The transition towards more sustainable energy systems poses new requirements on energy system models. New challenges include representing more uncertainties, including short-term detail in long-term planning models, allowing for more integration across energy sectors, and dealing with increased model complexities. SpineOpt is a flexible, open-source, energy system modelling framework for performing operational and planning studies, consisting of a wide spectrum of novel tools and functionalities. The most salient features of SpineOpt include a generic data structure, flexible temporal and spatial structures, a comprehensive representation of uncertainties, and model decomposition capabilities to reduce the computational complexity. These enable the implementation of highly diverse case studies. SpineOpt's features are presented through several publicly -available applications. An illustrative case study presents the impact of different temporal resolutions and stochastic structures in a co-optimised electricity and gas network. Using a lower temporal resolution in different parts of the model leads to a lower computational time (44%-98% reductions), while the total system cost varies only slightly (-1.22-1.39%). This implies that modellers experiencing computational issues should choose a high level of temporal accuracy only when needed.