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At least 1,711 records · Page 95
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Close substellar-mass companions in stellar wide binaries: discovery and characterization with APOGEE and Gaia DR2

We present a search for close, unresolved companions in a subset of spatially resolved Gaia wide binaries containing main-sequence stars within 200 pc of the Sun, utilizing the APOGEE–Gaia Wide Binary Catalog. A catalogue of 37 wide binaries was created by selecting pairs of stars with nearly identical Gaia positions, parallaxes, and proper motions, and then confirming candidates to be gravitationally bound pairs using APOGEE radial velocities. We identify close, unresolved stellar and substellar candidate companions in these multiple systems using (1) the Gaia binary main sequence and (2) observed periodic radial velocity variations in APOGEE measurements due to the influence of a close substellar-mass companion. The studied wide binary pairs reveal a total of four stellar-mass close companions in four different wide binaries, and four substellar-mass close companion candidates in two wide binaries. The latter are therefore quadruple systems, with one substellar-mass companion orbiting each wide binary component in an S-type orbit. Taken at face value, these candidate systems represent an enhancement of an order of magnitude over the expected occurrence rate of ~2 percent of stars having substellar companions >2 M Jup within ~100-d orbits; we discuss implications and possible explanations for this result. Finally, we compare chemical differences between the components of the wide binaries and the components of the candidate higher-order systems and find that any chemical influence or correlation due to the presence of close companions to wide binary stars is not discernible.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Type Ia supernova magnitude step from the local dark matter environment

ABSTRACT Residuals in the Hubble diagram at optical wavelengths and host galaxy stellar mass are observed to correlate in type Ia supernovae (SNe Ia) (‘magnitude step’). Among possible progenitor channels for the associated explosions, those based on dark matter (DM) have attracted significant attention, including our recent proposal that ‘normal’ SNe Ia from bare detonations in sub-Chandrasekhar white dwarf stars are triggered by the passage of asteroid-mass primordial black holes (PBHs): the magnitude step could then originate from a brightness dependence on stellar properties, on DM properties, or both. Here, we present a method to estimate the local DM density and velocity dispersion of the environment of SN Ia progenitors. We find a luminosity step of $0.52\pm 0.11\,$ mag corresponding to bins of high versus low DM density in a sample of 222 low-redshift events from The Open Supernova Catalog. We investigate whether the magnitude step can be attributed to local DM properties alone, assuming asteroid-mass PBHs. Given the inverse correlation between SN Ia brightness and PBH mass, an intriguing explanation is a spatially inhomogeneous PBH mass function. If so, a strong mass segregation in the DM density-dependent PBH mass scale is needed to explain the magnitude step. While mass segregation is observed in dense clusters, it is unlikely to be realized on galactic scales. Therefore, if DM consists of asteroid-mass PBHs, the magnitude step is more likely to exist, and dominantly to be attributed to local stellar properties.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Transitioning from Stage-III to Stage-IV: cosmology from galaxy×CMB lensing and shear×CMB lensing

ABSTRACT We examine the cosmological constraining power from two cross-correlation probes between galaxy and cosmic microwave background (CMB) surveys: the cross-correlation of lens galaxy density with CMB lensing convergence 〈δgκCMB〉, and source galaxy weak lensing shear with CMB lensing convergence 〈γκCMB〉. These two cross-correlation probes provide an independent cross-check of other large-scale structure constraints and are insensitive to galaxy-only or CMB-only systematic effects. In addition, when combined with other large-scale structure probes, the cross-correlations can break degeneracies in cosmological and nuisance parameters, improving both the precision and robustness of the analysis. In this work, we study how the constraining power of 〈δgκCMB〉 + 〈γκCMB〉 changes from Stage-III (ongoing) to Stage-IV (future) surveys. Given the flexibility in selecting the lens galaxy sample, we also explore systematically the impact on cosmological constraints when we vary the redshift range and magnitude limit of the lens galaxies using mock galaxy catalogs. We find that in our setup, the contribution to cosmological constraints from 〈δgκCMB〉 and 〈γκCMB〉 are comparable in the Stage-III data sets; but in Stage-IV surveys, the noise in 〈δgκCMB〉 becomes subdominant to cosmic variance, preventing 〈δgκCMB〉 to further improve the constraints. This implies that to maximize the cosmological constraints from future 〈δgκCMB〉 + 〈γκCMB〉 analyses, we should focus more on the requirements on 〈γκCMB〉 instead of 〈δgκCMB〉. Furthermore, the selection of the lens sample should be optimized in terms of our ability to characterize its redshift or galaxy bias instead of its number density.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Detection of spatial clustering in the 1000 richest SDSS DR8 redMaPPer clusters with nearest neighbor distributions

