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1. CyberGIS‐Jupyter for reproducible and scalable geospatial analytics

   https://doi.org/10.1002/cpe.5040  

   Yin, Dandong; Liu, Yan; Hu, Hao; Terstriep, Jeff; Hong, Xingchen; Padmanabhan, Anand; Wang, Shaowen (November 2018, Concurrency and Computation: Practice and Experience)

   Summary The interdisciplinary field of cyberGIS (geographic information science and systems (GIS) based on advanced cyberinfrastructure) has a major focus on data‐ and computation‐intensive geospatial analytics. The rapidly growing needs across many application and science domains for such analytics based on disparate geospatial big data poses significant challenges to conventional GIS approaches. This paper describes CyberGIS‐Jupyter, an innovative cyberGIS framework for achieving data‐intensive, reproducible, and scalable geospatial analytics using Jupyter Notebook based on ROGER, the first cyberGIS supercomputer. The framework adapts the Notebook with built‐in cyberGIS capabilities to accelerate gateway application development and sharing while associated data, analytics, and workflow runtime environments are encapsulated into application packages that can be elastically reproduced through cloud‐computing approaches. As a desirable outcome, data‐intensive and scalable geospatial analytics can be efficiently developed and improved and seamlessly reproduced among multidisciplinary users in a novel cyberGIS science gateway environment. 

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2. NotebookOS: A Replicated Notebook Platform for Interactive Training with On-Demand GPUs

   Carver, Benjamin; Zhang, Jingyuan; Wang, Haoliang; Mahadik, Kanak; Cheng, Yue (March 2026, The ACM International Conference on Architectural Support for Programming Languages and Operating Systems)

   Interactive notebook programming is universal in modern ML and AI workflows, with interactive deep learning training (IDLT) emerging as a dominant use case. To ensure responsiveness, platforms like Jupyter and Colab reserve GPUs for long-running notebook sessions, despite their intermittent and sporadic GPU usage, leading to extremely low GPU utilization and prohibitively high costs. In this paper, we introduce NotebookOS, a GPU-efficient notebook platform tailored for the unique requirements of IDLT. NotebookOS employs replicated notebook kernels with Raft-synchronized replicas distributed across GPU servers. To optimize GPU utilization, NotebookOS oversubscribes server resources, leveraging high inter-arrival times in IDLT workloads, and allocates GPUs only during active cell execution. It also supports replica migration and automatic cluster scaling under high load. Altogether, this design enables interactive training with minimal delay. In evaluation on production workloads, NotebookOS saved over 1,187 GPU hours in 17.5 hours of real-world IDLT, while significantly improving interactivity. 

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3. Building a Vision for Reproducibility in the Cyberinfrastructure Ecosystem: Leveraging Community Efforts

   https://doi.org/10.14529/jsfi200106  

   Chapp, D.; Stodden, V.; Taufer, M. (March 2020, Supercomputing Frontiers and Innovations)

   The scientific computing community has long taken a leadership role in understanding and assessing the relationship of reproducibility to cyberinfrastructure, ensuring that computational results - such as those from simulations - are "reproducible", that is, the same results are obtained when one re-uses the same input data, methods, software and analysis conditions. Starting almost a decade ago, the community has regularly published and advocated for advances in this area. In this article we trace this thinking and relate it to current national efforts, including the 2019 National Academies of Science, Engineering, and Medicine report on "Reproducibility and Replication in Science". To this end, this work considers high performance computing workflows that emphasize workflows combining traditional simulations (e.g. Molecular Dynamics simulations) with in situ analytics. We leverage an analysis of such workflows to (a) contextualize the 2019 National Academies of Science, Engineering, and Medicine report's recommendations in the HPC setting and (b) envision a path forward in the tradition of community driven approaches to reproducibility and the acceleration of science and discovery. The work also articulates avenues for future research at the intersection of transparency, reproducibility, and computational infrastructure that supports scientific discovery. 

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4. Reproducibility Starts at the Source: R, Python, and Julia Packages for Retrieving USGS Hydrologic Data

   https://doi.org/10.3390/w15244236  

   Hodson, Timothy O; DeCicco, Laura A; Hariharan, Jayaram A; Stanish, Lee F; Black, Scott; Horsburgh, Jeffery S (December 2023, Water)

   Much of modern science takes place in a computational environment, and, increasingly, that environment is programmed using R, Python, or Julia. Furthermore, most scientific data now live on the cloud, so the first step in many workflows is to query a cloud database and load the response into a computational environment for further analysis. Thus, tools that facilitate programmatic data retrieval represent a critical component in reproducible scientific workflows. Earth science is no different in this regard. To fulfill that basic need, we developed R, Python, and Julia packages providing programmatic access to the U.S. Geological Survey’s National Water Information System database and the multi-agency Water Quality Portal. Together, these packages create a common interface for retrieving hydrologic data in the Jupyter ecosystem, which is widely used in water research, operations, and teaching. Source code, documentation, and tutorials for the packages are available on GitHub. Users can go there to learn, raise issues, or contribute improvements within a single platform, which helps foster better engagement and collaboration between data providers and their users. 

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5. X-composer: enabling cross-environments in-situ workflows between HPC and cloud

   https://doi.org/10.1145/3468267.3470621  

   Li, Feng; Wang, Dali; Yan, Feng; Song, Fengguang (July 2021, Proceedings of the Platform for Advanced Scientific Computing Conference)

   As large-scale scientific simulations and big data analyses become more popular, it is increasingly more expensive to store huge amounts of raw simulation results to perform post-analysis. To minimize the expensive data I/O, “in-situ” analysis is a promising approach, where data analysis applications analyze the simulation generated data on the fly without storing it first. However, it is challenging to organize, transform, and transport data at scales between two semantically different ecosystems due to the distinct software and hardware difference. To tackle these challenges, we design and implement the X-Composer framework. X-Composer connects cross-ecosystem applications to form an “in-situ” scientific workflow, and provides a unified approach and recipe for supporting such hybrid in-situ workflows on distributed heterogeneous resources. X-Composer reorganizes simulation data as continuous data streams and feeds them seamlessly into the Cloud-based stream processing services to minimize I/O overheads. For evaluation, we use X-Composer to set up and execute a cross-ecosystem workflow, which consists of a parallel Computational Fluid Dynamics simulation running on HPC, and a distributed Dynamic Mode Decomposition analysis application running on Cloud. Our experimental results show that X-Composer can seamlessly couple HPC and Big Data jobs in their own native environments, achieve good scalability, and provide high-fidelity analytics for ongoing simulations in real-time. 

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