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

25

25

23

16

14

14

20

17

18

13

1915

19

15

1517

1517

13

13

13

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.