ABSTRACT Distances to the k-nearest-neighbor (kNN) data points from volume-filling query points are a sensitive probe of spatial clustering. Here, we present the first application of kNN summary statistics to observational clustering measurement, using the 1000 richest redMaPPer clusters (0.1 ≤ z ≤ 0.3) from the SDSS DR8 catalog. A clustering signal is defined as a difference in the cumulative distribution functions (CDFs) of kNN distances from fixed query points to the observed clusters versus a set of unclustered random points. We find that the k = 1, 2-NN CDFs of redMaPPer deviate significantly from the randoms’ across scales of 35 to 155 Mpc, which is a robust signature of clustering. In addition to kNN, we also measure the two-point correlation function for the same set of redMaPPer clusters versus random points, which shows a noisier and less significant clustering signal within the same radial scales. Quantitatively, the χ2 distribution for both the kNN-CDFs and the two-point correlation function measured on the randoms peak at χ2 ∼ 50 (null hypothesis), whereas the kNN-CDFs (χ2 ∼ 300, p = 1.54 × 10−36) pick up a much more significant clustering signal than the two-point function (χ2 ∼ 100, p = 1.16 × 10−6) when measured on redMaPPer. Finally, the measured 3NN and 4NN CDFs deviate from the predicted k = 3, 4-NN CDFs assuming an ideal Gaussian field, indicating a non-Gaussian clustering signal for redMaPPer clusters, although its origin might not be cosmological due to observational systematics. Therefore, kNN serves as a more sensitive probe of clustering complementary to the two point correlation function, providing a novel approach for constraining cosmology and galaxy–halo connection.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

The stellar parameters and elemental abundances from low-resolution spectra – I. 1.2 million giants from LAMOST DR8

As a typical data-driven method, deep learning becomes a natural choice for analysing astronomical data. In this study, we built a deep convolutional neural network (NN) to estimate basic stellar parameters $T\rm {_{eff}}$, log g , metallicity ([M/H] and [Fe/H]) and [α/M] along with nine individual elemental abundances ([C/Fe], [N/Fe], [O/Fe], [Mg/Fe], [Al/Fe], [Si/Fe], [Ca/Fe], [Mn/Fe], and [Ni/Fe]). The NN is trained using common stars between the APOGEE survey and the LAMOST survey. We used low-resolution spectra from LAMOST survey as input, and measurements from APOGEE as labels. For stellar spectra with the signal-to-noise ratio in g band larger than 10 in the test set, the mean absolute error (MAE) is 29 K for $T\rm {_{eff}}$, 0.07 dex for log g , 0.03 dex for both [Fe/H] and [M/H], and 0.02 dex for [α/M]. The MAE of most elements is between 0.02 and 0.04 dex. The trained NN was applied to 1210 145 giants, including sub-giants, from LAMOST DR8 within the range of stellar parameters 3500 K < $T\rm {_{eff}}$ < 5500 K, 0.0 dex < log g < 4.0 dex, −2.5 dex < [Fe/H] < 0.5 dex. The distribution of our results in the chemical spaces is highly consistent with APOGEE labels and stellar parameters show consistency with external high-resolution measurements from GALAH. The results in this study allow us to further studies based on LAMOST data and deepen our understanding of the accretion and evolution history of the Milky Way. The electronic version of the value added catalog is available at http://www.lamost.org/dr8/v1.1/doc/vac.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A multiwavelength study of the flat-spectrum radio quasar NVSS J141922−083830 covering four flaring episodes

