Working Titles

What do the most industrious people on earth read for fun?

BY LESLIE T. CHANG

Most of the officials in Qinglin spend their days playing mah-jongg and getting drunk, but Hou Weidong is determined to make something of himself. He sweeps the work team’s office every day. He organizes villagers to build a new road. Although he is drunk a fair amount—that’s a given for anyone in government service—he usually makes it home before he passes out.

The mountains around the fictional town of Qinglin, in southwestern China, consist of especially hard rock. And so in the first novel of a multivolume series about the life of Hou Weidong the protagonist invests in a stone quarry, even though officials are banned from commercial ventures. His timing is perfect: the county names 1994 the Year of Transport Construction, and demand for stone soars. But getting paid is another matter; anybody doing business has to bribe the government finance department in order to get the money he is owed. Hou Weidong learns how to do this, just as he learns how to win contracts that have not yet been announced and how to pay off the police. His bank account grows to three hundred and thirty-seven times his yearly civil servant’s salary. He buys a pager and then a Motorola mobile phone; his house is the first in town to have air-conditioning.
Eventually, Hou Weidong is detained and questioned in a corruption investigation. But he does not inform on his official patrons. After his release, friends get him elected deputy township chief. He makes plans to marry his college sweetheart, whose parents have long opposed the match. They change their minds after visiting his new fourteen-hundred-square-foot apartment with two bathrooms—a climactic scene that ends the first volume of “The Diary of Government Official Hou Weidong”:

Xiaojia said, “Husband, the two of us finally have a house.”
Hou Weidong said, “This is our little nest. We will spend 100,000 yuan to renovate it properly.”
Xiaojia said, “We should buy a full set of home appliances, a VCD player, a 29-inch television set, an automatic washing machine, an air-conditioner, and a complete set of wooden floors.” And so the door to happiness opened.
What do the Chinese, some of the hardest-working people on the planet, read in their spare time? Novels about work. The seventh volume of “The Diary of Government Official Hou Weidong” was published last July, with an initial print run of two hundred thousand copies. An official-looking red stamp on their covers proclaims that the books are a “Must-Read for Government Employees,” but managers and entrepreneurs read them, too. Zhichang xiaoshuo, or workplace novels, have topped best-seller lists in recent years. “Du Lala’s Promotion Diary,” by a corporate executive writing under the pen name Li Ke, is the story of a young woman who rises from secretary to human-resources manager at a Fortune 500 company. It has inspired three sequels, a hit movie, and a thirty-two-part television series. The books have sold five million copies. In “The Get-Rich Diary of China’s Poorest Guy,” an unemployed man becomes a millionaire in three years by selling electric cable; the book’s editor attributes its success to a clever title, a flashy cover, and the fact that “getting rich is the dream of all Chinese people.”

Certain professions have their own subgenres. The “commercial warfare novel” pits sales teams against each other in mortal combat over a large order. The “financial novel” wrings drama from stock prices. The “novel of officialdom,” which dates to imperial times, trades in the secrets and scandals of the bureaucracy.

Like their protagonists, these books strive to be efficient and useful. They include rules for getting ahead in the workplace:

Socialize with rich people. They know more than the poor.

Avoid unpromising work assignments by feigning illness. Women should fake pregnancy when necessary.

If your boss makes a pass at you, smile and flirt back.

Hire subordinates who are barely adequate or they’ll make you look bad.

When bribing an official, have your business partner deliver the money so your hands stay clean.

“Du Lala’s Promotion Diary” contains a long disquisition on how to calculate the budget for an office renovation. Elsewhere, the author interrupts the narrative to explain what a non-compete agreement is. “The Get-Rich Diary” puts entrepreneurial tips in boldface: “It takes many incidents to establish a reputation and only one to ruin it,” and “Selling the same item in a different location may increase your profits.”

In America, writers might feel pressured to add romance and sex to a novel; in China they’re told to take it out. “Traps and Links,” a thriller about sales teams competing to win a $1.7-million computer-equipment contract, was edited to tone down a love interest. “When we first saw this book, we told the author, ‘We don’t want to publish a romance novel. Can you make it more of a financial novel?,’ “ Zhang Lihong, the chief editor of Tsinghua University Press, which published the book, told me. “We knew that’s what would make it sell better.” The book has sold almost four hundred thousand copies and inspired two sequels.
Most workplace novelists do not have a literary background: one was a pioneer in the securities industry, and another sold computers for Dell. They typically begin writing anonymously on the Internet and are signed by publishers after they gain an online following. “The Diary of Government Official Hou Weidong” is published under a pseudonym, and the book jacket identifies the author only as “a certain deputy bureau director in a certain city in a certain province.” But in late 2010 newspaper reporters outed a mid-level functionary named Zhang Bing. He worked in Yongchuan District, one of the countless regions administered by the sprawling city of Chongqing. The author of the Hou Weidong series, which has sold three million copies, was the deputy director of the Bureau of Environmental Sanitation.

