Elucidation of interaction mechanisms between elements of complex biological systems often involves processing vast amounts of data, extracting meaningful information from heterogeneous data sources, generating, annotating, and refining research hypotheses. While various public databases, graphing software, and data mining methods are available, transferring data between these sources is not trivial. Limited support for querying is provided, and searching your own data along public datasets is often not possible. We developed Retina Workbench, a user-friendly software tool enabling biologists to easily store and manipulate public and private genetic data, query gene expression datasets and genetic networks based on the stored annotations as well as Gene Ontology annotations, and merge and reuse results obtained. Retina Workbench aided in our study of photoreceptor differentiation and development in mouse retina and showed to be a valuable tool automating the discovery and study of genetic regulatory networks.