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生物資訊與網路資源

生物資訊與網路資源. 生物資訊與網路資源. Bioinformatics and Web Resources. Department of Life Science Institute of Biotechnology National Dong Hwa University. David Shiuan. Bioinformatics. Bioinformatics (Computational Biology or Information Biology). Computational approaches to

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生物資訊與網路資源

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

  2. Bioinformatics Bioinformatics(Computational Biology or Information Biology) • Computational approaches to answer biological questions 使用電腦來解決生物學的問題

  3. Bioformaticscovers : • 型態、結構、顏色 morphology,color • DNA 及 基因體 genomes • 蛋白質、碳水化合物等大分子 Biomacromolecules, proteome • 生化、生理、遺傳、演化特性 biochemistry, physiology,genetics,evolution etc.

  4. NTHU清華大學 生物資訊與網路教學卓越計畫

  5. 清華大學 生物資訊與網路教學 卓越計畫

  6. Bioinformatics : Revelations from the Book of Life • …….BIOHRIACGTDSTRONGJKWISEGT • TUSH……MLGHSINCERITYGKJ……….. • CANCER • ……...FEBEAUTYRANTGGGGCUP………

  7. Bioinformatics • Information can be converted into knowledge • Promote human civilization and science achievements • Creat knowledge-based economics

  8. Bioinformatics Bioinformatics(Computational Biology or Information Biology) Why does it emerge so rapidly ? • 1. Explosion of sequence and structural information • 2. Advancement of Internet

  9. The Three Projects Affecting Human Civilization most • Menhatten Project 1940s • Apollo Project 1965s • Human Genome Project 1993-2003

  10. Human Genome Project1990-2003 • 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

  11. GOLD (Genomes OnLine Database)

  12. Internet (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

  13. Major Tasks of Bioinformatics 1. Establish data base 2. Search/retrieve bioinformations 3. Analysis of bioinformations

  14. From independent works to unified actions • Database • Data Retrieval • Data Analysis

  15. Major Disciplines • Algorithm, Graphics, Signal Processing, Statistics, Simulation, Computer Architecture, Database Management, Artificial Intelligence… • Biochemistry, Molecular Biology, Genomics, Proteomics, Physical Chemistry, Structural Biology/Physics

  16. Applications • 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

  17. Gene 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

  18. NCBI (National Center for Biotechnology Information) Established (1988) by US Congress • System for storing and analyzing • Advancing methods for data retrieval and analysis • Facilitation of the use

  19. NCBI • Database : GenBank • Database Retrieval Entrez, PubMed, Locus Link, Taxonomy Browser • Data Analysis BLAST, Electronic PCR, ORF Finder, UniGene, dbSNP, 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).

  20. GenBank • Created (1982) by NIGMS/NIH • Los Alamos National Lab - annotates & organizes • IntelliGenetics (1987-) • NCBI (1988-)

  21. NCBI

  22. Human Genome, Alzheimer disease

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

  24. NCBI - ORF Finder, M. hyopneumoniae PTSI

  25. NCBI – ORF Finder, PTSI

  26. NCBI – BLAST, PTSI

  27. NCBI – Structure, MMDB, PTSI

  28. NCBI – Cn3D, PTSI structure

  29. ExPASy

  30. ExPASy - 2o structureprediction, GOR IV, PTSI

  31. ExPASy –2o structureprediction, GOR IV, PTSI

  32. ExPASy – Topology prediction, SOSUI

  33. ExPASy – Topology prediction, SOSUI

  34. ExPASy – Topology prediction, SOSUI

  35. PDB

  36. PDB

  37. Web 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

  38. Conclusion • Tremendous information on the web • Promote biological sciences • Solving problems and creating new hints/problems • Use the information andgenerate new information

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