Zhang Bing doesn’t smoke, doesn’t drink at lunch, and doesn’t praise the Communist Party. He is forty-one years old but, with his sturdy round face, crewcut, and keen black eyes, he resembles a schoolboy eager for trouble. He is like no Chinese official I’ve ever met. In literary circles, Zhang Bing is famous for earning royalties of two million yuan, almost three hundred thousand dollars. His day job is to oversee the disposal of the three hundred tons of garbage that Yongchuan District generates every day. He has a staff of twenty-two, a crew of six hundred trash collectors, and a fleet of trucks. “Our job is to collect garbage, transport garbage, and treat garbage. This is what I do,” Zhang Bing told me. “And at night I write.”

On a spring morning, I accompanied him on an inspection of the old city dump, whose surrounding area is a popular getaway for residents. The dump was closed three years ago, because, as Zhang Bing explained, it “did not suit the atmosphere of a leisure area.” The trash was buried under a long field that slopes down to a stone dam.

Old Zhao, the foreman of the site’s work crew, approached. Zhang Bing pointed to a patch of land below the dam. “I want to make sure no water seeps into the ground here,” he said.

“There won’t be much water,” Old Zhao assured him. “Don’t worry about that.”

Zhang Bing worried. “What if there’s a sudden rainstorm and twenty millimetres of rain falls? How much water will collect in this spot?”

Old Zhao did some quick mental arithmetic. A hundred cubic metres, he said.

“So I’d need ten trucks to get rid of all the wastewater. I want you to build another channel to drain off more of the water,” Zhang Bing said. Old Zhao nodded. “If you spend money now, you’ll spend less later,” Zhang Bing told him.

Like the hero of his books, Zhang Bing started out supervising road maintenance and family planning in the farming villages around Yongchuan. He joined the district’s forestry department in 2007 and began to write a novel the following year, anonymously posting chapters online. In the series’ ninth installment, Hou Weidong will become the Party secretary of a major city. As a district deputy bureau director, Zhang Bing is four grades below that in the civil service. “The series will end there,” he told me. “I don’t really understand the world above that, so if I keep writing it won’t be authentic.”

Zhang Bing has never considered quitting his job to write full time. The economics of publishing are poor: in China’s fragmented market, a successful book may sell ten thousand copies and pay five thousand dollars in royalties before taxes. “If you add up the income of the ten top-earning writers, it’s not as much as the profit an average building brings a developer in a third-tier city,” Zhang Bing, then No. 22 on the list, said in a newspaper interview. But his reluctance is also a question of generations. He was born during the Cultural Revolution, when a person’s fate could be determined by political whim. He came of age during Deng Xiaoping’s economic reforms, which brought opportunity but also opened up a gulf between winners and losers in a hyper-competitive economy.

I asked Zhang Bing if the series had a moral. “Maybe professional writers stand on higher ground and look at things from that vantage point,” he said. “But I write about very real, very practical things. I don’t write about theory. I just want to tell a story.”

The first success manuals to appear in China were American imports. In the late nineteen-eighties, some people abandoned their government jobs to start businesses of their own. Dale Carnegie’s “How to Win Friends and Influence People” (translated into Chinese as “The Weaknesses of Human Nature”) was popular, as was L. Ron Hubbard’s “Dianetics” (“Techniques for Psychological Adjustment”). Over the next two decades, though, many Chinese authors rejected the sunny self-actualization message of the American self-help movement. A favorite among factory workers was “Square and Round,” which preached how to get ahead through manipulation and deceit. “Do not show concern for others,” it advised. “It insults your self-respect and will only make other people look down on you.”
Competition in the workplace is a new experience. For decades, people inhabited familiar and stable settings—the village, the school, the work unit. A nationwide system that assigned jobs to all college graduates was abolished only in the late nineteen-nineties. A decade later, promoting oneself in meetings and interviews still feels unnatural; one person’s advancement means that everyone else is left behind. Workplace novels present white-collar jobs as a form of gladiatorial combat, because to most people that’s how it feels. In “Traps and Links,” which in 2006 inaugurated the commercial-warfare genre, the drama of duelling sales departments is treated as a fight to the death. “Sales is like war: in some cases it’s better to die on the battlefield than to suffer defeat,” Zhang Lihong, of Tsinghua University Press, told me. “I did not enjoy reading this book and couldn’t finish it,” she admitted. “It’s so brutal—people behave like animals! But it’s very authentic.” The novel is based on a true story in which all but one person in a company’s fifteen-member sales department were fired when a rival team won a computer contract.

This Darwinian view of the workplace is widespread. Yu Zhenghua, a professional investor, wrote a best-seller called “The Stock Picker.” In 1993, when the government opened the market to institutional investors, it organized a training program to teach executives at a few select firms how to handle the trades. Of the thirty-three people in that class, Yu Zhenghua is the only one who still works in finance. “Some have gone to jail, some have fled abroad, some have lost their faith and are now driving taxicabs,” he told me.

“Are those the only options?” I asked.

“Oh, and some have committed suicide.”

