基礎計算生物学_E

Instructor(s) 
T. Sakurai, M. Shoji, Y. Inagaki, S. Makino, M. Sato, K. Morikuni

EMail 
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 

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 

relation degree program competence 
Knowledge Utilization Skills,Research Skills,Expert Knowledge 
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 
 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
Maximumparsimony, distance, maximumlikelihood, 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 

References 

Evaluation 

TF / TA 

Misc. 
