科目名 Course Title	バイオインフォマティクス［26C5067］ Bioinformatics
授業言語 Language	English
科目区分・科目種	情報科学科	クラス	情報科学科
コンピテンシー	◎問題解決力	ｶﾗｰｺｰﾄﾞ
単位数	2.0単位	履修年次	3〜4年

担当教員	オベル加藤　ナタナエル
学期	前期
曜日・時限・教室	木曜 7 〜 8 限 共3-408【情報科学講義室2】

受講条件・その他注意
Prerequisite: None, but familiarity with the Python programming language will help.

授業の形態
講義

教科書・参考文献
References: - Bioinformatics Programming Using Python, by Mitchell L Model, Publisher: O'Reilly Media, Inc. ISBN: 978-0596154509 - The Biopython tutorial, available at biopython.org

ＡＬＨ区分
ＡＬＨを実施しない

アクティブラーニングの技法
問題基盤型学習（PBL：Problem Based Learning）

評価方法・評価割合
小論文（レポート）=70%，授業への参加態度=30%

主題と目標

Bioinformatics is the application of information science techniques to biological data. In recent years, the amount of data generated by biological research has skyrocketed, and the use of automated data analysis has become necessary. This class will give an overview of the required biological concepts, then provide concrete exemples of applications, ranging from sequence alignment to time series analysis. Exercices will rely on the Python programming language.

授業計画
第1回	Introduction to Bioinformatics; overview
第2回	Biology fundamentals: Cell, Genome, Protein, DNA, RNA and the central dogma
第3回	Biological sequence data in Python: encoding and manipulation
第4回	Sequence alignment I: dynamic programming
第5回	Sequence alignment II: BLAST
第6回	Homology discovery
第7回	Unsupervised learning methods: clustering
第8回	Supervised learning methods
第9回	Phylogenetic trees
第10回	Gene regulatory networks
第11回	WeiGhted Correlation Network Analysis (WGCNA)
第12回	Modeling cells
第13回	Protein 3D folding
第14回	Nucleic acid folding algorithms
第15回	Overview of other bioinformatics applications: data mining, cell tracking, ...

時間外学習
Time will be given in class to attempt the programming exercises. Students may find it beneficial to have a look at the references outside of class

学生へのメッセージ

Bioinformatics is an exciting field of application of computer sciences tools. The goal of this class is mostly to help students bridge the gap toward interdisciplinary studies. No prior knowledge of biology nor python is required. While the class is taught in English, interactions in Japanese are possible if required. Depending on the number of participants, the class will either take place in person or partially online.