We present multiwavelength observations and a model for flat-spectrum radio quasar (FSRQ) NVSS J141922−083830, originally classified as a blazar candidate of unknown type (BCU II object) in the Third Fermi-LAT AGN Catalog. Relatively bright flares (>3 magnitudes) were observed on 2015 February 21 (MJD 57074) and 2018 September 8 (MJD 58369) in the optical band with the MASTER Global Robotic Net telescopes. Optical spectra obtained with the Southern African Large Telescope on 2015 March 1 (MJD 57082), during outburst, and on 2017 May 30 (MJD 57903), during quiescence, showed emission lines at 5325 Å and at ≈3630 Å that we identified as the Mg II III] 1909 Å lines, respectively, and hence derived a redshift z = 0.903. Analysis of Fermi-Large Area Telescope (LAT) data was performed in the quiescent regime (5 yr of data) and during four prominent flaring states in 2014 February–April, 2014 October–November, 2015 February–March, and 2018 September. We present spectral and timing analysis with Fermi-LAT . We report a hardening of the gamma-ray spectrum during the last three flaring periods, with a power-law spectral index Γ = 2.0–2.1. The maximum gamma-ray flux level was observed on 2014 October 24 (MJD 56954) at (7.57 ± 1.83) × 10 −7 ph cm −2 s −1 . The multiwavelength spectral energy distribution (SED) during the 2015 February–March flare supports the earlier evidence of this blazar to belong to the FSRQ class. The SED can be well represented with a single-zone leptonic model with parameters typical of FSRQs, but also a hadronic origin of the high-energy emission cannot be ruled out.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Clustering with general photo- z uncertainties: application to Baryon Acoustic Oscillations

ABSTRACT Photometric data can be analysed using the 3D correlation function ξp to extract cosmological information via e.g. measurement of the Baryon Acoustic Oscillations (BAO). Previous studies modeled ξp assuming a Gaussian photo-z approximation. In this work we improve the modeling by incorporating realistic photo-z distribution. We show that the position of the BAO scale in ξp is determined by the photo-z distribution and the Jacobian of the transformation. The latter diverges at the transverse scale of the separation s⊥, and it explains why ξp traces the underlying correlation function at s⊥, rather than s, when the photo-z uncertainty σz/(1+ z) ≳ 0.02. We also obtain the Gaussian covariance for ξp. Due to photo-z mixing, the covariance of ξp shows strong off-diagonal elements. The high correlation of the data causes some issues to the data fitting. None the less, we find that either it can be solved by suppressing the largest eigenvalues of the covariance or it is not directly related to the BAO. We test our BAO fitting pipeline using a set of mock catalogs. The data set is dedicated for Dark Energy Survey Year 3 (DES Y3) BAO analyses and includes realistic photo-z distributions. The theory template is in good agreement with mock measurement. Based on the DES Y3 mocks, ξp statistic is forecast to constrain the BAO shift parameter α to be 1.001 ± 0.023, which is well consistent with the corresponding constraint derived from the angular correlation function measurements. Thus, ξp offers a competitive alternative for the photometric data analyses.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Photometric calibration in u -band using blue halo stars

ABSTRACT We develop a method to calibrate u-band photometry based on the observed colour of blue Galactic halo stars. The Galactic halo stars belong to an old stellar population of the Milky Way and have relatively low metallicity. The ‘blue tip’ of the halo population – the main sequence turn-off (MSTO) stars – is known to have a relatively uniform intrinsic edge u-g colour with only slow spatial variation. In SDSS data, the observed variation is correlated with Galactic Latitude, which we attribute to contamination by higher metallicity disc stars and fit with an empirical curve. This curve can then be used to calibrate u-band imaging if g-band imaging of matching depth is available. Our approach can be applied to single-field observations at |b| > 30°, and removes the need for standard star observations or overlap with calibrated u-band imaging. We include in our method the calibration of g-band data with ATLAS-Refcat2. We test our approach on stars in KiDS DR 4, ATLAS DR 4, and DECam imaging from the NOIRLab Source Catalog (NSC DR2), and compare our calibration with SDSS. For this process, we use synthetic magnitudes to derive the colour equations between these data sets, in order to improve zero-point accuracy. We find an improvement for all data sets, reaching a zero-point precision of 0.016 mag for KiDS (compared to the original 0.033 mag), 0.020 mag for ATLAS (originally 0.027 mag), and 0.016 mag for DECam (originally 0.041 mag). Thus, this method alone reaches the goal of 0.02 mag photometric precision in u-band for the Rubin Observatory’s Legacy Survey of Space and Time (LSST).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

How the dynamical properties of globular clusters impact their $γ$-ray and X-ray emission

