IIST (Institute of Integrated Science and Technology)

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GNM500D1(ゲノム科学 / Genome science 500)
Introduction to Bioinformatics
バイオインフォマティクス入門

Antonio TSUNESHIGE

Class code etc
Faculty/Graduate school IIST (Institute of Integrated Science and Technology)
Attached documents
Year 2022
Class code YD952
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Term
Day/Period
Class Type
Campus 小金井 / Koganei
Classroom name 各学部・研究科等の時間割等で確認
Grade
Credit(s) 2
Notes
Class taught by instructors with practical experience

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Outline and objectives

This introductory course is offered to students in general. No previous knowledge of molecular biology or chemistry, although recommended, is not required, as most basic topics will be presented in a concise manner. Processes covering from gathering scientific information, to sequencing of genomic material will be presented.

Goal

After the completion of this course, the student should be able:
(1) to understand the basic concepts and principles of bioinformatics, and how they are applied routinely;
(2) to acquire basic and relevant information in the literature
by cross-referencing;
(3) to retrieve and analyze genomic and protein sequences from
their respective databases; and
(4) to interpret the processed data, especially with emphasis on the current pandemic situation.

Default language used in class

英語 / English

Method(s)(学期の途中で変更になる場合には、別途提示します。 /If the Method(s) is changed, we will announce the details of any changes. )

This course consists of fourteen lectures. Relevant material
(personal notes, scientific articles, all in English) for the lectures will be provided as needed using the Hoppii system. Part of the classes
will emphasize on problem-solving situations with guidance.

Active learning in class (Group discussion, Debate.etc.)

あり / Yes

Fieldwork in class

なし / No

Schedule

授業形態/methods of teaching:対面/face to face

※各回の授業形態は予定です。教員の指示に従ってください。

1[オンライン/online]:What is
bioinformatics?
-Part 1

Why is bioinformatics so relevant nowadays? Introduction to
NCBI, Expasy, and other bioinformatics resource sites.

2[対面/face to face]:What is
bioinformatics?
-Part 2

Understanding the span and imitations of bioinformatics. Pending issues.

3[対面/face to face]:What is Life? Living
organisms.

Introduction to basic concepts in biology. Chemistry of Life.

4[対面/face to face]:Rules of the Game.
Part 1

Variety of life forms. Basic concepts in molecular biology.

5[対面/face to face]:Rules of the Game.
Part 2

Basic concepts in molecular biology (continued).

6[対面/face to face]:Rules of the Game.
Part 3

Basic concepts in molecular biology (continued).
Terminology and processes.

7[対面/face to face]:Analyzing a protein
sequence. Part 1

Retrieval of a
protein sequence.

8[対面/face to face]:Analyzing a protein
sequence. Part 2

Pairwise and Multiple sequence alignment.
BLAST and Clustal.
PAM and BLOSUM scoring systems.

9[対面/face to face]:Nucleotide
sequences. Part 1

Chemistry of DNA and RNA molecules.

10[対面/face to face]:Nucleotide
sequences. Part 2

Analyzing DNA and RNA
composition.

11[対面/face to face]:Evolution and
phylogenetic trees. Part 1.

Biological basis of evolution and phylogenetics at
molecular level.

12[対面/face to face]:Evolution and
phylogenetic trees. Part 2.

Phylogenetic tree construction methods. Distance-based methods.

13[対面/face to face]:Evolution and
phylogenetic trees. Part 3.

Interpretation
of phylogenetic trees.

14[対面/face to face]:Role of Bioinformatics in the COVID-19 era.

How SARS-CoV-2 evolves and attempts to persist in our world.

Work to be done outside of class (preparation, etc.)

Standard study time outside of class for preparation and review: approximately 5 hours.
During classes, a personal computer will be required to login and access database sites, retrieve specific information. Also, you will be asked to work using specific analysis software on relevant data, and interpret the obtained results.

Textbooks

"Bioinformatics for Dummies", J.-M. Claverie, C. Notredame,
Wiley Publishing Inc., 2007.
"Essential Bioinformatics", Jin Xiong, Cambridge University Press, 2006.
Purchase of these books is not necessary. Lectures are based on a
collection of books and articles from several sources. Therefore, material will be provided. Information is widely available on the internet.

References

Relevant scientific articles will be provided prior classes. However, the scope of these will be tailored to the capabilities of the student.

Grading criteria

Reports (40%) are to be submitted as requested within deadline
limit.
Final exam (40%) at the end of course.
Active participation in class (20%) is strongly encouraged.
Some of the reports require the student to link to a server to retrieve
data and perform the appropriate analysis.

Changes following student comments

Due to the manageable number or students in each session, a
one-on-one interaction during classes has been always possible.
This provides a real-time feedback to adjust, in a bespoke manner, the content of each lecture, to overcome the wide diversity of backgrounds of the students. In a such a way, this course, although introductory, can be offered to any student holding any background, and personal interest stands as the only requirement.
Due to the current COVID-19 pandemic, for the current year of 2022, this course has been also implemented for real-time online delivery, that allows attendance of overseas students. Should conditions permit, in addition to the online format, in-person classes could be easily implemented, previous arrangement.

Equipment student needs to prepare

A personal computer with audiovisual capabilities, and internet access is highly recommended. All handouts, study material, assignments will be uploaded, and reports will be submitted via the Hoppii system.