Results for “open” — Page 8

NASA NTRS2024

Tracking Community Building in Open Science

Open Science is enabled by a vibrant community of researchers who regularly engage with the data, from its production to its organization, curation, archiving, dissemination, analysis, and publication. This presentation will examine community building in open science. The NASA Open Science Data Repository (OSDR) makes data available to the public following the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles. OSDR takes open science further with the OS Analysis Working Groups (AWGs) that facilitate community development and promotion. The primary activity of each AWG is to establish and validate analytical processes to generate higher-order data from data housed in OSDR. There are a number of these groups on various topics, including the Animal AWG, Plant AWG, Microbial AWG, Multi-Omics AWG, AI/ML AWG, and the Ames Life Sciences Data Archive (ALSDA) AWG. The international volunteers participating in these AWGs come from academia, citizen science initiatives, industry, and government. They include researchers, principal investigators, professors, trained hobbyists, and students from various domains and disciplines. Anyone may request to join the AWGs, and membership requests are vetted monthly by the group organizers before granting admission. Core to membership is demonstrated expertise through records of training, integrity, work in the professed domain(s), and good community standing. Regular virtual meetings are held for each AWG, with a varying cadence depending on the group's needs and goals. AWG communities share their expertise in research including cutting edge tools, software, frameworks, data formats, and libraries accelerating research collectively. This collaborative approach helps community members cross technology gaps and identify emerging challenges. These diverse communities encompass a wide range of individuals hailing from various sectors within the Science Mission Directorate and beyond. They serve as a means to promote and enhance transparency, accessibility, and inclusion. An annual AWG Symposium brings contributors together in person. Participation in AWGs can be synchronous or asynchronous, with some groups performing most of their work in off hours. Participants gain valuable skills and connections that allow them to add value to their communities and new organizations that they join, resulting in an expanded return on investment for the space life science community. Open science is increasingly a federal mandate and initiatives like NASA's Transform to Open Science and instruments like the Decadal Survey of Biological and Physical Sciences in Space demonstrate the need to carefully consider best practices in this domain. Here, we present greater detail about the makeup and participation metrics of the various AWGs affiliated with OSDR and details of successful peer-reviewed publication campaigns.

Christina M Johnson↗

NASA NTRSDate not supplied

Developing Open-Source Training Materials for AI/ML and Space Biological Sciences Using NASA Cloud-Based Data

Artificial Intelligence (AI) and Machine Learning (ML) has gained significant traction in the biological and biomedical research fields, in part due to a culture of open data sharing and reuse. AI/ML methodology is well-suited to recognize and predict biological patterns from high-dimensional next-generation sequencing data (e.g. whole genome sequencing, transcriptomic sequencing), as well as from biological or medical imaging data (e.g. microscopy, computed tomography, ultrasound, magnetic resonance imaging, radiography). These methodologies hold particular promise for space biosciences research and automated space health monitoring systems. However, there are key considerations for properly training, validating, and testing a machine learning model in biological research or clinical application. Inexperienced researchers can produce models that perform poorly outside of the training dataset. Open Science principles such as data sharing and open-source code must go hand-in-hand with publicly available, high-quality training curricula in best practices, with modules centered on real-life scientific use cases and data so future AI/ML practitioners gain experience on real problems. Here we present the development of open-source training materials for AI/ML and space biosciences, as part of the NASA Transform to Open Science Training (TOPST) initiative. We develop 4 independent training programs, focused on the following topics: 1) Fundamentals of Machine Learning and Space Biosciences Domain, 2) Open Science, Artificial Intelligence, and Ethical Best Practices for Data Sharing and Analysis, 3) Using AI/ML Classification to Identify Gene Networks Affected By Space Exposure in Mouse Liver, and 4) Using Neural Networks to Find DNA Damage Patterns in Immune Cells after Radiation. All programs leverage cloud-based NASA biological datasets. The curriculum we present will enable worldwide access to training in AI/ML and scientific analysis.

