Elisha M. Wood-Charlson, Christopher Henry, Paramvir Dehal, Gazi Mahmud, Ben Allen, Kathleen Beilsmith, D. Dakota Blair, Shane Canon, Mikaela Cashman, Dylan Chivian, Robert W. Cottingham, Zach Crocket, Ellen Dow, Meghan Drake, Janaka N. Edirisinghe, José P. Faria, Andrew P. Freiburger, Tianhao Gu, Prachi Gupta, AJ Ireland, Sean Jungbluth, Roy Kamimura, Keith Keller, Ahmed Khan, Dileep Kishore, Dan Klos, Filipe Liu, David Lyon, Christopher J. Neely, Katherine O’Grady, Gavin Price, Priya Ranjan, William J. Riehl, Boris Sadkhin, Sam Seaver, Gwyneth A. Terry, Yue Wang, Pamela Weisenhorn, Ziming Yang, Shinjae Yoo, Adam P. Arkin
The U.S. Department of Energy's Systems Biology Knowledgebase (KBase; www.kbase.us) is an open, collaborative platform that integrates data, models, and analysis tools to accelerate discovery in microbiology, plant biology, and environmental systems. Recently, KBase expanded as a comprehensive, multi-omics ecosystem. KBase enables representation of scientific samples, long-read sequence analysis, protein structure integration, and scalable modeling of microbial communities across diverse environments. KBase also generates digital notebooks as citable, executable research objects that link data, methods, and interpretation. KBase also supports a global education community focused on training the next generation of scientists to use high-performance computational tools. Together, these advances position KBase as a central hub for open, reproducible systems biology. In turn, this enables us to integrate many of the emerging advances in data federation, semantic interoperability, and agent-assisted analysis, paving the way for KBase to support the next generation of AI-driven discovery tools.