Fluxviz - Cytoscape plug-in for visualization of flux distributions in networks.
Fluxviz - Cytoscape plug-in for visualization of flux distributions in networks.
复制标题
DOI：
10.1142/9781848166585_0008
复制
发表时间：
2010
期刊：
影响因子：
--
通讯作者：
M. König;H. Holzhütter
中科院分区：
文献类型：
--
作者：
M. König;H. Holzhütter
动力学方法如FBA和动力学建模被广泛用于计算代谢网络中的通量。为了分析和理解模拟结果和实验测量的通量，网络环境中的可视化软件是必不可少的。结果我们推出了Flux Viz，这是一个开源的Celloscape插件，用于可视化分子相互作用网络中的通量分布。FluxViz支持（i）以各种格式（SBML、GML、XGMML、SIF、BioPAX、PSI-MI）导入网络（ii）以CSV、Cytoscape属性或瓦尔文件的形式导入通量分布（iii）将视图限制为通量携带反应（通量子网）或网络属性（如本地化）（iv）导出生成的视图（SVG、EPS、PDF、BMP、PNG）。虽然FluxViz主要是作为代谢网络中通量的可视化和FASIMU模拟结果分析的工具而开发的，FASIMU是一种用于大型代谢网络中批量通量平衡计算的灵活软件，但它不仅限于生化反应网络和FBA，而且可以应用于任意图形中任意通量的可视化。可用性平台无关的程序是一个开源项目，在GNU公共许可证下可在http://sourceforge.net/projects/fluxvizplugin/免费获得，包括手册、教程和示例。
MOTIVATION Methods like FBA and kinetic modeling are widely used to calculate fluxes in metabolic networks. For the analysis and understanding of simulation results and experimentally measured fluxes visualization software within the network context is indispensable. RESULTS We present Flux Viz, an open-source Cytoscape plug-in for the visualization of flux distributions in molecular interaction networks. FluxViz supports (i) import of networks in a variety of formats (SBML, GML, XGMML, SIF, BioPAX, PSI-MI) (ii) import of flux distributions as CSV, Cytoscape attributes or VAL files (iii) limitation of views to flux carrying reactions (flux subnetwork) or network attributes like localization (iv) export of generated views (SVG, EPS, PDF, BMP, PNG). Though FluxViz was primarily developed as tool for the visualization of fluxes in metabolic networks and the analysis of simulation results from FASIMU, a flexible software for batch flux-balance computation in large metabolic networks, it is not limited to biochemical reaction networks and FBA but can be applied to the visualization of arbitrary fluxes in arbitrary graphs. AVAILABILITY The platform-independent program is an open-source project, freely available at http://sourceforge.net/projects/fluxvizplugin/ under GNU public license, including manual, tutorial and examples.