Organizations: Applied Math & Computational Research Division · Bakar Comp. Health Sciences Institute, UC San Francisco · Berkeley Institute for Data Science, UC Berkeley
Abstract
The increasing complexity of modern computational environments often burdens researchers with infrastructure management, authentication protocols, and container deployments. We present Sci-Orchestra, a layered orchestration framework designed to fully automate experimental workflows, allowing scientists to prioritize scientific discovery over backend operations. By abstracting execution through an API-driven interface, the system assumes responsibility for secure authentication, resource management, and scalable deployment across diverse high-performance computing environments using Kubernetes architectures. A key innovation of Sci-Orchestra is its autonomous marketplace, which serves as a catalyst for cross-institutional collaboration. Through an intuitive user interface, researchers can rapidly deploy and share specialized services via simple selections, eliminating the need for complex installations and technical setups. This modular infrastructure is specifically designed to facilitate industry partnerships as it provides a secure execution environment and allows external collaborators to test and validate proprietary tools without the need for source-code exchange. This ``black-box'' interoperability protects intellectual property while enabling seamless integration into broader scientific pipelines, ultimately accelerating the transition from laboratory prototypes to industrial-scale applications.
Human involvement is critical in training and deploying AI systems in high-stakes defence and security contexts. However, real-time interaction is impractical in HPC environments due to compute intensity and resource constraints. We present a workflow framework that enables asynchronous human-AI collaboration across hybrid infrastructures, including HPC clusters, local machines, and cloud platforms. Workflows can pause at defined checkpoints for human input without halting underlying compute jobs, preventing idle resources and enabling non-blocking supervision. The framework supports interaction with SLURM-based scheduling, containerized and native tasks, and is customized for scenarios requiring human judgment and adaptability. We demonstrate its application in model training on systems like MareNostrum 5, highlighting benefits in portability, efficiency, and oversight in operational AI workflows.
High-performance computing (HPC) clusters remain the backbone of large-scale scientific computation, traditionally executing deterministic, linear pipelines optimised for predictable performance. However, the pervasive integration of artificial intelligence (AI) and foundation models into scientific research has introduced a fundamentally new computational paradigm. AI-driven workflows are characteristically iterative, data-driven, and probabilistic, introducing unique challenges regarding data gravity, heterogeneous resource management, and complex workflow orchestration. This guide provides twelve practical tips designed to help researchers design efficient, scalable, and reproducible AI-driven HPC workflows. By addressing critical system-level bottlenecks - such as containerisation for environment portability, strategic deployment of job arrays, explicit feedback loop mechanics, and I/O optimisation for small files - this article offers a framework for transitioning from rigid execution pipelines to adaptive, intelligent computational environments. While these architectural principles are broadly applicable across distributed environments, they are particularly tailored to the resource-intensive throughput demands of modern computational biology.
This paper details two novel frameworks for developing autonomous, agentic AI in scientific workflows. Both systems leverage a hybrid Local Body, Remote Brain architecture via Google Colab, utilizing Python-based local orchestrators to invoke large language model (LLM) cloud backends. The first agent, DeepTS/DeepCollector, automates the large-scale curation, extraction, and deduplication of time-series datasets. The second, DeepScribe, is an autonomous presentation analyzer that converts visually dense, mathematically complex physics lectures into structured scientific reports. Through practical systems engineering-such as granular attribute extraction (Cellular RAG), remote data inspection, and distributed concurrency controls-we demonstrate how agentic AI can overcome the context and reasoning limitations of current state-of-the-art systems to rigorously support scientific workflows. Finally, we outline a generalization of DeepTS to support deep knowledge graphs and discuss the application of this conceptual approach to high-energy physics (DeepQCD).