François Modave

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Class meetings: Monday, Wednesday, 1.30-2.50pm in room CS321.
Instructor: Dr. François Modave
Room: 207
Tel: (915) 747 5564
Email: fmodave (at) utep (dot) edu
Office hours: by appointment

Course Description: Over the last decade, the development of high-throughput technologies and sensor technologies has radically changed how research is done in the data-driven sciences. This is particularly true for biological sciences and systems biology, from the smaller scales (molecular and cellular biology), to the larger scales (ecology, ecosystems).

Systems biology is an interdisciplinary field that studies complex interactions between biological entities, at all scales, ranging from protein-gene interactions, to ecosystems interactions. The field is inherently data-driven, and the data come from numerous sources: DNA microarrays, gene sequencing techniques, sensors etc.

The aim of this class is to present and investigate various computational and mathematical methods that can be used for systems biology, for various scales.

Questions we would like to answer:
•    What are the properties of a given network (understand network in a general sense)?
•    How do networks interact with one another?
•    How does a networks evolve over time?
•    How is stability reached? How is it preserved?
We will look at several approaches to give (often partial) answers to these questions:
•    Statistical approaches (including an introduction to R)
•    Stochastic approaches
•    Machine learning approaches
•    Intelligent systems approaches
Text book: no text book is required for this class, however, the students will have numerous reading assignments to complement the material studied in class
Grading:
•    2 tests (10% each)
•    7 homeworks (10% each, discarding the lowest grade – They ALL have to be turned in)
•    Project 20%
Notes: Attending class is mandatory. If you arrive more than 5 minutes late, you will not be allowed to enter class and this will count as an absence. You will receive an F if you have more than 5 unexcused absences. To pass the class, the homeworks and the project have to be turned in on time.
Scaling:
1.    80% or higher is an A
2.    70% and under 80% is a B
3.    60% and under 70% is a C
4.    50% and under 60% is a D
5.    Below 50% is an F

These criteria may be adjusted based on the overall class performance
Standards of conduct: you are expected to conduct yourself in a professional and courteous manner (this means for example, being on time for class) as prescribed by the Standards of conduct. Graded work is to be done independently and should be unmistakably your own work, although you may discuss your work with other students in a general way. You may not represent as your own work, material that is transcribed or copied from an other person, book, web page, or any other source. Professors are required –and will- report academic dishonesty and any other violation of the Standards of conduct to the dean of students.
Disabilities: if you feel that you may have a disability that requires accommodation, contact the disabled student service office at 747-5184, Room 106E Union, or email dss@utep.edu.

The class I will be teaching in the Spring 2009 is:

• CS 4390 / CS 5390 – Introduction to Systems Biology,
  MW,  1:30 – 2:50 in Room CS321