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.

  • NOTE: This tutorial is on an archival version of BiologicalNetworks and will not be updated due to licensing issues.

    You will learn:

    • to use BiologicalNetworks Graphical User Interface
    • how to explore KEGG curated pathways
    • how to search Biological Networks to create curated pathways
    • how to add experimental data to create your own biological pathway diagrams
    • how to load and visualize microarray expression data


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Ye Olde Tutorials : These tutorials are those that are no longer being updated due to various reasons: the resource is not being updated or maintained any longer, is no longer licensed, etc.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

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

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

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

Komurov Kakajan et al., NetWalker: a contextual network analysis tool for functional genomics. BMC Genomics (2012) doi:10.1186/1471-2164-13-282

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