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All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Open-Source and FAIR Research Software for Proteomics

Scientific discovery relies on innovative software as much as experimental methods, especially in proteomics, where computational tools are essential for mass spectrometer setup, data analysis, and interpretation. Since the introduction of SEQUEST, proteomics software has grown into a complex ecosystem of algorithms, predictive models, and workflows, but the field faces challenges, including the increasing complexity of mass spectrometry data, limited reproducibility due to proprietary software, and difficulties integrating with other omics disciplines. Closed-source, platform-specific tools exacerbate these issues by restricting innovation, creating inefficiencies, and imposing hidden costs on the community. Open-source software (OSS), aligned with the FAIR Principles (Findable, Accessible, Interoperable, Reusable), offers a solution by promoting transparency, reproducibility, and community-driven development, which fosters collaboration and continuous improvement. In this manuscript, we explore the role of OSS in computational proteomics, its alignment with FAIR principles, and its potential to address challenges related to licensing, distribution, and standardization. Drawing on lessons from other omics fields, we present a vision for a future where OSS and FAIR principles underpin a transparent, accessible, and innovative proteomics community.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS1995

Joint ROSAT-Compton GRO observations of the X-ray bright Seyfert galaxy IC 4329A

We report a simultaneous ROSAT and Gamma Ray Observatory (GRO) observation of the X-ray-bright Seyfert galaxy IC 4329A. For the GRO Oriented Scintillation Spectrometer Experiment (OSSE) detector, we also present the sum of the data for this and earlier observations. The overall spectrum is very well described as a power law with an energy spectral index of approximately 1 absorbed at low energies plus a strong Compton reflection component, typical for Seyfert 1 galaxies. The low energy absorption can be well described by a sum of a neutral column density of approximately 3 x 10(exp 21)sq cm, most of which is associated with the edge-on galactic disk of IC 4329A, plus an edgelike feature at approximately 700 eV; this feature implies either complex absorption (due to additional ionized material, or due to a partial covering), or a soft excess. The data only weakly constrain the presence of a high-energy cutoff in the underlying power law; they are compatible with an exponential cutoff at any energy E(sub c) approximately greater than 100 keV. The relative steepness of the OSSE data, with the power-law energy index of 1.6 +/- 0.2, can be accounted for entirely by the contribution of the high-energy tail of the reflection component when E(sub c) approaches infinity. (We find that the definite cutoff at an energy E(sub c)approximately 130 keV suggested in the recently published analysis of the OSSE data for this subject is due to a data reduction error.) Including nonsimultaneous Ginga observations with 2 keV fluxes matching well that of ROSAT gives us likely broad-band X-ray/gamma-ray spectra of the object from approximately 0.1 keV up to several hundred keV. We also report the ROSAT spectrum of the companion object to the Seyfert galaxy, the elliptical galaxy IC 4329.

Madejski, G. M.↗
NASA NTRS1995

Observations of a large flare in GX 1+4 with the Compton gamma ray observatory

The pulsating X-ray binary GX 1+4 (4U 1728-24) was observed by Oriented Scintillation Spectrometer Experiment (OSSE) onboard the Compton Gamma Ray Observatory (CGRO) from 9 to 21 September 1993 as a target of oppurtunity after Burst and Transient Source Experiment (BATSE) had detected the onset of a large flare by the greatly increased pulsed flux at the period of approximately 2 min. The total flux in the 40-100 keV range as observed by the OSSE reached its maximum of 83 mCrab on 14/15 September, after which it fell sharply to about 31 mCrab within 2 days. The spectrum is well described by thermal type spectra. The characteristic temperature of the average OSSE spectrum for a thermal Bremsstrahlung model is kT = (35.5 +/- 0.5) keV. A single power law can be ruled out. There is evidence for a hardening of the spectrum with decreasing intensity at the end of the flare. The barycentric pulse period was (120.567 +/- 0.005) s on 5 September. The average spin-down rate as taken from the standard BATSE analysis was dP/dt = 0.0105 s/day, and constant over the time of the flare. A further target of oppurtunity (TOO) observation with the ROSAT Position Sensitive Proportional Counter (PSPC) on 18 September led to the first detection of the source with a reflecting X-ray telescope and to a signifcantly improved position: RA(2000) = 17h 32m 2.1s and DEC(2000) = -24 deg 44 min 44 sec. This position 3.5 sec from V2116 Oph, with a 90% error radius of 8 sec is the most accurate so far obtained with an X-ray instrument, thus confirming the identification with the suspected stellar counterpart.

