KBase: Open-source Platform for Collaborative Biological Data Analysis and Publication
Elisha M. Wood‐Charlsona, Christopher Scott Henryb, Paramvir Dehala, Gazi Mahmuda, Benjamin H. Allenc, Kathleen R. Beilsmithb, D. Dakota Blaird, Richard Shane Canona, Mikaela Cashmana, Dylan C. Chiviana, Robert W. Cottinghamc, Zachary Crockett
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Abstract
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.
TL;DRKBase's Systems Biology Knowledgebase is an open, collaborative platform that integrates data, models, and analysis tools to accelerate discovery in microbiology, plant biology, and environmental systems, and it enables many of the emerging advances in data federation, semantic interoperability, and agent-assisted analysis. (Semantic Scholar)