The X-ray and $γ$-ray emission of globular clusters (GCs) is attributed to their large fraction of compact binary systems, especially those with millisecond pulsars (MSPs). We analyse a population of 124 Galactic GCs to investigate how their dynamical properties affect the formation and evolution of compact binary systems and how this can be translated into the clusters’ observed X-ray and γ-ray emission. We use mainly Chandra X-ray Observatory and Fermi Large Area Telescope observations to achieve our goals and start by detecting 39 GCs in γ rays, seven of which are not listed in previous Fermi -LAT catalogs. Additionally, we find that the total number of X-ray sources within a GC and its γ-ray luminosity are linearly correlated with the stellar encounter rate, indicating that compact binary systems are mainly formed via close stellar encounters. We also find an unexpected rise in the number of X-ray sources for GCs with low rates of stellar encounters, suggesting that there is a dynamical threshold where the formation of X-ray sources is dominated by stellar encounters. Furthermore, we use the Heggie-Hills law to find that subsequent stellar encounters in these compact binaries will, on average, make the binaries even harder, with basically no possibility of binary ionization. Finally, we find that all GCs are point-like sources in γ rays, indicating that the MSPs are concentrated in the clusters’ cores, likely due to dynamical friction.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

A general framework for removing point-spread function additive systematics in cosmological weak lensing analysis

ABSTRACT Cosmological weak lensing measurements rely on a precise measurement of the shear two-point correlation function (2PCF) along with a deep understanding of systematics that affect it. In this work, we demonstrate a general framework for detecting and modelling the impact of PSF systematics on the cosmic shear 2PCF and mitigating its impact on cosmological analysis. Our framework can detect PSF leakage and modelling error from all spin-2 quantities contributed by the PSF second and higher moments, rather than just the second moments, using the cross-correlations between galaxy shapes and PSF moments. We interpret null tests using the HSC Year 3 (Y3) catalogs with this formalism and find that leakage from the spin-2 combination of PSF fourth moments is the leading contributor to additive shear systematics, with total contamination that is an order-of-magnitude higher than that contributed by PSF second moments alone. We conducted a mock cosmic shear analysis for HSC Y3 and find that, if uncorrected, PSF systematics can bias the cosmological parameters Ωm and S8 by ∼0.3σ. The traditional second moment-based model can only correct for a 0.1σ bias, leaving the contamination largely uncorrected. We conclude it is necessary to model both PSF second and fourth moment contaminations for HSC Y3 cosmic shear analysis. We also reanalyse the HSC Y1 cosmic shear analysis with our updated systematics model and identify a 0.07σ bias on Ωm when using the more restricted second moment model from the original analysis. We demonstrate how to self-consistently use the method in both real space and Fourier space, assess shear systematics in tomographic bins, and test for PSF model overfitting.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2023

Planting a Lyman alpha forest on ABACUSSUMMIT

The full-shape correlations of the Lyman alpha (Ly$α$) forest contain a wealth of cosmological information through the Alcock Paczynski effect. However, these measurements are challenging to model without robustly testing and verifying the theoretical framework used for analyzing them. Here, we leverage the accuracy and volume of the $N$-body simulation suite ABACUSSUMMIT to generate high-resolution Ly$α$ skewers and quasi-stellar object (QSO) catalogs. One of the main goals of our mocks is to aid in the full-shape Ly$α$ analysis planned by the Dark Energy Spectroscopic Instrument (DESI) team. We provide optical depth skewers for six of the fiducial cosmology base-resolution simulations ($L$ box = 2 $h$ -1 Gpc, $N$ = 6912 3 ) at $z$ = 2.5. We adopt a simple recipe based on the Fluctuating Gunn-Peterson Approximation (FGPA) for constructing these skewers from the matter density in an $N$-body simulation and calibrate it against the 1D and 3D Ly$α$ power spectra extracted from the hydrodynamical simulation IllustrisTNG (TNG; $L$ box = 205 $h$ -1 Mpc, $N$ = 2500 3 ). As an important application, we study the non-linear broadening of the baryon acoustic oscillation (BAO) peak and show the cross-correlation between DESI-like QSOs and our Ly$α$ forest skewers. We find differences on small scales between the Kaiser approximation prediction and our mock measurements of the Ly$α$×QSO cross-correlation, which would be important to account for in upcoming analyses. The ABACUSSUMMIT Ly$α$ forest mocks open up the possibility for improved modelling of cross correlations between Ly$α$ and cosmic microwave background (CMB) lensing and Ly$α$ and QSOs, and for forecasts of the 3-point Ly$α$ correlation function. Furthermore, our catalogues and skewers are publicly available on Globus via the National Energy Research Scientific Computing Center (NERSC) (full link under Data Availability).

