SiGN-BN Download
Latest Release
| SiGN-BN HC+BS: | 1.8.2 |
| SiGN-BN NNSR: | 0.16.7 |
| SiGN-BN Para-OS: | 0.1.2 |
| SiGN-Proc: | 0.22.6 |
See Change History for the history of the releases.
Human Genome Center Shirokane 5
The latest binary and related files can be found in the author's home directory
at ~tamada/sign/.
You do not need to download the binary and install it by yourself.
RIKEN R-CCS Fugaku computer and its compatible systems
SIGN-BN NNSR
- Release 0.16.7D (signbnnnsr.0.16.7D.gz) on Feb. 8, 2021.
- Compiled with lang environment "4.3.1 tcsds-1.2.29"
- Example of the job script: fugaku_job.sh.gz
- With the settings as in the above script and the sample data set below (GN-10k-500.edf.txt), Fugaku took less than 30 minutes to finished the network estimation (T=100,000).
- The degree of parallelism with a sufficient accuracy was confirmed up to 6144 processes (128 nodes × 48 processes/node, Flat MPI). Note: The number of processes affects the accuracy of the network estimation.
- This work used computational resource of Fugaku throught the HPCI System Research Project (Project ID: hp200194).
- Older release (Dec. 1, 2020): signbnnnsr.0.16.7C.gz compiled with lang environment "4.3.0a tcsds-1.2.28".
RIKEN AICS K COMPUTER and its compatible systems
SiGN-BN HC+Bootstrap
- Release 1.5.5 K-1.2.0-17 (signbn-hcbs.1.5.5_K-1.2.0-17.zip)
- Compiled with MPI+OpenMP hybrid parallelization.
- Compiled under the language environment K-1.2.0-17.
- This is not the open source software. DO NOT re-distribute the binary file.
SiGN-BN NNSR
- Release 0.14.2 K-1.2.0-17 (signbn-nnsr.0.14.2_K-1.2.0-17.zip)
- Compiled with MPI+OpenMP hybrid parallelization.
- Compiled under the language environment K-1.2.0-17.
- Set environment variable OMP_NUM_THREADS=8 in your job script.
- This is not the open source software. DO NOT re-distribute the binary file.
SiGN-BN Para-OS
- Release 0.1.2 K-1.2.0-21 (signbn-paraos.0.1.2_K-1.2.0-21.zip)
- Compiled with MPI+OpenMP hybrid parallelization.
- Compiled under the language environment K-1.2.0-21.
- Set environment variable OMP_NUM_THREADS=n in your job script where n represents the number of threads per CPU. Use n=8 for K computer.
- This is not the open source software. DO NOT re-distribute the binary file.
SiGN-Proc
- Release 0.21.1 binary for Linux x86-64 (signproc.0.21.1.gz)
- DO NOT RE-DISTRIBUTE THIS BINARY WITHOUT PERMISSION.
- Gzipped binary compiled for Linux x86-64, and hopefully works on general intel 86-64 linux systems.
- Confirmed it works on the following environments.
- RIKEN AICS K computer login node.
- Oakleaf login node (Fujitsu FX-10 installed on Univ. Tokyo).
Sample Data
For SiGN-BN HC+BS
- GN-527-100.edf.txt.gz - 527 nodes (genes) x 100 samples in gzipped EDF format (222,051 Bytes).
- GN-527-500.edf.txt.gz - 527 nodes (genes) x 500 samples in gzipped EDF format (1,095,070 Bytes).
- GN-527-120-DY.edf.txt.gz - 527 nodes (genes) x 40 samples x 3 replicates for dynamic Bayesian networks in gzipped EDF format (232,855 Bytes).
- GN-527-24-DY.edf.txt.gz - 527 nodes (genes) x 8 samples x 3 replicates for dynamic Bayesian networks in gzipped EDF format (49,067 Bytes).
- GN-527.sgn3.gz - Gene network with 527 nodes (genes) used to generate above datasets
in gzipped SGN3 format (11,312 Bytes).
For SiGN-BN NNSR
These files are the same as ones used in Tamada et al. (2011).
- GN-10k-500.edf.txt.gz - 10540 nodes (genes) x 500 samples in gzipped EDF format (21,979,935 Bytes)
- GN-10k-true.sgn3.gz - 10540 nodes (genes) gene network used to generate the above sample data set in gzipped SGN3 format (226,489 Bytes).
For SiGN-BN Para-OS