In the opening pages of “Du Lala’s Promotion Diary,” the heroine lands an entry-level job in the China office of an American telecommunications company. At first, Lala works hard and doesn’t complain. Then, realizing that her American bosses don’t value her at all, she takes charge of a seven-hundred-thousand-dollar office renovation. (In the literature of the Chinese workplace, renovation is an obsession akin to inheritance in the Victorian novel.) Afterward, she hectors her boss for a promotion:

She swallowed and said, “The project is finished. Will there be a bonus?”
“Our chairman hates when people talk of money. It’s not good to speak of money.” . . .
Lala said to herself: “If I don’t fight for myself, I can’t count on others to defend me.” She gathered up her courage and said, “Boss, can I have a raise?”
Modernity is the book’s true theme. Lala advances to management by learning how to promote herself, to speak up in meetings, to be pushy and friendly at the same time—in other words, to act like an American. She masters the corporate-speak of management consultants—SWOT analysis, SMART objectives. “Multinationals in China represent advanced ideas and systems,” Cai Mingfei, who edited the Du Lala books, told me. “If you understand these ideas, they can help you no matter what kind of place you work in.” While Americans try to learn from China’s economic rise, the Chinese still look to the West for inspiration. “Du Lala” is filled with English phrases that, taken together, offer a paean to the mixed blessings of globalization:

value-added

C.E.O.

sexual harassment

cubicle

we wish him a bright future

HBO

Nike

condom

Foreign Corrupt Practices Act

pay for it

Louis Vuitton

The novel is also striking for what it leaves out. Lala is an attractive single woman in her late twenties who lacks a social life; we never see her gossiping with friends, because she doesn’t have any. A romantic interest finally appears—an arrogant sales supervisor who threatens to derail Lala’s renovation—but their love scenes are less impassioned than their discussions of sales targets. People spend all their waking hours in conference rooms and cubicles, because this is what it takes to survive. We never even learn what Lala’s company sells.

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The fierce pursuit of success once figured in the plotlines of American fiction, too. Horatio Alger published more than a hundred novels intended as success manuals for youths during the late nineteenth century, an era of industrialization and economic growth that had much in common with China today. Theodore Dreiser’s Sister Carrie strives for material possessions as hungrily as any Chinese factory girl or office worker. “Here was the splendid dining chamber, all decorated and aglow, where the wealthy ate,” Carrie observes on entering a fine restaurant for the first time. “What a wonderful thing it was to be rich.” But the literature of America’s rise was told in moral terms. In a typical Alger story, a poor young man impresses a wealthy benefactor with his virtue and is rewarded with a job that promises middle-class respectability. When Carrie becomes a leading stage actress, she learns that wealth and fame do not bring happiness.
China was once a country governed by morals. Its emperor ruled through righteous example; by showing himself to be above corruption, he assured a virtuous administration and a peaceful empire. One of history’s first success manuals was the work of a fifth-century-B.C. moralist. “The Analects of Confucius” was a guide to zuoren, how to behave properly: “Riches and rank are what every man craves; yet if the only way to obtain them goes against his principles, he should desist from such a pursuit.” Today, the focus is on zuoshi, how to get things done. All the rules for getting ahead can be reduced to one: Do anything to survive, because you’re on your own.

If sales is war, so is publishing. Many Chinese publishers wait to see how a book sells in its first week before deciding whether to promote it; many writers respond to this pressure by buying hundreds of copies of their own works. Some contracts actually stipulate that an author purchase a set number of copies of his book and sell them however he can. Sales in China’s eleven-billion-dollar publishing industry grew nineteen per cent in 2010, according to the monitoring firm Beijing OpenBook Company, but almost seventy per cent of the trade is in textbooks. What’s more, the retail price of an average book is about four dollars and has barely budged in a decade. “People are willing to spend a lot of money to go out to dinner or to sing karaoke, but they are used to having books be very cheap,” Peggy Yu, of dangdang.com, China’s largest online book retailer, told me.

The cutthroat nature of the business is on display in any bookstore. “Du Lala’s Promotion Diary” was followed by “Hu Keke’s Beijing Success Diary,” “Tian Duoduo’s Civil Service Exam Diary,” and “Su Changchang’s Struggle to Get a Raise Diary.” Is it enough to have one novel called “Mayor’s Secretary”? Apparently not, because there’s also “County Party Secretary,” “Inspection Committee Party Secretary,” and “Municipal Party Committee Secretary.” The undisputed king of the genre is Wang Xiaofang. He has written fourteen books drawing on his experience working for Ma Xiangdong, the former vice-mayor of Shenyang, who was executed in 2006 for corruption. You can’t buy that kind of publicity.

These works owe their existence to a sweeping liberalization of the publishing business. In a push to modernize its culture and media industries, the government recently gave publishers more autonomy. Bureaucrats formerly bought books; now editors act as aggressive scouts. The Shanghai Translation Publishing House, the largest publisher of translated books in China, releases titles that it wouldn’t have touched before, such as Lawrence Wright’s “The Looming Tower” (too much religion) and the novels of Haruki Murakami (too much sex). “In the past, we preferred to avoid trouble at all costs. If you were punished, all the people involved from the managing director on down would be fired,” Zhang Jiren, an editor at the firm, told me. “Now we’re willing to take risks.”

