From Shiu Lab
Jump to: navigation, search



Course number PLB/MMG/BMB 400 (undergraduate)
PLB/MMG 810 (graduate)
Offerred Spring, 2009
Class hours/location TR – 1-2:20pm, Plant Biology 151 (east end of building).
Instructor Shin-Han Shiu
Office S-306 Plant Biology Bldg. (south end of building)
Email shius at msu dot edu (I’ll respond in 24 hours)
Office phone 353-7196 (prefer email)
Office hours TR 2:20-4pm or by appointment. To make an appointment, you can either stop by my office or email.


The availability of genome sequences and large-scale functional characterization datasets has drastically transformed the biomedical research enterprise. With the ability to examine the whole genome and tens of thousands of genes at the same time, the major challenge is how to extract information from these enormous amounts of data. Bioinformatics, the science and techniques for organizing and analyzing biological data, allows us to meet the challenges of the genomics era. This course will provide an introduction for the datasets available, current tools for analysis, the quantitative concepts behind these tools, and hands-on experiences on how to develop simple bioinformatic tools for biological data analysis.


The goals of this course are:

  • Introduce the quantitative concepts that utilized in bioinformatic tools such as programs for sequence alignments, motif search, phylogenetic reconstruction, and others.
  • Enhance understanding of the bioinformatic algorithms with weekly exercises that emphasize self-directed learning, critical thinking, and writing skills.
  • Develop bioinformatic tools in interactive lecture sessions with inquiry-based research problems.
  • Have students working on group projects that require team work, enhance their problem solving skills, and relate what you learn to real-world applications.


  • A introductory statistics course (such as STT200, 201, 231, 315, or 421).
  • Biology courses covering organisms, ecology, evolution, genetics, molecular and cell biology (e.g. BioSci 110/111 sequence).
  • Or permission from the instructor.

Text books


Grading & other general policies

About your grades

Exams (300pt)
They will consist of multiple choice and questions requiring essay-type answers. The material of each exam will cover lectures and readings of the preceding one-third of the course with a total of 300 points.
Exercises (100pt)
8 exercises will be given, 12.5 points each. They are to be solved by each student individually or as a group. In the later case, names of collaborators need to be included. Plagiarism is usually very easy to spot so please do not attempt. One point will be deducted from past due exercise and addition one point will be deducted every 12 hours.
Final project (125pt)
A project with 2-4 members will be carried out with 100 points. The project topics can be subjects related to your research projects or interests. The project is graded based on the following -
  1. Project justification (20 points): a one-page document with background, significance of the project, and the planned approaches, and the expected outcome.
  2. Progress report (20 points): a two-page document with 1/2 page on the background of the project and the rest with some details on the approach and the finding so far. Also need to provide information how the labor will be divided among team members.
  3. Final report (45 points): a 5-8 page document written in the scientific paper format (strictly enforced) with introduction, methods, results, discussion, figures, figure legends, and references. Also need to include information how the labor are divided among team members.
  4. Final presentation (40 points): a presentation with introduction, methods, results, implications, and future directions.
  • The total is 525points, which translated to 105%, not a mistake. The extra 5% serves as extra credits.

Attendance Policy

  • You are required by University regulation to attend every lecture.
  • You are expected to take examinations as scheduled.
  • Make-up examinations will only be given upon receipt of a medical excuse signed by a physician or approval of the instructor. If you cannot take an examination when scheduled, contact the instructor by e-mail or telephone when possible.

Academic Integrity (mind you, I didn't come up with this...)

  • The principles of truth and honesty are fundamental to the educational process and the academic integrity of the University; therefore, no student shall:
    1. claim or submit the academic work of another as one's own.
    2. procure, provide, accept or use any materials containing questions or answers to any examination or assignment without proper authorization.
    3. complete or attempt to complete any assignment or examination for another individual without proper authorization.
    4. allow any examination or assignment to be completed for oneself, in part or in total, by another without proper authorization.
    5. alter, tamper with, appropriate, destroy or otherwise interfere with the research, resources, or other academic work of another person.
    6. fabricate or falsify data or results.

Related courses in MSU

  • MMG 433: This course is a great genomics course with a focus on microbial genomes available and the use of tools for analyzing genomes.
  • BMB 960: This is traditionally a graduate level genomics course on various exciting developments in the field of genomics and systems biology. For more info, check the BMB course page.
  • BMB 961: This is traditionally an advanced bioinforamtic course in the area of structural bionformatics and others. For more info, check the BMB course page.
  • CSE 231: Introductory programming class teaching python by Bill Punch.