Objective

Students will apply advanced data structures and algorithms, object-oriented programming, software engineering principles, and parallel programming techniques in solving a real world computational modeling problem, which integrates Boolean logic, graph representation and search, markup languages, and the Message Passing Interface for parallel programming. Specific project topics will vary from semester to semester. Although the project is not specific to a particular type of applications, the current application will involve high-dimensional time-course data sets generated from modern high throughput biology.

Students will inherit legacy code from pervious student senior projects, revise existing and design new software components using efficient algorithms for generating, reconstructing, simulating from, testing, and creating a user interface for Boolean networks. The software will be used to model gene regulatory networks in the Halobacteria using microarray gene expression data.

Prerequisites

Senior standing and consent of instructor.

Course Information

Instructor: Joe Song, joemsong@cs.nmsu.edu, 505-646-4299, Office: SH 141, Office hours: Tuesday and Thursday 3:00pm-4:00pm.

Meeting time: Lecture–Room SH 113, Tuesday and Thursday 4:00pm-5:15pm; Lab–Room SH 118B Thursday 5:25pm-7:15pm

Course web page: http://www.cs.nmsu.edu/~joemsong/448

Important Dates

First class meets on ............................................................. Thursday August 23, 2007

Last day to withdraw with a “W” .............................................. (Tuesday) October 16, 2007

No class (Thanksgiving) ................................. ................................. 11/20/07, 11/22/07

Final presentation ............................................................... SH 124 December 6, 2007

Final project due ....................................................................... December 10, 2007

Grading Policies

• Progress 20% (attendance, weekly report, and progressive demonstration)
• Programming 50%: (sufficient amount of coding, correctness, readability, independent test code)
• Presentations (intermediate and final) 10%: (clarity, organization)
• Document 20%: (software requirement analysis, software design document, technical report, user manual)

Topics

1. Concepts in Boolean networks
2. Simulation of trajectories for a given Boolean networks
3. Random generation of Boolean networks
4. Reconstruction of Boolean networks from trajectories
5. Parallelization of Boolean network reconstruction
6. Analyze previous student code
7. Biology topics:
   • Molecular biology basics
   • Halobacteria gene expression data
   • Systems biology markup language

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 505-646-3635 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 505-646-6840 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.