Officially, all book publishers in China belong to the state; in reality, private entrepreneurs have been operating as publishers for years. Independent presses, which invented and dominate lucrative categories such as young-adult novels, were the first to send sales teams to bookstores. They’ve published many of the workplace novels and were instrumental in establishing the novel of officialdom. The first such work, titled “Painting,” was published in 1998 by the state-owned People’s Literature Publishing House. It arose out of an older genre known as the “anti-corruption novel,” whose story line typically involved the punishment of officials who flagrantly abused their power. But where those earlier stories blamed graft on a few greedy individuals, with justice prevailing in the end, “Painting” showed how deeply corruption was embedded in the Chinese political system. The government was not happy with the book, and state-owned publishers shied away from the market, but private presses quickly took over.
“The private companies were braver and less accountable than the state publishers because they are not part of the regulatory structure,” Jo Lusby, the managing director of Penguin China, told me. She is publishing Wang Xiaofang’s “Notes of a Civil Servant” in English. “Now these novels are such an established part of the literary culture that the government can’t do anything about it.”

That loss of control hasn’t been good for the bureaucracy’s image. In the Hou Weidong series, officials skip work for days to play mah-jongg, or they show up only to drink tea, read newspapers, and enjoy the air-conditioning. Every meeting is an excuse to eat and drink at public expense, and there are endless descriptions of cadres throwing up—on themselves, on dining tables, in public toilets, on country roads. They set up illegal companies and profit from sweetheart deals. Hou Weidong marvels at the scale of bribery but quickly masters the etiquette of the payoff. The corruption of a young man by the wide world has rarely been presented in such triumphant terms. An egalitarian universe, the author implies, is one in which even an unconnected nobody can learn to buy off officials and subvert the law.

For a man who wrote a best-selling novel that has a giant gold ingot on the cover, Lao Kang is surprisingly modest. Only a few friends know that he is the author of “The Get-Rich Diary of China’s Poorest Guy,” and his wife has not read the book. “She likes Korean soap operas,” he told me. He owns a small company that sells electrical wiring, and he agreed to meet me on a rainy afternoon in his native Chongqing, on the condition that I not take his photograph. He never told me his real name.

Lao Kang is forty years old. He has a big, open square face with a wispy goatee, like a peasant crossed with an artist. He rejects the get-rich gospel and boldface success tips advocated by his own book, which he conceived as the story of a self-made man’s struggle to overcome hardship. “The publisher packaged the book as a manual for success, which I very much disagreed with,” he told me. He was asked to rewrite the ending to emphasize the protagonist’s material wealth.

“I worry that the book will mislead young people,” he said. “It will make them focus too much on making money. If everyone in our country focussed only on getting rich, that would be a very dangerous thing.”

“But aren’t we already at that point?” I asked.

He was silent for a moment and then laughed in embarrassment, as if the national ethos were a personal failing. “But I think this will change,” he said. “A lot of people are already changing their thinking. They want to spend time with their loved ones, and to travel. They don’t need too many material goods—just enough not to have worries.”

“The Get-Rich Diary” tells the story of an educated man who has been out of work for several years and is estranged from his wife and son. He is inspired to pursue success after watching an “American Idol”-type reality show on television. “They were not necessarily good singers, but they made the attempt and took action,” the narrator says. “This was the origin of their success. So I must take action.” He finds work as a laborer on a construction site, assembling scaffolding for buildings. (“If you don’t act,” the book counsels, “you’ll be poor forever.”) In his spare time, he starts distributing construction materials, sets up a sales showroom, and eventually buys a scaffolding factory. (“A person’s job opportunity is to be found in the midst of work, not through sitting and imagining it.”) In three years, his company achieves sales of a million yuan. His wife returns home and they buy an apartment together. (In the Chinese workplace novel, the climax often involves an apartment purchase.)

The book describes how it feels to be a failure in a place as ambition-mad as China:

I am thirty years old.
I don’t own an apartment but live with my wife’s parents.
Every day I sleep until ten, cook a huge bowl of noodles to ravenously fill my stomach, then leave and “go to work.” . . . My work involves finding an Internet café to go online. I read the news, roam the online forums, or play some computer games.
If I have no money to go online, I will go alone to an out-of-the-way place and sit quietly staring into space. This is also part of my daily work.

At any rate, I will avoid people’s gaze, and I have gone into hiding from everyone I know.
Lao Kang reluctantly agreed to take me on a sales visit that he assured me would be of no interest. “All we’ll do is go in and sign a piece of paper,” he told me. It was his second meeting with Boss Peng, and he hoped to close a deal to supply Internet cable to a prison in the city of Fuling. Boss Peng’s office was a drafty room in an unfurnished apartment, lit by a flickering fluorescent bulb. The pounding of a hammer next door started up like a welcoming orchestra the moment we arrived.

“I’m not making money on this project, because the construction company is paying me such a low price,” Boss Peng, a stocky man with a meaty crewcut head, said.

“I’m not making money on this deal, either, because my costs are so high,” Lao Kang replied.

Having taken their vows of poverty, the men got down to negotiations. (“Any business opportunity needs two people: one who wants to spend money and another who wants to earn it.”) Boss Peng wanted to pay only ten per cent up front; Lao Kang required a twenty-per-cent down payment. Boss Peng protested—“I thought we had already agreed on this point last Friday”—and pulled out a brick of hundred-yuan bills, like a showgirl flashing a bit of leg. The brick disappeared almost immediately into the breast pocket of his windbreaker. Lao Kang stood firm. Next door, an interval of silence was followed by a second movement: power drilling.

