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The curriculum
Two basic profiles of computational expertise are developed through this program. The first is intended to produce a computational expert well versed in computer science, numerical methods and computer architecture who would be conversant in at least one application area. The other profile is intended to produce a specialist in a certain application area (such as molecular biophysics) who would be aware of the most advanced concepts in computing. There is considerable intersection of the curricula of these two profiles. This includes a common introductory background in advanced computing concepts provided by a course developed by Keck Center faculty, CAAM 420 (Introduction to Computational Science). Through this approach, students will learn the nature of interdisciplinary work first hand.
Depending on the background of the individual students, courses will be required from those listed below to ensure a sound background in basic biology or biophysics and computational methodologies. After the first year, the student will choose a thesis research mentor (who might be their Keck Center faculty mentor or another faculty member). The student will be supervised by a committee with faculty members as required by the home department, but with representation from the computational biology faculty at other institutions as well. Students will also be required to attend seminars, workshops, conferences, and present their work at least once a year in a student seminars, programs or retreats. Students entering from computational backgrounds will be required to take at least three semester courses in biology/biochemistry/ biophysics areas. Conversely, students entering from biological backgrounds will be required to take at least three semester courses in computational areas. The Keck Center Training Co-Directors, Drs. Chiu (Baylor), Pettitt (UH), and Phillips (Rice) will set the specific courses to be taken by each student, after consultation with the students and their potential mentors. Students will have to maintain certain performance standards (grade point average of 3.0 or better and solid research progress), consistent with the policies of their home departments.
Faculty have been chosen whose research is truly focused in the area of computational biology or the development of high performance computing algorithms and technologies applicable. The students in this program will work at the interface between biology and comp uter science to develop new techniques for visualizing biological complexes, including novel uses of optical video microscopy, three-dimensional electron microscopy, X-ray crystallography, and magnetic resonance methods; to develop DNA and protein sequenc e analysis, including alignment of sequences for genome construction, identification of coding regions, homology searching and prediction of structure; to develop advanced simulations, including molecular dynamics and Brownian motion, genetic information propagation, and other biological phenomena. The courses we have assembled, outlined above and in the appendix, are a unique training resource.
Rice University, Baylor College of Medicine, and the University of Houston have a uniquely rich teaching environment, including the following courses that are directly appropriate for this program:
Advanced Compilation for Vector and Parallel Processors
Biochemistry Cell Biology
Computational Methods for Molecular Biology
Computational Numerical Analysis Computational Methods in Non-linear Systems
Design and Analysis of Algorithms
Enzymology
Genetic Engineering
Graphics and Visualization
Introduction to Computational Sciences
Immunology
Macromolecular Design and Analysis
Membrane Biology
Molecular Biophysics I and II
Molecular Gene Expression and Regulation
Molecular Genetics
Molecular Mechanics and Modeling
Operating Systems and Concurrent Processing
Protein Chemistry
Statistical Mechanics
Virology
In addition to taking formal courses, students in the program will be required to attend the Keck-sponsored seminar series, which averages about two to three speakers per month. The speakers are selected on the basis of their involvement in computational biology. Students are encouraged to remain after the s eminars to discuss scientific issues with the speaker and with each other. This series has been a key component in building communication between different disciplines, and will be continued.
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