so far. And both companies reported earnings last month that topped forecasts.
Content delivery network company Akamai (AKAM) is the third-best performer in the S&P 500, up nearly 20%. And nearly all of that move came on Thursday, after Akamai blew away forecasts for earnings and revenue and gave bullish guidance.
Before the solid results, investors had been worrying that Apple (AAPL) was planning to build its own CDN to compete with Akamai. But this earnings report seems to put those fears to rest. For now.
Video game developer Electronic Arts (EA) is the seventh-best gainer in the S&P 500 this year. The Madden maker also posted earnings that beat estimates. And Facebook (FB) is the ninth-best performing stock in the S&P 500, up nearly 15%. It's no secret why. Facebook's growth in mobile users and ad revenue was phenomenal.
Related: No Terrible Twos for Facebook stock
Both of those companies are in CNNMoney's Tech 30. Two other standouts in our index that are up this year thanks to strong financial results are Netflix (NFLX) and Google (GOOG).
This all goes to show that investors shouldn't always obsess about the macro picture. Sure, emerging market fears and worries about the U.S. economy may be dragging down the market broadly.
But concerns about the Fragile Five don't appear to be having any impact on advertising growth at Facebook. I doubt that anyone canceled their Netflix streaming subscription because of this week's tepid ISM manufacturing number ... especially with season 2 of "House of Cards" just eight days away!
In this passively managed ETF world we live in, investors often forget that the market is a collection of individual stocks. And guess what? There is still value in doing fundamental analysis.
Of course, there are risks to stock-picking. Twitter (TWTR) fans aren't too pleased after its outlook underwhelmed.
And other stocks in the Tech 30 that have lagged the market this year also have had either disappointing earnings or weak guidance, most notably ARM Holdings (ARMH), Amazon (AMZN) and Yahoo (YHOO).
Related: Slower smartphone growth hits ARM sales ... and stock
Trying to identify winners and losers is not easy. You have to do your homework. Valuation matters too.
It's simpler to just plop some money down in the SPY, QQQ or other ETFs ... like GLD perhaps? Gold, after all, has outperformed stocks this year!
But maybe that's a column for next week.
Reader Comment of the Week ... pour it in my hand for a dime! I tweeted on Wednesday about how a sales miss at Buffalo Wild Wings (BWLD) had investors crying fowl. (Sorry!)
One reader brought to mind a hilarious scene from the late 80s parody classic "I'm Gonna Git You Sucka." The scene featured a then-relatively unknown comic by the name of Chris Rock. I'd embed the clip. But there is an F-bomb. And this is still a family column.
You got change for a hundred? Congratulations, LifeSciencesMkt! (What is your real name, pray tell?) This is your second RCOTW win already this year. Does
@BostonBroker33 have some competition for first-ballot induction in the Buzz Reader Hall of Fame?


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Thanks to everyone who came out to the January food swap, which will took place on January 12 and was hosted by Mac & Cheese Productions. Everyone enjoyed this smaller, more intimate event and the offerings were as amazing as usual! Huge thanks to our generous gift bag sponsors, Argo Tea, Cabot Creamery and the Savory Spice Shop. Everyone was blown away by the great swag! Congratulations to Maddie and Mike who took home the raffle prize, a Ball FreshTECH Automatic Jam and Jelly Maker.
Emily will be distributing recipes from the swap to all attendees next week. If you attended the January swap and would like to have your recipe included, please email it to Emily as soon as possible. To read more about the January swap, be sure to check out the recap on swapper Kelly's blog.
Argo Tea, a Chicago-based company that sells delicious teas and healthy food, recently supported the Chicago Food Swap with a contribution to the gift bags for the January swap. Right now, Emily is partnering with Argo Tea on her blog, West of the Loop, to give away two $50 Argo Tea gift certificates. Just leave a comment on the post to enter. In addition, you can find a coupon for a free oatmeal with purchase of a signature drink at any Argo Tea cafe. That's a great offer! Be sure to check it out and show some love for our sponsors.
Upcoming Events:
- Sunday January 19 at 2 pm -- the Northshore Chicago Food Swap will be holding their second swap in Evanston. Perfect for those located on the North Shore or who missed the January 12 swap! You can register here.
