Download Slide 1

2007 【IBM developerWorks 開發者大會】
演繹生化科技新樂章
－生醫研發整合平台
October 30, 2007
呂政欣 Joe Lu, Ph.D.
Life Sciences Center of Excellence
Software Group, IBM Taiwan
[email protected]
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
IBM Taiwan – Life Sciences Center of Excellence
 Established
in September, 2002 and under the support of
Ministry of Economics Affairs.
 Based
in the Nankang Software Park, Taipei.
 The
first and only IBM life science and healthcare solution
development and enabling center in Asia Pacific region
beside Japan.
 Develop
and construct a flexible, on demand bioinformatics
common platform based on open standards.
 Linkage
2
and bridge to IBM worldwide research capacity.
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
The Current Problems in Biomedical Studies
How can I utilize
&
link Analysis
tools on
Data
different sites ??
How can I integrate
information
from
Data
Integration
different data
resources ??
How can I do with
Computation
limited
computing
Power
power ??
3
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
The Current Problems in Biomedical Studies
 Data
Analysis
– Multiple bioinformatics tools for an analysis process.
– Bioinformatics tools on various websites and systems.
– Not unified user interfaces or data formats.
 Data
Integration
– Require to integrate information to gain global view.
– Dispersed data in different websites, database systems and without
standard.
 Computation
Power
– Require powerful and flexible system and environment to support
bioinformatics analyses and data integration.
4
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
LSCE’s Approaches to Tackle the Problems
 Data
Analysis
– Integrated workplace and unified interface.
– The “Lego” type workflow and workflow engine.
– Web Services as standard.
 Data
Integration
– Federated data integration.
– Easy data query and search for end users.
 Computation
Power
– High performance computing.
– Grid computing architecture.
5
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
LSCE’s Approaches to Tackle the Problems
 Data
Analysis
– Integrated workplace and unified interface.
– The “Lego” type workflow and workflow engine.
– Web Services as standard.
 Data
Integration
– Federated data integration.
– Easy data query and search for end users.
 Computation
Power
– High performance computing.
– Grid computing architecture.
6
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Web Services as Unified Standards
Nature. 2002 May 9;417(6885):119-20
adapted from a keynote speech given by Lincoln Stein
at the 2002 O’Reilly Open Bioinformatics Conference
7
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
“Lego” Type Component and Workflow
Traditional Approach
Tool 2
Tool 1
Tool 3
Tool
Tool 4
4
LINUX
Our Approach
Tool 2
Tool 1
Site A
LINUX
8
Site B
MS
Site C
UNIX
Site A
MS
IBM developerWorks| Oct 2007
Site E
LINUX
Tool 3
Site X
LINUX
Tool
Tool 4
4
Site Z
UNIX
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
LSCE Static Workflow
Bioinformatics
tools
9
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Traditional Analysis Process
Format conversion
input
output
Format conversion
output
input
input
Format conversion
output
input
output
Sequence
Alignment
Multiple Sequence
Alignment
Sequence
Relation Analysis
Sequence
Distance Analysis
BLAST
ClustalW
Protdist
Neighbor
Individual
Websites
US
NCBI
UK
EBI
France
Phylip
Germany
Max-Planck
Analysis Time
10
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
IBM Bioinformatics Common Platform
IBM Bioinformatics Common Platform
Phylogenic Analysis
Web Services
Sequence
Alignment
Multiple Sequence
Alignment
Sequence
Relation Analysis
ClustalW
Protdist
BLAST
Save time for
tool searching
Save time for
format conversion
Unified user
interface
Sequence
Distance Analysis
Neighbor
Reduce
manual error
Analysis time
11
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Bioinformatics Common Platform
– Resource Sharing
A
B
C
D
E
IBM Bioinformatics Common Platform
Workflow A
Workflow B
workflow C
workflow D
workflow E
Tool 38
Tool 24
Bioinformatics Tool 36
Analysis Tools
Web Services Pool
12
Tool 36
Tool
Tool 27
27
Tool 19
Tool 81
Tool
Tool 21
21
Tool 7
Tool 65
Tool 77
Tool 79
Tool 14
Tool 4
Tool 68
IBM developerWorks| Oct 2007
Tool 48
Tool 52
Tool 19
Tool 3
Tool 8
Tool
Tool 31
31
Tool 55
Tool 72
Tool 25
Tool 6
Tool 1
Tool 49
Tool 43
Tool 57
Tool 72
Tool 43
Tool 61
Tool 13
Tool 42
Tool 19
Tool 5
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
LSCE Dynamic Workflow
Adaptors to link components
Bioinformatics database access
Bioinformatics analysis tools
13
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
14
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
15
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Bioinformatics analysis tools
Adaptors to link components