In the next hour, Boss Peng requested that the boxes of cable be delivered to the construction site that afternoon. Lao Kang said he needed two days. Boss Peng explained that he had only fifteen days to finish the job. Seeing his advantage, Lao Kang said he could guarantee delivery the next day if Boss Peng paid him on the spot. The brick of cash reappeared and changed hands. The drilling continued and the hammer joined back in, building to a crescendo as the two men signed the contract.

This negotiation had taken two hours. “I’m very tired,” Boss Peng said.

“I’m very tired, too,” Lao Kang said. “In our next life, let’s not do business. Let’s be government officials instead.” For supplying six thousand dollars’ worth of Internet cable to Boss Peng, Lao Kang earned less than fifty dollars—a profit margin of seven-tenths of one per cent.

As we drove back to his office, Lao Kang told me that he could imagine a different way of life. His wife’s sister and her husband have lived and worked in the United States for years. “They don’t focus on money,” he said. “All they care about is living a pleasant life. Every weekend, they drive somewhere on an outing.”

I suggested that he could also spend weekends this way.

“Yes,” he said. “But every time I think about doing it I immediately think I should be doing something more meaningful. Like working.”

In a nation that so worships material success, even the heretics are high achievers. Zhao Xing is a twenty-six-year-old executive at an American public-relations firm in Beijing who also writes a blog aimed at office workers in their twenties. But Zhao Xing does not offer tips on becoming a manager or a millionaire. Instead, she advises readers on how to fulfill their dreams while surviving the workplace—an explicit rejection of the work-obsessed society she lives in. “We disagree with Du Lala,” she told me. “All she does is fight. It is very tiring. I keep telling my readers that we don’t have to be like that. If we’re just like our elders, society will never develop.”

Zhao Xing’s first book, which comes out in China this spring, is not about work. It’s about an eleven-day trip that she made to Taiwan in 2010, sleeping on the couches of families she met online. Chinese tourists are not allowed to travel to Taiwan except in organized groups, so the book, which sold well in Taiwan, is getting a lot of attention. “It’s been my dream to visit Taiwan since I was seventeen,” she told me. A second book, combining essays and fiction about the workplace, is due out later this year.

Zhao Xing is part of what the Chinese call bawuhou, the post-1985 generation. Accustomed to a life of material comfort and choice, they don’t define success in the standard ways. “We grew up along with China’s reforms,” she said. “You can’t motivate us with money—you have to appeal to our dreams. For example, a post-’85 may quit a job so he can take a trip. This is unimaginable to the older generation.” Readers often write her about their aspirations: to be a good teacher, to buy Louis Vuitton, to direct films, to take their parents on a plane trip for the first time.
Zhao Xing would like to visit “the places other people cannot go, like Iceland, Fiji, and the Vatican.” She wants to improve her piano-playing. She was the only workplace writer I met who offered her own definition of success. “Success means that you can live the way you want, that you can be yourself and not the person others want you to be,” she told me. “I can’t say I’ve achieved this, but I’m pursuing it.”

“Don’t get wrapped up in your title and the words on your business card,” she tells readers in one blog post. “Life is not lived for the sake of those few words. . . . You can change the company, you can change the profession, but your own youth comes only once, and of your own inner being you have only one. Don’t sacrifice your soul and your ideas for anything. You must have diligent behavior and a brave heart.”

Though Zhao Xing represents something new in contemporary fiction, she is also a throwback to an earlier generation of Chinese writers: those who were concerned not with how to work but with how to live. ♦

Division of Medical Sciences at Harvard Medical School (DMS)

Bioinformatics and Integrative Genomics (BIG)

The Bioinformatics and Integrative Genomics (BIG) Program enrolls PhD students with exceptional training in quantitative sciences and strong interest in biomedical applications. Research areas encompass computational analysis and mathematical modeling of data generated by DNA sequence, gene expression, structural, proteomics, and metabolite-assaying technologies. In applied projects, they may also include integration of clinical and population data from electronic health records. Both bioinformatics and genomics are tightly linked to the mathematical and biophysical modeling of complex biological systems and experimental validation of computational predictions. Graduate students will conduct original research in the development of novel approaches and new technologies to address fundamental biological questions, and they will acquire the skills to be leaders in the field of bioinformatics and genomics. Students will be joint members of BIG and a “home program” chosen from one of the four DMS programs (BBS, Immunology, Neuroscience, Virology). BIG students will follow the curriculum and participate in activities of the home program, which will be supplemented with BIG programmatic and curricular offerings.

Terminology

1.fold-coverage

the theoretical “fold-coverage” of a shotgun sequencing experiment:

<number of reads> * <read length> / <target size>

2.Amplicon

An amplicon is a piece of DNA or RNA that is <the source and/or product of natural or artificial amplification or replication events>.

It can be formed using various methods including polymerase chain reactions (PCR), ligase chain reactions (LCR), or natural gene duplication.

