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At least 379 records · Page 21
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Characterizing natural fractures and sub-seismic faults for well completion of Marcellus shale in the MSEEL Consortium project, West Virginia, USA

The Middle Devonian Marcellus shale play has emerged as a major world-class hydrocarbon accumulation and represents one of the largest and most prolific shale plays in the world. According to many outcrop studies in the region, natural fractures are well developed in the Marcellus Shale. However, evaluating fractures in the subsurface is often a significant challenge due to a lack of sufficient data. Therefore, in the Marcellus Shale Energy and Environment Laboratory (MSEEL) consortium project, significant efforts have been made to acquire high-quality image logs in the Marcellus laterals. The project provided tremendous opportunities to characterize the natural fractures and sub-seismic faults and to evaluate their impact on well stimulation. In this study, about 70,000 ft of acquired high-resolution logging while drilling (LWD) acoustic images from five long laterals located in Monongalia County, West Virginia, were processed and interpreted. In addition, the study used high-quality micro-resistivity images from a pilot well, allowing the evaluation of natural fractures in the entire Marcellus vertical sequence. Based on the available acoustic images, the natural fractures were classified into three basic categories: high-amplitude fractures, low-amplitude fractures, and faults. Further, larger open fractures can also be determined when a low-amplitude fracture is evident on caliper images. The fractures in the Marcellus usually have a medium to high angle dip; however, multiple fracture sets in terms of strike orientation were clearly observed in all the laterals. The fracture set with a strike at NE-SW (or 60-240 deg) seems to be the predominant one in all the wells. A few other sets, including those with N-S, NWW-SEE, and E-W strikes, were also observed. Several sub-seismic faults, with mostly a low dip angle and a NE-SW strike, have also been seen in two of the laterals. The fracture density is variable across all the laterals, ranging from very low (or none) to very high (up to 5 fractures per ft). The average fracture density for all the laterals is about 1 fracture per 10 ft. In the vertical sequence, the natural fracture development showed a clear preference for shale or shaly facies over carbonate-rich or thin limestone layers. The interpreted fracture and fault data were used as input data for the stimulation design with the purpose of better understanding the fractures’ impact on well stimulation. Production data from the laterals were also used to evaluate the natural fractures’ influence on well performance. The quality image database and the consistent interpretation results for the entire project enabled a systematic approach to characterizing fractures and, more importantly, to evaluating the impact of fractures on well stimulation and production.

03 NATURAL GAS↗
DOE OSTI2023

Overestimated prediction using polygenic prediction derived from summary statistics

When polygenic risk score (PRS) is derived from summary statistics, independence between discovery and test sets cannot be monitored. We compared two types of PRS studies derived from raw genetic data (denoted as rPRS) and the summary statistics for IGAP (sPRS). Two variables with the high heritability in UK Biobank, hypertension, and height, are used to derive an exemplary scale effect of PRS. sPRS without APOE is derived from International Genomics of Alzheimer’s Project (IGAP), which records ΔAUC and ΔR 2 of 0.051 ± 0.013 and 0.063 ± 0.015 for Alzheimer’s Disease Sequencing Project (ADSP) and 0.060 and 0.086 for Accelerating Medicine Partnership - Alzheimer’s Disease (AMP-AD). On UK Biobank, rPRS performances for hypertension assuming a similar size of discovery and test sets are 0.0036 ± 0.0027 (ΔAUC) and 0.0032 ± 0.0028 (ΔR 2 ). For height, ΔR 2 is 0.029 ± 0.0037. Considering the high heritability of hypertension and height of UK Biobank and sample size of UK Biobank, sPRS results from AD databases are inflated. Independence between discovery and test sets is a well-known basic requirement for PRS studies. However, a lot of PRS studies cannot follow such requirements because of impossible direct comparisons when using summary statistics. Thus, for sPRS, potential duplications should be carefully considered within the same ethnic group.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2003

Unlocking the Mystery of Columbia's Tragic Accident Through Materials Characterization

The wing and underbelly reconstruction of Space Shuttle Columbia took place at the Shuttle Landing Facility Hangar after the accident which destroyed STS-107. Fragments were placed on a grid according to their original location on the orbiter. Some Reinforced Carbon-Carbon (RCC) panels of the left wing leading edge and other parts from both leading edges were recovered and incorporated into the reconstruction. The recovered parts were tracked on a database according to a number and also tracked on a map of the orbiter. This viewgraph presentation describes the process of failure analysis undertaken by the Materials and Processes (M&P) Problem Resolution Team. The team started with factual observations about the accident, and identified highest level questions for it to answer in order to understand where on the orbiter failure occured, what component(s) failed, and what was the sequence of events. The finding of Columbia's MADS/OEX data recorder shifted the focus of the team's analysis to the left wing leading edge damage. The team placed particular attention on slag deposits on some of the RCC panels. The presentation lists analysis techniques, and lower level questions for the team to answer.

