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Old 06-02-2009, 10:17 PM   #1
cafeblue
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Wink Hi from China

Hi everybody!

I am cafeblue from QIBEBT, CAS. There is a 454 titanium in our lab and there will be a Solexa GAIIx at the end of this month. I am new to these instruments and I am new to all the data generated by them. Hope we can communicate well here.
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Old 06-06-2009, 01:43 AM   #2
takout
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I am takeout , from shanghai china

中国人多不多这里?
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Old 06-06-2009, 05:18 PM   #3
cafeblue
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Shanghai? SCBIT? ?www.chgc.sh.cn?

我也不知道多不多,我也是刚刚注册,还没有到处逛逛呢。
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Old 06-06-2009, 05:43 PM   #4
takout
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当然不是。

不是专业人士

只是对这行非常有兴趣

我大概看了一下。

中国的不少不少于20-25%

甚至30%

美国和中国最多了。

欧洲不多。

欧洲人是比利时和德国看到几个。波兰和俄国都是零星的。

看来中国和美国在这方面是巨人。

我看到kenome是用BGI服务的。

这方面政府投资了不少钱。谁让我们有钱呢。
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Old 06-06-2009, 06:05 PM   #5
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哈!就是啊!钱是花了不少,不过在技术上还是受制于人。

晕倒,我不知道kenome是什么东西啊?还有BGI。看来我是土了点。
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Old 06-06-2009, 06:28 PM   #6
takout
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kenome应该是第一家做商业sequencing的。350kUSD
现在大概100K左右
有家庭优惠套餐

BGI是华大呀
兄弟,他们刚进了solex 12台

你那个是啥时候定的货?月底才到?
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Old 06-06-2009, 06:30 PM   #7
takout
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不好意思写错了
KNOME
not kenome

sorry
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Old 06-06-2009, 07:06 PM   #8
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哦,我们的454已经在用了,今天刚刚出了些数据,我刚才在分析。

那个solexa 这个月的月底会到货,到真正使用可能还需要一点时间。

我们这是国家事业单位,至于定货,我还不清楚,反正一年前就在酝酿着买了,彻底决定买大概是两三个月前吧。
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Old 07-07-2009, 07:36 AM   #9
ivy1985732
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hi i am chinese but at sanger now, work on bioinformatics, assembly


how about the development of bioinformatics in China


thanks
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Old 07-22-2009, 09:33 PM   #10
Melissa
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Quote:
Originally Posted by takout View Post
当然不是。

不是专业人士

只是对这行非常有兴趣

我大概看了一下。

中国的不少不少于20-25%

甚至30%

美国和中国最多了。

欧洲不多。

欧洲人是比利时和德国看到几个。波兰和俄国都是零星的。

看来中国和美国在这方面是巨人。

我看到kenome是用BGI服务的。

这方面政府投资了不少钱。谁让我们有钱呢。
Thanks for the statistics. Would prefer you guys PM (private message) each other next time for personal discussion in Chinese.
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Old 07-31-2009, 01:51 AM   #11
MicroHimalaya
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我也是呵呵!今年刚接触这个领域。
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Old 08-23-2009, 01:12 AM   #12
polyhedron
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大家好,我也報到,基本沒有接觸過(除了看過一些454測序的數據)。
請問中國國內有哪些對外服務測序中心?南方、北方和華大?華大現在只在深圳了?都各有什麽測序手段?分享一下經驗吧!
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Old 09-26-2009, 06:30 PM   #13
node
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我是“子江” ,现在中国深圳! 来自BGI。

To 楼上:
国内提供散样测序的公司现在很多,大大小小的,很多都是新组建的;
提供高通量测序服务以及后期的数据分析服务的以BGI为主 !
BGI现在核心部分在深圳,主要以solexa用来做项目和生产,同时有solid 。
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Old 10-17-2009, 04:19 AM   #14
genomechina
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hahaha,这么多中文啊
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Old 10-17-2009, 07:27 AM   #15
takout
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hi genomechian what means FAFU?
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Old 10-17-2009, 02:04 PM   #16
Josliu
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I am from SoftGenetics, a USA based bioinformatics company at State College, Pennsylvania.

