Learn to use BiologicalNetworks, a software platform created to analyze and visualize molecular interaction networks, metabolic and signaling pathways with experimental data, genomic sequences, 3D structure information, ontologies and taxonomies. The functionality built into this tool allows users to analyze complex molecular interactions at the systems level. In addition, BiologicalNetworks also has a built in tool for pathway analysis of microarray expression data. For researchers who investigate molecular interactions, this resource allows you to combine curated pathways with your own experimental data to create biological pathways tailored to your research needs.
This tutorial is a part of the tutorial group Interaction resources. You might find the other tutorials in the group interesting:
Pathway Interaction Database: A resource of pathway and network data and displays
MINT: Molecular Interaction Database
Cytoscape: An open-source software platform used for visualization and analysis of molecular interaction and network data
BioSystems: Database of Biological Systems
Reactome Legacy: Older version of the current Reactome knowledgebase of biological processes.
Reactome: Knowledgebase of biological processes
GeneMANIA: GeneMANIA: Fast Gene Function Predictions
GenMAPP: A freely available open source software application for visualizing microarray data in the context of biological pathways.
VisANT: A web-based or downloadable software platform used for visualization and analysis of networks and interaction pathways
InterPro: A comprehensive protein signature resource
IntAct protein interaction database: IntAct is an open source database and analysis resource for protein interaction data
KEGG: KEGG, The Kyoto Encyclopedia of Genes and Genomes
Ye Olde Tutorials : These tutorials are those that are no longer being updated due to various reasons: the resource is not being updated or maintained any longer, is no longer licensed, etc. Some people may be running legacy copies, however. References to the use of these tools in the literature may be found, and without examples of the tool features the details may be difficult to understand. The materials are still useful, therefore, and are offered to our users as an additional resource.
Open source molecular modeling--finally?: My Bio SmartBrief newsletter today had a reference to a paper in a rather...um...obscure journal. Maybe it is just something I have missed over the years, but the Journal of the Royal Society Interface...
Recent BioMed Central research articles citing this resource
Pavlopoulos A. Georgios et al., Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future. GigaScience (2015) doi:10.1186/s13742-015-0077-2
Sfakianaki Pepi et al., Semantic biomedical resource discovery: a Natural Language Processing framework. BMC Medical Informatics and Decision Making (2015) doi:10.1186/s12911-015-0200-4
Moulos Panagiotis et al., The KUPNetViz: a biological network viewer for multiple -omics datasets in kidney diseases Networks analysis. BMC Bioinformatics (2013) doi:10.1186/1471-2105-14-235
Lopes Pedro et al., COEUS: “semantic web in a box” for biomedical applications. Journal of Biomedical Semantics (2012) doi:10.1186/2041-1480-3-11
Komurov Kakajan et al., NetWalker: a contextual network analysis tool for functional genomics. BMC Genomics (2012) doi:10.1186/1471-2164-13-282