Staubert, R.↗
NASA NTRS2000

Education and Public Outreach

This Annual Report is a summary of nearly 400 Education and Public Outreach (E/PO) products and activities developed or carried out in FY2000 under NASA's Office of Space Science (OSS) E/PO program. It includes products and activities developed by OSS missions and research programs, innovative space science concepts developed under the Initiative to Develop Education through Astronomy and Space Science (IDEAS) Program, projects initiated under the Minority University Education and Research Partnership Initiative in Space Science, and a number of additional comprehensive or special purpose programs managed by OSS at NASA Headquarters. Taking into account the fact that many of the activities reported involve multiple events that took place in a variety of venues, the total number of E/PO events reported for FY2000 is over 1,500, with events having taken place in all 50 states, the District of Columbia, one US Territory (Guam), and four foreign nations (Australia, Canada, Mexico, and Peru).

Sakimoto, Philip↗
NASA NTRS2002

Observing System Simulation Experiments to Define Lidar Wind Requirements

Since the advent of meteorological satellites in the 1960's, numerous experiments have been conducted in order to evaluate the impact of these and other data on atmospheric analysis and prediction. Such studies have included both OSE'S and OSSE's. The OSE's were conducted to evaluate the impact of specific observations or classes of observations on analyses and forecasts. Such experiments have been performed for selected types of conventional data and for various satellite data sets as they became available. (See for example the 1989 ECMWF/EUMETSAT workshop proceedings on "The use of satellite data in operational numerical weather prediction" and the references contained therein.) The OSSE's were conducted to evaluate the potential for future observing systems to improve Numerical Weather Prediction (NWP) and to plan for the Global Weather Experiment and more recently for EOS ( [1], [2], [3]). In addition, OSSE's have been run to evaluate trade-offs in the design of observing systems and observing networks ([4], [5]), and to test new methodology for data assimilation ([6]).

Atlas, Robert↗
NASA NTRS2002

Recent Observing System Simulation Experiments at the NASA DAO

Since the advent of meteorological satellites in the 1960's, numerous experiments have been conducted in order t o evaluate the impact of these and other data on atmospheric analysis and prediction. Such studies have included both OSE'S (Observing System Experiments) and OSSE's (Observing System Simulation Experiments). The OSE's were conducted to evaluate the impact of specific observations or classes of observations on analyses and forecasts. Such experiments have been performed for selected types of conventional data and for various satellite data sets as they became avail- able. (See for example the 1989 ECMWF/EUMETSAT workshop proceedings on "The use of satellite data in operational numerical weather prediction" and the references contained therein.) The OSSE's were con- ducted to evaluate the potential for future observing systems to improve Numerical Weather Prediction (NWP) and to plan for the Global Weather Experiment and more recently for EOS. In addition, OSSE's have been run t o evaluate trade-offs in the design of observing systems and observing net-works, and to test new methodology for data assimilation.

Atlas, Robert↗
NASA NTRS2004

The Impact of Current and Future Polar Orbiting Satellite Data on Numerical Weather Prediction at NASA/GSFC

The lack of adequate observational data continues to be recognized as a major factor limiting both atmospheric research and numerical prediction on a variety of temporal and spatial scales. Since the advent of meteorological satellites in the 1960's, a considerable research effort has been directed toward the design of space-borne meteorological sensors, the development of optimal methods for the utilization of these data, (and an assessment of the influence of existing satellite data and the potential influence of future satellite observations on numerical weather prediction. This has included both Observing System Experiments (OSEs) and Observing System Simulation Experiments (OSSEs). OSEs are conducted to evaluate the impact of specific observations or classes of observations on analyses and forecasts. While OSEs are performed with existing data, OSSEs are conducted to evaluate the potential for future observing systems to improve-NWP, as well as to evaluate trade-offs in observing system design, and to develop and test improved methods for data assimilation. At the conference, results from OSEs to evaluate satellite data sets that have recently become available to the global observing system, such as AIRS and Seawinds, and results from OSSEs to determine the potential impact of space-based lidar winds will be presented.