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2023

Full forward model of galaxy clustering statistics with AbacusSummit light cones

ABSTRACT Novel summary statistics beyond the standard 2-point correlation function (2PCF) are necessary to capture the full astrophysical and cosmological information from the small-scale (r < 30h−1Mpc) galaxy clustering. However, the analysis of beyond-2PCF statistics on small scales is challenging because we lack the appropriate treatment of observational systematics for arbitrary summary statistics of the galaxy field. In this paper, we develop a full forward modelling pipeline for a wide range of summary statistics using the large high-fidelity AbacusSummit light cones that account for many systematic effects as well as remain flexible and computationally efficient to enable posterior sampling. We apply our forward model approach to a fully realistic mock galaxy catalog and demonstrate that we can recover unbiased constraints on the underlying galaxy–halo connection model using two separate summary statistics: the standard 2PCF and the novel k-th nearest neighbour (kNN) statistics, which are sensitive to correlation functions of all orders. We will demonstrate its strong constraining power on extended galaxy–halo connection models and cosmology in follow up papers. We expect this to become a powerful approach when applying to upcoming surveys such as DESI where we can leverage a multitude of summary statistics across a wide redshift range to maximally extract information from the non-linear scales.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2025

OpenUniverse2024: a shared, simulated view of the sky for the next generation of cosmological surveys

The OpenUniverse2024 simulation suite is a cross-collaboration effort to produce matched simulated imaging for multiple surveys as they would observe a common simulated sky. Both the simulated data and associated tools used to produce it are intended to uniquely enable a wide range of studies to maximize the science potential of the next generation of cosmological surveys. We have produced simulated imaging for approximately 70 deg 2 of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) Wide-Fast-Deep survey and the Nancy Grace Roman Space Telescope High-Latitude Wide-Area Survey, as well as overlapping versions of the ELAIS-S1 Deep-Drilling Field for LSST and the High-Latitude Time-Domain Survey for Roman. OpenUniverse2024 includes (i) an early version of the updated extragalactic model called Diffsky, which substantially improves the realism of optical and infrared photometry of objects, compared to previous versions of these models; (ii) updated transient models that extend through the wavelength range probed by Roman and Rubin; and (iii) improved survey, telescope, and instrument realism based on up-to-date survey plans and known properties of the instruments. It is built on a new and updated suite of simulation tools that improves the ease of consistently simulating multiple observatories viewing the same sky. The approximately 400 TB of synthetic survey imaging and simulated universe catalogs are publicly available, and we preview some scientific uses of the simulations.

large-scale structure of Universe↗
DOE OSTI2025

Galaxy-multiplet clustering from DESI DR2

We present an efficient estimator for higher-order galaxy clustering using small groups of nearby galaxies, or multiplets. Using the Luminous Red Galaxy (LRG) sample from the Dark Energy Spectroscopic Instrument (DESI) Data Release 2, we identify galaxy multiplets as discrete objects and measure their cross-correlations with the general galaxy field. Our results show that the multiplets exhibit stronger clustering bias as they trace more massive dark matter halos than individual galaxies. When comparing the observed clustering statistics with the mock catalogs generated from the N-body simulation AbacusSummit, we find that the mocks underpredict multiplet clustering despite reproducing the galaxy two-point auto-correlation reasonably well. This discrepancy indicates that the standard Halo Occupation Distribution (HOD) model is insufficient to describe the properties of galaxy multiplets, revealing the greater constraining power of this higher-order statistic on galaxy-halo connection and the possibility that multiplets are specific to additional assembly bias. We demonstrate that incorporating secondary biases into the HOD model improves agreement with the observed multiplet statistics, specifically by allowing galaxies to preferentially occupy halos in denser environments. Our results highlight the potential of utilizing multiplet clustering, beyond traditional two-point correlation measurements, to break degeneracies in models describing the galaxy-dark matter connection.

cosmology↗
DOE OSTI2023

Phosphate Limitation Responses in Marine Green Algae Are Linked to Reprogramming of the tRNA Epitranscriptome and Codon Usage Bias

