[Seminars] PSB event reminder

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Calendar Name: seminars
Scheduled for: Thursday, March 25 2010, 10:00 - 12:00
Event text:    Mini-Symposium on "BGI and Genomics in China - 'Life
	       Sciences for all' in the 21st Century"
Details:       10:00 - 10:40
	       "BGI and Genomics in China - Life Sciences in the 21st
	       Century"
	       Huanming Yang, Ph.D.
	       Professor & President
	       BGI (Beijing Genomics Institute)-Shenzhen, China
	       
	       The recent progresses in biotechnology, such as iPS and
	       stem cell research, animal cloning and bio-plants,
	       synthetic biology and many others, have made it even
	       more obvious that life sciences would have significant
	       impact on every respect of our life and society in the
	       21st Century.  
	       
	       It is also widely accepted that reading and decoding
	       genome sequences of an organism is the basis and
	       beginning for any biological studies on it. Based on its
	       persistent belief that “life is of sequence” and “life
	       is digital”, BGI, a flagship in genomics in China for
	       the decade, has built its powerful capacity in
	       sequencing and bio-computing with its young and
	       innovative teams, and greatly contributed to the global
	       genomics and to the future development of biotechnology
	       as one of the biggest and most influential genomics
	       centers in the world.
	       
	       As a later comer in the modern life sciences, the growth
	       of BGI is deeply rooted in the Chinese tradition and
	       Culture, for example:
	       
	       1)      Foresight:  “Success could not be made without
	       foresight, failure from no prediction”.
	       2)      Persistence:  “Winners are only those with
	       persistence”.
	       3)      Learning:  “Among those three passing by, at
	       least one is qualified to be your teacher”.
	       4)      Confidence:  “The later comers always do a
	       better job because of the pioneers ahead”.
	       5)      Collaboration:	“Nobody could be a hero without
	       three partners”.
	       6)      Appreciation: “When you drink sweet water, never
	       forget those helped dig the well”.
	       
	       As an institute in the developing part of the world, BGI
	       has been raising the banner of both science and
	       humanity, and actively participating in the discussion
	       on HELSOC issues (Humanitarian, Ethical, Legal, SOcial,
	       and Cultural issues) that are essential to “life science
	       for all” in the 21st century.
	       
	       10:40 - 11:20 
	       "Harvest the fruits of genomics - to upgrade agriculture
	       with new breeding tools"
	       Sanwen Huang, Ph.D.
	       Key Laboratory of Genomics, Ministry of Agriculture
	       Chinese Academy of Agricultural Sciences (CAAS)
	       and Beijing Genomics Institute (BGI)
	       
	       The global food security is in menace because of the
	       rapidly growing human population, the depletion of
	       agricultural resources as arable land, water, and
	       petroleum-based pesticide and fertilizer, and the
	       climatic changes. The genetic improvement of crops is
	       the most viable approach by which food production can
	       try to keep pace with the anticipated growth of the
	       human population. The efficiency of crop breeding relies
	       on our knowledge on the biology of the ~60 species that
	       uses about 95% of the arable land and a dozen of
	       livestocks. The most fundamental biological knowledge of
	       a crop is stored in its genome.
	       
	       Next generation sequencing (NGS) technologies, such as
	       Illumina GA, SOLiD, and 454, made it feasible and
	       economical acceptable to sequence genomes of all crops.
	       However, as NGS often produces millions of shorter reads
	       in a single run, it also meet computational and
	       algorithmic challenges. BGI constructed a powerful
	       platform mainly based on sequencing-by-synthesis
	       technology, including >30 Illumina GA II, a 10,000-CPU
	       cluster, and a software package, Short Oligonucleotide
	       Analysis Program (SOAP). The genomes of cucumber (350
	       Mb), Brassica rapa (500Mb), potato (830Mb), duck (2 Gb),
	       and even giant panda (2.3 Gb)have been assembled and
	       analyzed, giving the first set of examples that NGS can
	       be used in de novo sequencing of large plant and animal
	       genomes. Large scale germplasm resequencing was
	       conducted on rice, silkworm, and cucumber, which
	       produced millions of SNPs and structural variations and
	       identified hundreds of genes that  likely underwent
	       selection during domestications and breeding.
	       
	       With the newly established Key Laboratory of Genomics
	       (MOA), BGI, CAAS, and other agricultural research
	       institutions will sequence 100 crops, 100 species of
	       livestocks and insects, core collection of every
	       important species, and also perform genome-scan of over
	       400,000 accessions of various crops are stored in the
	       National Seed Bank. Combined with genetic analysis and
	       robust phenotyping, this huge resource will lead to
	       high-throughput isolation of trait genes. The knowledge
	       of trait genes will give rise to new breeding tools that
	       can be used to deliberately design crops and animals
	       that suit to various environment, agricultural
	       practices, and applications. 
	       
	       
	       11:20 - 12:00 
	       "More than just sequencing - Bioinformatics tools
	       developed at BGI"
	       Ruibang LUO, B.S.
	       Bioinformatics project manager
	       BGI (Beijing Genomics Institute)-Shenzhen, China
	       
	       “The day is not far off when more biology will be done
	       at the computer than at the bench!” Roos et al. said in
	       2002.
	       
	       Nowadays, with the rapid development of information
	       technology, not only the computational resources but
	       also talents of this field could be acquired much more
	       easily. It has also demonstrated its powerful ability in
	       assistance of solving complex biological, especially
	       genomic problems. BGI, a flagship in genomics in China
	       for the decade, has created our own series of tools and
	       pipelines for the analysis including the genome, SNP,
	       structural variation, methylation, RNA, assembly and
	       etc.
	       
	       Next-generation massively parallel DNA sequencing
	       technologies provide ultra-high throughput at a
	       substantially lower unit data cost; however, the data is
	       very short read length sequences, making de novo
	       assembly extremely challenging. We’ve just described a
	       novel method for de novo assembly of large genomes from
	       short-read sequences. We successfully assembled both the
	       Asian and African human genome sequences, achieving an
	       N50 contig size of 7.4 and 5.9 Kb and scaffold of 446.3
	       and 61.9 Kb, respectively. Comparison of these
	       assemblies to the NCBI reference genome demonstrated the
	       capability of accurate identification of structural
	       variations, especially small deletions and insertions
	       that are difficult to identify using a resequencing
	       method. The development of this de novo short-read
	       assembly method creates new opportunities for building
	       reference sequences and carrying out accurate analyses
	       of unexplored genomes in a cost effective way.

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