基礎計算生物学_E
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Instructor(s) |
T. Sakurai, M. Shoji, Y. Inagaki, S. Makino, M. Sato, K. Morikuni
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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, morikuni@cs.tsukuba.ac.jp |
URL |
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Office hours |
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Cource# |
01CH107,02RA210 |
Area |
Information Mathematics and Modeling |
Basic/Advanced |
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Course style |
Lecture |
Term |
Fall AB |
Period |
Thu1,2 |
Room# |
3B301 |
Keywords |
Computational Science, Computational Biology, High Performance Computing |
Prerequisites |
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relation degree program competence |
Knowledge Utilization Skills,Research Skills,Expert Knowledge |
Goal |
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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 |
- 1st week: Mathematical modeling and algorithms (1)
Overview of the course, mathematical modeling and numerical simulation - 2nd week: Mathematical modeling and algorithms (2)
Computational algorithms, molecular simulaiton and eigenvalue solver - 3rd week: Biodiversity
Biodiversity on earth and global eukaryotic phylogeny - 4th week: Basics of molecular phylogeny
Maximum-parsimony, distance, maximum-likelihood, and heuristic tree search - 5th week: Theoretical methods for biology
Methods and applications of classical molecular dynamics - 6th week: Quantum mechanics for biology
Methods and applications of quantum mechanical methods - 7th week: Independent component analysis and blind signal separation
Basic theory of independent component analysis and its application to blind signal separation - 8th week: Sparse component analysis and blind signal separation
Basic theory of sparse component analysis and its application to blind signal separation - 9th week: High performance computing technology (1)
Parallel processing and parallel systems - 10th week: High performance computing technology (2)
Parallel programming, and trends of high performance computing |
Textbook |
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References |
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Evaluation |
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TF / TA |
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Misc. |
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