Transcript IBM Healthcare and Life Sciences

Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Wang Yadong
Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Computer science: a multidisciplinary science
• Seeking to develop intelligent machine
Blaise Pascal:1642
Charles Babbage:1833
ENIAC:1944
Fig.from www.sciencemuseum.org.uk
System
(64 cabinets, 64x32x32)
IBM: Blue Gene
A massively parallel
supercomputer
Cabinet
(32 Node boards, 8x8x16)
Node Board
(32 chips, 4x4x2)
16 Compute Cards
Compute Card
(2 chips, 2x1x1)
180/360 TF/s
16 TB DDR
Chip
(2 processors)
90/180 GF/s
8 GB DDR
2.8/5.6 GF/s
4 MB
5.6/11.2 GF/s
0.5 GB DDR
2.9/5.7 TF/s
256 GB DDR
From:http://www.research.ibm.com
Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Computer science: a multidisciplinary science
• Seeking to make machine more intelligent
―Boolean logic
―Finite state machines
―Formal grammars
―Turing machines
―Recursion
―Garbage collection
―Complexity theory
―Machine learning
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
The emerging multidisciplinary research in C.S
Internet and WWW(World Wide Web)
Grid computing
Pervasive computing
intelligent searching
Service computing
…
from http://discovermagazine.com/
Human Genome Map
Genome informatics
Bioinformatics
From http://www.fotosearch.com/
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Bioinformatics on demand
• Human Genome Project
Then the “omics”
revolution
• Genomes
•
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•
•
Challenge
• Genome Annotation
• Sequence Assembly
• Physical Mapping
• Protein folding / Docking
• Protein-protein interaction
• Finding Binding Site Motifs
• Transcriptional Regulation
• Post-transcriptional Regulation
• Histone modification
• DNA methylation
• Drug discovery
Proteomes
Transcriptomes
Epigenetics(-omics)
“Whatever”omes (...?)
• GenBank database
Bioinformatics
• EMBL database
• BLAST
• Algorithm for high-throughout data analysis
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
What’s next?
• From “omics” to system biology
• From bench to bedside
• From data to knowledge
• Computational System biology
• Translational bioinformatics
• Bio Knowledge engineering
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Computational system biology: on demand
Challenge: how to construct descriptive and predictive
models and interacting systems from the “omics” data.
Gene regulatory network
Protein-Protein
interaction network
Metabolic Network
Signaling network
Cell Simulation
Key Areas: represenattion, visualization, modeling, networks of
biological entities, and construct interacting systems .
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Translational bioinformatics
The Human Genome – A Starting Point Not an Endpoint.
But now the real challenge – translating this base of
knowledge into meaningful diagnostics and innovative
new therapies and treatments, and to achieve the
promise of personalized medicine….Information
technology will play a decisive, transformative role.
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Translational bioinformatics
Challenge 1: Managing huge volume of Data
P e t a b y t e s
More Data Over the
Genomics
Last 3 Years Than
Digital Pathology
Previous 40,000 years
Digital Radiology
Combined
E-Health Initiatives/Linkages
40,000 BCE
cave paintings
Electronic Medical Record
bone tools 3500
writing 0 C.E.
Digital Cardiology
paper 105
1450
printing
1870
electricity, telephone
transistor 1947
computing 1950
Late 1960s
Internet
1993
The Web
1999
Source: UC Berkeley, School of Information Management and Systems.
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2003
Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Translational bioinformatics
Challenge 2: Reducing the knowledge gap
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Translational bioinformatics
The goal of translational bioinformatics is to enable the
transformation of increasingly voluminous genomic and
biological data into diagnostics and therapeutics for the clinician
Key research areas:
• Data : Integration of increasingly voluminous biological
and clinical data
•Knowledge: Newly found knowledge from these
integrative efforts that can be represented, stored,
retrieved, and disseminated
• Algorithm: To integrate genetic, genomic, proteomic,
animal model, and clinical measurements are needed for
the next step
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
A human phenome-interactome network of protein
complexes implicated in genetics disorders
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
The Bioinformatics In Harbin Institute of Technology
 2001 established the Bioinformatics Division,
2001 Set up the bachelor program. This program provides three
areas of study
• computer science
• molecular biology
• bioinformatics
 2001 established the center for bio-computing, research focus on
•Biometrics and Computer aided traditional Chinese medicine diagnoses.
•Biomedical informatics
•Simulation of biology structure
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Tongue diagnoses system
Pulse diagnoses system
Computer aided
traditional Chinese
medicine diagnoses
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Bioinformatics in HIT
Computer Science and
Bioinformatics
MiR2Disease:
Database and
predication system
Gene expression levels Transcriptional initiation
MotifModeler:
Identify transcription
factor and miRNA
binding site
Transcription factors
5’ upstream regulatory region
mRNA degradation
microRNA-induced
mRNA degradation
3’ un-translated region
Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Bioinformatics in HIT
Computer Science and
Bioinformatics
• Gene Mining: A Novel and Powerful
Ensemble Decision Approach to
Hunting for Disease Genes Using
Microarray Expression Profiling.
Virtual heart
Petri nets based e-cell
Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
Bioinformatics Technology supported by
National High Technology Program Supported
Seven Research Directions: (2001-2005)
• Technology for Bio-Data Acquisition and Mining
• Technology for Bio-Data Application
• Structure Genomics and Proteomics
• Molecular and Drug Design
• Bio-Chip
• High-Throughput Drug Screening
• Novel Drugs
Total budget: ~40 million USD
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
Computer Science and
Bioinformatics
New Budget Launch Into Bioinformatics Field from
the 863 program (2006-2010)
• Topic Program : Bioinformatics and Bio-computing
• Key Program: Drug design and Molecular design
• National Program:

Functional genomics and protoemics
 Major disease related molecular genotype and personal
health care
Total budget: ~70 million USD
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Harbin Institute of Technology
Second US-China Computer Science
Leadership Summit
THANK YOU
Harbin Institute of Technology