Agents for Everyone: A Workshop Framework for Building Agentic AI Capabilities in a Distributed Curation Community
Authors: Seth Carbon, Sierra Moxon, Kimberly Van Auken, Pascale Gaudet, Christopher J. Mungall
Organizations: Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA · Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA · Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland
Agentic AI has the potential to accelerate curation of biological databases and knowledge bases. However, uptake has been hindered by a number of challenges and obstacles, including access to agents and appropriate training. Here we describe how we have attempted to address and mitigate these challenges and obstacles through the deployment of a cloud-based agentic environment, and the development of an interactive training workshop for the Gene Ontology Consortium. Our cloud environment for agentic-assisted curation was based on the JupyterHub platform, and utilized Claude Code as a universal harness. This allows curators to interact with an agent session through a terminal running in the browser, and has additional benefits such as centralization of access through a single API gateway, removing the need for participants to manage subscriptions or install software locally. We created four training modules, walking participants through basic agentic tool use first and then working up to agentic biological pathway curation using the existing GO-CAM (GO Causal Activity Model) curation tool. Thirty-seven participants took part in the four-hour workshop. Our key takeaway from this workshop is that building community capability with agentic AI is primarily a problem of access, workflow design, and training. Removing technical barriers, introducing capabilities gradually, grounding exercises in familiar curation tasks, and giving curators direct experience evaluating agent output can provide a practical route toward building shared agentic AI capability in distributed scientific communities.
Agentic code generation has the potential to accelerate the development of computational workflows while also reducing barriers to entry. However, a key gap remains: existing coding agents focus on code generation and do not address the entire workflow lifecycle, including deployment and sharing. As a result, users develop and stitch modules independently while managing deployment on their own. To address this gap, we propose CURATE (Composition, User-in-the-loop, Reuse, and Automated Task Execution), a novel human-in-the-loop multi-agent system that uses LLM agents to manage and develop composable workflows across their entire lifecycle. A key feature of the system is a catalog that allows for the storage and reuse of modules across workflows. Module catalogs provide a foundation that can be expanded to support FAIR principles by facilitating the sharing and reuse of curated modules and subgraphs. We demonstrate the feasibility of our system with an initial prototype and 6 experiments.
Nolan Cutler, Chia-Chen Kuo, Nanda Velugoti +2
School of EECS Oregon State University · School of CBEE Oregon State University
Agentic systems large language model (LLM) based architectures capable of reasoning, planning, acting, and coordinating with tools and other agents are rapidly transitioning from research prototypes to production scale deployments across domains such as software engineering, scientific discovery, and finance. While academic work has emphasized benchmarks and algorithmic innovation, deployment raises new challenges around robustness, safety, and reliability. This tutorial brings together researchers and practitioners to explore advances in reasoning and planning, multi agent coordination, and evaluation, highlighting open challenges arising from deployment experience. Through applied case studies in pharmaceutical discovery and financial systems, we analyze common design patterns that make agentic systems successful, and discuss practical mitigation strategies for failure modes, such as verification pipelines, fallback mechanisms, and human in the loop supervision. Attendees will gain a comprehensive view of the field along with concrete design patterns, evaluation checklists, and templates for safe and reliable deployment across industries.
Grace Hui Yang, Pranav N. Venkit, Hooman Sedghamiz +3
Georgetown University · Washington, D.C., USA · Salesforce +7
Curating training data is among the most consequential yet labor-intensive parts of modern AI development: practitioners iteratively propose, implement, evaluate, and revise data policies against noisy benchmark feedback. We ask whether generalist coding agents can automate this data-curation loop. We introduce Curation-Bench, an agent-centric benchmark that fixes the model, training recipe, and evaluation suite while giving agents command-line access to inspect data, implement policies, submit them to a fixed training/evaluation pipeline, and revise. In a vision-language instruction-tuning instantiation, out-of-the-box agents reach strong published data-selection baselines within ten iterations. However, trajectory analysis reveals a persistent execution-research gap: agents mainly tune local policy variants rather than explore new policy families, even when given strategy guides and paper references. Scaffolds requiring each iteration to cite, instantiate, and adapt a prior method shift agents toward method-guided exploration. The scaffolded agent autonomously composes -- without human design input -- a data-selection policy that outperforms strong published baselines at one-tenth their data budget. Overall, current agents can run the curation loop, but reliable data research requires scaffolded method adaptation, not open-ended prompting alone. Code and benchmark are open-sourced.
Feiyang Kang, Hanze Li, Adam Nguyen +5
1Virginia Tech · University of Illinois Urbana-Champaign · University of Wisconsin-Madison +1