3.Whole genome mapping

A Whole Genome Map is a high-resolution, ordered, whole genome restriction map generated from single DNA molecules extracted from bacteria, yeast, or other fungi. Whole Genome Mapping is a novel technology with unique capabilities in the field of microbiology, with specific applications in the areas of Comparative Genomics, Strain Typing, and Whole Genome Sequence Assembly. Whole Genome Maps are generated de novo, independent of sequence information, require no amplification or PCR steps, and provide a comprehensive view of whole genome architecture. A Whole Genome Map is displayed in the MapCode pattern where the vertical lines indicate the locations of restriction sites, and the distance between the lines represent the restriction fragment size.

4.Radiation hybrid mapping

A theory is developed to predict marker retention and conditional retention or loss in radiation hybrids. Applied to multiple pairwise analysis of a human chromosome 21 data set, this theory fits much better than proposed alternatives and gives a physical map consistent with other evidence and robust with respect to errors to typing. Radiation hybrids have great promise to provide order and physical location at two levels of resolution, spanning the techniques of linkage and restriction fragments and not limited to polymorphic loci.

5.dna barcoding

DNA barcoding is a taxonomic method that uses a short genetic marker in an organism’s DNA to identify it as belonging to a particular species

6.metric space

In mathematics, a metric space is a set for which distances between all members of the set are defined. Those distances, taken together, are called a metric on the set.

7.Pseudometric space

In mathematics, a pseudometric space is a generalized metric space in which the distance between two distinct points can be zero.

8.pyrosequencing

Pyrosequencing is a method of DNA sequencing (determining the order of nucleotides in DNA) based on the “sequencing by synthesis” principle. It differs from Sanger sequencing, in that it relies on the detection of pyrophosphate release on nucleotide incorporation, rather than chain termination with dideoxynucleotides.The desired DNA sequence is able to be determined by light emitted upon incorporation of the next complementary nucleotide by the fact that only one out of four of the possible A/T/C/G nucleotides are added and available at a time so that only one letter can be incorporated on the single stranded template (which is the sequence to be determined). The intensity of the light determines if there are more than one of these “letters” in a row. The previous nucleotide letter (one out of four possible dNTP) is degraded before the next nucleotide letter is added for synthesis: allowing for the possible revealing of the next nucleotide(s) via the resulting intensity of light (if the nucleotide added was the next complementary letter in the sequence). This process is repeated with each of the four letters until the DNA sequence of the single stranded template is determined.

9.n-gram(k-mer)

In the fields of computational linguistics and probability, an n-gram is a contiguous sequence of n items from a given sequence of text or speech. The items can be phonemes, syllables, letters, words or base pairs according to the application. The n-grams typically are collected from a text or speech corpus.

 

DNA sequencing:base pair

…AGCTTCGA…

…, A, G, C, T, T, C, G, A, …

…, AG, GC, CT, TT, TC, CG, GA, …

…, AGC, GCT, CTT, TTC, TCG, CGA, …

10.sequence space

In evolutionary biology, sequence space is a way of representing all possible sequences (for a protein, gene or genome).

11.k-mer distance

1.li,lj,表示两条序列

2.τ:表示一个k-mer的一个子序列,

ni(τ),nj(τ):表示该子序列在两条序列的k-mer中的个数。

3.ki,j:表示这两条序列k-mer的相似度

12.optical map(ordered restriction map)

Optical mapping is a technique for constructing ordered, genome-wide, high-resolution restriction maps from single, stained molecules of DNA, called “optical maps”. By mapping the location of restriction enzyme sites along the unknown DNA of an organism, the spectrum of resulting DNA fragments collectively serve as a unique “fingerprint” or “barcode” for that sequence.

13.Restriction map

A restriction map is a map of known restriction sites within a sequence of DNA. Restriction mapping requires the use of restriction enzymes. In molecular biology, restriction maps are used as a reference to engineer plasmids or other relatively short pieces of DNA, and sometimes for longer genomic DNA.

14.Expressed sequence tag

An expressed sequence tag or EST is a short sub-sequence of a cDNA sequence.They may be used to identify gene transcripts, and are instrumental in gene discovery and gene sequence determination. The identification of ESTs has proceeded rapidly, with approximately 74.2 million ESTs now available in public databases (e.g. GenBank 1 January 2013, all species).

15.Multiple Sequencing Alignment

A Multiple Sequence Alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a lineage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences’ shared evolutionary origins. Visual depictions of the alignment as in the image at right illustrate mutation events such as point mutations (single amino acid or nucleotide changes) that appear as differing characters in a single alignment column, and insertion or deletion mutations (indels or gaps) that appear as hyphens in one or more of the sequences in the alignment. Multiple sequence alignment is often used to assess sequence conservation of protein domains, tertiary and secondary structures, and even individual amino acids or nucleotides.

16.POA(Partial Order Alignment)

Partial order alignment (POA) has been proposed as a new approach to multiple sequence alignment (MSA), which can be combined with existing methods such as progressive alignment. This is important for addressing problems both in the original version of POA (such as order sensitivity) and in standard progressive alignment programs (such as information loss in complex alignments, especially surrounding gap regions).

17.Progressive Alignment

This approach begins with the alignment of the two most closely related sequences (as determined by pairwise analysis) and subsequently adds the next closest sequence or sequence group to this initial pair [37,7]. This process continues in an iterative fashion, adjusting the positioning of indels in all sequences. The major shortcoming of this approach is that a bias may be introduced in the inference of the ordered series of motifs (homologous parts) because of an overrepresentation of a subset of sequences.