We have done a lot the data analysis in last couple of years. NextGENe is developed. Contact us in Chinese if you have any questions regarding the sequence data analysis. liu@softgenetics.com.
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Old 10-19-2009, 01:40 PM   #17
yli
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Default hello from california

hello everyone. i am currenly working on whole transciptome sequencing using roche 454.

i am working at roche diagnostics in california and am chinese.
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Old 10-22-2009, 04:19 AM   #18
genomechina
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Smile

Quote:
Originally Posted by takout View Post
hi genomechian what means FAFU?
let me put this simple,福建
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Old 11-15-2009, 06:52 PM   #19
Y.Y. LEUNG
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I am from Hong Kong.

BGI in 深圳?
what are you working on? algorithms or wet-lab experiments?
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Old 11-15-2009, 07:14 PM   #20
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somthing about BGI

Sequencing, Sequencing, Sequencing






BGI-Shenzhen tackles the cute, the edible, and pretty much everything else.

By Alissa Poh

November 12, 2009 | SHENZHEN, CHINA—Boxing Day 2008: The Luohu border between Hong Kong and mainland China is crowded, smoky, and noisy. With my visitor’s visa to Shenzhen in hand, I’m cleared to visit the Beijing Genomics Institute’s (BGI’s) Shenzhen-based sequencing facility. Accompanied by my father and brother-in-law, I wave down the nearest cab. The cab driver doesn’t have the faintest idea where BGI is located. As none of us can handle his thick Mandarin accent, I’m forced to call Zhuo Li, vice president of BGI’s health care division. I hand the phone to the driver, and happily we’re deposited at BGI’s main entrance. It’s a tall gray-and-glass structure, distinctly newer and shinier than the neighboring buildings. My companions head across the street for a late breakfast (frog legs), and I wander in to meet Li.

The lobby lacks a smiling receptionist, tasteful paintings, or piped-in music. Save for supercomputers humming away within a glass-enclosed area and several ping-pong tables—naturally—in a corner, it’s Spartan. My sense is BGI’s staff wasn’t going to spend any time on décor that they could otherwise devote to research.

Li is tall, lean, and intense. He greets me in immaculate English, and escorts me on a whirlwind tour of the institute. It’s eleven floors of long hallways, each with its respective research unit—cloning, bioinformatics and the like—on one side, posters papering the opposite wall. Lab-coated staff are everywhere, poring over printouts, peering into cell-culture hoods, shuttling racks of test tubes from one lab to another. Most ignore me, apart from the occasional half-diffident glance.
BGI Beginnings
Li succinctly answers my questions, but as I discover, Chinese scientists are rather more close-mouthed than their Western colleagues. Getting them to elaborate beyond the facts is akin to tooth extraction.

It all started in August 1998 with the Human Genome Project, which geneticist Yang Huanming and three like-minded countrymen, all recently returned from U.S. postdocs, saw as the perfect way to position China on the genomics and sequencing stage. Yang’s plan was to utilize the Chinese Academy of Sciences (CAS), as its Institute of Genetics already had its own Human Genome Center. But he quickly concluded that CAS, bound by traditions, was lagging behind the rest of the world. In early 1999, he broke away, setting up BGI as a private, non-profit research organization. A few months later, at a conference at the Wellcome Trust Sanger Institute in the U.K., Yang announced China’s intention of becoming a global player in genomics.

Naturally, he was asked whether he had the money to realize his vision. As he later confessed to Science, he lied. Just four months after the conference, CAS funded three Chinese sequencing centers to tackle 1 percent of the human genome, with BGI receiving over half of the total award. But Yang didn’t know it at the time, standing at the podium and looking out at a sea of skeptical faces. He gambled on the funds somehow materializing, figuring that what the audience didn’t know couldn’t hurt them, or BGI’s image.

