Systemic Theoretic Process Analysis (STPA) Used for Cyber Security and Agile Software Development
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An Agile/XP software development process for modernizing the accelerator control system at Fermilab
Fermilab is undergoing the most ambitious upgrade to its accelerator control system of the 21st century. As part of the ACORN project, hundreds of legacy control system applications written in C/C++ will be re-imagined and developed from the ground up. In addition, applications to support Fermilab’s new super-conducting linear accelerator are already under construction. To manage the development of modern controls applications, the Controls department has adopted an Agile software development process based on eXtreme Programming. In this paper we will describe our process and detail our experience applying it to the development of two case studies.
Diamond, John [Fermilab]↗
GDSA PFLOTRAN Development (FY2021)
The Spent Fuel & Waste Science and Technology (SFWST) Campaign of the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Spent Fuel & Waste Disposition (SFWD) is conducting research and development (R&D) on geologic disposal of spent nuclear fuel (SNF) and high-level nuclear waste (HLW). A high priority for SFWST disposal R&D is to develop a disposal system modeling and analysis capability for evaluating disposal system performance for nuclear waste in geologic media. This report describes fiscal year (FY) 2021 advances of the PFLOTRAN Development group of the SFWST Campaign. The mission of this group is to develop a geologic disposal system modeling capability for nuclear waste that can be used to probabilistically assess the performance of generic disposal concepts. In FY 2021, development proceeded along three main thrusts: software infrastructure, code performance, and process model advancement. Software infrastructure improvements included implementing an Agile software development framework and making improvements to the QA Test Suite. Code performance improvements included development of advanced linear and nonlinear solvers as well as design of flexible smoothing algorithms for capillary pressure functions. Process modeling advancements included the addition of flexible thermal conductivity function definitions and refinement of multi-continuum reactive transport to support Sandia’s participation in DECOVALEX
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
PFLOTRAN Development FY2021
The Spent Fuel & Waste Science and Technology (SFWST) Campaign of the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Spent Fuel & Waste Disposition (SFWD) is conducting research and development (R&D) on geologic disposal of spent nuclear fuel (SNF) and high-level nuclear waste (HLW). A high priority for SFWST disposal R&D is to develop a disposal system modeling and analysis capability for valuating disposal system performance for nuclear waste in geologic media. This report describes fiscal year (FY) 2021 advances of the PFLOTRAN Development group of the SFWST Campaign. The mission of this group is to develop a geologic disposal system modeling capability for nuclear waste that can be used to probabilistically assess the performance of generic disposal concepts. In FY 2021, development proceeded along three main thrusts: software infrastructure, code performance, and process model advancement. Software infrastructure improvements included implementing an Agile software development framework and making improvements to the QA Test Suite. Code performance improvements included development of advanced linear and nonlinear solvers as well as design of flexible smoothing algorithms for capillary pressure functions. Process modeling advancements included the addition of flexible thermal conductivity function definitions and refinement of multi-continuum reactive transport to support Sandia’s participation in DECOVALEX. This report fulfills the GDSA PFLOTRAN Development Work Package Level 3 Milestone – PFLOTRAN Development, FY2021, M3SF-21SN010304072.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Approaches for Synthesis and Deployment of Controller Models on Automated Vehicles for Car-following in Mixed Autonomy
This paper describes the software design patterns and vehicle interfaces that were employed to transition vehicle controllers from simulation environments to open-road field experiments. The approach relies on a life cycle that utilizes model-based design and code generation, along with agile software development, and both software and hardware-in-the-loop testing, with additional safety margins. Autonomous designs should consider the dynamics of mixed autonomy in traffic to safely operate among humans. The software that provides a vehicle’s behavior intelligence is often developed through simulation, which may have a mismatch between dynamics, or as a result of a reinforcement learning workflow, which may be a black box with challenges to analyze. In each of these cases, it is important to have research interfaces that provide strongly typed data streams accessible to researchers who are not software experts while continuing to satisfy safety and liveness constraints. This paper describes how we design the hardware platform interfaces and software design process for a mixed autonomy traffic experiment with a leader-follower scenario. Controller synthesis for these vehicles requires clearly articulated vehicle interfaces and software design patterns for successful onboard deployment. Testing strategies for such controllers are also described before algorithms are transitioned to full-scale field experiments with safety operators for the vehicles. Testing strategies include software-in-the-loop simulation testing, hardware-in-the-loop simulation, ghost-car testing, and read-only testing in live traffic. With our approach, we were not only able to validate our controller synthesized in scripts and simulation, but also able to scale deployment to multiple vehicles.
