This course is offered in English.
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<br>本課程採英文授課.
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<br> 一、課程說明(Course Description)
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<br>“Throughout the foreseeable future, research in medicine, molecular biology, and biotechnology will be dominated by scientific advancements resulting from the Human Genome Project. Knowledge of genomes will elucidate disease patterns and promises improved and personalized treatments. Food and drug development will be revolutionized by the focused manipulated of genes and biochemical process.”
<br>– by Prof. Eberhard O. Voit.
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<br>In this course, we will introduce essential servers, databases and online tools in Bioinformatics. We will also conduct hand-on exercises in functional genomics and protein analyses.
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<br>本課程兼重學理與實作，藉由習題與範例，使學員能熟悉網路上各種生物資訊之取得及應用，並針對各種常用生物資料庫作概略性的介紹，包括 NCBI, Protein Data Bank (PDB)、 KEGG、ExPasy 等生物資料庫。 課程中將連線上網，實際操作、演練各種輔助軟體 (Browser, viewer, molecular displayer...)。
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<br>Parts of the contents require basic knowledge in Molecular and cellular biology.
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<br>部分內容需具有生科系本科生大二基礎
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<br>二、指定用書(Text Books)
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<br>None
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<br> 三、參考書籍(References)
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<br>1. Bioinformatics: a practical guide to the analysis of genes and proteins
<br>Third Edition -- Gene Module
<br>(http://as.wiley.com/WileyCDA/WileyTitle/productCd-0471478784.html)
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<br> 四、教學方式(Teaching Method)
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<br>Lectures and hand-on training will be offered in Life Science computer room.
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<br>在電腦教室上課，課堂講解示範與學生實地操做並行。
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<br> 五、教學進度(Syllabus)
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<br>Gene Module- 
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<br>1.	Introduction to Bioinformatics: history and usage in industry - 
<br>2.	Information retrieval from biological database - 
<br>3.	Sequence alignment and database searching - 
<br>4.	Genomic mapping and mapping databases - 
<br>5.	Predictive methods using DNA sequences – 
<br>6.	Expressed sequence tags (ESTs) – 
<br>7.	Sequence assembly and finishing methods – 
<br>8.	Phylogenetic analysis – 
<br>9.	Comparative genome analysis – 
<br>10.	Large-scale genome analysis – 
<br>Special Topic: Using PERL to facilitate biological analysis - 
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<br>Midterm
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<br>Protein Module – 
<br>(Text and tools to be found in NTHU-Life Alpha Server)
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<br>1.	Protein function prediction by similarity (homology) to characterized proteins
<br>2.	Identifying related protein family members 
<br>3.	Multiple sequence alignment: methods and interpretation
<br>4.	Hidden Markov models: use in homolog identification, structure prediction, and multiple sequence alignment
<br>5.	Protein structure prediction methods
<br>6.	Motif detection 
<br>7.	Predicting binding pocket and other critical functional positions in proteins 
<br>8.	Subfamily classification 
<br>9.	Experimental methods for determining protein structure & function
<br>10.	Public databases of protein structure and function
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<br>Final 
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<br> 六、成績考核(Evaluation)
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<br>Grading policy - Homework 50% / Midterm and final Exam. 30% / Projects 20% 
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<br>10% credit will be deducted for late homework. Homework submission shall be be delayed for more than 3 days. 
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<br>總成績 算法 — Homework 50% / Midterm and final Exam. 30% / Projects 20% 
<br>Homework 遲交一天扣該次 homework 成績10%，遲交三天視同未交。
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<br>Do not be late for the class. Two counts of late arrival will be marked as 1 x absence (10% credit deduction for the final score.) Three absences will result in a "F" of the final grade.
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<br>上課時間 — 請勿遲到 
<br>遲到兩次以曠課一次論，曠課一次扣總成績十分，曠課三次以不及格論。 
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<br> 七、可連結之網頁位址 (Links)
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<br>NTHU E-Learning System:  http://lms.nthu.edu.tw/
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<br>NTHU LS Alpha server: http://alpha.life.nthu.edu.tw/
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