Objective

To learn and develop computational systems biology modeling methodologies for high throughput data generated with modern biotechnology and build system models to explain underlying biological mechanisms.

Overview

This course introduces algorithms for state-of-the-art statistical and mathematical modeling in systems biology. Cellular and molecular processes, such as metabolism and signal transduction, are studied as systems and networks quantitatively. The central theme along which this course develops is how to construct various system models from high throughput measurements of above life processes. Examples of data include genomes, transcriptomes, proteomes, interactomes. Principles of assessing statistical significance of reconstructed networks will also be discussed. Topics include dynamic Bayesian networks, generalized logical networks, and discrete dynamic system models. Basic concepts of molecular biology will be reviewed at the beginning of the course. Homework and team projects will be assigned. Each group will make several presentations of their projects during the semester.

Prerequisites: graduate or undergraduate standing in biology, biochemistry, computer science, mathematics, electrical & computer engineering, physics, or permission of instructor. A previous exposure in two of the following four subjects at undergraduate level is highly recommended: programming in C/C++, Java, R/Splus, or MATLAB; molecular biology; probability and statistics; and differential equations.

Course Information

• Meeting time: 4:00 pm - 5:15 pm Monday & Wednesday in Science Hall 115
• Instructor: Prof. Joe Song, joemsong@cs.nmsu.edu, 575-646-4299, Office: SH 141
• Course web page: http://www.cs.nmsu.edu/~joemsong/479, or
  http://www.cs.nmsu.edu/~joemsong/579
• Office hours: 5:15 pm - 6:00 pm Monday & Wednesday (right after class) or by appointment.

Text

• [recommended] Klipp et al., Systems Biology in Practice, Wiley, 2005.
• [recommended] Alberts et al., Essential Cell Biology - An Introduction to the Molecular Biology of the Cell, Graland Publishing, 1998.
• [recommended] T.A. Brown, Genomes, 2nd Ed., Wiley-Liss, 2002.
• Journals articles from Bioinformatics, J. of Computational Biology, J. of Bioinformatics and Computational Biology, Nucleic Acid Research, Genome Research, J. of Molecular Biology, and etc.
• Conference papers from ISMB, RECOMB, CSB, ECCB, PSB and etc.
• Internet resources: http://www.systems-biology.org

Important Dates

First class meets on .................................................................. January 16, 2008 (W)

Martin Luther King holiday ......................................................... January 21, 2008 (M)

Last day to withdraw with “W” at NMSU .............................................March 10, 2008 (M)

Spring break ............................................................................ March 24-28, 2008

Last class meets on .....................................................................April 30, 2008 (W)

Final presentation on .......................................................................... (TBA)

Grading

• Homework (20%).
• Project:
  • Progress reports (20%)
  • Final presentation (10%)
  • Final project report (20%)
  • Program performance and quality (30%)
• Grading policies:
  • Late homework will not be accepted.
  • Incomplete grades will be given only for legitimate reasons.
  • Contributions of individual students in the same group must be documented. They must be balanced. Thus, members in the same group may not necessarily receive the same grade.

Topics

• Review of molecular biology and biochemistry (Klipp et al., 2005)
• Generalized logical networks (Song et al., 2007)
• Discrete dynamic systems (Song et al., 2007; Klipp et al., 2005.)
• Dynamic Bayesian networks (Friedman et al., 2004)
• Quantization of continuous random variables to discrete ones (handout)
• Dynamic system simulation (handout)
• Performance evaluation (handout)

Plagiarism and Code of Conduct

Please see the “Student Code of Conduct” in the current “Student Handbook.” (URL http://www.nmsu.edu/%7Evpsa/SCOC/misconduct.html) regarding academic misconduct and plagiarism. The penalty for plagiarism or other forms of academic misconduct (as defined in the Student Code of Conduct) leads to failure of the course.

Non-Discrimination Policy

Feel free to call Jerry Nevarez, Director of Institutional Equity, at 575-646-3635 with any questions you may have about NMSU’s Non-Discrimination Policy and complaints of discrimination, including sexual harassment.

Students with Disabilities

Feel free to call Michael Armendariz, Coordinator of Services for Students with Disabilities, at 575-646-6840 with any questions you may have on student issues related to the Americans with Disabilities Act (ADA) and/or Section 504 of the Rehabilitation Act of 1973. All medical information will be treated confidentially.