Abstract
SummaryThe complexity of molecular networks makes them difficult to navigate and interpret, creating a need for specialized software. MINERVA is a web platform for visualization, exploration and management of molecular networks. Here, we introduce an extension to MINERVA architecture that greatly facilitates the access and use of the stored molecular network data. It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform’s visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats. To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities. In the article, we demonstrate the plugins for interactive tree traversal of molecular networks, for enrichment analysis and for mapping and visualization of known disease variants or known adverse drug reactions to molecules in the network.Availability and implementationPlugins developed and maintained by the MINERVA team are available under the AGPL v3 license at https://git-r3lab.uni.lu/minerva/plugins/. The MINERVA API and plugin documentation is available at https://minerva-web.lcsb.uni.lu.
Highlights
One of the goals of systems biology is to model molecular networks of biological systems
It allows to incorporate such data in analytical pipelines via a programmatic access interface, and to extend the platform’s visual exploration and analytics functionality via plugin architecture. This is possible for any molecular network hosted by the MINERVA platform encoded in well-recognized systems biology formats
To showcase the possibilities of the plugin architecture, we have developed several plugins extending the MINERVA core functionalities
Summary
One of the goals of systems biology is to model molecular networks of biological systems. To efficiently interpret and harvest knowledge stored in complex molecular networks, a support from computational pipelines is needed. MINERVA enables visualization of expression data and cross-linking of molecules to external resources, including drug, chemical or microRNA interaction databases. Such a platform needs to account for a plethora of different analytical and visualization techniques in order to support translational medicine research. Programmatic access and manipulation of hosted data, and (ii) a plugin architecture allowing to flexibly extend existing functionality of the web interface
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