FluKB is a knowledge-based system that supports influenza vaccine discovery. It contains influenza sequence data, T-cell epitope, and B-cell epitope data, along with a set of tools for the analysis of targets of immune responses. Standardized nomenclature and dictionaries were developed and implemented to enable automated analysis queries and automation of updates. FluKB was built using a modular framework allowing the implementation of analytical workflows. FluKB supports the discovery of vaccine targets, analysis of viral diversity and of cross-reactivity and cross-neutralization of T-cells and neutralizing antibodies.