Systems biology is a data intensive science, with high-throughput experiments, in particular those from genomics-based technologies, generating extremely large and heterogenous datasets that are challenging to manage let alone analyze. We introduce here the new Systems Biology Knowledgebase (KBase), a collaborative effort designed to enable scientists and researchers to work with their data, and in the process allowing them to build new knowledge, test hypotheses, design experiments, and share their findings. The KBase is developed for microbes, microbial communities, and plants resources, and designed to meet the computational requirements for accelerating fundamental discoveries in bioenergy and climate research. Built on extensible and scalable open-source software frameworks, and application systems, KBase will integrate commonly used core tools and their associated data, while including new capabilities on top of the integrated data. It will be community-driven and will provide free and open access to data, models and simulations. The project will leverage the power of cloud computing, as well as high-performance computing resources across the DOE system of labs to handle the anticipated rapid growth in data volumes and computing requirements of the KBase.