The article introduces the DOE Systems Biology Knowledgebase (KBase), an open-source software and data platform designed to integrate and analyze complex biological data from microbes, plants, and their communities. KBase addresses the challenge of integrating heterogeneous and distributed data into predictive models of biological functions. It maintains an extensive reference database, including microbial genomes, plant genomes, media formulations, and metabolic reactions, which can be integrated with user data. KBase features a web-based user interface that supports data provenance, reproducibility, and collaboration. Key features include a flexible system for sharing data and workflows, an integrated database of genomes and biochemistry, a point-and-click interface for building and sharing complex analyses, and a software development kit for external developers. KBase supports a wide range of scientific applications, such as genome assembly, annotation, metabolic modeling, and community analysis. The platform has been used by over 3,000 users, creating more than 5,000 narratives, and has been published in over 30 peer-reviewed publications. Future developments aim to enhance social aspects, data discovery, and knowledge-discovery capabilities.The article introduces the DOE Systems Biology Knowledgebase (KBase), an open-source software and data platform designed to integrate and analyze complex biological data from microbes, plants, and their communities. KBase addresses the challenge of integrating heterogeneous and distributed data into predictive models of biological functions. It maintains an extensive reference database, including microbial genomes, plant genomes, media formulations, and metabolic reactions, which can be integrated with user data. KBase features a web-based user interface that supports data provenance, reproducibility, and collaboration. Key features include a flexible system for sharing data and workflows, an integrated database of genomes and biochemistry, a point-and-click interface for building and sharing complex analyses, and a software development kit for external developers. KBase supports a wide range of scientific applications, such as genome assembly, annotation, metabolic modeling, and community analysis. The platform has been used by over 3,000 users, creating more than 5,000 narratives, and has been published in over 30 peer-reviewed publications. Future developments aim to enhance social aspects, data discovery, and knowledge-discovery capabilities.