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At least 19 records

The Journal of Open Source Software (JOSS): Bringing Open-Source Software Practices to the Scholarly Publishing Community for Authors, Reviewers, Editors, and Publishers

Open-source software (OSS) is a critical component of open science, but contributions to the OSS ecosystem are systematically undervalued in the current academic system. The Journal of Open Source Software (JOSS) contributes to addressing this by providing a venue (that is itself free, diamond open access, and all open-source, built in a layered structure using widely available elements/services of the scholarly publishing ecosystem) for publishing OSS, run in the style of OSS itself. A particularly distinctive element of JOSS is that it uses open peer review in a collaborative, iterative format, unlike most publishers. Additionally, all the components of the process—from the reviews to the papers to the software that is the subject of the papers to the software that the journal runs—are open. We describe JOSS’s history and its peer review process using an editorial bot, and we present statistics gathered from JOSS’s public review history on GitHub showing an increasing number of peer reviewed papers each year. We discuss the new JOSSCast and use it as a data source to understand reasons why interviewed authors decided to publish in JOSS. JOSS’s process differs significantly from traditional journals, which has impeded JOSS’s inclusion in indexing services such as Web of Science. In turn, this discourages researchers within certain academic systems, such as Italy’s, which emphasize the importance of Web of Science and/or Scopus indexing for grant applications and promotions. JOSS is a fully diamond open-access journal with a cost of around US$\$$5 per paper for the 401 papers published in 2023. The scalability of running JOSS with volunteers and financing JOSS with grants and donations is discussed.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION

Measured opening characteristics of an electromagnetically opened diaphragm for the Langley expansion tunnel

Results from an experimental study of the opening characteristics of an electromagnetically opened, 15.24 cm diameter diaphragm are presented. This diaphragm consists of a polyester film bonded to a preformed wire and is opened by passing a current pulse (capacitor discharge) through the wire. The diaphragm separates the acceleration section of the expansion tunnel from the nozzle so that the nozzle may be at a lower pressure than the acceleration section prior to a test. Opening times and cleanness of the opened area were examined for dependence on diaphragm thickness, on wire diameter, on technique of bonding the wire to the diaphragm, and on voltage and energy level of the energy source. Time histories of the pitot pressure measured at the expansion-tunnel nozzle entrance location are presented for (1) no diaphragm, (2) a flow-opened diaphragm, and (3) an electromagnetically opened diaphragm.

Moore, J. A.

Open e2e Testing Initiative with Open MCT

Open MCT (Open Mission Control Technologies) is a next-generation mission control framework for visualization of data on desktop and mobile devices. It is developed at NASA’s Ames Research Center, and is being used by NASA for data analysis of spacecraft missions, as well as planning and operation of experimental rover systems. This advanced application needs an advanced battery of tests… and you! In this talk, we’ll outline how the Open MCT project is leveraging the testing community to write mission critical e2e tests. We’ll start with the unique (and not so unique) requirements of Open MCT test automation and how they’re addressed with Playwright. Next, we’ll detail the approach to open sourcing the tests and associated challenges. We’ll end with some lessons learned and detail how you can get started testing NASA Open MCT — no previous experience with javascript or web testing required!

John Hill

Open Science for Plants in Space: Improvements in NASA's Open Science Data Repository

Upcoming deep space missions will rely on plants for crew and ecosystem health. Open access space biology data enables scientists to examine the biological responses of plants to ionizing radiation, altered gravity, elevated CO2, and many other abiotic stressors. NASA has declared 2023 as the ‘Year of Open Science’ and created a 5-year Transform to Open Science (TOPS) initiative designed to rapidly transform the agency toward an inclusive culture of open science. NASA’s Open Science Data Repository (OSDR) combines two databases, GeneLab and Ames Life Sciences Data Archive (ALSDA) to maximize access to standardized ‘omics (e.g., transcriptomics, proteomics) and phenotypic data (e.g., microscopy, biomass), respectively. Current OSDR standards include the ISA (Investigation-Study-Assay) experiment model, assay metadata configurations, and standardized terminology and ontologies. In 2024 OSDR will include a new suite of features for improved FAIR compliance including downloadable plant metadata templates, data submission tools and overall improved AI-readiness of plant datasets. AI/ML methods can be helpful tools to overcome the inherent challenges of space biology research (small sample size, sparse and heterogeneous data etc.). However these methods are built on an assumption of normalized and well-curated data. OSDR’s new curation tools will improve users ability to leverage ML and AI methods to model space biology data and better understand the complex effects of spaceflight on living systems across hierarchical biological levels. We look forward to sharing our advances with the spaceflight community.

