title: BisoGenet: a new tool for gene network building, visualization and analysis.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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/.
authors.affiliation: Center for Genetic Engineering and Biotechnology, Havana, Cuba.
authors.forename: Alexander
authors.initials: A
authors.lastname: Martin
authors.forename: Maria E
authors.initials: ME
authors.lastname: Ochagavia
authors.forename: Laya C
authors.initials: LC
authors.lastname: Rabasa
authors.forename: Jamilet
authors.initials: J
authors.lastname: Miranda
authors.forename: Jorge
authors.initials: J
authors.lastname: Fernandez-de-Cossio
authors.forename: Ricardo
authors.initials: R
authors.lastname: Bringas
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D020869:Gene Expression Profiling / Q000379:methods*; D008954:Models, Biological; D025941:Protein Interaction Mapping / Q000379:methods*; D020543:Proteome / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D014584:User-Computer Interface
chemical_list: D020543:Proteome