SPNConverter: a new link between static and dynamic complex network analysis
SPNConverter: a new link between static and dynamic complex network analysis
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DOI：
10.1093/bioinformatics/btt421
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发表时间：
2013-10
期刊：
影响因子：
5.8
通讯作者：
Jennifer E. Dent;Xinyi Yang;C. Nardini
中科院分区：
文献类型：
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作者：
Jennifer E. Dent;Xinyi Yang;C. Nardini
信令Petri网（SPN）模拟器，旨在提供洞察分子的活动水平响应于外部刺激的趋势，有助于分析大规模细胞网络的动态的系统生物学的必要性。在免费软件BioLayout Express（3D）中实现，模拟器是公开可用的，易于使用，前提是输入文件以GraphML格式准备，通常使用网络编辑软件yEd和软件特定的标准。然而，使用其他系统生物学格式化语言（流行的软件，如CellDesigner和Cytoscape）表示的复杂网络的分析需要手动操作，这一步骤容易出错，并限制了BioLayout Express（3D）中SPN模拟器的使用。为了克服这一点，我们提出了一个Cytoscape插件，使用户能够自动转换网络分析与SPN模拟器从标准的系统生物学标记语言。这个步骤的自动化将SPN模拟器开放给比以前可能的更大的用户组。可用性和实施根据http://apps.cytoscape.org/apps/spnconverter上的GNU通用公共许可证第3版分发。
SUMMARY The signaling Petri net (SPN) simulator, designed to provide insights into the trends of molecules' activity levels in response to an external stimulus, contributes to the systems biology necessity of analyzing the dynamics of large-scale cellular networks. Implemented into the freely available software, BioLayout Express(3D), the simulator is publicly available and easy to use, provided the input files are prepared in the GraphML format, typically using the network editing software, yEd, and standards specific to the software. However, analysis of complex networks represented using other systems biology formatting languages (on which popular software, such as CellDesigner and Cytoscape, are based) requires manual manipulation, a step that is prone to error and limits the use of the SPN simulator in BioLayout Express(3D). To overcome this, we present a Cytoscape plug-in that enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language. The automation of this step opens the SPN simulator to a far larger user group than has previously been possible. AVAILABILITY AND IMPLEMENTATION Distributed under the GNU General Public License Version 3 at http://apps.cytoscape.org/apps/spnconverter.