#Cytoscape networks with bisogenet software#
As the amount of biological data increase, software tools able to visualize biological-meaningful abstract representations of these data at different levels of details are valuable to biologists. These databanks can be seen as repositories of biological entities and their functional relations. On the other hand databases like KEGG, Reactome, BioCyc, NCI Nature PID and others provide information on both metabolic and signaling pathways. Data retrieved from high-throughput experiments and literature are available from several databases, such as, DIP, BIND, HPRD, BioGRID, MINT and Intact, which represent the major repositories of protein-protein interacions from multiple organisms. New models for data integration, standard specifications for data exchange and the development of new tools for data visualization and analysis are crucial and represent one of the most challenging tasks for bioinformaticians.ĭata repositories such as NCBI's Entrez Gene and Ensembl maintain annotation on whole genomes, including sequences, gene location, transcripts, classification and links to several external databases. Network representation of relationships among biomolecules is an intensive field of research of in silico System Biology. This feature facilitates the integration of our software with other tools available in the Cytoscape platform. In addition, an option is provided to allow other networks to be converted to BisoGenet. The client application includes network analysis tools and interactive network expansion capabilities. This feature could be instrumental to achieve a finer grain representation of the bioentities and their relationships. A feature of Bisogenet is the possibility to include coding relations to distinguish between genes and their products. ConclusionīisoGenet is able to build and visualize biological networks in a fast and user-friendly manner. The client tier is a Cytoscape plugin, which manages user input, communication with the Web Service, visualization and analysis of the resulting network. 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. In the data tier, an in-house database stores genomics information, protein-protein interactions, protein-DNA interactions, gene ontology and metabolic pathways. ResultsīisoGenet is a multi-tier application for visualization and analysis of biomolecular relationships. 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.
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 increasing availability and diversity of omics data in the post-genomic era offers new perspectives in most areas of biomedical research.
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