- Saturday February 8 at 2 pm -- Registration is now open for the next Chicago Food Swap which will take place at 2 pm on February 8 at All Natural Chicago Catering. All Natural Chicago is a new local catering company that specializes in healthy and flavorful cuisine. All Natural Chicago provides breakfasts and lunches for corporate gatherings as well as parties and other special events. Owners Tess and Micky are very excited to welcome our group to their cool loft space. The February 8 swap is 2/3 full, so do not wait to register! As always, we will keep a waitlist once all the spots are full.


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Persistent depressive disorder is a type of affective disorder. It is also called mood disorder. It often resembles a less severe, yet more chronic form of major (clinical) depression. It was previously referred to as dysthymia or dysthymic disorder. However, people with persistent depressive disorder may also experience major depressive episodes at times.
Depression is a mood disorder that involves a child's body, mood, and thoughts. It can affect and disrupt eating, sleeping, or thinking patterns. It is not the same as being unhappy or in a "blue" mood. It is also not a sign of personal weakness or a condition that can be willed or wished away. Children with a depressive illness cannot merely "pull themselves together" and get better. Treatment is often necessary and many times crucial to recovery.
There are 3 primary types of depression, including:
Major depression (clinical depression)
Bipolar disorder (manic depression)
Persistent depressive disorder (dysthymia)
Persistent depressive disorder occurs in about 11% of 13- to 18-year-olds.
The following are the most common symptoms of persistent depressive disorder. However, each adolescent may experience symptoms differently. Symptoms may include:
Persistent feelings of sadness
Feeling hopeless or helpless
Having low self-esteem
Feeling inadequate
Excessive guilt
Feelings of wanting to die
Difficulty with relationships
Sleep disturbances (like insomnia or hypersomnia)
Changes in appetite or weight
Decreased energy
Difficulty concentrating
Irritability, hostility, aggression
A decrease in the ability to make decisions
Suicidal thoughts or attempts
Frequent physical complaints (like headache, stomachache, or fatigue)
Running away or threats of running away from home
Loss of interest in usual activities or activities once enjoyed
Hypersensitivity to failure or rejection
For a diagnosis of persistent depressive disorder to be made, a depressed or irritable mood must last for at least 1 year in children or adolescents. It must be accompanied by at least 2 other major depressive symptoms. The symptoms of persistent depressive disorder may resemble other medical problems or psychiatric conditions. Always talk with your adolescent's health care provider for a diagnosis.
Depression has been shown to often coexist with other psychiatric disorders, like substance abuse or anxiety disorders. Early diagnosis and treatment is crucial to the recovery of your adolescent.
A child psychiatrist or other mental health professional usually diagnoses persistent depressive disorder following a complete psychiatric evaluation. An evaluation of the adolescent's family, when possible, in addition to information provided by teachers and care providers may also be helpful in making a diagnosis.
Specific treatment for persistent depressive disorder will be decided by your adolescent's health care provider based on:
Your adolescent's age, overall health, and medical history
Extent of your adolescent's symptoms
Your adolescent's tolerance for specific medicines or therapies
Expectations for the course of the condition
Your opinion or preference
Mood disorders, including persistent depressive disorder, can often be effectively treated. Treatment should always be based on a complete evaluation of the adolescent and family. Treatment may include 1, or more, of the following:
Antidepressant medicines. These have been shown to be very effective in the treatment of depression in children and teens, especially when combined with psychotherapy.
Psychotherapy (most often cognitive-behavioral and/or interpersonal therapy) for the adolescent. This should focus on changing the adolescent's distorted views of himself or herself and the environment around him or her. It should also help him or her work through difficult relationships. Identifying stressors in the adolescent's environment and learning how to avoid them should be another goal of the adolescent's psychotherapy.
Family therapy
Consultation with the adolescent's school
Parents play a vital supportive role in any treatment process.
Persistent depressive disorder is associated with an increased risk for major depression if a child or adolescent does not receive appropriate treatment. Persistent depressive disorder also increases the risk for a child or adolescent to develop other mental health disorders. Appropriate treatment helps to reduce the severity of symptoms and the risk for relapse of another depressive episode.
Because episodes of persistent depressive disorder may last for longer than 5 years, long-term, continued treatment may help to prevent the depressive symptoms from returning.
Vidant Health can connect you to health care professionals to help you understand your condition and guide you through the treatment process. Let's chat.


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Phil Hughes, Twins agree to three-year deal, report says
The Minnesota Twins continue to address their desperate need for starting pitching.
The team has agreed to a three-year, $24 million with free-agent RHP Phil Hughes, according to the Minneapolis Star Tribune.