Bhadani, Rahul↗
Agile Acceleration of LLVM Flang Support for Fortran 2018 Parallel Programming
The LLVM Flang compiler ("Flang") is currently Fortran 95 compliant, and the frontend can parse Fortran 2018. However, Flang does not have a comprehensive 2018 test suite and does not fully implement the static semantics of the 2018 standard. We are investigating whether agile software development techniques, such as pair programming and test-driven development (TDD), can help Flang to rapidly progress to Fortran 2018 compliance. Because of the paramount importance of parallelism in high-performance computing, we are focusing on Fortran’s parallel features, commonly denoted “Coarray Fortran.” We are developing what we believe are the first exhaustive, open-source tests for the static semantics of Fortran 2018 parallel features, and contributing them to the LLVM project. A related effort involves writing runtime tests for parallel 2018 features and supporting those tests by developing a new parallel runtime library: the CoArray Fortran Framework of Efficient Interfaces to Network Environments (Caffeine).
Rasmussen, Katherine↗
Agile Project Management for Research Software [Slides]
Scrum is an agile process that allows us to focus on delivering the highest business value in the shortest time. It allows us to rapidly and repeatedly inspect actual working software (every two weeks to one month). The business sets the priorities. Teams self-organize to determine the best way to deliver the highest priority features. Every two weeks to a month anyone can see real working software and decide to release it as is or continue to enhance it for another sprint.
97 MATHEMATICS AND COMPUTING↗
Verification and Validation of START: A Spent Nuclear Fuel Routing and Decision Support Tool
This is a technical presentation that does not take into account contractual limitations or obligations under the Standard Contract for Disposal of Spent Nuclear Fuel and/or High-Level Radioactive Waste (Standard Contract) (10 CFR Part 961). For example, under the provisions of the Standard Contract, spent nuclear fuel in multi-assembly canisters is not an acceptable waste form, absent a mutually agreed to contract amendment.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Agile collaboration: Citizen science as a transdisciplinary approach to heliophysics
Citizen science connects scientists with the public to enable discovery, engaging broad audiences across the world. There are many attributes that make citizen science an asset to the field of heliophysics, including agile collaboration. Agility is the extent to which a person, group of people, technology, or project can work efficiently, pivot, and adapt to adversity. Citizen scientists are agile; they are adaptable and responsive. Citizen science projects and their underlying technology platforms are also agile in the software development sense, by utilizing beta testing and short timeframes to pivot in response to community needs. As they capture scientifically valuable data, citizen scientists can bring expertise from other fields to scientific teams. The impact of citizen science projects and communities means citizen scientists are a bridge between scientists and the public, facilitating the exchange of information. These attributes of citizen scientists form the framework of agile collaboration. In this paper, we contextualize agile collaboration primarily for aurora chasers, a group of citizen scientists actively engaged in projects and independent data gathering. Nevertheless, these insights scale across other domains and projects. Citizen science is an emerging yet proven way of enhancing the current research landscape. To tackle the next-generation’s biggest research problems, agile collaboration with citizen scientists will become necessary.
79 ASTRONOMY AND ASTROPHYSICS↗
An Extensible Software and Communication Platform for Distributed Energy Resource Management
This paper introduces a novel Distributed Extensible Grid Control (DEGC) software and communication platform to facilitate the control of distributed energy resources on electric grids. The DEGC software platform leverages state-of-the-art advances in secure, distributed communication and decentralized authorization and authentication. We discuss how these advances enable the kind of robust and secure communication required for a distributed grid control platform, and show how DEGC applies these technologies to the agile development and deployment of grid software through an extensible and flexible API. Here, we describe how DEGC can implement both Volt-VAR voltage magnitude control and Phasor-Based Control as sample applications and demonstrate the DEGC platform in hardware with the demanding Phasor-Based Control test case, and provide performance metrics.
