title: SiGN-SSM: open source parallel software for estimating gene networks with state space models.
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.
  
  
  BACKGROUND
  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.
  
  
  BACKGROUND
  tamada@ims.u-tokyo.ac.jp.
authors.affiliation: 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
authors.forename: Yoshinori
authors.initials: Y
authors.lastname: Tamada
authors.forename: Rui
authors.initials: R
authors.lastname: Yamaguchi
authors.forename: Seiya
authors.initials: S
authors.lastname: Imoto
authors.forename: Osamu
authors.initials: O
authors.lastname: Hirose
authors.forename: Ryo
authors.initials: R
authors.lastname: Yoshida
authors.forename: Masao
authors.initials: M
authors.lastname: Nagasaki
authors.forename: Satoru
authors.initials: S
authors.lastname: Miyano
mesh_terms: D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D015233:Models, Statistical; D012984:Software