The deal, which is expected to be announced this week, would mark the second major contract handed out to a free agent pitcher by the Twins this offseason. RHP Ricky Nolasco and Minnesota agreed to terms on a four-year, $49 million deal Wednesday.
The Nolasco contract is the biggest deal ever given by the Twins to an outside free agent, and the Hughes deal would be the second biggest, the Star Tribune reports. It doesn't come without risk.
Hughes, 27, has spent his entire seven-year career with the New York Yankees. He struggled badly in 2013, going 4-14 with a 5.19 ERA and 1.455 WHIP. Much of the damage was done at Yankee Stadium, where he allowed 17 home runs and had a 6.32 ERA, so the Twins are betting a change of scenery to pitcher-friendly Target Field will help his effectiveness.
Hughes was an All-Star in 2010 when he went 18-8 with a 4.19 ERA and was shaping up as a building block for the Yankees' rotation. He was a former first-round draft pick and a once coveted young pitcher by many teams. Among them was the Twins, who had discussions with the Yankees about Hughes headlining a package for ace Johan Santana after the 2007 season.
The Yankees eventually pulled out of the talks, in part because of how highly they thought of Hughes, and the Twins sent Santana to the Mets.
But Hughes developed shoulder problems in 2011 that limited him to 17 starts and has been underwhelming the past two seasons while also dealing with back problems.
Overall, Hughes is 56-50 with a 4.54 ERA and a 1.322 WHIP.
According to the newspaper, the Twin also might re-sign RHP Mike Pelfrey, who went 5-13 with a 5.19 ERA in his first season back from Tommy John surgery.
The Associated Press contributed to this report.


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Scenes From Meatopia 2013, San Antonio, TX
This year, Meatopia eschewed its New York City roots and headed straight for Texas. Hungry masses and an impressive roster of chefs gathered in San Antonio on Sunday for Josh Ozersky's celebrated meat-centric festival.
It would be hard to argue against turning this year's location into the event's annual home base. As we've seen on more than one occasion, food festivals are fraught with peril in NYC, due to logistical challenges and the vagaries of inclement weather. Indeed, last year's Meatopia was the victim of a storm of biblical proportions. The one before that was hit with a massive heatwave. But in San Antonio, picture-perfect blue skies and 75° weather set the perfect stage for this year's orgy of meat.
Josh Ozersky outdid himself this time around, pulling together an impressive cadre of chefs and sponsors. The event was held at the Pearl Brewery; the adjacent Culinary Institute of America's kitchens served as the ideal staging and prep area. In total, 32 chefs from around the country cooked beef, veal, pork, lamb, and more, serving 'em up from nose to tail. But perhaps the biggest star was the city of San Antonio, which provided visitors with a warm welcome and an intoxicating exuberance.
Take a look throughout the slideshow to see highlights from the event »
All products linked here have been independently selected by our editors. We may earn a commission on purchases, as described in our affiliate policy.


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1. Manifest locations for web archivestommysdk Apr 16, 2011 3:39 PM (in response to tommysdk)
Recap on the discussions on the JIRA issue.
WebArchive war = ShrinkWrap.create(WebArchive.class, "test.war")
.addAsManifestResource("test-persistence.xml", "persistence.xml");
... will give the following output:
The question is how to handle web archive WEB-INF/ and WEB-INF/classes. E.g. Service provider registrations appear in /META-INF/services/ rather than in /WEB-INF/classes/META-INF/services/. There are many frameworks that requires that WEB-INF/classes/META-INF exists, e.g. persistence spec, JSF and service providers. Therefore it should be possible to add content to the /WEB-INF/classes/META-INF and /WEB-INF/classes/META-INF/services.
My proposal after looking into this is:
war.addAsManifestResource() -> /META-INF/ (keep as is)
war.addAsWebManifestResource() -> /WEB-INF/classes/META-INF/
war.addAsServiceProvider() -> /WEB-INF/classes/META-INF/services/ (instead of /META-INF/services)
war.setManifest() -> /META-INF/MANIFEST.MF
It would also make sense to provide a method that puts a MANIFEST.MF in WEB-INF/classes/META-INF/ just as the setManifest method:
war.setWebManifest() --> /WEB-INF/classes/META-INF/


text:
After 'Smash' crash, songwriters savor success
LOS ANGELES >> Marc Shaiman and Scott Wittman have strong opinions about the demise of "Smash," the highly anticipated but ultimately much maligned TV series about the making of Broadway musicals.
But to borrow from one of the duo's lyrics, they'd rather just smile and look back.