Bioinformatics database access
16
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
DynaFlow – Unified Interface
Mouse over component box to select
command for:
“Set Inputs”
“Set Options”
“Set Outputs”
17
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
DynaFlow – User Interface
Ready State
Running State
After all parameters being set,
press “Run” button to run this step
18
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
DynaFlow – User Interface
19
Finish State
Error State
When everything goes well
When process fails
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
DynaFlow – Adaptor
20
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Integration of Bioinformatics Tools
Bioinformatics Analysis Workflows:
– 16 bioinformatics analysis workflows.
– Applications for Microarray, EST, Transcription Factor Binding Site,
Protein Structure, Antigenic Site, Alternative Splicing Site,
Phylogenetic Analyses, etc.
Bio Web Services and Data integration:
– 68 bioinformatics & 25 data integration web services components.
– Bioinformatics web services components include BLAST, CAP3,
ClustalW, GLAM, Glimmer, HEMMER, Modeller, RasMol,
RepeatMasker, SIM4, TMHMM, Vectorstrip and etc.
– Data Integration web services components include NR, Unigene,
LocusLink, dbEST, KEGG, Pfam, GO, JASPAR, InParanoid and etc.
 Value Added Database:
– Developed 6 Value Added Databases.
– VAD includes Microarray Primer Analysis, Protein–Protein Interaction,
Repeat Sequences and SCA disease and etc.
21
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
LSCE’s Approaches to Tackle the Problems
 Data
Analysis
– Integrated workplace and unified interface.
– The “Lego” type workflow and workflow engine.
– Web Services as standard.
 Data
Integration
– Federated data integration.
– Easy data query and search for end users.
 Computation
Power
– High performance computing.
– Grid computing architecture.
22
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Federated Data Integration
MySQL
Information Integrator (II)
PALS
Pfam
HMMER
Oracle
KEGG
BLAST
MS SQL
Sybase
DB2
Unigene
Mitochondria
NT
E.coli lamda
LocusLink
dbEST
rRNA
CGAP
HUGO
FASTA
NR
Homologene
IBM II supported wrappers
LSCE developed wrappers
23
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Example
 Looking
for genes expressed in human liver from UniGene
Database.
 Is
there any gene expression difference in normal tissue and
tumor??
I
am only interested in genes involved in signal transduction.
 My
research is focus on chromosome 9, 19 and 22.
I
also want to know their roles on Gene Ontology and
biological pathway.
 Do
these genes have information on OMIM disease
database??
24
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Data Integration & Query System
Data Discovery & Query Builder (DDQB)
Information Integrator (II)
25
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Click and Select Query Condition
26
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Click and Select Output Data
27
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Query Management
28
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Query Results
—
29
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
LSCE’s Approaches to Tackle the Problems
 Data
Analysis
– Integrated workplace and unified interface.
– The “Lego” type workflow and workflow engine.
– Web Services as standard.
 Data
Integration
– Federated data integration.
– Easy data query and search for end users.
 Computation
Power
– High performance computing.
– Grid computing architecture.
30
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
LSCE System Architecture
Portal
Layer
WebSephere Portal Server
Contents, Collaboration, Applications based on personalization
Application Integration
31
Other
Applications
DDQB
Application
Layer
…
Workflows
IDA
MAA
BLAST
EMBOSS
SOAP
WS II
Database
Layer
EAP
CAP3
WSDL
KEGG
GO
Hugo
UniGene
GRID Service MGMT
Others
DynaFlow Engine
Phred
…
R
Others
XML
Federated Database Access & Integration
Database Sources
DB2
…
CREPP
MPL
Web Services
SOA
Computing
Layer
Bioinformatics Common Platform
WebSphere Application Server
SwissPro ……
dbEST
Pfam
GRID Security Svc
DB2
Value Added Database
PALS
SCAdb
GRID Prog. Service
CHANGE ……
PPI
GRID Registry Svc
Globus Tool Kit
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
Collaboration & Implementation
新竹生醫園區
32
IBM developerWorks| Oct 2007
© 2007 IBM Corporation
2007 【IBM developerWorks 開發者大會】
For More Information
33

IBM Taiwan, Life Sciences Center of Excellence
– /http://www.petridish.cc/

IBM Healthcare and Life Sciences
– http://www-03.ibm.com/industries/healthcare/index.jsp

IBM Research
– http://www.research.ibm.com/

The World Community
– www.worldcommunitygrid.org

The Genographic Project
– https://www5.nationalgeographic.com/genographic/
IBM developerWorks| Oct 2007
© 2007 IBM Corporation