バイオインフォマティクス[22C5067]

科目名
Course Title
バイオインフォマティクス[22C5067]
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
CCBM キャリアデザイン  
単位数 2.0単位 履修年次 34

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 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,対面授業のみ

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

ALH区分
通常授業として実施(11・12限等)

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
Sequence similarity searching
第7回
Sequence motif analysis
第8回
Clustering: Hierarchical clustering, k-means and PCA
第9回
Supervised learning methods I: Logistic regression model
第10回
Supervised learning methods II: k-Nearest Neighbors
第11回
Phylogenetics visualization
第12回
Protein 3D modeling: data format and analysis
第13回
Protein 3D folding
第14回
Overview of other bioinformatics applications: data mining, cell tracking, ...
第15回
Conclusion

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.