Not that there's been much time for reflection.
A month after the final "Smash" episode aired on NBC in late May, the Tony-winning Shaiman and Wittman ("Hairspray") added a new hit to their list of credits: They supplied songs to the stage adaptation of Roald Dahl's much-loved and twice film-adapted children's book, "Charlie and the Chocolate Factory." The musical opened in London to such strong ticket demand that the show's run was extended by six months, to the end of May 2014.
Then Shaiman and Wittman received more good news: an Emmy nomination for outstanding original music and lyrics for one of their "Smash" songs, the ballad "Hang the Moon."
"(It's great) that Scott and I get to represent 'Smash' with this nomination because it is now no longer," Shaiman said. "(But) there were millions of people who really were enjoying the show, or, certainly, certain parts of the show."
"Hang the Moon" imagines a musical meeting of Marilyn Monroe with her estranged mother, who expresses regret over leaving her daughter alone so often during childhood.
"We knew that Marilyn's mom was a film cutter," Shaiman said. "So we had this great concept where she said, 'If I could only re-edit our lives."'
Sitting at a piano in his Hollywood Hills recording studio, Shaiman sang the opening verse:
"If our lives were a movie/ I'd know what to do/ I'd write every scene with my heart/ An RKO picture that stars me and you/ And this time I'd learn my part."
Shaiman said he learned that "Smash" suffered from having too many cooks in the kitchen.
"And too many chefs all loved it," he said, soon to be cut off by the ringing of a phone.
"That's them, calling, saying, 'Stop talking about us!"' Shaiman joked.
As for "Charlie," Wittman confirmed the musical is bound for Broadway, but said its arrival will be delayed until director Sam Mendes completes the next James Bond movie.
The biggest challenge for the songwriters was meeting the expectations of fans of the previous takes on the novel. Fortunately, Shaiman said, the original Dahl text is "so full of wild, great, extravagant and emotional ideas that musicalizing the book was actually a walk in the park."
The Academy of Television Arts & Science's prime-time creative-arts ceremony will be held Sept. 15 in Los Angeles.
Shaiman predicted that he and Wittman won't be walking away with an Emmy, given the competition this year.
But little matter. If nothing else, "Hang the Moon" will always serve as the duo's pitch-perfect love letter to a smash that just wasn't meant to be. Shaiman played and sang it out:
"As the final reel ends/ We might both shed a tear/ For the ending is coming up soon/ But as the screen fades to black/ We can smile and look back/ And for you, darling, I'll hang the moon."


text:
Our SLIG guest blogger this week is Kory Meyerink, coordinator for Course 5: Research in the Midwestern United States.
Researching in the Midwest states is one of the most important areas to learn about when doing U.S. genealogy for several reasons. That's why the Midwest course has been one of the most popular courses in the history of the Salt Lake Institute of Genealogy. In fact, Midwest research is important even if you don't have research in the eight states included in this course!
That's a strong statement; can I back it up? Certainly. But first, let's identify the eight states covered in the 2012 Institute course: Ohio, Michigan, Indiana, Illinois, Wisconsin, Minnesota, Iowa and Missouri. Well, what's so special about those states? That list includes two of the most populous states in the nation (Ohio and Illinois) as well as an ethnic diversity that can't be found elsewhere in America. More immigrants settled in the Midwest than any other region in the country and, since all Americans are descended from immigrants, the discussion of immigration sources and strategies will pertain to all American research.
In addition the Midwest (especially Ohio and Missouri) is the gateway to the west. The vast majority of families who settled west of the Mississippi and Missouri rivers came through the Midwest and often lived there for several years. But, beyond that, the record collections and research strategies for Midwestern research pertain to almost all of the "western" states. Consider the following: Land records in the Midwest are all public domain lands, just as they are in the western states. Vital records in the Midwest set a pattern followed by most of the western states. The same is true of newspapers and other published records, including local histories and biographical sources. Their commercial success in the Midwest encouraged their development in the west, and even in the southern and eastern states.
But, it's not just about the west. Many of our ancestors lived in large cities all over the country, but the Midwest has the most. Once you've learned about research in Chicago, Detroit, St. Louis, Cincinnati, Cleveland, etc., then you'll be prepared for any other city, from New York to Atlanta to New Orleans. You see, it's not about specific localities, but rather research principles that pertain to the Midwest that apply elsewhere. Ports of arrival may not be in the Midwest, but we certainly will be discussing passenger lists because of the flood of immigrants to the Midwest. The same principles for research ethnic and religious records in the Midwest pertain to other U.S. research areas.