Three years later, the genomics world took notice when BGI metamorphosed from one man’s intangible dream to the cover of Science, having outraced its global competition to shotgun-sequence the indica rice genome. A reform-minded China proved that the will to succeed, spirited nationalism, and sheer manpower can be a potent combination. BGI split its sequencing team into 12-hour shifts so the machines could run 24/7 for the 74 days it took to finish indica. Dispensing with the commute between workplace and home, staff catnapped in hallways or simply dozed in their chairs.

By 2002, BGI had outgrown its initial home and relocated to an industrial park in Beijing, with an additional campus in Hangzhou. The original Beijing unit assumed responsibility for all commercial and outsourcing projects, while the Hangzhou branch focused on sequencing and academic research. Then in 2007, BGI made a major investment in next-gen sequencing technology—Illumina’s Solexa—and moved its headquarters to Shenzhen. The director is 33-year-old Jun Wang, a handsome, highly decorated Ph.D. from Peking University whose interest in genomics dates back a decade to the Human Genome Project.
The Chinese Way
New employees at BGI-Shenzhen don’t need reminding about the institute’s game plan. It’s right in their faces: poster-style and of billboard proportions, spanning an entire hallway. Printed in giant font, dead center, is a four-word slogan—“Sequencing is the basic!” It’s the foundation for moving into broader biological systems and processes—analysis of DNA variation and global methylation, protein networks, and metagenomics, ultimately providing individualized health care and agricultural advances.

Large-scale research is a mainstay of BGI-Shenzhen, and the “Tree of Life” project among its most prominent. Silkworms, cucumbers, chickens, and pigs are but a few examples of organisms large and small that the institute’s scientists have already sequenced. On the wall-sized poster, they’re lumped into three groups: animals, plants, and microorganisms. Animals are labeled “economic” (ducks, for instance); “endangered” (the Chinese river dolphin); or “model” (Drosophila). Similarly, microorganisms are categorized as industrial, pathogenic, or environmental. Projects past, present, and future are annotated, respectively, by red flags, green stars, and yellow circles.

BGI-Shenzhen is perhaps best known for the panda genome, as well as a Han-Chinese individual whose genome was but the third announced and published worldwide, after Watson and Venter.

Back in February 2008, the institute launched its International Giant Panda Genome project, aiming to sequence and assemble the draft sequence within six months. The honor fell to Jingjing, the prototype for the Beijing Olympics’ panda mascot. The project was wrapped up by October. This ranked among China’s top ten technology accomplishments for 2008, and is viewed as a major step toward understanding why pandas eat only bamboo and have poor libido. It also suggested that rather than being related to raccoons, they likely hail from the bear family.

The first (human) Asian sequence is the starting point for BGI-Shenzhen’s Yanhuang project—so named for the Mandarin saying yan huang zi sun, or “descendants of Yan and Huang,” two emperors from ancient times that many Chinese consider their earliest ancestors. The institute has its sights set on sequencing at least 100 additional Chinese genomes, to better study genetic variations among China’s different populations.

“It got a lot of media attention,” Li says of the November 2008 publication in Nature. “Not long afterwards, we received RMB10 million [$1.46 million] from an anonymous Chinese donor. He’s interested in decoding personal genetic information to improve biomedical research, and wants to help this project move forward.”

Information gleaned from Yanhuang will contribute to the 1000 Genomes project, aimed at creating the most finely-tuned reference map of human genetic variation to date, down to the 1 percent level. BGI-Shenzhen is one of the key players in this undertaking.
Other initiatives include a “strategic alliance,” since early 2008, with Knome, George Church’s personal genomics company. The latter gets prime access to BGI’s capabilities in whole-genome sequencing, assembly, and annotation for its private clients. BGI-Shenzhen is also one of 13 academic and industrial participants in MetaHIT, a four-year project financed by the European Commission to study connections between genes of the human intestinal microbiota and our health, zooming in on inflammatory bowel disease and obesity. In addition, a Sino-Danish diabetes project involves deep-sequencing of exons and other conserved genomic regions from more than 4,000 individuals, in an attempt to discover genetic variations linked with obesity, type 2 diabetes and hypertension.

