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Bioinformatics. 2011 Apr 15;27(8):1172-3. doi: 10.1093/bioinformatics/btr078. Epub 2011 Feb 10.

SiGN-SSM: open source parallel software for estimating gene networks with state space models.

Author information

1
Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. tamada@ims.u-tokyo.ac.jp

Abstract

SiGN-SSM is an open-source gene network estimation software able to run in parallel on PCs and massively parallel supercomputers. The software estimates a state space model (SSM), that is a statistical dynamic model suitable for analyzing short time and/or replicated time series gene expression profiles. SiGN-SSM implements a novel parameter constraint effective to stabilize the estimated models. Also, by using a supercomputer, it is able to determine the gene network structure by a statistical permutation test in a practical time. SiGN-SSM is applicable not only to analyzing temporal regulatory dependencies between genes, but also to extracting the differentially regulated genes from time series expression profiles.

AVAILABILITY:

SiGN-SSM is distributed under GNU Affero General Public Licence (GNU AGPL) version 3 and can be downloaded at http://sign.hgc.jp/signssm/. The pre-compiled binaries for some architectures are available in addition to the source code. The pre-installed binaries are also available on the Human Genome Center supercomputer system. The online manual and the supplementary information of SiGN-SSM is available on our web site.

CONTACT:

tamada@ims.u-tokyo.ac.jp.

PMID:
21317140
DOI:
10.1093/bioinformatics/btr078
[Indexed for MEDLINE]

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