Molecular dynamics calculation

Software	Chief Developer	Homepage
GENESIS	Yuji Sugita (RIKEN)
With two programs – spdyn for massively parallel all-atom molecular dynamics calculations, and atdyn for generalized-ensemble calculations (e.g. replica exchange method) and all-atom / coarse-grained model calculations, GENESIS covers a wide range of research areas, from cellular-scale simulations to free-energy calculations in an in vivo reaction.
MARBLE	Mitsunori Ikeguchi (Graduate School of Medical Life Science, Yokohama City University)
A molecular dynamics method using an all-atom molecular model is employed in massively parallel calculations, and behaviors of proteins in solution or bio-membrane are simulated in collaboration with various structural biology experiments.
SCUBA	Hisashi Ishida (Japan Atomic Energy Agency)
Molecular dynamics simulations are run with all-atom model calculations, targeting biological polymers such as nucleic acids and proteins.
CafeMol	Syouji Takada (Graduate School of Science, Kyoto University)
A molecular dynamics method using a molecular model that is more coarse-graining than atom-level models for simulating the dynamics of biological polymers that are difficult to research using experimental techniques is employed in massively parallel calculations.
MP-CAFEE	Hideaki Fujitani (Research Center for Advanced Science and Technology)
An all-atom molecular dynamics method based on the non-equilibrium statistical method for calculating the binding free energy of a low-molecular drug candidate compound to a target protein that causes disease is employed in massively parallel calculations.
μ2lib	Akinori Kidera (Yokohama City University / RIKEN)
Biomolecules, such as proteins, nucleic acids and drugs, are targeted for calculation. A multi-copy and multi-scale molecular simulation method based on statistical mechanics is used to reproduce bio-molecular interactions and accompanying conformational changes that are difficult to track with conventional molecular dynamics methods due to long-time scale events such as chemical reactions (millisecond to second).

 

Simulation of in vivo reactions

Software	Chief Developer	Homepage
pSpatiocyte	Koichi Takahasi (RIKEN)
This is designed to solve reaction-diffusion equations with a lattice-based Monte Carlo method and simulate biochemical reaction systems, such as intracellular signaling pathways, in a single protein molecule level and on a cellular scale.

 

Cranial nerve simulation

Software	Chief Developer	Homepage
NEST	Kenji Doya (Okinawa Institute of Science and Technology Graduate University)
This is designed to estimate basal ganglia model parameters and simulate cortex basal ganglia loops using approximately 100,000 conductance-base Hodgkin-Huxley type neurons on a large scale.

 

Simulation of whole human body musculoskeletal systems

Software	Chief Developer	Homepage
K-BODY	Yoshihiko Nakamura (Graduate School of Information Science and Technology, The University of Tokyo)
This is designed to build detailed skeletal muscle models and dynamic calculation models for whole human body musculoskeletal systems in view of the volume effects of the former. Simulations are then made on the presumption that signals enter from the cranial nerve system. K-BODY can identify and analyze input from human motion measurement data.
Hi-Muscle	Syu Takagi (School of Engineering, The University of Tokyo)
This is a multi-scale skeletal muscle simulator designed to compute contraction at the muscle fiber-level with signals from motor neurons and the whole skeletal muscle.

 

Heart simulation

Software	Chief Developer	Homepage
UT-HEART	Toshiaki Hisada (Graduate School of Frontier Sciences, The University of Tokyo)
This is designed to build a heart employing a cardiomyocyte model in which electrochemical and mechanical phenomena are reproduced on a subcellular functional protein level so that heartbeat, blood flow and coronary circulation can be reproduced.

 

Blood clot simulation

Software	Chief Developer	Homepage
EX-THROM	Syu Takagi (School of Engineering, The University of Tokyo)
This is designed to simulate molecular-level binding between the GP1ba on the surface of blood platelets and von Willebrand factor, and recreate the complex biochemical reactions from the activation of blood platelets to coagulation.

 

Next-generation sequencer data analysis

Software	Chief Developer	Homepage
GHOST-MP	Yasusi Akiyama (Graduate School of Information Science and Engineering, Tokyo institute of Technology)
This is homology analysis software designed to search homologous sequences in a large amount of base sequences, usually given by next-generation DNA sequencers, against an amino-acid sequence database. The base sequences are converted to amino-acid sequences with six reading frames, and homologous sequences are searched from the amino-acid sequence database with very high sensitivity.
Genomon	Satoru Miyano (The Institute of Medical Science, The University of Tokyo)
System abnormality caused by cancer is revealed extensively and comprehensively on the sequence and transcriptome levels through analyses of exome, RNA sequence data and all genome sequence data of cancer genomes, and estimation of single nucleotide variants(SNV), copy number variations(CNV), fusion genes and so on.

 

Biomolecular network analysis

Software	Chief Developer	Homepage
SiGN-BN	Satoru Miyano (The Institute of Medical Science, The University of Tokyo)
SiGN-BN is gene network estimation software using the Bayesian network model and nonparametric regression. It is capable of estimating regulatory dependencies between genes as gene networks from expression data such as individual cell samples, gene knocked-down cell samples, drug-stimulated time series (time course) samples, and so on.
SiGN-L1	Satoru Miyano (The Institute of Medical Science, The University of Tokyo)
SiGN-L1 is network estimation software using sparse learning. It applies L1-regularization for simultaneous parameter estimation and selection of statistical graphical models such as graphical Gaussian and vector autoregressive models.
SiGN-SSM	Satoru Miyano (The Institute of Medical Science, The University of Tokyo)
SiGN-SSM is open source gene network estimation software. It estimates a state space model (SSM), a statistical dynamic model suitable for analyzing short-time and/or replicated time series gene expression profiles.
BENIGN	Hideo Matuda (Graduate School of Information Science and Technology, Osaka University)
BENIGN estimates networks that show the dependencies of biomolecules, such as DNA or RNA, from biomolecule expression data under various conditions with the Bayesian network method, and enables comparison of the estimated networks.
EEM	Atsudhi Niida (The University of Tokyo)
Using gene set information, EEM extracts co-expression gene groups and co-expression modules in mRNA expression data.

 

ISLiM software group

Please see an open website of software that is developed in the ISLiM (Next Generation Integrated Simulation of Living Matter) program.

 

Others

Software	Chief Developer	Homepage
GROMACS
This is a molecular dynamic simulator designed to analyze the dynamic behaviors of molecules, such as protein and/or DNA, calculate free energy, and so on.
GROMACS-Viewer	RIKEN HPCI Program for Computational Life Sciences
This is a molecular visualization program designed to display and analyze various data produced by GROMACS. Using 3-D graphics, it is capable of displaying molecular dynamics in synchronization with time-course and other data produced by GROMACS.
R (GNU R)
This is a software suite designed to manipulate, compute and display data with a statistical analysis language and in its execution environment.
Blat OpenMP Patch	Satoshi Ito (The Institute of Medical Science, The University of Tokyo)
This patch applies OpenMP thread parallelization to blat.