http://www.biosino.org
Introduction of bioinformatics
research and service in China
Yixue LI
email: yxli@sibs.ac.cn
Bioinformatics center of Shanghai
Institutes for Biological Sciences
Chinese Academy of Sciences
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http://www.biosino.org
Outline
‹ Main
bioinformatics center in China
‹ Organization of the bioinformatics
society in China
‹ Funding status for bioinformatics
research and service in China
‹ Few Thoughts on Collaborations
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Main bioinformatics centers in China
Center of Bioinformatics, Peking
University,http://www.cbi.pku.edu.cn
‹ Bioinformation Center, Shanghai Institutes for
Biological Sciences (SIBS), CAS
http://www.biosino.org
‹ Beijing Genomics Institute, Genomics &
Bioinformatics Center,CAS
http://www.genomics.org.cn
‹ Shanghai Center for Bioinformatics
Technology. http://www.scbit.org.cn
‹
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http://www.biosino.org
Main bioinformatics centers in China
Center of Bioinformatics, Peking University
http://www.cbi.pku.edu.cn
‹ The first bioinformation center in China
‹ Chinese node for EMBnet since 1996
‹ Focus on mirror site setup for international public
databases
‹ Develop and install data analysis tools supplied
through web servers
‹ Annual national training for scientists and students
interested in bioinformatics
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Bioinformation Resources of Beijing University
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Mirror Site of Public Databases
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Bioinformation Tools in CBI
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Bioinformatics Centers in China
Bioinformation Center, Shanghai Institutes for
Biological Sciences (SIBS), CAS
http://www.biosino.org
‹ Focused on general and specialized database
construction and services in SIBS,CAS
‹ Customized development of data analysis tools
for post-genomics research in SIBS
‹ Routine local training for scientists and
students interested in bioinformatics
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http://www.biosino.org
Bioinformatics Center, Shanghai Institutes for
Biological Sciences (SIBS), CAS
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BioSino DNA Sequence Database
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BioSino DNA Chips Database
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BioSino SNPs Database
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BioSino 2D-Page Database
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On going work for an integrated datawarehouse
system of proteomics research
User queries
(GUI)
Mediator
Relevance
module
http://www.biosino.org
Query
planner
Schema
translate
Knowledge base
of databases
Result
analyzer
DB schemas
Query
evaluator
Peptide
mapping
Object Request Broker Interface
PDB
driver
PIR
driver
Swiss-prot
driver
Oracle
driver
2D-page
driver
PSTs
driver
PDB
PIR
Swissprot
Genome
DB
2D-Page
RCP
PSTs
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On going project: High-throughput peptide mapping based de
novo sequencing
Experiment
Mass spectrum
M/Z
Human Genome
人类基因组
DB
相关蛋白库
Theoretical
Digested protein
Human Genome
related
Protein DB
DB
Theoretical
Mass spectrum
M/Z
High
throughput
peptide
mapping
through
special
algorithm
Matched candidate proteins
Novel proteins
Function annotation
Function
Annotation
related DB
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In Silico Cloning
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Annotaion System based on Java+Oracle.Used by web.
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EMBOSS server at www.biosino.org
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Ensembl server at www.biosino.org
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http://www.biosino.org
SRS server at www.biosino.org
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http://www.biosino.org
BIOINFORMATICS Is Important to Associate All Information
>several thousands Gene
Sequences from genome
Similar to
known
Proteins
Homology
to known Gene
Predict
Gene
Function
Associate
genes to
QTLor dieses
Gene
Expression
profilingMicroarray
Proteomics,
Protein
Interactions
Under-expression
Over-expression
Understand
Gene
Regulation
and Discover
Promoters
Associate
unknown
genes to
known genes
Discover
of confirm
Gene
Function
BIOINFORMATICS
A few Interesting Genes
Leptospira interrogence: genome sequencing and annotation, submitted to Nature
Japanic rice chromosome 4: sequencing and annotation, accepted by Nature.
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http://www.biosino.org
Bioinformatics Centers in China
Beijing Genomics Institute, Genomics &
Bioinformatics Center,CAS
http://www.genomics.org.cn
‹ Focused on specialized rice genome database
construction and services in Beijing, China
‹ Development of data analysis tools for
sequence assembling and genomics research
‹ Training courses for scientists and students
interested in bioinformatics
Indica rice genome was sequenced and
released by this center on May
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New Bioinformatics Center in China
Support by local government , Shanghai:
Shanghai Center for Bioinformatics Technology (SCBIT)
http://www.scbit.org
Main goal will be:
Focused on general datawarehouse and specialized
databases construction and services in Shanghai, China
‹ Customized development of data analysis tools for postgenomics research
‹ Routine local training for scientists and students interested in
bioinformatics
‹ Promote sharing biological data produced by
Chinese biological research institutes and genome centers
from Shanghai and China
‹ Open Source and Grid based e-Biologist’s workbench
development
‹
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http://www.biosino.org
Organization of the bioinformatics
society in China
Beijing:
under the Society of Bioengineering
Shanghai:
under the Society of Cell Biology
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Funding status for bioinformatics in China
‹ Government
funding for the next 5 years:
Total Budget from 863 Plan: 25 million EURO
1. Development of database and data analysis tools
2. Bioinformatics related to functional genomics:
structure biology, proteomics, protein-protein
interactions, gene regulation networks, small
molecule drug design and molecular design .
3. From information biology to novel drug
development: including target discovery, novel
screening methodology and drug design ⇒genome
based drug targets screening and validation
‹ National
Bioinformation Center + National
High Performance Computational Grid:
the future of bioinformatics infrustructure in China
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http://www.biosino.org
At End, a Few Thoughts on Collaborations
Identify our strengths, create win-win Collaborations
UK: Genome Technologies, integrated biological databases,
bioinformatics software systems, high performance computer
systems, e- Biologist’s workbench.
CHINA: Biodiversity resources, rice biology,disease related
heredity resources
Possible collaborations
Genome annotation－gene prediction,expression profiling
analysis,proteomics, Structure genomics
Genome based drug discovery－mapping disease related genes,
screening and validating candidate drug targets
Bioinformatics － integrated database system, real time mirror
site, BioGrid, e- Biologist’s workbench etc.
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http://www.biosino.org
Thank you!
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BioChips Research and Industry in China
• National Research Engineering Center for
Beijing Biochip Technology, Beijing, China
total budget: ~50 million EURO.
http://www.capitalbiochip.com
• Shanghai Research Engineering Center for
Biochip Technology, Shanghai, China
total budget: ~10 million EURO.
• Several Universities have also own biochip
research center (North-western University,
South-Eastern University, etc.)
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http://www.biosino.org
National Research Engineering Center for
Beijing Biochip Technology, Beijing, China
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BioChips Research and Industry in China
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http://www.biosino.org
National Research Engineering Center for
Beijing Biochip Technology, Beijing, China
Capital Biochip Co., Ltd, Beijing
http://www.capitalbiochip.com
Main goal:Active biochips applicable to
biological analyses and drug discovery.
Proposed main products: chips for drug
screening, chips for clinical diagnosis,
chips for analeptic examination.
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BioChips Research and Industry in China
Shanghai HealthDigit Co.,Ltd , Shanghai
http://www.health-digit.com
Health-Digit developed Protein Chip System
for Multi-tumor Marker Detection. This Multitumor marker detection protein chip is the first
product of this kind used in the clinical diagnosis
in the world.
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BioChips Research and Industry in China
• BioStar Genechip Inc., Shanghai
http://www.ugbiostar.com
Main products: 1. Human gene expression
chip, 2. Cancer related gene expression chip,
3. Mouse gene expression chip.
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