生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa...

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生生生生生生生生生 生生生生生生生生生 Department of Life S cience Institute of Biotec hnology National Dong Hwa Unive rsity David Shiuan 生生生生生生生生生 生生生生生生生生生 Bioinformatics and Web Resources Bioinformatics and Web Resources

Transcript of 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa...

Page 1: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

生物資訊與網路資源生物資訊與網路資源

Department of Life Science Institute of BiotechnologyNational Dong Hwa University

David Shiuan

生物資訊與網路資源生物資訊與網路資源Bioinformatics and Web ResourcesBioinformatics and Web Resources

Page 2: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

BioinformaticsBioinformatics(Computational Biology (Computational Biology

or Information Biology)or Information Biology)

Computational approaches to

answer biological questions

使用電腦來解決生物學的問題

BioinformaticsBioinformatics

Page 3: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

BioformaticsBioformatics covers :covers :

1. 型態、結構、顏色 morphology,color

2. DNA 及 基因體 genomes

3. 蛋白質、碳水化合物等大分子 Biomacromolecules, proteome

4. 生化、生理、遺傳、演化特性 biochemistry, physiology,genetics,evolution etc.

Page 4: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NTHUNTHU 清華大學 生物資訊與網路教學卓越計清華大學 生物資訊與網路教學卓越計畫畫

Page 5: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

清華大學 生物資訊與網路教學 卓越計畫清華大學 生物資訊與網路教學 卓越計畫

Page 6: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.
Page 7: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.
Page 8: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.
Page 9: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Bioinformatics : Bioinformatics : Revelations from Revelations from the Book of Lifethe Book of Life

…….BIOHRIACGTDSTRONGJKWISEGT

TUSH……MLGHSINCERITYGKJ……….. CANCER

……...FEBEAUTYRANTGGGGCUP………

Page 10: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

BioinformaticsBioinformatics

Information can be converted into

knowledge

Promote human civilization and

science achievements

Creat knowledge-based economics

Page 11: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

BioinformaticsBioinformatics(Computational Biology (Computational Biology

or Information Biology)or Information Biology)

Why does it emerge so rapidly ?

1. Explosion of sequence and structural information

2. Advancement of Internet

BioinformaticsBioinformatics

Page 12: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

The Three Projects Affecting The Three Projects Affecting Human Civilization mostHuman Civilization most

Menhatten Project 1940s

Apollo Project 1965s

Human Genome Project 1993-2003

Page 13: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Human Genome ProjectHuman Genome Project 1990-20031990-2003

Unravelling the 3 x 109 bp genome

Goals 1. Understanding Life Science 2. Disease Diagnosis and Treatment Legal and Ethical Challenges 1. Human rights 2. Health insurance

Page 14: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

GOLD GOLD (Genomes OnLine Database)(Genomes OnLine Database)

Page 15: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.
Page 16: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.
Page 17: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Internet Internet (International Network)(International Network)

1972 - ARPAnet (created by Defense Advanced Research Projects Agency), cold war network

1979 - Usenet (the first News Distribution protocol)

1982 - TCP/IP (Transmission Control Protocol/ Internet Protocol), with routing capability

1987 - NSFnet (TCP/IP based, connecting university supercomputers, evolved into Inernet today)

1990 - Commercial links to Internet, and popularization of WWW

Page 18: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Major Tasks of Major Tasks of BioinformaticsBioinformatics

1. Establish data base

2. Search/retrieve bioinformations

3. Analysis of bioinformations

Page 19: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

From independent works From independent works to unified actionsto unified actions

1. Database

2. Data Retrieval

3. Data Analysis

Page 20: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Major DisciplinesMajor Disciplines

Algorithm, Graphics, Signal Processing, Statistics, Simulation, Computer Architecture, Database Management, Artificial Intelligence…

Biochemistry, Molecular Biology, Genomics, Proteomics, Physical Chemistry, Structural Biology/Physics

Page 21: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ApplicationApplicationss

Database Construct, Database Query, Genome Mapping and Comparison, Gene Identification and Annotation

Sequence Alignment, Molecular Evolution

Structure Alignment and Comparison, Structure Prediction, Structure-Based Drug Design, Molecular Modeling and Simulation

Page 22: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Gene AnnotationGene Annotation

定序 DNA Sequencing

組合 Assemble DNA Sequence

確認基因 Gene Identification

功能註解 Gene Annotation

資料庫 GenBank

使用分析 Retrieval and Analysis

Page 23: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBINCBI (National Center for (National Center for Biotechnology Information)Biotechnology Information)

Established (1988) by US Congress

1. System for storing and analyzing

2. Advancing methods for data retrieval and analysis

3. Facilitation of the use

Page 24: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBINCBI1. Database : GenBank

2. Database Retrieval Entrez, PubMed, Locus Link, Taxonomy Browser

3. Data Analysis BLAST, Electronic PCR, ORF Finder, UniGene, dbS

NP, Human Genome Sequencing, Human MapViewer, Intrer Genomes, Cancer Chromosome Aberration Project (CCAP), Gene Expression Omnibus (GEO), Online Online Mendelian Inheritance in Man (OMIM), The Molecular Modeling DataBase (MMDB), and the Conserved Domain Database (CDD).

Page 25: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

GenBankGenBank

Created (1982) by NIGMS/NIH

Los Alamos National Lab - annotates & organizes

IntelliGenetics (1987-)

NCBI (1988-)

Page 26: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBINCBI

Page 27: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Human Genome, Human Genome, Alzheimer diseaseAlzheimer disease

Page 28: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Human Genome Map, Human Genome Map, Presenilin 2 ( Alzheimer disease 4)Presenilin 2 ( Alzheimer disease 4)

Page 29: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBI - ORF Finder, NCBI - ORF Finder, M. hyopneumoniaeM. hyopneumoniae PTSI PTSI

Page 30: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBI – ORF Finder, PTSINCBI – ORF Finder, PTSI

Page 31: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBI – BLAST, PTSINCBI – BLAST, PTSI

Page 32: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBI – Structure, MMDB, PTSINCBI – Structure, MMDB, PTSI

Page 33: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

NCBI – Cn3D, PTSI structureNCBI – Cn3D, PTSI structure

Page 34: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ExPASyExPASy

Page 35: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ExPASy - 2ExPASy - 2o structure prediction, GOR IV, PTSI

Page 36: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ExPASy –ExPASy – 22o structure prediction, GOR IV, PTSI

Page 37: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ExPASy – Topology prediction, SOSUI

Page 38: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ExPASy – Topology prediction, SOSUI

Page 39: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ExPASy – Topology prediction, SOSUI

Page 40: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

PDBPDB

Page 41: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

PDBPDB

Page 42: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

Web ResourcesWeb Resources

Organization : NCBI/NIH, EBI/EMBL, SIB

Database : GenBank, ExPASy, PDB

Societies/Agencies : WHO, ASM

Universities : NIH, CDC, Pasteur, 國衛院 , 高速電腦中心 , 清華 , 陽明

Firms : Celera, Human Genome Sciences

Page 43: 生物資訊與網路資源 Department of Life Science Institute of Biotechnology National Dong Hwa University David Shiuan 生物資訊與網路資源 Bioinformatics and Web Resources.

ConclusionConclusion

Tremendous information on the web

Promote biological sciences

Solving problems and creating new hints/problems

Use the information and generate new information