Atlas, Robert↗
NASA NTRS2013

Ionospheric Simulation System for Satellite Observations and Global Assimilative Modeling Experiments (ISOGAME)

ISOGAME is designed and developed to assess quantitatively the impact of new observation systems on the capability of imaging and modeling the ionosphere. With ISOGAME, one can perform observation system simulation experiments (OSSEs). A typical OSSE using ISOGAME would involve: (1) simulating various ionospheric conditions on global scales; (2) simulating ionospheric measurements made from a constellation of low-Earth-orbiters (LEOs), particularly Global Navigation Satellite System (GNSS) radio occultation data, and from ground-based global GNSS networks; (3) conducting ionospheric data assimilation experiments with the Global Assimilative Ionospheric Model (GAIM); and (4) analyzing modeling results with visualization tools. ISOGAME can provide quantitative assessment of the accuracy of assimilative modeling with the interested observation system. Other observation systems besides those based on GNSS are also possible to analyze. The system is composed of a suite of software that combines the GAIM, including a 4D first-principles ionospheric model and data assimilation modules, an Internal Reference Ionosphere (IRI) model that has been developed by international ionospheric research communities, observation simulator, visualization software, and orbit design, simulation, and optimization software. The core GAIM model used in ISOGAME is based on the GAIM++ code (written in C++) that includes a new high-fidelity geomagnetic field representation (multi-dipole). New visualization tools and analysis algorithms for the OSSEs are now part of ISOGAME.

Pi, Xiaoqing↗
NASA NTRS2014

Applied Meteorology Unit (AMU) Quarterly Report First Quarter FY-14

NASA's LSP and other programs at Vandenberg Air Force Base (VAFB) use wind forecasts issued by the 30th Operational Support Squadron (30 OSS) to determine if they need to limit activities or protect property such as a launch vehicle due to the occurrence of warning level winds at VAFB in California. The 30 OSS tasked the AMU to provide a wind forecasting capability to improve wind warning forecasts and enhance the safety of their customers' operations. This would allow 30 OSS forecasters to evaluate pressure gradient thresholds between pairs of regional observing stations to help determine the onset and duration of warning category winds. Development of such a tool will require that solid relationships exist between wind speed and the pressure gradient of one or more station pairs. As part of this task, the AMU will also create a statistical climatology of meteorological observations from the VAFB wind towers.

Forecasting↗
NASA NTRS2019

Uncertainty of Observation Impact Estimation in an Adjoint Model Investigated with an Observing System Simulation Experiment

Adjoint models are often used to estimate the impact of different observations on short-term forecast skill. A common difficulty with the evaluation of short term forecast quality is the choice of verification fields. The use of self-analysis fields for verification is typical but incestuous, and introduces uncertainty due to biases and errors in the analysis field. In this study, an observing system simulation experiment (OSSE) is used to explore the uncertainty in adjoint model estimations of observation impact. The availability of the true state for verification in the OSSE framework in the form of the Nature Run allows calculation of the observation impact without the uncertainties present in self-analysis verification. These impact estimates are compared to estimates calculated using self-analysis verification. The Global Earth Observing System version 5 (GEOS-5) forecast model with Gridpoint Statistical Interpolation (GSI) is used with the National Aeronautics and Space Administration Global Modeling and Assimilation Office (NASA/GMAO) OSSE capability. The adjoint model includes moist processes, with total wet energy selected as the norm for evaluation of observation impacts. The results show that there are measurable but small discrepancies in the adjoint model estimation of observation impact. In general, observations of temperature and winds tend to have overestimated impacts with self-analysis verification, while observations of humidity and moisture-affected observations tend to have underestimated impacts. The small magnitude of the differences in impact estimates supports the robustness of the adjoint method of estimating observation impacts.

N C Prive↗
NASA NTRS2021

Origins Survey Spectrometer: revealing the hearts of distant galaxies and forming planetary systems with far-IR spectroscopy

The Origins Survey Spectrometer (OSS) is a multi-purpose far-IR spectrograph for Origins. Operating at the photon background limit, OSS covers the 25- to 588-μm wavelength range instantaneously at a resolving power (R) of 300 using six logarithmically spaced grating modules. Each module couples at least 30 and up to 100 spatial beams simultaneously, enabling true [three-dimensional (3D)] spectral mapping. In addition, OSS provides two high-resolution modes. The first inserts a long-path Fourier-transform spectrometer (FTS) into a portion of the incoming light in advance of the grating backends, enabling R up to 43,000 × [λ/112 μm] , while preserving the grating-based sensitivity for line detection. The second incorporates a scanning etalon in series with the FTS to provide R up to 300,000 for the 100-to 200-μm range.

