The United States Department of Energy (DOE) has developed KBase, an open-source software and data platform that enables data sharing, integration, and analysis of microbes, plants, and their communities. KBase provides a comprehensive set of tools for scientists to analyze complex and heterogeneous data sets, integrate their data and results with others, and rapidly propagate new data and conclusions. KBase maintains an internal reference database that consolidates information from widely used external data repositories, including over 90,000 microbial genomes, over 50 plant genomes, over 300 Biolog media formulations, and >30,000 reactions and compounds from KEGG, BIGG, and MetaCyc. These public data are available for integration with user data where appropriate. KBase links these diverse data types with a range of analytical functions within a web-based user interface. The platform's primary user interface, the Narrative Interface, provides a user experience distinct from other analysis platforms, allowing users to upload data, search and retrieve public reference data, access data shared by others, share their data, select and run applications, view and analyze results, and record their thoughts and interpretations. These activities take place within a point-and-click 'notebook' environment. A finished Narrative is a precise record of everything the authors did to complete their analysis. Narratives can be shared or made public, enabling other users to copy and rerun them on their own data or modify them for their scientific needs. KBase's data model is fundamental to supporting reproducibility and collaboration. It is built upon an object-oriented data model where each object instance is automatically versioned and linked to provenance information. This data model enhances interoperability by requiring apps to operate on a common data representation. KBase has over 160 apps offering diverse scientific functionality for (meta)genome assembly, contig binning, genome annotation, sequence homology analysis, tree building, comparative genomics, metabolic modeling, community modeling, gap-filling, RNA-seq processing, and expression analysis. These apps interoperate seamlessly to enable a range of scientific workflows. KBase is designed to be an extensible community resource, supported by the KBase Software Development Kit (SDK), which enables any developer to build, test, register, and deploy new or existing software as KBase apps. KBase has been used by over 3,000 users, who have created over 5,000 Narratives containing over 250,000 data objects. Science done within KBase has been published in over 30 peer-reviewed publications. KBase's integration of data and tools has the potential to empower scientists in a broad range of application areas for systems biology, including environmental analysis, biosystems design, and human health.The United States Department of Energy (DOE) has developed KBase, an open-source software and data platform that enables data sharing, integration, and analysis of microbes, plants, and their communities. KBase provides a comprehensive set of tools for scientists to analyze complex and heterogeneous data sets, integrate their data and results with others, and rapidly propagate new data and conclusions. KBase maintains an internal reference database that consolidates information from widely used external data repositories, including over 90,000 microbial genomes, over 50 plant genomes, over 300 Biolog media formulations, and >30,000 reactions and compounds from KEGG, BIGG, and MetaCyc. These public data are available for integration with user data where appropriate. KBase links these diverse data types with a range of analytical functions within a web-based user interface. The platform's primary user interface, the Narrative Interface, provides a user experience distinct from other analysis platforms, allowing users to upload data, search and retrieve public reference data, access data shared by others, share their data, select and run applications, view and analyze results, and record their thoughts and interpretations. These activities take place within a point-and-click 'notebook' environment. A finished Narrative is a precise record of everything the authors did to complete their analysis. Narratives can be shared or made public, enabling other users to copy and rerun them on their own data or modify them for their scientific needs. KBase's data model is fundamental to supporting reproducibility and collaboration. It is built upon an object-oriented data model where each object instance is automatically versioned and linked to provenance information. This data model enhances interoperability by requiring apps to operate on a common data representation. KBase has over 160 apps offering diverse scientific functionality for (meta)genome assembly, contig binning, genome annotation, sequence homology analysis, tree building, comparative genomics, metabolic modeling, community modeling, gap-filling, RNA-seq processing, and expression analysis. These apps interoperate seamlessly to enable a range of scientific workflows. KBase is designed to be an extensible community resource, supported by the KBase Software Development Kit (SDK), which enables any developer to build, test, register, and deploy new or existing software as KBase apps. KBase has been used by over 3,000 users, who have created over 5,000 Narratives containing over 250,000 data objects. Science done within KBase has been published in over 30 peer-reviewed publications. KBase's integration of data and tools has the potential to empower scientists in a broad range of application areas for systems biology, including environmental analysis, biosystems design, and human health.