Bonnet Eric, Calzone Laurence, Rovera Daniel, Stoll Gautier, Barillot Emmanuel, Zinovyev Andrei
Institut Curie, 26 rue d'Ulm, Paris, F-75248, France.
BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.
Public repositories of biological pathways and networks have greatly expanded in recent years. Such databases contain many pathways that facilitate the analysis of high-throughput experimental work and the formulation of new biological hypotheses to be tested, a fundamental principle of the systems biology approach. However, large-scale molecular maps are not always easy to mine and interpret.
We have developed BiNoM (Biological Network Manager), a Cytoscape plugin, which provides functions for the import-export of some standard systems biology file formats (import from CellDesigner, BioPAX Level 3 and CSML; export to SBML, CellDesigner and BioPAX Level 3), and a set of algorithms to analyze and reduce the complexity of biological networks. BiNoM can be used to import and analyze files created with the CellDesigner software. BiNoM provides a set of functions allowing to import BioPAX files, but also to search and edit their content. As such, BiNoM is able to efficiently manage large BioPAX files such as whole pathway databases (e.g. Reactome). BiNoM also implements a collection of powerful graph-based functions and algorithms such as path analysis, decomposition by involvement of an entity or cyclic decomposition, subnetworks clustering and decomposition of a large network in modules.
Here, we provide an in-depth overview of the BiNoM functions, and we also detail novel aspects such as the support of the BioPAX Level 3 format and the implementation of a new algorithm for the quantification of pathways for influence networks. At last, we illustrate some of the BiNoM functions on a detailed biological case study of a network representing the G1/S transition of the cell cycle, a crucial cellular process disturbed in most human tumors.
近年来，生物途径和网络的公共知识库有了极大的扩展。这类数据库包含许多途径，有助于高通量实验工作的分析以及有待检验的新生物学假设的形成，这是系统生物学方法的一项基本原则。然而，大规模分子图谱并不总是易于挖掘和解读。
我们开发了BiNoM（生物网络管理器），这是一个Cytoscape插件，它提供了一些标准系统生物学文件格式的导入-导出功能（从CellDesigner、BioPAX Level 3和CSML导入；导出到SBML、CellDesigner和BioPAX Level 3），以及一组用于分析和降低生物网络复杂性的算法。BiNoM可用于导入和分析用CellDesigner软件创建的文件。BiNoM提供了一组功能，不仅允许导入BioPAX文件，还能搜索和编辑其内容。因此，BiNoM能够有效地管理大型BioPAX文件，如整个途径数据库（例如Reactome）。BiNoM还实现了一系列强大的基于图形的功能和算法，如路径分析、按实体参与度进行分解或循环分解、子网聚类以及将大型网络分解为模块。
在此，我们深入概述了BiNoM的功能，还详细介绍了一些新特性，如对BioPAX Level 3格式的支持以及用于影响网络途径量化的新算法的实现。最后，我们通过一个详细的生物学案例研究来说明BiNoM的一些功能，该案例研究涉及一个代表细胞周期G1/S转换的网络，这是一个在大多数人类肿瘤中受到干扰的关键细胞过程。