FAIR

NASA Open Science Data Repository: Open Science for Life in Space

Space biology and health data are critical for the success of deep space missions and sustainable human presence off-world. At the core of effectively managing biomedical risks is the commitment to open science principles, which ensure that data are findable, accessible, interoperable, reusable, reproducible and maximally open. The 2021 integration of the Ames Life Sciences Data Archive with GeneLab to establish the NASA Open Science Data Repository significantly enhanced access to a wide range of life sciences, biomedical-clinical, and mission telemetry data alongside existing ‘omics data from GeneLab. This paper describes the new database, its architecture, and new data streams supporting diverse data types and enhancing data submission, retrieval, and analysis. Features include the Biological Data Management Environment for improved data submission, a new user interface, controlled data access, an enhanced API, and comprehensive public visualization tools for environmental telemetry, radiation dosimetry data, and ‘omics analyses. By fostering global collaboration through its Analysis Working Groups and training programs, the Open Science Data Repository promotes widespread engagement in space biology, ensuring transparency and inclusivity in research. It supports the global scientific community in advancing our understanding of spaceflight's impact on biological systems, ensuring humans will thrive in future deep space missions.

OSDR

Data for A Fluorescence-Based Transient Expression Assay for the Analysis of Upstream Open Reading Frames in Plants

Scripts for the manuscript "A fluorescence-based transient expression assay for the analysis of upstream open reading frames in plant" by Haas et al. Upstream open reading frames (uORFs) are regulatory elements present in the 5′ leaders of mRNA that can significantly impact downstream gene expression in eukaryotes. In crop engineering, editing of uORFs can provide an avenue to upregulate expression of native genes without the need to add persistent transgenic copies. Even with genome- wide methods to identify translated uORFs such as ribosome profiling, their functional characterization depends on validation through reporter gene assays and mutagenesis studies. Current screening methods for plants use luciferases or protoplasts to measure differential gene expression between wild- type and mutated transcript leaders, which requires tissue processing and/or substrate addition. Here, we present a time- and cost- efficient alternative to investigate transcript leaders by co- expression of two fluorescent proteins in Nicotiana benthamiana leaf tissue and test our assay on genes involved in photoprotection, editing of which could provide a pathway to increase CO2 assimilation during sun–shade transitions.

Gene Editing

Diesel Fuel Consumption in Prominent U.S. Open-Pit Mines: Site-Level Estimates

This report presents a comprehensive framework for estimating diesel fuel consumption and prices at open-pit mines in the United States. The framework includes transparent methods for calculating site-level diesel energy use when direct reporting is unavailable, and a structured confidence evaluation for each method. The framework is demonstrated to estimate current diesel consumption at 21 open-pit mines in the United States. Initial findings support ongoing efforts to strengthen the competitiveness and security of the U.S. industrial base by supporting data-driven supply chain analysis and decision-making, improved transparency in mining sector energy use, and targeted deployment of energy innovation and cost-reduction strategies. Future updates to the dataset—coupled with expanded data transparency and method validation—will help ensure that the findings remain relevant as the sector continues to evolve.