Paula Warren's discussions of research repositories and manuscript collections will open everyone's eyes and make you think about similar collections elsewhere in America. Yes, it's true. Midwestern research is a foundation for your successful research in the rest of the U.S. and even elsewhere (consider Canada, Ireland, Germany, England, etc.). It's also a favorite area for people taking the Accredited Genealogist exams, because so many potential clients have Midwest ancestry.
So, review the course listing for the Midwest course and sign up. We'll see you in January!
Visit the UGA website for more information about how to register for Course 5 (or any of our other offerings at the 2012 Salt Lake Institute of Genealogy).
If you enjoyed this article we invite you to share it via your favorite social networking media using the appropriate icon below. You may also reprint this article in any email or print newsletters you wish to distribute provided you include the date of original publication and the following text:
This article reprinted with permission of the Utah Genealogical Association. To learn more about the Utah Genealogical Association (UGA) or the Salt Lake Institute of Genealogy (SLIG), please visit their website at: ugagenealogy.org.


text:
How to pronounce Vikram Chandra: Vik (rhymes with sick)-rum, Chund-rah
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Bio::Gonzales::Project::Functions - organize your computational experiments
Inspired by A Quick Guide to Organizing Computational Biology Projects this module makes it easy to organise computational biology projects.
$ gonzp init human_genome
$ cd human_genome/analysis
$ gonzp analysis genome_assembly
$ cd genome_assembly
# set up scripts, Makefile, etc.
# ...
$ make human_genome_assembly
$ gonzp analysis genome_annotation # finds the project directory automatically
$ cd ../genome_annotation
# set up scripts, Makefile, etc.
# ...
$ make human_genome_annotation
Project Layout
Create it with
gonzp init <project_name>
A project consists of a root directory, containing everything, the paper-draft, analyses, 3rd-party documentation (and perhaps literature), scripts, etc. The whole system is based on Makefiles (to start the different analysis steps) and perl modules (surprise, surprise!!).
The documentation goes into the
README file, in whatever format (plain text, markdown, textile, ...) you prefer.
Thus, the basic layout is of an
example project is:
example/Makefile (a Makefile to start single analyses)
example/README (a overview documentation of the computational experiment)
example/analysis/ (all analyses go in here)
example/data/ (3rd-party data, such as the uniprot database or
experimental results, common to the whole computational
experiment go in here)
example/paper/ (the paper draft goes in here)
example/doc/ (3rd-party documentation)
example/lib/ (if some scripts or analyses have a lot in common,
creating a module/library might be helpful)
Create it with
gonzp analysis <analysis_name>
The analysis directory contains all analyses that have been done. One directory per analysis. The layout in
example/analysis is therefore:
./important_computational_experiment/Makefile (the Makefile to start single analysis steps)
./important_computational_experiment/av (the analysis version)
./important_computational_experiment/README (some analysis-specific documentation)
./important_computational_experiment/gonz.conf.yml (configuration stuff, e.g. file locations or parameters)
./important_computational_experiment/2014-01-28/ (the analysis directory derived from the version stored in "av")
./important_computational_experiment/data/ (analysis-specific data)
./important_computational_experiment/playground/ (here you can try stuff)
./important_computational_experiment/bin/ (a directory to store the scripts)
the analysis version
The analysis version is just a single string and defaults to the day the analysis was created. The contents of the
av file are e.g.:
$ cat important_computational_experiment/av
Cange it to whatever you want. A common use case is to change input data or parameters without clobbering the previous results. Therefore, change the analysis version to a different date and rerun the whole analysis.
