Bioinformatics Center - TIGP--Bioinformatics Program

powerfultennesseeΒιοτεχνολογία

2 Οκτ 2013 (πριν από 4 χρόνια και 9 μέρες)

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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

Bioinformatics

Center

Bioinformatics

edu. program

Bioinformatics

research

Infrastructure

for genome
research

Educational supports

Sequencing

Center

Gene
Expression

Center

Proteomics

Center

Bioinformatics

Center

Bioinformtics

Program

Provide :

1. Computing


resource

2. Database &


mirrors


3. Raw data

4. Lab.


Experience

5. Practical training


program

Infrastructure

PC
-
cluster

Oct. 1, 1999

High performance

computing

Dec. 28, 2001

Storage Area

Network (SAN)

Dec. 15, 2002

Biomed Grid

New job
distribution
policy

Ongoing

Biomed Grid

http://binfo.ym.edu.tw/grid/

Globus server

PC
-
cluster 1:

PC
-
cluster 2:

Sun E450

clone

Server &

disk array

Server &

disk array

IBM p690

Compaq

XP1000

National Research Program for
Genomic Medicine

Information

Technology

Application

service

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

Bioinformatics

Center

Bioinformatics

edu. program

Bioinformatics

research

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 project

Comparative genomics

Functional & cellular roles

Gene map viewer

Gene lists

Protein domain family

Structural modeling

Second year

Second semester

biopathways, …
etc.

Gene ontology

Graphics

Basic sequence
analysis,

database & cgi

Information
integration

Protein
analysis

Viewer

analysis
comparison

Microarray
Database

Microarray data

Metabolic pathways

Gene variation &
disease databases

annotation
normalization

Signal transduction pathways

Regulatory pathways

Proteomics data

Molecular interaction

Literature

Gene Ontology
TM

Functional classification

Cellular 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 databases

Related pathways can be discovered by looking for


shared components among pathways

25

25

23

16

14

14

20

17

18

13

19

15

19

15

15

17

15

17

13

13

13

18

13

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
proteome 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

Bioinformatics

Center

Bioinformatics

edu. program

Bioinformatics

research

Three years of experience in
running bioinformatics program.

Posters for recruiting

students


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

1

2

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
Bioinformatics 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 poster

session to promote

communication

Systems Biology

The first and second

systems biology symposia

and 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
in 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
Municipal Rapid Transit station. Have shuttle bus to MRT
station, too.