Charles M. Bradford↗
NASA NTRSDate not supplied

Open-Source Science-led Development of the Atmosphere Observing System (AOS) Mission Science Data System (SDS)

The Earth System Observatory (ESO) Atmosphere Observing System (AOS) mission will provide space-based and suborbital observations of collocated cloud, dynamic, precipitation and aerosol processing leading to improved weather, air quality, and climate predictions. The AOS Science Data System (SDS) will be a system of systems developed within the Cloud to manage the research and operational processing of AOS mission orbital and suborbital sensors and curate these data for reprocessing (e.g., in near real-time or by collection) and transfer them to a NASA Distributed Active Archive Center (DAAC) for long-term storage. Further, AOS SDS will follow guidelines provided by NASA Earth Science Data Systems (ESDS) program including standard conventions for data file formats, naming, and metadata to improve data interoperability, interpretability, usability, discovery, provenance, and spatiotemporal representativeness. The AOS mission follows NASA’s lead in making a commitment to Open-Source Science (OSS) including the sharing of data, software, and knowledge in an open and timely manner. Each of the AOS SDS system components will be developed with open-source concepts including components of SDS itself as well as AOS mission algorithms. Further, the AOS SDS assumes the role to lead and facilitate OSS activities for the AOS mission. This presentation describes the framework of the AOS SDS and its integral part in facilitating OSS within the AOS mission.

David Giles↗
NASA NTRSDate not supplied

Open-Source Science-led Development of the AOS Mission Science Data System (SDS)

The Earth System Observatory (ESO) Atmosphere Observing System (AOS) mission will provide space-based and suborbital observations of collocated cloud, dynamic, precipitation and aerosol processing leading to improved weather, air quality, and climate predictions. The AOS Science Data System (SDS) will be a system of systems developed within the Cloud to manage the research and operational processing of AOS mission orbital and suborbital sensors and curate these data for reprocessing (e.g., in near real-time or by collection) and transfer them to a NASA Distributed Active Archive Center (DAAC) for long-term storage. Further, AOS SDS will follow guidelines provided by NASA Earth Science Data Systems (ESDS) program including standard conventions for data file formats, naming, and metadata to improve data interoperability, interpretability, usability, discovery, provenance, and spatiotemporal representativeness. The AOS mission follows NASA’s lead in making a commitment to Open-Source Science (OSS) including the sharing of data, software, and knowledge in an open and timely manner. Each of the AOS SDS system components will be developed with open-source concepts including components of SDS itself as well as AOS mission algorithms. Further, the AOS SDS assumes the role to lead and facilitate OSS activities for the AOS mission. This presentation describes the framework of the AOS SDS and its integral part in facilitating OSS within the AOS mission.

David M. Giles↗
NASA NTRS2015

Observing System Simulation Experiments

This presentation gives an overview of Observing System Simulation Experiments (OSSEs). The components of an OSSE are described, along with discussion of the process for validating, calibrating, and performing experiments. a.

OSSE↗
NASA NTRS2015

On the Feasibility of Monitoring Carbon Monoxide in the Lower Troposphere from a Constellation of Northern Hemisphere Geostationary Satellites (PART 1)

By the end of the current decade, there are plans to deploy several geostationary Earth orbit (GEO) satellite missions for atmospheric composition over North America, East Asia and Europe with additional missions proposed. Together, these present the possibility of a constellation of geostationary platforms to achieve continuous time-resolved high-density observations over continental domains for mapping pollutant sources and variability at diurnal and local scales. In this paper, we use a novel approach to sample a very high global resolution model (GEOS-5 at 7 km horizontal resolution) to produce a dataset of synthetic carbon monoxide pollution observations representative of those potentially obtainable from a GEO satellite constellation with predicted measurement sensitivities based on current remote sensing capabilities. Part 1 of this study focuses on the production of simulated synthetic measurements for air quality OSSEs (Observing System Simulation Experiments). We simulate carbon monoxide nadir retrievals using a technique that provides realistic measurements with very low computational cost. We discuss the sampling methodology: the projection of footprints and areas of regard for geostationary geometries over each of the North America, East Asia and Europe regions; the regression method to simulate measurement sensitivity; and the measurement error simulation. A detailed analysis of the simulated observation sensitivity is performed, and limitations of the method are discussed. We also describe impacts from clouds, showing that the efficiency of an instrument making atmospheric composition measurements on a geostationary platform is dependent on the dominant weather regime over a given region and the pixel size resolution. These results demonstrate the viability of the "instrument simulator" step for an OSSE to assess the performance of a constellation of geostationary satellites for air quality measurements.

