University of Tsukuba | Grad. Scho. Syst. and Info. Eng. | Dept. Comp. Sci. | List of Courses
基礎計算生物学_E
Instructor(s)
T. Sakurai, M. Shoji, Y. Inagaki, S. Makino, M. Sato
E-Mail sakurai@cs.tsukuba.ac.jp, yuji@ccs.tsukuba.ac.jp, mshoji@ccs.tsukuba.ac.jp, maki@tara.tsukuba.ac.jp, msato@cs.tsukuba.ac.jp
URL
Office hours
Cource# 01CH107,02RA210
Area Information Mathematics and Modeling
Basic/Advanced
Course style Lecture
Term Fall AB
Period Thu1,2
Room# 3B301
Keywords Computational Science, Computational Biology, High Performance Computing
Prerequisites
Goal
Outline In this lecture, we will understand basic methods to solve a wide variety of problems by using a program in the field of biology. Explain molecular phylogenetic analysis molecular dynamics method, modelization and algorithm of a phenomenon, high- performance computation (HPC), and component analysis.
Course plan
  1. 1st week: Mathematical modeling and algorithms (1)
    Overview of the course, mathematical modeling and numerical simulation
  2. 2nd week: Mathematical modeling and algorithms (2)
    Computational algorithms, molecular simulaiton and eigenvalue solver
  3. 3rd week: Biodiversity
    Biodiversity on earth and global eukaryotic phylogeny
  4. 4th week: Basics of molecular phylogeny
    Maximum-parsimony, distance, maximum-likelihood, and heuristic tree search
  5. 5th week: Theoretical methods for biology
    Methods and applications of classical molecular dynamics
  6. 6th week: Quantum mechanics for biology
    Methods and applications of quantum mechanical methods
  7. 7th week: Independent component analysis and blind signal separation
    Basic theory of independent component analysis and its application to blind signal separation
  8. 8th week: Sparse component analysis and blind signal separation
    Basic theory of sparse component analysis and its application to blind signal separation
  9. 9th week: High performance computing technology (1)
    Parallel processing and parallel systems
  10. 10th week: High performance computing technology (2)
    Parallel programming, and trends of high performance computing
Textbook
References
Evaluation
TF / TA
Misc.
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