基礎計算生物学_E

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

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 
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 
 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. 