James Casaletto↗

NASA NTRSDate not supplied

Tracking Community Building in Open Science

Open Science is enabled by a vibrant community of researchers who regularly engage with the data, from its production to its organization, curation, archiving, dissemination, analysis, and publication. This presentation will examine community building in open science. The NASA Open Science Data Repository (OSDR) makes data available to the public following the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles. OSDR takes open science further with the OS Analysis Working Groups (AWGs) that facilitate community development and promotion. The primary activity of each AWG is to establish and validate analytical processes to generate higher-order data from data housed in OSDR. There are a number of these groups on various topics, including the Animal AWG, Plant AWG, Microbial AWG, Multi-Omics AWG, AI/ML AWG, and the Ames Life Sciences Data Archive (ALSDA) AWG. The international volunteers participating in these AWGs come from academia, citizen science initiatives, industry, and government. They include researchers, principal investigators, professors, trained hobbyists, and students from various domains and disciplines. Anyone may request to join the AWGs, and membership requests are vetted monthly by the group organizers before granting admission. Core to membership is demonstrated expertise through records of training, integrity, work in the professed domain(s), and good community standing. Regular virtual meetings are held for each AWG, with a varying cadence depending on the group's needs and goals. AWG communities share their expertise in research including cutting edge tools, software, frameworks, data formats, and libraries accelerating research collectively. This collaborative approach helps community members cross technology gaps and identify emerging challenges. These diverse communities encompass a wide range of individuals hailing from various sectors within the Science Mission Directorate and beyond. They serve as a means to promote and enhance transparency, accessibility, and inclusion. An annual AWG Symposium brings contributors together in person. Participation in AWGs can be synchronous or asynchronous, with some groups performing most of their work in off hours. Participants gain valuable skills and connections that allow them to add value to their communities and new organizations that they join, resulting in an expanded return on investment for the space life science community. Open science is increasingly a federal mandate and initiatives like NASA's Transform to Open Science and instruments like the Decadal Survey of Biological and Physical Sciences in Space demonstrate the need to carefully consider best practices in this domain. Here, we present greater detail about the makeup and participation metrics of the various AWGs affiliated with OSDR and details of successful peer-reviewed publication campaigns.

Christina M Johnson↗

DOE OSTI2022

Open port sampling interface

A system for sampling a sample material includes a probe which can have an outer probe housing with an open end. A liquid supply conduit within the housing has an outlet positioned to deliver liquid to the open end of the housing. The liquid supply conduit can be connectable to a liquid supply for delivering liquid at a first volumetric flow rate to the open end of the housing. A liquid exhaust conduit within the housing is provided for removing liquid from the open end of the housing. A liquid exhaust system can be provided for removing liquid from the liquid exhaust conduit at a second volumetric flow rate. A droplet dispenser can dispense drops of a sample or a sample-containing solvent into the open end of the housing. A sensor and a processor can be provided to monitor and maintain a liquid dome present at the open end.

Van Berkel, Gary J.↗

DOE OSTI2023

Open port sampling interface

A system for sampling a sample material includes a probe which can have an outer probe housing with an open end. A liquid supply conduit within the housing has an outlet positioned to deliver liquid to the open end of the housing. The liquid supply conduit can be connectable to a liquid supply for delivering liquid at a first volumetric flow rate to the open end of the housing. A liquid exhaust conduit within the housing is provided for removing liquid from the open end of the housing. A liquid exhaust system can be provided for removing liquid from the liquid exhaust conduit at a second volumetric flow rate. A droplet dispenser can dispense drops of a sample or a sample-containing solvent into the open end of the housing. A sensor and a processor can be provided to monitor and maintain a liquid dome present at the open end.

Van Berkel, Gary J.↗

DOE OSTI2024

Open port sampling interface

A system for sampling a sample material includes a probe which can have an outer probe housing with an open end. A liquid supply conduit within the housing has an outlet positioned to deliver liquid to the open end of the housing. The liquid supply conduit can be connectable to a liquid supply for delivering liquid at a first volumetric flow rate to the open end of the housing. A liquid exhaust conduit within the housing is provided for removing liquid from the open end of the housing. A liquid exhaust system can be provided for removing liquid from the liquid exhaust conduit at a second volumetric flow rate. A droplet dispenser can dispense drops of a sample or a sample-containing solvent into the open end of the housing. A sensor and a processor can be provided to monitor and maintain a liquid dome present at the open end.

