Priority Issue on Post-K computer. Integrated Computational Life Science to Support Personalized and Preventive Medicine
 

This is an old revision of the document!


List of Software

This page shows the software information developed with K computer in Next-Generation Integrated Simulation of Living Matter and  the Strategic Programs for Innovative Research Field 1 Supercomputational Life Science.

Supercomputational Life Science software group

Simulation of whole human body musculoskeletal systems

Software Chief Developer
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 Developer Website
UT-HEART Toshiaki Hisada (UT-Heart Inc.) UT Heart XB Modeler
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
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
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 whole 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
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 Institute of Medical Science, The University of Tokyo)
Using gene set information, EEM extracts co-expression gene groups and co-expression modules in mRNA expression data.

OThers

Software Chief Developer
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.        


Next-Generation Integrated Simulation of Living Matter

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


Use of Software

About Licence

Please note that licenses of software provided in this website are granted by the respective copyright holders and therefore different depending on the software. For details of the copyrights of the software provided in this website, please check with the persons in charge of its development.

Copyright © 2016 Integrated Computational Life Science to Support Personalized and Preventive Medicine