GigaScience is an online open access, open data, open peer-review journal. Our focus covers ‘big data’ research from the life and biomedical sciences, including the growing range of work that uses difficult-to-access large-scale data, such as imaging, neuroscience, ecology, cohort, systems biology, and other new types of sharable data. We are unique in the publishing industry as we publish ALL research objects (data, software tools, and workflows) and do this within the context of a variety of article types, including Research, Data Notes, Technical Notes, Reviews and Commentaries. Our goal is to revolutionize publishing by improving research reproducibility and data dissemination, organization, understanding, and re-use. To achieve our goals, the journal has a novel publication format: one that links standard manuscript publication with an extensive database that hosts all associated data, provides data analysis tools and cloud-computing resources. Coupled with this, we have also built a Galaxy-based data analysis platform to host computational methods and workflows, maximizing use of the data, tools and workflows in our articles in a more accessible and reproducible environment.