Van Berkel, Gary J.↗

NASA NTRS2017

An Evolving Worldview: Making Open Source Easy

NASA Worldview is an interactive interface for browsing full-resolution, global satellite imagery. Worldview supports an open data policy so that academia, private industries and the general public can use NASA's satellite data to address Earth science related issues. Worldview was open sourced in 2014. By shifting to an open source approach, the Worldview application has evolved to better serve end-users. Project developers are able to have discussions with end-users and community developers to understand issues and develop new features. New developers are able to track upcoming features, collaborate on them and make their own contributions. Getting new developers to contribute to the project has been one of the most important and difficult aspects of open sourcing Worldview. A focus has been made on making the installation of Worldview simple to reduce the initial learning curve and make contributing code easy. One way we have addressed this is through a simplified setup process. Our setup documentation includes a set of prerequisites and a set of straight forward commands to clone, configure, install and run. This presentation will emphasis our focus to simplify and standardize Worldview's open source code so more people are able to contribute. The more people who contribute, the better the application will become over time.

open dat↗

DOE OSTI2023

Operator Growth in Open Quantum Systems

The spreading of quantum information in closed systems, often termed scrambling, is a hallmark of many-body quantum dynamics. In open systems, scrambling competes with noise, errors, and decoherence. Here, in this work, we provide a universal framework that describes the scrambling of quantum information in open systems: we predict that the effect of open-system dynamics is fundamentally controlled by operator size distributions and independent of the microscopic error mechanism. This framework allows us to demonstrate that open quantum systems exhibit universal classes of information dynamics that fundamentally differ from their unitary counterparts. Implications for the Loschmidt echo, nuclear magnetic resonance experiments, and the classical simulability of open quantum dynamics will be discussed.

Physics↗

DOE OSTI2022

The Open Cluster Chemical Abundances and Mapping Survey. V. Chemical Abundances of CTIO/Hydra Clusters Using The Cannon

Open clusters are key chemical and age tracers of Milky Way evolution. While open clusters provide significant constraints on galaxy evolution, their use has been limited due to discrepancies in measuring abundances from different studies. We analyze medium-resolution ( R ~ 19,000) Cerro Tololo Inter-American Observatory/Hydra spectra of giant stars in 58 open clusters using The Cannon to determine [Fe/H], [Mg/Fe], [Si/Fe], [Al/Fe], and [O/Fe]. This work adds an additional 55 primarily southern hemisphere open clusters calibrated to the Sloan Digital Sky Survey/Apache Point Observatory Galactic Evolution Experiment DR16 metallicity system. This uniform analysis is compared to previous studies [Fe/H] measurements for 23 clusters and we present spectroscopic metallicities for the first time for 35 open clusters.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

NASA NTRS2017

Open-Source RTOS Space Qualification: An RTEMS Case Study

NASA space-qualification of reusable off-the-shelf real-time operating systems (RTOSs) remains elusive due to several factors notably (1) The diverse nature of RTOSs utilized across NASA, (2) No single NASA space-qualification criteria, lack of verification and validation (V&V) analysis, or test beds, and (3) different RTOS heritages, specifically open-source RTOSs and closed vendor-provided RTOSs. As a leader in simulation test beds, the NASA IV&V Program is poised to help jump-start and lead the space-qualification effort of the open source Real-Time Executive for Multiprocessor Systems (RTEMS) RTOS. RTEMS, as a case-study, can be utilized as an example of how to qualify all RTOSs, particularly the reusable non-commercial (open-source) ones that are gaining usage and popularity across NASA. Qualification will improve the overall safety and mission assurance of RTOSs for NASA-agency wide usage. NASA's involvement in space-qualification of an open-source RTOS such as RTEMS will drive the RTOS industry toward a more qualified and mature open-source RTOS product.

Real-time operating system↗

NASA NTRS2018

Building a Community of Open Source Contributors

In 2014, a software development team from NASA's Ames Research Center (ARC), working in collaboration with mission teams at the Jet Propulsion Laboratory (JPL), set out to build a new software system for data visualization for missions. Our functional goal was to build a modular multi-mission software system that empowered users to build and compose their own visualizations of data across mission domains, with no programming required from the users to assemble these displays. Beyond the basic functional requirements for missions, we specified a requirement to make the software open source. This requirement was included to enable flexible use, and reduce or eliminate the proprietary nature of software that can impede collaboration. By making it open source, we also benefit from increased productivity and draw on the innovation of the open source developer community. We want to build and empower a community of contributors and enable broad use both inside and outside the space community to glean insights from cross domain usage. The open source software is called Open Mission Control Technologies, it is available on GitHub (https://github.com/nasa/openmct).

