学府共通教育プログラム
Course Title: AgriBio Global Exercise II
Subtitle: Practical Application of Bioinformatics Analysis Using Genomic Information
Language: English/Japanese
Lecturer: Dr. Hideki Hirakawa （Kazusa DNA Research Institute）
https://www.kazusa.or.jp/en/
Credits: 1 credit
Dates: 1/16 (on demand), 1/23 (face-to-face in 3&4 hours), 1/24 (face-to-face in 2&3 hours), 1/30 (Zoom in 3&4 hours)
Enrollment Requirements:
This course is open to students enrolled in the Faculty of Bioresource and Bioenvironmental Sciences. It is an advanced course designed for students interested in genome analysis or actively involved in genomic analysis. Students are required to bring a Windows PC (laptop), and in case of limited availability (limited number of PCs may be provided).
Number of Participants:
Up to 15 students.
Course Objectives:
Introduce the latest methods for genome decoding and analysis, databases, and subsequently engage in practical exercises in bioinformatics analysis. Provide a forum for students to ask questions related to the on-going analysis and strive for solutions. The goal is for students to be able to independently perform bioinformatics analysis through this course.
Keywords:
Bioinformatics, Genome Decoding, Genome Analysis, Databases, DX (Digital Transformation)
Required Materials:
Slide presentations
Personal computer (PC windows) (for exercises including genome analysis and programming).
Course Schedule:
(1st.class on demand on Jan 16) Introduction to Genome Decoding and Analysis Methods, Databases
Learn about the latest methods and analysis techniques for genome decoding using next-generation sequencers and explore various databases containing data obtained from genome decoding.
(2nd class on demand on Jan 16) Introduction to Bioinformatics Analysis
Study bioinformatics analysis necessary for genome decoding, such as genome assembly, gene prediction, and gene function prediction.
(3rd. 3rd hour on Jan 23@room224 on site) Bioinformatics Analysis Practical Exercise (1)
Discuss the setup of the PC environment required for bioinformatics analysis and learn about operations in Linux necessary for analysis.
Topics include: Windows Terminal, Bioconda, program installation, commands, editors, shell scripts.
(4.４th hour on site on Jan 23@room224 対面) Bioinformatics Analysis Practical Exercise (2)
Learn basic sequence analysis methods, including sequence similarity searches.
Tools include: BLAST, FASTA, ClustalW2, FigTree.
(5.2限on site on Jan 24@room 223 対面) Bioinformatics Analysis Practical Exercise (3)
Learn methods for genome assembly using next-generation sequencer data.
Tools include: MultiQC, hifiasm, Flye, HiCanu, D-Genies, Unicycler, Augustus, EggNOG.
(6.３限on site on Jan 24@room 223 対面) Bioinformatics Analysis Practical Exercise (4)
Learn methods for polymorphism analysis using next-generation sequencer data.
Tools include: Bowtie2, HISAT2, StringTie, SAMtools, SnpEff, VarScan.
(7. ３限on line live on Jan 24) Bioinformatics Analysis Practical Exercise (5)
Explore various methods using next-generation sequencer data.
(8. ４限on line live on Jan 24) Question and Answer Session
Address questions related to the course and provide solutions to queries regarding students' ongoing research analyses.
Grading Method:
Report: Submission of a report after the completion of the course.
Attendance: Mandatory attendance and participation in online lectures.
Course Title: AgriBio Global Exercise II
Subtitle: Practical Application of Bioinformatics Analysis Using Genomic Information
Language: English/Japanese
Lecturer: Dr. Hideki Hirakawa （Kazusa DNA Research Institute）
https://www.kazusa.or.jp/en/
Credits: 1 credit
Dates: 1/16 (on demand), 1/23 (face-to-face in 3&4 hours), 1/24 (face-to-face in 2&3 hours), 1/30 (Zoom in 3&4 hours)
Enrollment Requirements:
This course is open to students enrolled in the Faculty of Bioresource and Bioenvironmental Sciences. It is an advanced course designed for students interested in genome analysis or actively involved in genomic analysis. Students are required to bring a Windows PC (laptop), and in case of limited availability (limited number of PCs may be provided).
Number of Participants:
Up to 15 students.
Course Objectives:
Introduce the latest methods for genome decoding and analysis, databases, and subsequently engage in practical exercises in bioinformatics analysis. Provide a forum for students to ask questions related to the on-going analysis and strive for solutions. The goal is for students to be able to independently perform bioinformatics analysis through this course.
Keywords:
Bioinformatics, Genome Decoding, Genome Analysis, Databases, DX (Digital Transformation)
Required Materials:
Slide presentations
Personal computer (PC windows) (for exercises including genome analysis and programming).
Course Schedule:
(1st.class on demand on Jan 16) Introduction to Genome Decoding and Analysis Methods, Databases
Learn about the latest methods and analysis techniques for genome decoding using next-generation sequencers and explore various databases containing data obtained from genome decoding.
(2nd class on demand on Jan 16) Introduction to Bioinformatics Analysis
Study bioinformatics analysis necessary for genome decoding, such as genome assembly, gene prediction, and gene function prediction.
(3rd. 3rd hour on Jan 23@room224 on site) Bioinformatics Analysis Practical Exercise (1)
Discuss the setup of the PC environment required for bioinformatics analysis and learn about operations in Linux necessary for analysis.
Topics include: Windows Terminal, Bioconda, program installation, commands, editors, shell scripts.
(4.４th hour on site on Jan 23@room224 対面) Bioinformatics Analysis Practical Exercise (2)
Learn basic sequence analysis methods, including sequence similarity searches.
Tools include: BLAST, FASTA, ClustalW2, FigTree.
(5.2限on site on Jan 24@room 223 対面) Bioinformatics Analysis Practical Exercise (3)
Learn methods for genome assembly using next-generation sequencer data.
Tools include: MultiQC, hifiasm, Flye, HiCanu, D-Genies, Unicycler, Augustus, EggNOG.
(6.３限on site on Jan 24@room 223 対面) Bioinformatics Analysis Practical Exercise (4)
Learn methods for polymorphism analysis using next-generation sequencer data.
Tools include: Bowtie2, HISAT2, StringTie, SAMtools, SnpEff, VarScan.
(7. ３限on line live on Jan 24) Bioinformatics Analysis Practical Exercise (5)
Explore various methods using next-generation sequencer data.
(8. ４限on line live on Jan 24) Question and Answer Session
Address questions related to the course and provide solutions to queries regarding students' ongoing research analyses.
Grading Method:
Report: Submission of a report after the completion of the course.
Attendance: Mandatory attendance and participation in online lectures.