課程資訊
課程名稱
 生物資訊相關軟體工程
Software Engineering for Bioinformatics 
開課學期
 102-1 
授課對象
 電機資訊學院  生醫電子與資訊學研究所  
授課教師
 高成炎 
課號
 CSIE5008 
課程識別碼
 922 U0080 
班次
  
學分
 3 
全/半年
 半年 
必/選修
 選修 
上課時間
 星期三6,7,8(13:20~16:20) 
上課地點
 資105 
備註
 限學士班三年級以上
總人數上限：50人 
Ceiba 課程網頁
 http://ceiba.ntu.edu.tw/1021bio_se 
課程簡介影片
 
核心能力關聯
 本課程尚未建立核心能力關連
課程大綱
為確保您我的權利,請尊重智慧財產權及不得非法影印
課程概述

THE COURSE CONSISTS OF TWO PARTS:
- SOFTWARE ENGINEERING
- PRACTICAL APPLICATIONS FOR BIOINFORMATICS
IN SOFTWARE ENGINEERING PART, WE WILL INTRODUCE MAIN DISCIPLINES WITHIN SOFTWARE ENGINEERING, INCLUDING:
(1) LIFE CYCLE PLANNING MODELS
(2) REQUIREMENT SPECIFICATION PROCESS
(3) DESIGN, IMPLEMENTATION, AND TEST
(4) QUALITY ASSURANCE
(5) PROJECT MANAGEMENT
(6) OBJECT ORIENTED ANALYSIS AND DESIGN
(7) COMPONENT BASED ENGINEERING (SOFTWARE IC)
(8) RAPID PROTOTYPING
(9) FUNCTIONAL & RULE-BASED PROGRAMMING LANGUAGE
(10) CASE (COMPUTER-AIDED SOFTWARE ENGINEER), ETC.
IN BIOINFORMATICS PART, WE WILL INTRODUCE SOME APPLICATIONS IN BIOLOGY, INCLUDING:
(1) GENE PREDICTION
(2) GENE CHIP (MICROARRAY) ANALYSIS
(3) SEQUENCE ALIGNMENT
(4) PROTEIN STRUCTURE PREDICTION AND FOLDING
(5) DOCKING AND DRUG DESIGN  

課程目標
 This is a project oriented course, students are required to design and implement real world usable software systems. 
課程要求
 A BIOINFORMATICS APPLICATIONS TERM PROJECT AND CONSISTS OF:
(1) REQUIREMENT SPECIFICATION
(2) DESIGN
(3) IMPLEMENTATION
(4) VERIFICATION
(5) PRESENTATION OF THE RESULT  
預期每週課後學習時數
  
Office Hours
 每週二 13:00~19:00
每週三 13:00~14:20 備註： 以上為TA Hours, 地點在資工系401室, 找老師請直接Email 
指定閱讀
  
參考書目
 Here are some useful books on software engineering:

•Frederick P. Brooks, Jr., The Mythical Man Month. Addison-Wesley, 1972. This
is the classical text on software engineering. It is short, witty and still
relevant after forty years.

•Sommerville, Ian, Software Engineering, Ninth Edition. Addison-Wesley, 2010.

•Pfleeger, Shari Lawrence, Software Engineering Theory and Practice, fourth
edition. Prentice- Hall 2009.

•Grady Booch, Robert A. Maksimchuk, Michael W. Engel, and Bobbi J. Young,
Object-Oriented Analysis and Design with Applications, third edition.
Benjamin/Cummings 2007.

•Grady Booch, James Rumbaugh, Ivar Jacobson, The Unified Modeling Language.
Addison-Wesley 1999.

•Rob Pooley, Perdita Stevens, Using UML Software Engineering with Objects and
Components, second edition. Addison-Wesley 2005.

•Bernd Bruegge and Allen H. Dutoit, Object-Oriented Software Engineering Using
UML, Patterns and Java, third edition. Prentice Hall, 2009.

•Mary Shaw and David Garlan, Software architecture: perspectives on an
emerging discipline. Prentice Hall, 1996.

•E. Gamma, R. Helm, R. Johnson, and J. Vlissides, Design Patterns: Elements of
Reusable Object-Oriented Software. Addison-Wesley, 1994. This is the standard
book on design patterns.

•Steve McConnell, Code Complete: A Practical Handbook of Software
Construction, Second Edition. Microsoft Press, 2004

•Armando Fox and David Patterson, Engineering Software as a Service: An Agile
Approach Using Cloud Computing, Strawberry Canyon LLC, 2013 
評量方式
(僅供參考)
  
No.
項目
百分比
說明
1. 
 專題參與度 
30% 
  
2. 
 課堂參與度 
20% 
  
3. 
 作業 
20% 
  
4. 
 報告 
30% 
  
 
課程進度
週次
日期
單元主題
第1週
 9/11  Introduction 
第2週
 9/18  Project management 
第3週
 9/25  Software Processes 
第4週
 10/02  Software Reuse 
第5週
 10/09  NGS Project Tools Demo - BLAST, Bowtie, VM 
第6週
 10/16  爐心熔毀大逃亡-上學期專題成果DEMO 
第7週
 10/23  System Modeling, Wireframe, MVC, Learning Resources 
第8週
 10/30  EBAR演算法與程式討論 
第9週
 11/06  期中考停課 
第10週
 11/13  軟體工程的歷史與地緣關係 
第11週
 11/20  期末專題問題與討論(老師出國) 
第12週
 11/27  網路創業, 1st Project Check Point 
第13週
 12/04  Software Testing, VIGS, IGV 
第14週
 12/11  Gerhard-Wilhelm Weber Talk 
第15週
 12/18  華聯生技產品部副理:劉家宏博士 演講, 分析肝癌反映路徑間之蛋白質交互作用發現一個嶄新預後標記 
第16週
 12/25  2ed Project Check Point 
第17週
 1/01  Final Project Demo