Open Source↗

DOE OSTI2022

Decoding the Gate Opening Mechanism of the Flexible Framework RPM3–Zn upon Hydrocarbon Inclusion

Although the existence of a gate-opening phenomenon in the flexible RPM3–Zn is well known, the actual mechanism remains a mystery. Here, we provide a full picture that unambiguously identifies and explains the gate-opening mechanism in RPM3–Zn upon exposure to various hydrocarbons—acetylene, ethylene, ethane, propane, and butane—by combining insights gained from calorimetry, adsorption isotherms, PXRD, in situ infrared spectroscopy, and ab initio simulations. We find that the key to gate opening in this framework is the stretching of a bond between an O and the Zn metal center (COO–Zn), acting as a “stabilizer”, which weakens the necessary support required for the structure to remain intact. Consequently, an increasing concentration of guest molecules exerts sufficient internal pressure to induce strong structural transformations in the unit cell shape and volume, thus triggering the gate opening. Here, our results are critical to understanding the gate opening in several other flexible frameworks and provide an opportunity to fine- tune hydrocarbon separation.

36 MATERIALS SCIENCE↗

DOE OSTI2023

Open-Shell Tensor Hypercontraction

The extension of least-squares tensor hypercontracted second- and third-order Møller–Plesset perturbation theory (LS-THC-MP2 and LS-THC-MP3) to open-shell systems is an important development due to the scaling reduction afforded by THC and the ubiquity of molecular ions, radicals, and other open-shell reactive species. The complexity of wavefunction-based quantum-chemical methods such as Møller–Plesset and coupled cluster theory is reflected in the steep scaling of the computational costs with the molecular size. The least-squares tensor hypercontraction (LS-THC) method is an efficient, single-step factorization for the two-electron integral tensor but can also be used to factorize the double excitation amplitudes, leading to significant scaling reduction. Herein we extend this promising method to open-shell variants of LS-THC-MP2 and -MP3 by using diagrammatic techniques and explicit spin summation. The accuracy of the resulting methods for open-shell species is benchmarked on standard test systems such as regular alkanes as well as realistic systems involving bond breaking, radical stabilization, and other effects. We find that open-shell LS-THC-MPn methods exhibit errors highly comparable to those produced by closed-shell LS-THC-MPn and are highly insensitive to particular chemical interactions, geometries, or even moderate spin contamination.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Neutralizing antibodies induced in immunized macaques recognize the CD4-binding site on an occluded-open HIV-1 envelope trimer

Broadly-neutralizing antibodies (bNAbs) against HIV-1 Env can protect from infection. We characterize Ab1303 and Ab1573, heterologously-neutralizing CD4-binding site (CD4bs) antibodies, isolated from sequentially-immunized macaques. Ab1303/Ab1573 binding is observed only when Env trimers are not constrained in the closed, prefusion conformation. Fab-Env cryo-EM structures show that both antibodies recognize the CD4bs on Env trimer with an ‘occluded-open’ conformation between closed, as targeted by bNAbs, and fully-open, as recognized by CD4. The occluded-open Env trimer conformation includes outwardly-rotated gp120 subunits, but unlike CD4-bound Envs, does not exhibit V1V2 displacement, 4-stranded gp120 bridging sheet, or co-receptor binding site exposure. Inter-protomer distances within trimers measured by double electron-electron resonance spectroscopy suggest an equilibrium between occluded-open and closed Env conformations, consistent with Ab1303/Ab1573 binding stabilizing an existing conformation. Studies of Ab1303/Ab1573 demonstrate that CD4bs neutralizing antibodies that bind open Env trimers can be raised by immunization, thereby informing immunogen design and antibody therapeutic efforts.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

The allosteric mechanism leading to an open-groove lipid conductive state of the TMEM16F scramblase