02 PETROLEUM

Open Power System Datasets and Open Simulation Engines: A Survey Toward Machine Learning Applications

A major factor behind the success of machine learning (ML) models in multiple domains is the availability and accessibility of large, labeled, and well-organized datasets for training and benchmarking. In comparison, power grid datasets face three major challenges: (i) real-world data is often restricted by regulatory constraints, privacy reasons, or security concerns, making it difficult to obtain and work with; (ii) synthetic datasets, which are created to address these limitations, often have incomplete information and are released using specialized tools, making them inaccessible to the broader community; and, (iii) input-output datasets are difficult to generate through simulation for non-experts because open-source simulators are not known outside the power system community. This survey addresses these challenges by serving as an entry point to publicly available datasets and simulators for researchers venturing in this area. We review the current landscape of open-source power network data, machine models, consumer demand profiles, renewable generation data, and inverter models. We also examine open-source power system simulators, which are crucial for generating high-quality, high-fidelity power grid datasets. We aim to provide a foundation for overcoming data scarcity and advance towards a structured web of datasets and simulators to support the development of ML for power systems.

42 ENGINEERING

The Open Data Repository - an Open Science Platform for Long-Tail Research Data

Introduction: ‘Long-tail’ research is performed by individual PIs and small research teams, producing what are often highly diverse, but relatively small da-tasets that span a variety of traditional scientific disci-plines. ‘Long-tail’ research is a fundamental part of realizing NASA’s goals in planetary sciences and a key input feeding into mission life cycles. The ‘long-tail’ has traditionally lacked the resources (available to larg-er groups and missions) to overcome barriers inhibit-ing the adoption of open science practices, including lack of acknowledgment, time, money, guidance, ex-pertise, and trust in available platforms1. Here we show how the Open Data Repository’s (ODR) data publish-ing platform could help lower some of these barriers and accelerate the adoption of open-science practices in planetary science.

‘Long-tail’ research

Beyond Fair: Engagement, Data Usability, and Open Community Productivity through the NASA Open Science Data Repository

The FAIR principle (findable, accessible, interoperable, and reusable) governs the storage and sharing of NASA space biology and health data[1]. These guiding principles maximize reuse of data and the reproducibility of scientific findings. The NASA Open Science Data Repository (OSDR; an expansion of NASA GeneLab) was built on the FAIR principles and houses over 500 studies and close to 1000 datasets from decades of space life sciences experiments. OSDR embodies the FAIR principles through data governance that includes mediated, embargoed, and fully open access data. The FAIR data governance principles were recently proposed to be expanded to encompass a FAIREST framework for assessing research data repositories (FAIR + Engagement, Social connections, and Trust)[2]. FAIREST emphasizes the importance of data repositories engaging with the scientific community and gaining the trust of researchers regarding data quality. Trust also refers to the TRUST principles developed for assessment of digital repositories: Transparency, Responsibility, User Focus, Sustainability, Technology[3]. We present the “Open Science for Life in Space” Analysis Working Groups (AWGs) as evidence regarding the power of engagement, social connections, and trust which has enhanced OSDR’s capabilities and productivity. AWG members engage in two main activities. One, members provide feedback on OSDR scientific standards for data ingestion, curation, and reuse (study, subject and assay metadata; processing pipelines; dataset formats and uniformed structures for machine-readability). Two, AWG members collaborate to mine-reuse OSDR data to conduct scientific analysis. With nearly 800 active members, the AWGs have resulted in 32 publications re-using OSDR data and contributed many papers in two major special issues in Cell (2020) and Nature (2024). AWGs also serve as networking groups, facilitate social connections between researchers at all levels of experience, and also have a social online ‘Forum’ used to keep members informed on projects and opportunities. This community-centric, productive, and trustworthy data culture has resulted in a broader effect with international space agencies, academics, and the commercial space sector wanting to submit their data to OSDR. Ten studies of Inspiration 4 data were recently publicly released by OSDR, as were some JAXA human data. Coming up soon in OSDR are data submissions from the European Space Agency, Virgin Galactic PIs, and SpaceX Polaris Dawn. A major benefit of OSDR is the array of standardized and uniformly formatted data (which was developed through AWG member consensus), from which visualization tools, analysis tools, and machine learning models can be built or trained. This talk will cover the Multi-Study Visualization Tool, the Environmental Data Application, RadLab, and a UCSF-NSF funded knowledge graph biomedical health discovery tool ‘SPOKE’ currently being integrated with OSDR. OSDR also provides training programs in bioinformatics and machine learning to improve the scientific community’s awareness of data availability and to boost their ability to perform data analysis. The increasing engagement of the scientific community and the public with technologies powered by artificial intelligence (AI) heightens the need for data analysis to be transparent. The AI for Life in Space initiative leverages the data products provided in OSDR to train AI models, with an emphasis on explainable and trustworthy AI, which would not be possible without FAIR data and metadata. Overall, here we will demonstrate the importance for NASA life sciences data repositories to adhere to the FAIREST framework, by providing examples and success stories from different aspects of OSDR.

