SiGN-SSM: open source parallel software for estimating gene networks with state space models
SiGN-SSM: open source parallel software for estimating gene networks with state space models
复制标题
SiGN-SSM：用于使用状态空间模型估计基因网络的开源并行软件
DOI：
10.1093/bioinformatics/btr078
复制
发表时间：
2011
期刊：
影响因子：
5.8
通讯作者：
S. Miyano
中科院分区：
文献类型：
--
作者：
Y. Tamada;R. Yamaguchi;S. Imoto;Osamu Hirose;Ryo Yoshida;Masao Nagasaki;S. Miyano
未标记
SiGN-SSM是一个开源的基因网络估计软件，能够在PC和大规模并行超级计算机上并行运行。该软件估计状态空间模型（SSM），即适用于分析短时间和/或重复时间序列基因表达谱的统计动态模型。SiGN-SSM实现了一种新的参数约束，有效地稳定估计模型。此外，通过使用超级计算机，能够在实际时间内通过统计排列测试确定基因网络结构。SiGN-SSM不仅适用于分析基因间的时间调控依赖关系，而且还适用于从时间序列表达谱中提取差异调控基因。
可用性
SiGN-SSM在GNU Affero通用公共许可证（GNU AGPL）第3版下发布，可以从http://sign.hgc.jp/signssm/下载。除了源代码之外，还提供了用于某些体系结构的预编译二进制文件。预装的二进制文件也可以在人类基因组中心的超级计算机系统上使用。SiGN-SSM的在线手册和补充信息可在我们的网站上查阅。
接触
tamada@ims.u-tokyo.ac.jp.
UNLABELLED
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.
影响因子：
5.8
作者：
Hirose, Osamu;Yoshida, Ryo;Miyano, Satoru
通讯作者：
Miyano, Satoru