TMEM16F is a Ca 2+ -activated phospholipid scramblase in the TMEM16 family of membrane proteins. Unlike other TMEM16s exhibiting a membrane-exposed hydrophilic groove that serves as a translocation pathway for lipids, the experimentally determined structures of TMEM16F shows the groove in a closed conformation even under conditions of maximal scramblase activity. It is currently unknown if/how TMEM16F groove can open for lipid scrambling. Here we describe the analysis of ~400 µs all-atom molecular dynamics (MD) simulations of the TMEM16F revealing an allosteric mechanism leading to an open-groove, lipid scrambling competent state of the protein. The groove opens into a continuous hydrophilic conduit that is highly similar in structure to that seen in other activated scramblases. The allosteric pathway connects this opening to an observed destabilization of the Ca 2+ ion bound at the distal site near the dimer interface, to the dynamics of specific protein regions that produces the open-groove state to scramble phospholipids.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Measurement of the work statistics of an open quantum system using a quantum computer

Abstract We report on the experimental measurement of the work statistics of a genuinely open quantum system using a quantum computer. Such measurement has remained elusive thus far due to the inherent difficulty in measuring the total energy change of a system-bath compound (which is the work) in the open quantum system scenario. We overcome this difficulty by applying the interferometric scheme, originally conceived for closed systems, to the open system case and implement it on a superconducting quantum computer, taking advantage of the relatively high levels of noise on current quantum hardware to realize an open quantum system. We demonstrate that the method can be used as a diagnostic tool to probe physical properties of the system-bath compound, such as its temperature and specific transition frequencies in its spectrum. Our experiments corroborate that the interferometric scheme is a promising tool to achieve the long-sought experimental validation of the Jarzynski equality for arbitrary open quantum systems.

Oftelie, Lindsay Bassman (ORCID:0000000335421553)↗

DOE OSTI2021

Invited: Bambu: an Open-Source Research Framework for the High-Level Synthesis of Complex Applications

This paper presents the open-source High-Level Synthesis research framework Bambu. The framework provides an open-source starting point to experiment with new ideas across High-Level Synthesis, high-level verification and debugging, FPGA/ASIC design, design flow space exploration, and parallel hardware accelerator design. The tool accepts as input standard C/C++ specifications and compiler intermediate representations (IRs) coming from the well-known Clang/LLVM and GCC com- pilers. The broad spectrum and flexibility of input formats allow the electronic design automation (EDA) research community to explore and integrate new transformations and optimizations. The easily extendable modular framework already includes many op- timizations and HLS benchmarks. The integration with synthesis and verification backends (commercial and open-source) allows researchers to quickly test any new finding and easily obtain performance and resource usage metrics for a given application. Different FPGA devices are supported from several different vendors: AMD/XILINX, Intel/Altera, Lattice Semiconductor, and NanoXplore. Finally, integration with the OpenRoad open-source end-to-end silicon compiler perfectly fits with the recent push towards open-source EDA.

Ferrandi, Fabrizio↗

DOE OSTI2022

Antibody Recognition of CD4-Induced Open HIV-1 Env Trimers

Human immunodeficiency virus type 1 (HIV-1) envelope (Env), a heterotrimer of gp120-gp41 subunits, mediates fusion of the viral and host cell membranes after interactions with the host receptor CD4 and a coreceptor. CD4 binding induces rearrangements in Env trimer, resulting in a CD4-induced (CD4i) open Env conformation. Structural studies of antibodies isolated from infected donors have defined antibody-Env interactions, with one class of antibodies specifically recognizing the CD4i open Env conformation. In this study, we characterized a group of monoclonal antibodies isolated from HIV-1 infected donors (V2i MAbs) that displayed characteristics of CD4i antibodies. Binding experiments demonstrated that the V2i MAbs preferentially recognize CD4-bound open Env trimers. Structural characterizations of V2i MAb-Env-CD4 trimer complexes using single-particle cryo-electron microscopy showed recognition by V2i MAbs using different angles of approach to the gp120 V1V2 domain and the β2/β3 strands on a CD4i open conformation Env with no direct interactions of the MAbs with CD4. We also characterized CG10, a CD4i antibody that was raised in mice immunized with a gp120-CD4 complex, bound to an Env trimer plus CD4. CG10 exhibited characteristics similar to those of the V2i antibodies, i.e., recognition of the open Env conformation, but showed direct contacts to both CD4 and gp120. Structural comparisons of these and previously characterized CD4i antibody interactions with Env provide a suggested mechanism for how these antibodies are elicited during HIV-1 infection.

60 APPLIED LIFE SCIENCES↗