data

Open Source Lessons Learned with Open MCT

Open source enables flexible use, and reduces or eliminates the proprietary nature of software that can impede collaboration. While still in the early stages, we have built a community of users and contributors, with participation inside and outside of the space community. The model for collaboration is to empower missions by enabling them to adopt the software as their own, make modifications and contributions, and see those contributions used in a larger space community. All missions benefit from the larger user base enabled by open source, as each critical eye on the software results in improvements. The Open MCT user base ranges from missions, to industry outside the space industry, to research and student projects.

Trimble, Jay

Using Open Standards and NASA Open Source Simulation Tools to Model Artemis Base Camp Mission Timelines

The United States’ National Aeronautics and Space Administration (NASA) has announced that the Artemis Program will return humans to the Moon, establishing a persistent presence with the Artemis Base Camp (ABC), and extend human exploration to Mars. The NASA Exploration Systems Simulations (NExSyS) team at NASA’s Johnson Space Center is using internationally developed simulation interoperability standards and NASA open source simulation tools to support Artemis concept, analysis, designs, development, training, and ultimately operations. The NExSyS team has been tasked to support early ABC architecture and mission analysis using mission time lines developed by the crew operations mission planning team. The NExSyS team is developing a distributed simulation framework with initial Artemis element implementations to model the ABC mission timelines using the international simulation interoperability standard High Level Architecture (HLA), the Simulation Interoperability Standards Organization’s Space Reference Federation Object Model (SpaceFOM), the NASA open source Trick Simulation Environment, and another NASA open source interface package called TrickHLA. The ABC architecture is composed of a number of key surface elements and resources. Some examples of modeled elements (also known as entities) are landers, habitats, rovers, logistics carriers, and astronauts. Some examples of modeled transferable and consumable resources are power, water, oxygen, nitrogen, scientific samples, and food. These entities and resources are modeled in a collection of individual simulations called Federates. A coordinated collection of interoperable federates is called a Federation and when these federates are tied together in a coordinated simulation run, it is referred to as a Federation Execution. The federates communicate through HLA using data exchange formats defined by a collection of machine readable files called Federation Object Models (FOMs). These FOM files are based on extensions to the SpaceFOM. This enables the instantiation and sharing of objects and interactions between federates in the federation. These provide for entity and resource tracking, object transfer, and data collection. Federate interactions are used to trigger events and notify federates of entity or resource transfers. For the initial implementation, the constituent federates are Trick-based simulations that use TrickHLA to provide the required HLA-base interoperability. These Trick-based simulations provide the required modeling for the individual Artemis elements along with the associated element resources. These federates provide a means to explore traverses between surface elements and exploration sites as scheduled in a mission timeline and explore the affects traverse times have on the overall mission timeline. The mission time lines are modeled using a Trick input file event handling capabilities. Each timeline operation is handled as individual simulation events, and triggered based on previous event status, time of operation, and simulated task completions. In addition, the ABC Federation can be used to perform Monte Carlo analysis. The Monte Carlo tool can vary the inputs, timings, and malfunctions to show how various contingencies in the mission can affect the mission timeline.