“We’re a completely private organization, with an annual budget of [$30 million],” Li says. “So to feed ourselves and carry out all our projects, we rely on revenue from these collaborations, and our spin-off companies [ten in total].” BGI-Shenzhen also benefits from the generous support of Shenzhen’s municipal government.
‘Omics Know-How
BGI-Shenzhen relies heavily on Illumina’s Genome Analyzers for its myriad sequencing projects; at last count, April 2009, their fleet had expanded to 29 (eight are in Hong Kong). The machines are kept in continuous production, churning out data at a daily rate of 60 gigabases (GB). “We could sequence the human genome 20 times a day,” Li says, “but we probably won’t load all our machines with just the one sample.” He’s not joking, and yet I wonder if one can’t take the last half of his statement as a bit of deadpan humor.

Might they eventually switch to another platform such as Life Technologies’ SOLiD system? “We’ve developed all our software and applications based on Illumina, which is why we mainly use their technology,” Li responds. “But we do have two SOLiD machines, and we may get more. It doesn’t necessarily mean we’ll switch; we’d like to make good use of both [technologies].”

The software developers work within BGI-Shenzhen’s energetic bioinformatics group, one of the largest in China, if not the world, directed by seven-year veteran Ruiqiang Li. “I don’t know any other place with so many bioinformaticians [200 and counting] under one roof,” Zhuo Li affirms, adding that many are 25 or younger, with some of the brightest stars barely out of college. Designing novel analysis tools capable of handling short-read sequences by the ton is among the group’s specialties. Their Short Oligonucleotide Analysis Package (SOAP), for instance, includes de novo software where assembling large genomes—panda, human and the like—takes just about two days.

BGI-Shenzhen also has an active health care platform, which Li manages. They’ve developed a variety of affordable, quality diagnostic tests—for instance, tissue-matching via the gold standard Sequencing-Based Typing (SBT). China is seeing an increasing number of bone marrow transplants, yet most diagnostic laboratories remain unequipped with the expensive SBT commercial kits. Hence BGI’s decision to manufacture their own SBT reagents and software.

Public health and smarter disease surveillance are additional foci, particularly “digitalized health,” complete with databases for personal health records. Li’s platform has successfully introduced this improved system to Chinese communities in Yunnan Province, Inner Mongolia, and Tibet—nearly 25,000 individuals in all—and with the support of their local government, they’re doing the same for residents in Shenzhen’s Yantian district, which surrounds the institute.

Not surprisingly, BGI dabbles in cloning and genetic engineering, mainly for agricultural and animal husbandry purposes. Researchers in this division use handmade cloning (HMC) technology—a cheaper and simpler alternative—to produce transgenic pigs. They’ve already created a porcine model of Alzheimer’s, collaborating with Danish scientists.
Looking Ahead
Rather than dwell on how many years they’ve been in existence, folks at BGI consider their institute “as young as genomics.” And much like the field itself—which has accelerated at lightning speed within the last decade—BGI now has five additional branches across China, plus a presence in Hong Kong, Denmark, and the U.S. (California). Coming from a tiny brick building devoid of staff, equipment, or money, it’s phenomenal growth. So what does BGI see in its future?

A “Personal Genomics Industry” by 2012, for starters. BGI believes the cost of human genome sequencing could drop below $1000 soon, making feasible an era where digitalized and personalized health records are affordable. They’ve estimated the Chinese market for such services at a fat RMB1 trillion ($146.5 billion).

And of course, more sequencing—of the cute, the edible, and anything else imaginable. BGI-Shenzhen scientists are already working on the emperor penguin, the Tibetan antelope, and the polar bear. “These [creatures] will help us understand how living organisms adapt to extreme environments,” Li says. “And we think it is fun as well. Actually, we want to sequence everything—and we will.”
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