18.核糖体小亚基(英文:Ribosomal Small Subunit,简称“SSU”)

是核糖体中较小的核糖体亚基。每个核糖体都由一个核糖体小亚基与一个核糖体大亚基共同构成。[1]小亚基在核糖体翻译过程中负责信息的识别。  原核细胞中的70S核糖体、真核细胞细胞质中的80S核糖体与真核细胞线粒体中的线粒体核糖体各拥有一种不同的核糖体小亚基:70S核糖体中包含30S核糖体亚基,80S核糖体中包含40S核糖体亚基,线粒体核糖体中则包含28S核糖体亚基。

原核细胞 (70S核糖体) 大亚基:50S亚基(包含5S rRNA及23S rRNA)  
  小亚基:30S亚基(包含16S rRNA)  
真核细胞 细胞质核糖体 (80S核糖体) 大亚基:60S亚基(包含5S rRNA、5.8S rRNA及28S rRNA)
    小亚基:40S亚基(包含18S rRNA)
  线粒体核糖体 39S大亚基(12S MT-RNR1)
    28S小亚基(16S MT-RNR2)

19.rare biosphere

Low-abundance high-diversity group is what is now called the “Rare Biosphere”.

20.Phred quality score

Phred quality scores were originally developed by the program Phred to help in the automation of DNA sequencing in the Human Genome Project. Phred quality scores are assigned to each nucleotide base call in automated sequencer traces.[1][2] Phred quality scores have become widely accepted to characterize the quality of DNA sequences, and can be used to compare the efficacy of different sequencing methods. Perhaps the most important use of Phred quality scores is the automatic determination of accurate, quality-based consensus sequences.

21.Base calling

Base calling is the process of assigning bases (nucleobases) to chromatogram peaks. One of the best computer programs for accomplishing this job is Phred base-calling, which is currently the most widely used basecalling software program by both academic and commercial DNA sequencing laboratories because of its high base calling accuracy

22.MIAME(Minimum Information About a Microarray Experiment)

describes the Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment.

1.The raw data for each hybridisation.

2.The final processed data for the set of hybridisations in the experiment (study)

3.The essential sample annotation, including experimental factors and their values

4.The experiment design including sample data relationships

5.Sufficient annotation of the array design

6.Essential experimental and data processing protocols

 

 

suffix array – 后缀数组(倍增算法实现版)

使用倍增算法,反复调用基数排序,最后得到’名次数组rank’;
使用’名次数组rank’最终得到’后缀数组sa‘。

倍增算法的倍增体现在,每次处理的字符串长度增长方式为:2^0,2^1,2^2…(a^b表示a的b次方);
rank[i]表示首指针为i的序列,排名第几;
sa[i]表示排名第i的序列,首指针是多少;
注意编号开始的位置。

时间复杂度:
O(n*log[2](n))
log2n为倍增次数,n为基数排序的次数;

注意两个很重要的边界:一个是单个数据的范围,一个是数据个数的范围;
即,每个数据的最小值最大值,和一共要处理的数据的个数;

Counting sort – 计数排序

原理:

假设待排序对象为整数,且范围为1…1000;

举例:2,3,3,4

首先统计每个数字出现的次数,用c[i]表示。i表示数字,c[i]表示数字i出现的次数;

c[1] = 0;  c[2] = 1;  c[3] = 2;  c[4]=1;

然后从小到大,统计比每个数小的数一共有多少,用a[i]表示。i表示数字,a[i]=c[1]+c[2]+c[3]…+c[i]

a[2] = 1;a[3] = 3;a[4]=4;

接着算出每个数字的序数;遍历每个数字,算出其序数,将这个数字直接放在数组rank中,其对应的位置上;

for(int i = 1;i <= n;i ++) rank[– c[a[i]]] = a[i];

整个过程并没有一个数组专门来存所有待排列数字,只有一个数组rank来存储排列好的数字,所有一样大的数字之间的顺序取决于代码实现的过程。

《算法设计编程实验》中提到使用计数排序来实现后缀数组中rank数组的计算(这里的rank是后缀数组的rank),其实是笔误,那里用的是基数排序。

 

How to Become a Bioinformatics Professional

1 Understand what Bioinformaticians do.

  • Broadly, computational biology is involved with developing and implementing tools in order to use and manage biological data.
  • The medical field is a major employer of Bioinformaticians, but they are also needed in industry and agriculture.

2 Stay abreast of new developments in Bioinformatics and biotechnology.

  • This highly technological field is undergoing rapid changes.
  • The Bioinformatics Organization offers continuing education courses.

3 Become proficient in computer science.

  • This includes database administration and programming skills.
  • UNIX is currently the preferred operating system platform.
  • Be able to write programs in computer languages such as PERL, SQL and C.
  • Learn to use genomic sequence analysis and molecular modeling programs.

4 Study college level biology.

  • Biology courses should include analytical techniques and molecular biology.

5 Take math courses, particularly those for biologists.

  • Biostatistics is an important discipline in Bioinformatics.

