計算生物學這門課主要在教導學生親自撰寫電腦程式來研究一些計算生物學上的演算法與研究課題，所以在課程的開始會先教導一些程式撰寫技巧，接著在課堂上我們將會介紹並演練序列比對、多重序列比對、結構比對、分群分類方法以及機器學習等課題。學生透過實際撰寫程式的研究方法並製作期末專題，必會對計算生物學有深刻的認知。
The course is a practical, hands-on approach to the field of computational molecular biology. Basic programming skill will be taught in the beginning of this course. Various existing methods will be critically described and the algorithm of each will be discussed. For example, dynamic programming, sequence alignment, multiple sequence alignment, clustering and machine learning method. Students will have practical assignments utilizing the tools described and have a final project of computational molecular biology.
先修科目Prerequisites
教學方式Teaching Methods
評量方式Assessment
Homework (30%), Midterm (20%) and Final project (50%)
參考書目Reference
1. Introduction to Computational Molecular Biology : 1997, edited by Joao Carlos Setubal, Joao Meidanis
2. Computational Molecular Biology (An Algorithmic Approach) : 2000, edited by Pavel A. Pevzner
教學進度Course Schedule
2017/09/18 計算生物學簡介
Introduction to computational biology
陸志豪(Chih-Hao Lu) 2017/09/25 基本程式設計
Basic programming
陸志豪(Chih-Hao Lu) 2017/10/02 基本程式設計
Basic programming
陸志豪(Chih-Hao Lu) 2017/10/09 雙十節彈性放假
Holiday
陸志豪(Chih-Hao Lu) 2017/10/16 陣列與排序
Array and sorting
陸志豪(Chih-Hao Lu) 2017/10/23 陣列與排序
Array and sorting
陸志豪(Chih-Hao Lu) 2017/10/30 邏輯與演算法
Logic and algorithm
陸志豪(Chih-Hao Lu) 2017/11/06 基因序列比對
Gene sequence alignment
陸志豪(Chih-Hao Lu) 2017/11/13 蛋白質序列比對
Protein sequence alignment
陸志豪(Chih-Hao Lu) 2017/11/20 序列相似度與一致性的計算
Sequence similarity and identity
陸志豪(Chih-Hao Lu) 2017/11/27 蛋白質結構檔案的讀取
PDB parser
陸志豪(Chih-Hao Lu) 2017/12/04 蛋白質中氫鍵的計算
Calculation of H-bonds
陸志豪(Chih-Hao Lu) 2017/12/11 原子間距離、角度、雙面角的計算
Calculation of distance, angle and torsion angle
陸志豪(Chih-Hao Lu) 2017/12/18 機器學習在單一細胞基因體的應用
Machine learning in single-cell genomics
林詩鈞 2017/12/25 機器學習在單一細胞基因體的應用
Machine learning in single-cell genomics
林詩鈞 2018/01/01 元旦
Holiday
陸志豪(Chih-Hao Lu) 2018/01/08 蛋白質與小分子的交互作用區域偵測
Protein binding site detection
陸志豪(Chih-Hao Lu) 2018/01/15 期末專題報告
Final project report
陸志豪(Chih-Hao Lu)