Marine algae are central to global carbon fixation, and their productivity is dictated largely by resource availability. Reduced nutrient availability is predicted for vast oceanic regions as an outcome of climate change; however, there is much to learn regarding response mechanisms of the tiny picoplankton that thrive in these environments, especially eukaryotic phytoplankton. Here, we investigate responses of the picoeukaryote Micromonas commoda, a green alga found throughout subtropical and tropical oceans. Under shifting phosphate availability scenarios, transcriptomic analyses revealed altered expression of transfer RNA modification enzymes and biased codon usage of transcripts more abundant during phosphate-limiting versus phosphate-replete conditions, consistent with the role of transfer RNA modifications in regulating codon recognition. To associate the observed shift in the expression of the transfer RNA modification enzyme complement with the transfer RNAs encoded by M. commoda, we also determined the transfer RNA repertoire of this alga revealing potential targets of the modification enzymes. Codon usage bias was particularly pronounced in transcripts encoding proteins with direct roles in managing phosphate limitation and photosystem-associated proteins that have ill-characterized putative functions in “light stress.” The observed codon usage bias corresponds to a proposed stress response mechanism in which the interplay between stress-induced changes in transfer RNA modifications and skewed codon usage in certain essential response genes drives preferential translation of the encoded proteins. Collectively, we expose a potential underlying mechanism for achieving growth under enhanced nutrient limitation that extends beyond the catalog of up- or downregulated protein-encoding genes to the cell biological controls that underpin acclimation to changing environmental conditions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

DRAM for distilling microbial metabolism to automate the curation of microbiome function

Abstract Microbial and viral communities transform the chemistry of Earth's ecosystems, yet the specific reactions catalyzed by these biological engines are hard to decode due to the absence of a scalable, metabolically resolved, annotation software. Here, we present DRAM (Distilled and Refined Annotation of Metabolism), a framework to translate the deluge of microbiome-based genomic information into a catalog of microbial traits. To demonstrate the applicability of DRAM across metabolically diverse genomes, we evaluated DRAM performance on a defined, in silico soil community and previously published human gut metagenomes. We show that DRAM accurately assigned microbial contributions to geochemical cycles and automated the partitioning of gut microbial carbohydrate metabolism at substrate levels. DRAM-v, the viral mode of DRAM, established rules to identify virally-encoded auxiliary metabolic genes (AMGs), resulting in the metabolic categorization of thousands of putative AMGs from soils and guts. Together DRAM and DRAM-v provide critical metabolic profiling capabilities that decipher mechanisms underpinning microbiome function.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Genomes OnLine Database (GOLD) v.10: new features and updates

The Genomes OnLine Database (GOLD; https://gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute is a comprehensive online metadata repository designed to catalog and manage information related to (meta)genomic sequence projects. GOLD provides a centralized platform where researchers can access a wide array of metadata from its four organization levels namely Study, Organism/Biosample, Sequencing Project and Analysis Project. GOLD continues to serve as a valuable resource and has seen significant growth and expansion since its inception in 1997. With its expanded role as a collaborative platform, it not only actively imports data from other primary repositories like National Center for Biotechnology Information but also supports contributions from researchers worldwide. This collaborative approach has enriched the database with diverse datasets, creating a more integrated resource to enhance scientific insights. As genomic research becomes increasingly integral to various scientific disciplines, more researchers and institutions are turning to GOLD for their metadata needs. To meet this growing demand, GOLD has expanded by adding diverse metadata fields, intuitive features, advanced search capabilities and enhanced data visualization tools, making it easier for users to find and interpret relevant information. This manuscript provides an update and highlights the new features introduced over the last 2 years.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

The secondary metabolism collaboratory: a database and web discussion portal for secondary metabolite biosynthetic gene clusters

Secondary metabolites are small molecules produced by all corners of life, often with specialized bioactive functions with clinical and environmental relevance. Secondary metabolite biosynthetic gene clusters (BGCs) can often be identified within DNA sequences by various sequence similarity tools, but determining the exact functions of genes in the pathway and predicting their chemical products can often only be done by careful, manual comparative analysis. To facilitate this, we report the first release of the secondary metabolism collaboratory (SMC), which aims to provide a comprehensive, tool-agnostic repository of BGC sequence data drawn from all publicly available and user-submitted bacterial and archaeal genome and contig sources. On the website, users are provided a searchable catalog of putative BGCs identified from each source, along with visualizations of gene and domain annotations derived from multiple sequence analysis tools. SMC’s data is also available through publicly-accessible application programming interface (API) endpoints to facilitate programmatic access. Users are encouraged to share their findings (and search for others’) through comment posts on BGC and source pages. At the time of writing, SMC is the largest repository of BGC information, holding 13.1M BGC regions from 1.3M source sequences and growing, and can be found at https://smc.jgi.doe.gov.

59 BASIC BIOLOGICAL SCIENCES↗