(Updated on 2012/12/27)
● Presentation materials for professionals of Japan Pharmaceutical Manufacturers Association (JPMA), etc.
Title
Presenter
Download
The status and target of software being developed in the grand challenge project
Ryutaro HIMENO, Associated program director
Progress of molecular simulation: Toward supercomputing
Akinori KIDERA, Team Leader
Large-scale genome network ewstimation software SiGN
Satoru MIYANO, Team Leader
RIKEN press conference (2011.6.24)
Ryutaro HIMENO, Associated program director
|
Application codes targeting multiscale simulation by the method of quantum mechanics (QM), molecular mechanics (MM), coarse grained model (CG), and coupled QM/MM and MM/CG. |
ID
Application
Code
Principal developer
Affiliation
M-1
Platypus-MM/CG
Akinori KIDERA
RIKEN
M-2
Platypus-REIN
Yuji SUGITA
RIKEN
M-3
MARBLE
Mitsunori IKEGUCHI
Yokohama City University
M-4
CafeMol
Shoji TAKADA
Kyoto University
M-5
ProteinDF
Fumitoshi SATO
University of Tokyo
M-6
Platypus-QM/MM-FE
Shigehiko HAYASHI
Kyoto University
M-7
Platypus-QM
Haruki NAKAMURA
Osaka University
M-8
Platypus-QM/MM
Haruki NAKAMURA
Osaka University
More details of each code are available here.
 |
The cell simulation integrated platform as a kernel of cell scale research. |
Simulation of intra-cell phenomena by the voxel dividing. |
ID
Application
Code
Principal developer
Affiliation
C-1
RICS
Hideo YOKOTA
RIKEN
More details of each code are available here.
|
The simulation-based support system for the next-generation medical treatment. For example, thrombosis simulator is developed through the introduction of the coupling method between continuum scale simulation for blood flow and cell level simulation for the aggregation of platelets. |
3D Fluid-Elastic Body-Elastic Wall Interaction |
ID
Application
Code
Principal developer
Affiliation
O-1
ZZ-EFSI
Shu TAKAGI
RIKEN
O-2
ZZ-DOSE
Kenichi ISHIKAWA
RIKEN
O-3
ZZ-HIFU
Kohei OKITA
Nihon University
O-4
UT-Heart
Toshiaki HISADA
University of Tokyo
More details of each code are available here.
|
The data analysis codes for explosive experimental data of genes and genomes, which cannot be realized without peta-scale computing and a peta-scale modeling technology based on data assimilation that fuses observational data and simulation models. |
Large-scale Genome Network Estimation |
ID
Application
Code
Principal developer
Affiliation
D-1
ParaHaplo
Tatsuhiko TSUNODA
RIKEN
D-2
NGS analyzer
Tatsuhiko TSUNODA
RIKEN
D-3
ExRAT
Tatsuhiko TSUNODA
RIKEN
D-4
SiGN-BN
Satoru MIYANO
University of Tokyo
D-5
SiGN-L1
Satoru MIYANO
University of Tokyo
D-6
SiGN-SSM
Satoru MIYANO
University of Tokyo
D-7
SBiP
Satoru MIYANO
University of Tokyo
D-8
LiSDAS
Tomoyuki HIGUCHI
Institute of Mathematical Statitics
D-9
MEGADOCK
Yutaka AKIYAMA
Tokyo Tech
More details of each code are available here.
|
The simulation study codes for the development and plasticity of single neurons, the dynamics of cortical neuron ensembles, and the processing of invertebrate's olfactory system and mammalian visual system. |
Whole Brain Simulation for Insect Olfactory System |
ID
Application
Code
Principal developer
Affiliation
B-1
NEST
Markus Diesmann
RIKEN
B-2
CMDN
Tomoki FUKAI
RIKEN
B-3
VSM
Shiro USUI
RIKEN
B-4
NeuroMorphoKit
Naoto YUKINAWA
Kyoto University
B-5
IOSSIM
Ryohei KANZAKI
University of Tokyo
More details of each code are available here.
|
The highly parallel software for the next-generation supercomputer system in addition to the parallelized libraries for the molecular dynamics, the molecular orbital method, the fluid/elastic mechanics, etc. as well as visualization and workflow tools. |
Massively Parallel Large-scale MD Calculation |
ID
Application
Code
Principal developer
Affiliation
H-1
cppmd
Yosuke OHNO
RIKEN
H-2
LSV
Kenji ONO
RIKEN
H-3
SPHERE
Kenji ONO
RIKEN
H-4
VLSVL
Kimito FUNATSU
University of Tokyo
More details of each code are available here.
No research team page is available.