Keaton Craig Dodd

Recent advances in coupled cluster computations of open-shell atomic nuclei

In this contribution, we report on recent progress in coupled-cluster simulations of open-shell atomic nuclei using interactions consistently derived from chiral effective field theory. In particular, we compare different coupled-cluster approaches by computing binding energies and electric dipole polarizabilities in medium-mass calcium isotopes.

Marino, Francesco [Johannes Gutenberg Univ., Mainz

Open Source Service Agent (OSSA) in the intelligence community's Open Source Architecture

The Community Open Source Program Office (COSPO) has developed an architecture for the intelligence community's new Open Source Information System (OSIS). The architecture is a multi-phased program featuring connectivity, interoperability, and functionality. OSIS is based on a distributed architecture concept. The system is designed to function as a virtual entity. OSIS will be a restricted (non-public), user configured network employing Internet communications. Privacy and authentication will be provided through firewall protection. Connection to OSIS can be made through any server on the Internet or through dial-up modems provided the appropriate firewall authentication system is installed on the client.

Fiene, Bruce F.

Capillary Flows Along Open Channel Conduits: The Open-Star Section

Capillary rise in tubes, channels, and grooves has received significant attention in the literature for over 100 years. In yet another incremental extension of such work, a transient capillary rise problem is solved for spontaneous flow along an interconnected array of open channels forming what is referred to as an 'open-star' section. This geometry possesses several attractive characteristics including passive phase separations and high diffusive gas transport. Despite the complex geometry, novel and convenient approximations for capillary pressure and viscous resistance enable closed form predictions of the flow. As part of the solution, a combined scaling approach is applied that identifies unsteady-inertial-capillary, convective-inertial-capillary, and visco-capillary transient regimes in a single parameter. Drop tower experiments are performed employing 3-D printed conduits to corroborate all findings.

Weislogel, Mark

De-Risking Exploration for Geothermal Plays in Magmatic Environments Through Open-Source Tools: An Open-Source Python Framework for 2D and 3D Play Fairway Analysis

The De-Risking Exploration for Geothermal Plays in Magmatic Environments (DEEPEN) project seeks to accelerate superhot geothermal development by reducing exploration risk through advanced open-source modeling tools. This work presents a novel Python-based framework, geoPFA, for conducting 2D and 3D play fairway analysis (PFA) tailored to superhot geothermal systems. Building on previous methodologies, the framework integrates thermo-hydro-mechanical-chemical simulation outputs from TReactMech, resulting in improved representation of subsurface properties that are critical to superhot resource producibility. The workflow has been applied to the Nesjavellir field in Iceland, a candidate site for the third Iceland Deep Drilling Project's superhot production scenarios. This application demonstrates the value of modular, transparent, and extensible workflows for integrating geological, geophysical, and simulation-derived datasets in high-enthalpy environments. Preliminary results indicate favorable zones consistent with known hydrothermal activity and suggest possible upflow from the Hengill volcanic system. The geoPFA library is publicly available, offering a scalable and reproducible approach to geothermal exploration across varied geological contexts.

15 GEOTHERMAL ENERGY

Au147(SPh)30(PPh3)12: A Geometrically Closed, but Electronically Open Triple‐Shell Icosahedral Gold Cluster and its Geometrically Open Counterpart

The aesthetic platonic solids have been known since ancient times, and the structure of all five platonic solids is also found in chemical compounds. While gold sub-nanometer clusters and gold nanoparticles with an icosahedral structure have been known for a long time to exist, a multi-shell icosahedral gold cluster at the intermediate size between 13 and thousands of atoms has been elusive. Here we present the synthesis and crystallographic characterization of the first triple-shell icosahedral metal cluster, Au147(SPh)30(PPh3)12 1. The gold core in 1 is stabilized by phosphines and thiolates, but surprisingly no staple motifs are formed. A second cluster, Au146(SPh)30(PPh3)12 2, cocrystallizes and is identified as having a closed electronic shell but can be considered as a geometrically open pendant of 1. The unique clusters are characterized experimentally by EDX, UV/vis, DLS, and EPR and theoretically by quantum chemical calculations.

Strienz, Markus