The analysis version is integral part of Bio::Gonzales::Project::Functions and therefore accessible via
- The Makefile
- Via an exported function of Bio::Gonzales::Project::Functions, nfi($filename)
For example you want to calculate the average number of leaves for 4 plant accessions. You have 3 replicates, so 12 records:
Input data
accession num_leaves ACC_001 3 ACC_001 4 ACC_001 6 ACC_002 8 ACC_002 14 ACC_002 12 ACC_003 18 ACC_003 10 ACC_003 12 ACC_004 10 ACC_004 4 ACC_004 7
#!/usr/bin/env perl # created on 2014-01-28 use warnings; use strict; use 5.010; use Bio::Gonzales::Project::Functions; use List::Util qw(sum); # read in some raw data open my $fh, '<', 'data/leaves.txt' or die "Can't open filehandle: $!"; my %num_leaves; <$fh>; # get rid of the header while ( my $line = <$fh> ) { chomp $line; my ( $acc, $num_leaves ) = split /\t/, $line; push @{ $num_leaves{$acc} }, $num_leaves; } close $fh; # nfi = new file in the current analysis version directory # here the result file will be e.g. "2014-01-28/avg_num_leaves.tsv", depending on the analysis version my $result_file = nfi("avg_num_leaves.tsv"); # open the result file open my $result_fh, '>', $result_file or die "Can't open filehandle: $!"; # calculate the result and write it while ( my ( $acc, $leaves ) = each %num_leaves ) { my $sum = sum @$leaves; my $count = scalar @$leaves; my $avg = $sum / $count; say $result_fh join( "\t", $acc, $avg ); } close $result_fh;
- Via an exported variable of Bio::Gonzales::Project::Functions, $ANALYSIS_VERSION
The script changes slightly, see here the changed lines:
use Bio::Gonzales::Project::Functions; ... # nfi = new file in the current analysis version directory # here the result file will be e.g. "2014-01-28/avg_num_leaves.tsv", depending on the analysis version my $result_file = nfi("avg_num_leaves.tsv");
use Bio::Gonzales::Project::Functions qw(:DEFAULT $ANALYSIS_VERSION); # CHANGED ... # here the result file will be e.g. "2014-01-28/avg_num_leaves.tsv", depending on the analysis version my $result_file = "$ANALYSIS_VERSION/avg_num_leaves.tsv"; # CHANGED
The configuration is stored in
gonz.conf.yml and accessible via commandline and perl functions. The format of the configuration is YAML. You can therefore freely store any configuration in various data formats, such as lists or dictionaries.
Access via commandline
The access via commandline is intended to be used in the
Makefile. The commandline script is called
gonzconf. See
gonzconf --help
for help.
gonzconf looks for the
gonzconf.yml and extracts parts of the configuration. Example:
- genotype_1
- genotype_2
- genotype_3
Make target:
GENOTYPES=$(shell gonzconf --flat genotypes)
for g in $(GENOTYPES); do \
echo "analysing $$g"; \
Access in perl
In perl scripts the configuration can be accessed via the
gonzconf function.
- my $config = gonzconf()
Calling the function without arguments returns the complete configuration. It can be accessed as normal perl array or hash (depending on the configuration).
#!/usr/bin/env perl use warnings; use strict; use 5.010; use Bio::Gonzales::Project::Functions; my $config = gonzconf(); my @genotypes = @{$config->{genotypes}}; for my $genotype (@genotypes) { say "analysing genotype $genotype"; }
- my $config_entry = gonzconf($entry)
gonzconfcan take one argument to access entries of the top layer directly. By "top layer", gonzconf assumes that the structure of the configuration is organised as hash/dictionary.
#!/usr/bin/env perl use warnings; use strict; use 5.010; use Bio::Gonzales::Project::Functions; my @genotypes = @{gonzconf("genotypes")}; for my $genotype (@genotypes) { say "analysing genotype $genotype"; }
Bio::Gonzales::Project::Functions comes with logging included. The logged info is stored in
$ANALYSIS_VERSION/gonzlog. Therefore every analysis has a different log file. 5 log levels are available: debug, info, warn, error, fatal
Access via commandline
gonzlog <namespace> <message>
to log something. The log level is hardcoded to "info".
Access via perl
Bio::Gonzales::Project::Functions exports the function
gonzlog by default. To log stuff you run
# or
my $log = gonzlog();
The namespace is the filename of the invoking script.
jw bargsten,
<joachim.bargsten at wur.nl>
2 POD Errors
The following errors were encountered while parsing the POD:
- Around line 172:
'=item' outside of any '=over'
- Around line 195:
You forgot a '=back' before '=head2'


text:
Event Archive - Open Mic
Wed. September 4th 2013 - Wed. September 4th 2013 @ Ocean Island Lounge (All Ages)
8:00pm - 11pm
Event CategoriesMusic: Open Mic / Jam / Karaoke
One of Victoria's longest-running Open Mic nights. Whether you're a folk singer, spoken word artist, jazz trombonist, beat-boxer, noisemaker or anything else, we want you to show us what you got! The musical madness starts at 8pm.
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Open Mic
Fairly self explanatory. Jump up on stage and show your stuff! Contact promoter or venue # indicated for details more info