6 Pursue higher education. Undergraduate degrees can be in biology, computer science or biotechnology.

  • In graduate school, find a program that combines both disciplines, if possible; however the emphasis seems to be on molecular biology study with the acquiring of information technology skills.
  • Bioinformatics or computational biology programs are still fairly new.
  • Researchers should have a doctorate in biology, statistics or math.

7 Learn to identify the right questions to ask in addition to the methodologies to apply.

听起来就是这么容易……

http://www.wikihow.com/Become-a-Bioinformatics-Professional

DNA Packaging: Nucleosomes and Chromatin

18847_6

At the top right portion of the diagram, a vertical double-ended arrow indicates that the DNA double helix strands are 2 nm apart. The strands are represented as gray ribbons connected by vertical colored bars that are either half red/half green or half yellow/half cyan.

As the DNA strand reaches the left side of the illustration, all colors are replaced by gray. Box 1 has the text “At the simplest level, chromatin is a double-stranded helical structure of DNA. The DNA strand turns down and goes back toward the right, still compacting along the way.

Below this is Box 2, with the text “DNA is complexed with histones to form nucleosomes.” Toward the center of the schematic are three sets of two brown discs, each disc quartered, and the cylinders are wrapped 1.65 times by the DNA, which has now compacted into a thick gray thread shape. Each nucleosome consists of eight histone molecules.

To the right of the first nucleosome complex is Box 3, with the text “Each nucleosome consists of eight histone proteins around which the DNA wraps 1.65 times.” The second nucleosome has a vertical red bar, about as long as the nucleosome is high, attached to the side of the nucleosome. This bar is labeled H1 histone. A horizontal, double-ended, black arrow indicates the nucleosome with DNA has a diameter of 11 nm. A third nucleosome to the right of the second is labeled “Chromatosome.” Above and to the right of the chromatosome is Box 4, with the text “A chromatosome consists of a nucleosome plus the H1 histone.”

Below this, the nucleosomes are folded in on each other to form a hollow, tube-like fiber, where many nucleosomes are arranged in parallel rings to form the tube’s outer layer. To the right of this is a vertical, double-ended, black arrow labeled 30 nm. To the right of this arrow is Box 5, with the text “The nucleosomes fold up to produce a 30-nm fiber…” The nucleosome tube continues to compact to form a gray spiral and gray squiggles as it continues leftward. Above this is Box 6 with the text “… that forms loops averaging 300 nm in length.” A black, vertical, double-ended arrow is labeled 300 nm. The squiggles compact further, going down and back toward the right, coiling like a telephone cord. Below this is Box 7 with the text “The 300-nm fibers are compressed and folded to produce a 250-nm-wide fiber.” A black, vertical, double-ended arrow is labeled 700 nm. Two, inward-pointing, black arrows indicate a gap labeled “250-nm-wide fiber.”

These coils continue to the right and compress further, forming a horizontal, X-shaped, chromosome. A black, vertical, double-ended arrow is labeled 1400 nm. Below this is Box 8 with the text “Tight coiling of the 250-nm fiber produces the chromatid of a chromosome.”

这里的欠缺在于,从图框6到图框8之间的折叠细节没有交代清楚。而且染色质\染色体的构象是随着时间在发生动态变化的,并非一成不变的。所以上述描述可以说是一个剪影。

http://www.nature.com/scitable/topicpage/DNA-Packaging-Nucleosomes-and-Chromatin-310

押棋新纪录

  1. 2016.5.4 二区间押分:172000(全押);获得:516000;收益:344000。总弈币:516000;
    2016-05-04_0203282016-05-04_020428
    判断依据:
    1. 前面八十手,选手’乌市少年宫’计算速度比’ltsoo’快许多,而且,在八十手之前,局面还是五五开,所以我决定押乌市少年宫;
    2. 看到2/3的人押ltsoo,我觉得我应该全押获得最大利润;
    3. 还有一个直觉,那就是我相信小孩子的战斗力;
    中盘的时候将双活看错了,于是以为白输棋了,当时伤心啊,还在对话区说,白输多了。想来也是不应该。别人对局时自己无论如何不该说话。
    白棋右下角当黑棋打入时的计算又快又准。左上角的做活堪称一绝。对黑棋的侵消是处处紧逼,恰到好处。这是我截止目前最高的弈币收入。我本来说,等我弈币上一百万,我的棋艺肯定会精进不少,因为押分能力增强了嘛。不过看来,对小孩子的偏信和运气能够使我很快到达一百万。看来得上一千万时我的棋艺才会通过押棋得到较大飞升。
  2. 2016.5.12 一区间押分:100000(小酌);获得:450000;收益:350000。总弈币:855460。
    这局棋押胜吧,我是开了sgo的。我把对局下载下来,然后用sgo判断,黑领先8目,当时,黑的赔率是4.5倍,所以我就押了十万,小酌一下,毕竟我的总弈币都有五十多万,押十万输了影响也不大。
    另外,弈币和人民币的汇率为:1元=1金币=40万弈币。

Excel 数据分析

  1. 回归分析
  2. 直线图
  3. 快速公式套用:
    1. 在一个格子内输入公式;
    2. 点击该格子,Ctrl+Shift+方向,选定所有需要套用的格子;
    3. Ctrl+D,完成计算。