GEOS-5↗
NASA NTRS2019

A Neural Network Correction to the Scalar Approximation in Radiative Transfer

The next generation of advanced high-resolution sensors in geostationary orbit will gather detailed information for studying the Earth system. There is an increasing desire to perform observing system simulation experiments (OSSEs) for new sensors during the development phase of the mission in order to better leverage information content from the new and existing sensors. Forward radiative transfer calculations that simulate the observing characteristics of a new instrument are the first step to an OSSE, and they are computationally intensive. The scalar approximation to the radiative transfer equation, a simplification of the vector representation, can save considerable computational cost, but produces errors in top of the atmosphere (TOA) radiance as large as 10% due to neglecting polarization effects. This article presents an artificial neural network technique to correct scalar TOA radiance over both land and ocean surfaces to within 1% of vector-calculated radiance. A neural network was trained on a database of scalar-vector TOA radiance differences at a large range of solar and viewing angles for several thousand realistic atmospheric vertical profiles that were sampled from a high resolution (7 km) global atmospheric transport model. The profiles include Rayleigh scattering and aerosol scattering and absorption. Training and validation of the neural network was demonstrated for two wavelengths in the ultraviolet-visible (US-Vis) spectral range (354 nm and 670 nm). The significant computational savings accrued from using a scalar approximation plus neural network correction approach to simulating TOA radiance will make feasible hyperspectral forward simulations of high-resolution sensors on geostationary satellites, such as TEMPO, GOES-R, GEMS, and SENTINEL-4.

TOA↗
NASA NTRSDate not supplied

Impacts of Assimilating Infrared Sounders from Geostationary Orbit

A set of observing system simulation experiments (OSSEs) was used to assess the impact of assimilating hyperspectral infrared (IR) radiances from geostationary platforms. This was done in preparation for the proposed National Oceanic and Atmospheric Administration (NOAA) Geostationary eXtended Observations (GeoXO) Sounder (GXS), expected to launch in the 2030s, using the National Aeronautics and Space Administration (NASA) Global Modeling and Assimilation Office (GMAO) OSSE framework. From a numerical weather prediction (NWP) perspective, a global “ring” of geostationary IR sounders was found to improve both the analysis and forecasts and provide beneficial impacts as measured by the forecast sensitivity observation impact (FSOI) metric.

Geostationary orbit↗
DOE OSTI2024

Applying a Phase-Separation Parameterization in Modeling Secondary Organic Aerosol Formation from Acid-Driven Reactive Uptake of Isoprene Epoxydiols under Humid Conditions

Secondary organic aerosol (SOA) from acid-driven reactive uptake of isoprene epoxydiols (IEPOX) contributes up to 40% of organic aerosol (OA) mass in fine particulate matter. Our previous work showed substantial conversions of particulate inorganic sulfates to surface-active organosulfates (OSs) by IEPOX decreases aerosol acidity and creates a viscous organic-rich shell that poses as a diffusion barrier, inhibiting additional reactive uptake of IEPOX. In this study, to account for this “self-limiting” effect, a phase-separation box model was developed to evaluate parameterizations of IEPOX reactive uptake against time-resolved chamber measurements of IEPOX-SOA tracers, including 2-methyltetrols (2-MT) and methyltetrol sulfates (MTS), at ~ 50% relative humidity. The phase-separation model was most sensitive to mass accommodation coefficient, IEPOX diffusivity in the organic shell, and ratio of the third-order reaction rate constants forming 2-MT and MTS (k MT /k MTS ). In particular, k MT /k MTS had to be lower than 0.1 to bring model predictions of 2-MT and MTS in closer agreement with chamber measurements, while prior studies reported values larger than 0.71. The model-derived rate constants favor more particulate MTS formation due to 2-MT likely off-gassing at ambient-relevant OA loadings. Incorporating this parametrization into chemical transport models is expected to predict lower IEPOX-SOA mass and volatility due to the predominance of OSs.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