24 POWER TRANSMISSION AND DISTRIBUTION↗
Algorithms and file structures to extend and enhance liquid chromatography and ion mobility mass spectrometry workflows (CRADA Final Report)
The purpose of this project was to continue supporting customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based protein and metabolite characterization. PNNL worked with Agilent to design, implement, evaluate, and demonstrate new algorithms and integrated them as functionalities into the PNNL-PreProcessor software. The project augmented PNNL’s capabilities to analyze complex proteomics and metabolomics samples. These capabilities are directly beneficial to DOE and PNNL efforts to characterize and analyze these compounds in microbial and plant communities. The project assisted Agilent in further developing improved instrument-software solutions combining liquid chromatography and ion mobility with mass spectrometry for widespread applications in life sciences and other fields.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Multi-Rigor Agile Verification and Rapid Prototyping for Formally Verified Software
We propose a novel approach to developing formally verified systems through Multi-rigor Agile Verification. Multi-rigor Agile Verification is rooted in the hypothesis of Rigor Independence, that a system’s specification and verification architecture depend primarily on the system requirements to be verified, and they depend very little on the rigor level of the methods used to verify those requirements. Due to its iterative nature, Multi-rigor Agile Verification promises to mitigate many of the high upfront design costs experienced by formally verified systems and to deliver a better-architected, and thus better-trusted, system in the end. We then discuss the tooling needed to perform Multi-rigor Agile Verification and go in depth to build one of those tools, which directly generates executable prototype code from declarative formal specifications using the Maude rewrite-logic framework.
97 MATHEMATICS AND COMPUTING↗
Algorithms and file structures to enhance software workflows for ion mobility mass spectrometry (IM-MS): CRADA 410 (Final Report)
This document is the final report for CRADA 410 (Project No. 72496). The purpose of this project was supporting customizations of algorithms and raw data file structures to enhance software workflows for liquid chromatography (LC), mass spectrometry (MS) and ion mobility mass spectrometry (IM-MS)-based metabolite characterization. PNNL worked with Agilent to evaluate and improve the integration of ion mobility into existing MS data analysis methods of Agilent software tools. The project augmented PNNL’s capabilities to analyze complex omics samples. These capabilities are directly beneficial to DOE and PNNL efforts to characterize and analyze compounds in microbial and plant communities. The project assisted Agilent in further developing improved instrument-software solutions combining ion mobility with mass spectrometry for widespread applications in life sciences and other fields.
97 MATHEMATICS AND COMPUTING↗
Tabletop Testing for EV Charging Ecosystem PKI (Project T34PKI Final Report)
To test the communications and cybersecurity functionality, Electric Vehicle and charging station vendors have had to ship their products to in-person testing events. This is cumbersome, expensive, inefficient, and an impediment to rapid time-to-deployment. In this project Sandia used COTS hardware and Open-Source Software to develop and demonstrate a more agile, productive approach: testing low-voltage controllers independently from high-voltage power delivery sub-systems. This approach allows communications controllers to be transported easily (e.g. shipped at low cost, checked as airline baggage); set up on a table-top (“bench testing”); and use ordinary 120 VAC outlets to conduct agile testing. Table-top platforms become end nodes that can connect to laboratory and cloud-based servers to test communications and cybersecurity, specifically Public Key Infrastructure (PKI) functionality and interoperability, separately from EV battery charging (power/energy transfer) functionality.
33 ADVANCED PROPULSION SYSTEMS↗
Agilent AgileBioFoundry CRADA (Final Report)
The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOF-MS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Therefore, our accomplishment in this CRADA improved the efficiency and accuracy of strain testing by developing and implementing fast analytical methods, robust processing tools, and software for predicting the best methods for UHPLC analysis.
