Class Schedule of Problem Solving in Bioinformatics (INFOINST 8010)

Time: 11:00 am - 12:15 pm; Location: Lafferre Hall E3508

Date

Topic

Instructor

Assignment

8/26, Wednesday

Introduction (lecture)

Jianlin Cheng

Review the human genome paper (due 8/28)

8/28, Friday

Genome sequencing and assembly (lecture)

Dong Xu

Review genome sequencing and assembly papers (due 9/2)

9/2, Wednesday

Protein structure prediction (lecture)

Jianlin Cheng

Review protein structure prediction papers (due 9/4)

9/4, Friday

Gene prediction (lecture)

Dong Xu

Review gene prediction papers (due 9/9)

9/9, Wednesday

Protein function prediction (lecture)

Toni Kazic / Jianlin Cheng

Review protein function prediction papers (due 9/11)

9/11, Friday

Protein interaction prediction (lecture)

Dmitry Korkin

Review protein interaction prediction papers (due 9/16)

9/16, Wednesday

Biological pathways networks (lecture)

Chi-Ren Shyu

Review biological pathway and network papers (due 9/18)

9/18, Friday

Introduction to a genome assembly and annotation project (lecture: data, rules and expectations)

Jianlin Cheng

 

9/23, Wednesday

Mid-term exam

Jianlin Cheng

 

9/25, Friday

Tasks & Solutions for assembling a bacteria genome (Discussion)

Dong Xu & Jianlin Cheng

Prepare a presentation-style report to describe tasks, solutions, and implementation plan (a group leader coordinates the group assignment, due 9/30)

9/30, Wednesday

Presentation and Discussion of solution / implementation plan for genome assembly and annotation. Presentation is given by a group leader.

Dong Xu & Jianlin Cheng

1.      Prepare a final plan of tasks, solutions and implementation led by a group leader (Due 10/2)

  1. Start implementation led by a group leader. (implementation is due 10/8)

10/2, Friday

Tasks & Solutions for gene prediction (Discussion)

Dong Xu & Jianlin Cheng

Prepare a presentation-style report to describe tasks, solutions, and implementation plan (due 10/7)

10/7, Wednesday

Presentation and Discussion of solution / implementation plan for gene prediction.

Dong Xu & Jianlin Cheng
  1. Prepare a final plan of tasks, solutions and implementation (due 10/9)
  2. Start implementation (due 10/19)

10/9, Friday

Assess and discuss the results of genome assembly (Discussion)

Dong Xu & Jianlin Cheng

Add assessment plan and results into the final progress report (due 10/14)

10/14, Wednesday

Tasks & Solutions for protein structure prediction (Discussion)

Jianlin Cheng

Prepare a presentation-style report to describe tasks, solutions, and implementation plan (due 10/16)

10/16, Friday

Presentation and Discussion of solution / implementation plan for protein structure prediction

Jianlin Cheng
  1. Prepare a final plan of tasks, solutions and implementation (due 10/21)
  2. Start implementation (due 10/29)

10/21, Wednesday

Assess and discuss the results of gene prediction (Discussion)

Dong Xu & Jianlin Cheng

Add assessment plan and results into the final progress report (due 10/26)

10/23, Friday

Tasks & Solutions for protein function prediction (Discussion)

Toni Kazic & Jianlin Cheng

Prepare a presentation-style report to describe tasks, solutions, and implementation plan (due 10/28)

10/28, Wednesday

Presentation and Discussion of solution / implementation plan for protein function prediction

Toni Kazic & Jianlin Cheng
  1. Prepare a final plan of tasks, solutions and implementation (due 10/30)
  2. Start implementation (due 11/11)

10/30, Friday

Assess and discuss the results of protein structure prediction (Discussion)

Jianlin Cheng

Add assessment plan and results into the final progress report (due 11/4)

11/4, Wednesday

Tasks & Solutions for protein interaction prediction (Discussion)

Dmitry Korkin & Jianlin Cheng

Prepare a presentation-style report to describe tasks, solutions, and implementation plan (due 11/6)

11/6, Friday

Presentation and Discussion of solution / implementation plan for protein interaction prediction

Dmitry Korkin & Jianlin Cheng
  1. Prepare a final plan of tasks, solutions and implementation (due 11/11)
  2. Start implementation (due 11/17)

11/11, Wednesday

Tasks & Solutions for biological pathway and networks (Discussion)

Chi-Ren Shyu & Jianlin Cheng

Prepare a presentation-style report to describe tasks, solutions, and implementation plan (due 11/13)

11/13, Friday

Presentation and Discussion of solution / implementation plan for biological pathway

Chi-Ren Shyu & Jianlin Cheng
  1. Prepare a final plan of tasks, solutions and implementation (due 11/18)
  2. Start implementation (due 11/26)

11/18, Wednesday

Assess and discuss the results of protein function prediction (Discussion)

Toni Kazic & Jianlin Cheng

Add assessment plan and results into the final progress report (11/23)

11/20, Friday

Assess and discuss the results of protein interaction prediction (Discussion)

Dmitry Korkin & Jianlin Cheng

Add assessment plan and results into the final progress report (11/25)

12/2, Wednesday

Discuss integration of the system and final report (Discussion)

Jianlin Cheng

Prepare a plan to integrate the system and write the final report (due 12/16)

12/4, Friday

Assess and discuss the results of pathway prediction (Discussion)

Chi-Ren Shyu & Jianlin Cheng

Add assessment plan and results into the final progress report (due 12/9)

12/9, Wednesday

Group presentation and discussion

All instructors