Constructing multi-step bioinformatics workflows, from read quality control through genome assembly to functional annotation, requires expertise in both biology and computational tool selection, creating a bottleneck for scalable and reproducible analysis. We present the KBase Research Agent, a multi-agent system for automating such workflows within the DOE Systems Biology Knowledgebase (KBase). Given a set of sequencing reads and a research objective, the agent constructs an analysis plan grounded in KBase documentation and a Knowledge Graph (KG) of the KBase application catalog, then selects, parameterizes, validates and executes appropriate KBase applications to carry out the workflow. The resulting analysis is preserved as a reproducible KBase Narrative. We evaluate the system's planning and execution quality against ground truth constructed from reference workflows derived from peer-reviewed Microbiology Resource Announcements. We further apply the agent to 100 previously unanalyzed bacterial isolate genomes from the JGI IMG/M database, where it autonomously performed read quality control, genome assembly, taxonomic classification with GTDB-Tk, and downstream analysis producing annotated genomes, reproducible Narratives, and draft manuscripts without human intervention. Across these experiments, the KBase Research Agent demonstrates the feasibility of domain-grounded, end-to-end scientific workflow automation in a production bioinformatics platform.
Gupta, P., Riehl, W. J., Cashman, M., Chivian, D., Neely, C. J., Canon, S. R., Cottingham, R., Henry, C., Arkin, A. P., Dehal, P. S.
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