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License

SiGN-SSM is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

Source Code

2020-09-14; release 1.3.0; SiGN-SSM.1.3.0.tgz (Latest release)

Precompiled Binaries

See below to install these binaries.

K computer (rel 1.2.1. compiled on K-1.2.0-15)
Mac OS X 10.8- (Intel) (rel 1.2.1. MPI, multi-thread supported)
Linux x86-64 (rel 1.0.2. Multi-thread supported, MPI support not enabled)

The reason why the linux binary does not support MPI is that there are lots of implementations of MPI and you need to compile SiGN-SSM with one of these implementations.

Windows Vista/7 without multi-thread support (32bit)

Compiled by MinGW with Netlib BLAS/LAPACK. Not optimized so much and very slow.

Windows Vista/7 with multi-thread support (32bit)

Compiled by MinGW with Netlib BLAS/LAPACK. Not optimized so much and very slow.
This includs pthreadGC2.dll developed by Pthreads-win32 project. It is an LGPL library and required to run multi-thread applications by OpenMP. Go to the project web site to obtain the source code.

Other tools

signssm_plot.sh

A shell script to generate PDFs containing the plots of one-ahead prediction of the results. You need Gnuplot that supports PDFs to run this script.

Sample Data

Sample short time triplicate data file: sample.tsv

This is also included in the above source/binary packages.

COMPILE AND INSTALL

Source Code

See Readme.txt and Makefile in the source code archive for details. SiGN-SSM does not automatically configure for your environment to compile the source code. You need to set some paths and variables for your own environment in Makefile by yourself.

The Makefile for the following environments are prepared. Edit Makefile to read the appropriate file.

R-CCS Fugaku computer (sequential only)
R-CCS K computer
GCC + Netlib LAPACK
Linux + Intel icc + MKL (x86_64)
Mac OS X 10.9 - 10.6 (Xcode)
HGC Supercomputer System (Intel icc + MKL)
RIKEN RICC (x86_64, fcc + SSL II)
Fujitsu FX1 (Solaris 10 with SPARC64 VII, Fujitsu fcc + SSL II)

We cannot support your compilation. Please do not ask us how to compile in your environment.

Pre-compiled Binary

To install the binary package, untar/unzip the binary package, then copy files to the appropriate folder (Windows) or execute "make INSTALLDIR=dir install" to install the binary to dir, or simply "make install" to install to /usr/local/bin (Unix-like systems).

USING ON HGC AND "K COMPUTER"

Pre-installed binaries are available in the HGC supercomputer system. You do not need to copy the binary to your directory. These binaries are installed under the different license. Redistribution and copying of them are not permitted. Permutation test and differentially regulated gene extraction described in ABOUT SSM and HOW TO USE pages is implemented only on these binaries. The multi-thread mode is disabled for these binaries.