  Omics technologies enable unbiased investigation of biological systems
through massively parallel sequence acquisition or molecular measurements,
bringing the life sciences into the era of Big Data. A central challenge posed
by such omics datasets is how to transform this data into biological knowledge.
For example, how to use this data to answer questions such as: which functional
pathways are involved in cell differentiation? Which genes should we target to
stop cancer? Network analysis is a powerful and general approach to solve this
problem consisting of two fundamental stages, network reconstruction and
network interrogation. Herein, we provide an overview of network analysis
including a step by step guide on how to perform and use this approach to
investigate a biological question. In this guide, we also include the software
packages that we and others employ for each of the steps of a network analysis
workflow.
