Center for Genetic Engineering and Biotechnology, Havana, Cuba.
BMC Bioinformatics. 2010 Feb 17;11:91. doi: 10.1186/1471-2105-11-91.
The increasing availability and diversity of omics data in the post-genomic era offers new perspectives in most areas of biomedical research. Graph-based biological networks models capture the topology of the functional relationships between molecular entities such as gene, protein and small compounds and provide a suitable framework for integrating and analyzing omics-data. The development of software tools capable of integrating data from different sources and to provide flexible methods to reconstruct, represent and analyze topological networks is an active field of research in bioinformatics.
BisoGenet is a multi-tier application for visualization and analysis of biomolecular relationships. The system consists of three tiers. In the data tier, an in-house database stores genomics information, protein-protein interactions, protein-DNA interactions, gene ontology and metabolic pathways. In the middle tier, a global network is created at server startup, representing the whole data on bioentities and their relationships retrieved from the database. The client tier is a Cytoscape plugin, which manages user input, communication with the Web Service, visualization and analysis of the resulting network.
BisoGenet is able to build and visualize biological networks in a fast and user-friendly manner. A feature of Bisogenet is the possibility to include coding relations to distinguish between genes and their products. This feature could be instrumental to achieve a finer grain representation of the bioentities and their relationships. The client application includes network analysis tools and interactive network expansion capabilities. In addition, an option is provided to allow other networks to be converted to BisoGenet. This feature facilitates the integration of our software with other tools available in the Cytoscape platform. BisoGenet is available at http://bio.cigb.edu.cu/bisogenet-cytoscape/.
在后基因组时代，组学数据的可用性不断增加且种类日益丰富，为大多数生物医学研究领域提供了新的视角。基于图的生物网络模型捕捉了分子实体（如基因、蛋白质和小分子）之间功能关系的拓扑结构，为整合和分析组学数据提供了合适的框架。开发能够整合来自不同来源的数据并提供灵活的方法来重建、表示和分析拓扑网络的软件工具是生物信息学中的一个活跃研究领域。
BisoGenet 是一个用于可视化和分析生物分子关系的多层应用程序。该系统由三个层次组成。在数据层，内部数据库存储基因组学信息、蛋白质-蛋白质相互作用、蛋白质-DNA 相互作用、基因本体论和代谢途径。在中间层，在服务器启动时创建一个全局网络，代表从数据库中检索到的生物实体及其关系的全部数据。客户端层是 Cytoscape 的一个插件，用于管理用户输入、与 Web 服务的通信、可视化和分析生成的网络。
BisoGenet 能够快速、用户友好地构建和可视化生物网络。BisoGenet 的一个特点是能够包含编码关系，以区分基因与其产物。此功能对于实现更精细的生物实体及其关系表示非常有用。客户端应用程序包括网络分析工具和交互式网络扩展功能。此外，还提供了将其他网络转换为 BisoGenet 的选项。此功能有助于将我们的软件与 Cytoscape 平台中提供的其他工具集成。BisoGenet 可在 http://bio.cigb.edu.cu/bisogenet-cytoscape/ 获得。