97 MATHEMATICS AND COMPUTING↗
Development and implementation of high-throughput proteomic and metabolomics assays by using advanced chromatographic and mass spectrometric systems (CRADA Final Report)
The mission of this CRADA with Agilent was to couple powerful MS platforms (QQQ, IM-QTOFMS) with Agilent’s novel Ultra-High-Performance Liquid Chromatography (UHPLC) fast metabolomic workflows and perform ABF Machine Learning (ML) to generated datasets. Agilent transferred UHPLC methods to PNNL and LBNL and methods were implemented and demonstrated in both labs, achieving total acquisition times of < 10 min. Metabolites analyzed using Agilent’s shared methods included metabolites from central carbon metabolism, common across hosts, and metabolites unique to engineered strains. Standards were acquired in an UHPLC-Drift Tube Ion Mobility Mass Spectrometer (DTIMS) system for the first time within the context of ABF and methods were optimized based on Agilent’s protocols. Samples from ABF hosts Pseudomonas putida, Aspergillus pseudoterreus, Aspergillus niger and Rhodosporidium toruloides were analyzed using the UHPLC-DTIMS platform for a total of 276 runs. A data analysis workflow compatible with the Experimental Data Depot (EDD) and completely shareable was developed for the acquired UHPLC-DTIMS data. Samples were analyzed using a Data Independent Acquisition Approach (DIA), which for most of the standards provided more transitions therefore increasing detection confidence. Using the data acquired by PNNL, LBNL, and Agilent’s specifications from previous ML projects, SNL applied an ensemble ML strategy to pick the best performing model for automated LC-method selection. Finally, with the contribution of the participant labs and Agilent, SNL developed an Automated Method Selection (AMS) software tool to predict the best liquid chromatography method for analysis of any new molecules of interest. Samples with novel pathways and new metabolite targets of interest are generated at a high pace in the ABF. Overall, the project advanced rapid metabolomics by combining liquid chromatography, ion mobility spectrometry, and data-independent mass spectrometry with machine learning. This multidimensional approach uses retention time, collision cross-section, precursor mass, and fragment-ion information to distinguish chemically similar metabolites that can be difficult to resolve using conventional liquid- or gas-chromatography methods. The resulting workflow also provided automated metabolite-identification error estimates, addressing a recognized need for statistical confidence measures in metabolomics.
Petzold, Christopher [Lawrence Berkeley National L↗
Continuous Integration, In-Code Documentation, and Automation for Nuclear Quality Assurance Conformance
The Multiphysics Object Oriented Simulation Environment (MOOSE) is an open-source, finite element framework for solving highly coupled sets of nonlinear equations. The development of the framework and applications occurs concurrently using an agile, continuous-integration software package. Included in the framework is an in-code, extensible documentation system. Using these two tools in union with the repository management tools GitHub and GitLab, a software quality plan was created and followed such that MOOSE and a MOOSE-based application (BISON) have been shown to meet the American Society of Mechanical Engineers’ Nuclear Quality Assurance-1 standard. The approach relies heavily on automation for both testing and documentation. The resulting effort demonstrates that a rigorous software quality plan may be implemented that incurs a minimal impact on day-to-day development of the software, satisfying the stringent guidelines necessary to operate the software in a safety function within a nuclear facility.
97 MATHEMATICS AND COMPUTING↗
Host Onboarding Tool (HObT) v1.0.0
The Host OnBoarding Tool (Hobt) is a publicly accessible, web-based software designed to organize and share information about microbial hosts under development at the Agile BioFoundry (ABF). It streamlines the assessment, tracking, and sharing of information related to microbial host development and provides a centralized platform where users can rapidly evaluate hosts' readiness for various bio processes. HObT leverages the Tier System, a standardized host development framework that organizes and assesses microbial hosts based on their readiness for biomanufacturing. Each tier outlines key targets—including genetic tools, growth conditions, omics data, and predictive models—needed to transform new or emerging microbes into established production platforms. By applying clear criteria for advancement, the Tier System helps users quickly evaluate each organism's current development status, identify gaps in available knowledge or tools, and prioritize future strain improvement efforts. Through its user-friendly interface, HObT encourages contributions of new data and insights from researchers, fostering collaboration and accelerating host development. By providing structured guidance for microbial strain advancement, HObT and the Tier System support more systematic, rapid, and cost-effective development of non-traditional microbial hosts, ultimately enhancing the efficiency and impact of biomanufacturing research and applications.
Plahar, Hector [Lawrence Berkeley National Laborat↗