a research university that focused on biomedical research submited only two proposals and won both...
TRANSCRIPT
A research university that focused on biomedical research
Submited only two proposals and won both out of the 200+ applied projects in “Program to promote academic excellence” that are sponsored by Ministry of Education in Taiwan.
Bioinformatics Part of the “Program to Promote Academic Excellence”
Genome-based biomedical research for the 21st century
Infrastructure Scientific program
Educational program
BioinformaticsCenter
Bioinformaticsedu. program
Bioinformaticsresearch
Infrastructurefor genome research
Educational supports
SequencingCenter
Gene Expression
Center
ProteomicsCenter
BioinformaticsCenter
BioinformticsProgram
Provide :1. Computing resource2. Database & mirrors
3. Raw data4. Lab. Experience5. Practical training program
Infrastructure
PC-clusterOct. 1, 1999
High performancecomputing
Dec. 28, 2001
Storage AreaNetwork (SAN)Dec. 15, 2002
Biomed Grid
New job distribution policy
Ongoing
Biomed Gridhttp://binfo.ym.edu.tw/grid/
Globus server PC-cluster 1: PC-cluster 2:
Sun E450 clone
Server & disk array
Server & disk arrayIBM p690
Compaq XP1000
National Research Program for Genomic Medicine
InformationTechnology
Applicationservice
Education
Bioinformatics Core
Bioinformatics Part of the “Program to Promote Academic Excellence”
Genome-based biomedical research for the 21st century
Infrastructure Scientific program
Educational program
BioinformaticsCenter
Bioinformaticsedu. program
Bioinformaticsresearch
Try to be in the frontier of bioinformatics research
User-centric environment
Integration and data mining
Information-driven biomedical research
Genome researches is the driving force for bioinformatics study
Human
Vibrio vulnificus
Mycoplasma fermentan
Ling-Chi(Ganoderma
lucidum)
Importance of team work “Special Topics in Bioinformatics” course
Broaden your horizon and learn how to manage a projectComparative genomics
Functional & cellular rolesGene map viewer
Gene lists Protein domain family
Structural modeling
Second yearSecond semester
biopathways, … etc.
Gene ontology Graphics
Basic sequence analysis,
database & cgi
Information integration
Protein analysis
Viewer
analysis comparison
Microarray Database
Microarray data
Metabolic pathwaysGene variation & disease databases
annotation normalization
Signal transduction pathways
Regulatory pathways
Proteomics data
Molecular interaction
Literature Gene OntologyTM
Functional classificationCellular role assignment
Goal: Establish a user-centric bioinformatics environment for microarray data analysis
Understand the diversity of life
Information “ integration” will make new discovery
Knowledge can be transformed into technology
Web service and workflow
communication protocols:
WDDX,XML-RPC,
SOAP.
Examples of the next generation bioinformatics
software
http://palsdb.ym.edu.tw/cgi-bin/palsdb/project_xml.cgi
Decoding the life
• Life can be described in a multi-dimensional space
• The above information is compressed and stored in the one-dimensional “sequence”
• To decompress the sequence information, you need to have enough dimensions
• Tissue and developmental stages are the most important dimensions.
Sequence information
decompress
Expression level
Tissue (spatial)
Development(temporal)Genes
From gene expression and protein interaction toward pathway
?
Cell., 100(1):57–70 Review, 2000.
PNAS, Vol. 95, 14863-14868
Science. Vol 292. May,2001
Pathway study is the one of most fundamental problems for biological research at molecular level
• Metabolism• Signal transduction• Biosynthesis of
macromolecules (mechanism study)– Replication
– Transcription
– RNA processing
– Translation
Gene, cellular location, tissue, development ontologies
Directed acyclic graph(DAG)
為一種重要的資料結構 , 亦即一個路徑中的每個元件不可以同時是起點也是終點 .
More value-added databasesRelated pathways can be discovered by looking for
shared components among pathways
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23
16
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1915
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1517
1517
13
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1813
Shared
Component
Pathway1 Pathway2 Index
pdgfPathway egfPathway 1.96e-40
pdgfPathway tpoPathway 9.89e-27
pdgfPathway igf1Pathway 2.26e-22
pdgfPathway insulinPathway 2.26e-22
egfPathway igf1Pathway 2.26e-22
egfPathway insulinPathway 2.26e-22
pdgfPathway ngfPathway 2.20e-22
… … …
Only those pathways that are
expressed in the same tissue
can be integrated / merged
PDGF 11
EGF 11
TNF 21
EGF/PDGF 16
ALL 4
Integrating genome, transcriptome, and prot
eome information
Modification, expression, interaction, structure
DNA
RNA
transcription
translation
protein
Genomic seq.
EST, SAGE,Gene chips
Annotation,comparison
Components Pathways and regulatory circuits Hypothetical cell
Bioinformatics Part of the “Program to Promote Academic Excellence”
Genome-based biomedical research for the 21st century
Infrastructure Scientific program
Educational program
BioinformaticsCenter
Bioinformaticsedu. program
Bioinformaticsresearch
Three years of experience in running bioinformatics program.
Posters for recruitingstudents – more and more locally generated results
Bioinformatics Program Is Supported by Four Institutes in Three Colleges
3. Institute of Health Informatics and Decision Making, College of Medicine
2. Institute of Biotechnology in Medicine, College of Medical Technology and Engineering
1. Institute of Biochemiistry, Institute of Genetics, College of Life Science
Bioinformatics Program
12
3
Active academic activities
• Routine seminar for two years (i.e. 4 semesters)• Symposia & workshops
– 2000: Shoba Ranagnathan (vice president of APBioNet), Cathy Wu (Director of PIR)
– 2001: Michael Zhang (Cold Spring Harbor)– 2002: Kanehisa (previous president of Japanese Bioinf
ormatics Society) & Miyano (present president)– 2003: Gribskov (President of International Society of
Computational Biology), Wilfred Li (EOL), Ming Li
Bioinformatics in Taiwan (BIT)
The first bioinformatics symposium that has postersession to promote communication
Systems Biology
The first and secondsystems biology symposiaand workshop in Taiwan
The niche of YMU• A research university which is strong in biomedical sciences
– Institute of Bioinformatics– Institute of Health informatics (may change to Medica informatics i
n the future)
• Have close relation with Veterans General Hospital• Strong brain research• Infrastructure supports
– genome research center– bioinformatics research center
• Try to be in the frontier of bioinformatics research• Good collaboration with industry, such as IBM and HP• Excellence transportation: Within walking distance to Muni
cipal Rapid Transit station. Have shuttle bus to MRT station, too.