VANTED v2: a framework for systems biology applications

TLDR

Experimental datasets are growing larger and more complex across multiple data domains, and networks provide a foundation for integrating, analyzing, and visualizing multi‑omics data. The authors present Vanted v2, a systems biology framework comprising seven main tasks. The framework implements seven tasks—including network reconstruction, data visualization, multi‑type data integration, network simulation, and data exploration—combined to allow users to view comprehensive datasets from multiple perspectives while supporting systems biology standards. Vanted is a stand‑alone, Java‑based open‑source framework that aids scientists in data analysis and interpretation, and is available at www.vanted.org.

Abstract

Experimental datasets are becoming larger and increasingly complex, spanning different data domains, thereby expanding the requirements for respective tool support for their analysis. Networks provide a basis for the integration, analysis and visualization of multi-omics experimental datasets. Here we present Vanted (version 2), a framework for systems biology applications, which comprises a comprehensive set of seven main tasks. These range from network reconstruction, data visualization, integration of various data types, network simulation to data exploration combined with a manifold support of systems biology standards for visualization and data exchange. The offered set of functionalities is instantiated by combining several tasks in order to enable users to view and explore a comprehensive dataset from different perspectives. We describe the system as well as an exemplary workflow. Vanted is a stand-alone framework which supports scientists during the data analysis and interpretation phase. It is available as a Java open source tool from http://www.vanted.org