Shah, Sandeep↗
NASA NTRS2019

CHIANTI-An Atomic Database for Emission Lines. XV. Version 9, Improvements for the X-Ray Satellite Lines

CHIANTI contains a large quantity of atomic data for the analysis of astrophysical spectra. Programs are available in IDL and Python to perform calculation of the expected emergent spectrum from these sources. The database includes atomic energy levels, wavelengths, radiative transition probabilities, rate coefficients for collisional excitation, ionization, and recombination, as well as data to calculate free–free, free–bound, and two-photon continuum emission. In Version 9, we improve the modeling of the satellite lines at X-ray wavelengths by explicitly including autoionization and dielectronic recombination processes in the calculation of level populations for select members of the lithium isoelectronic sequence and Fe XVIII–XXIII. In addition, existing data sets are updated, new ions are added, and new total recombination rates for several Fe ions are included. All data and IDL programs are freely available at http://www.chiantidatabase.org or through SolarSoft, and the Python code ChiantiPy is also freely available at https://github.com/chianti-atomic/ChiantiPy.

X-rays (general)↗
NASA NTRS2009

Sequential Imaging of Earth by Astronauts: 50 Years of Global Change

For nearly 50 years, astronauts have collected sequential imagery of the Earth. In fact, the collection of astronaut photography comprises one of the earliest sets of data (1961 to present) available to scientists to study the regional context of the Earth s surface and how it changes. While today s availability of global high resolution satellite imagery enables anyone with an internet connection to examine specific features on the Earth s surface with a regional context, historical satellite imagery adds another dimension (time) that provides researchers and students insight about the features and processes of a region. For example, one of the geographic areas with the longest length of record contained within the astronaut photography database is the lower Nile River. The database contains images that document the flooding of Lake Nasser (an analog to today s flooding behind China s Three Gorges Dam), the changing levels of Lake Nasser s water with multiyear cycles of flood and drought, the recent flooding and drying of the Toshka Lakes, as well as urban growth, changes in agriculture and coastal subsidence. The imagery database allows investigations using different time scales (hours to decades) and spatial scales (resolutions and fields of view) as variables. To continue the imagery collection, the astronauts on the International Space Station are trained to understand basic the Earth Sciences and look for and photograph major events such as tropical storms, landslides, and volcanic eruptions, and document landscapes undergoing change (e.g., coastal systems, cities, changing forest cover). We present examples of selected sequences of astronaut imagery that illustrate the interdependence of geological processes, climate cycles, human geography and development, and prompt additional questions about the underlying elements of change.

Evans, Cynthia A.↗
NASA NTRSDate not supplied

Decision Framework for Classifying the State of Knowledge for Pharmaceutical Stability in Spaceflight

The currently approved medication formulary for exploration-class spaceflight missions presently exceeds 200pharmaceuticals. However, these medications' physical and chemical stability during long-term exposure to the spaceflight environment remains uncharacterized. A multi-disciplinary team of pharmacy and spaceflight subject matter experts (SMEs) collaborated to develop a decision framework that will prioritize medications for future stability research. This framework prioritizes the physical stability, drug quality, and safety of the active pharmaceutical ingredient of finished drug products selected for specific design reference mission (DRM) drug formularies. The United States Pharmacopeia (USP) defines drug stability as "the extent to which a drug product retains, within specified limits, and throughout its period of storage and use, the same properties and characteristics that it possessed at the time of its manufacture.1"The candidate medication is assessed by applying a sequence of drug agnostic questions to evaluate the limits of stability information pertinent to spaceflight. The answers to these questions ultimately lead to one of three characterizations: green (not prioritized for further research for this DRM), yellow (requires further literature review/additional studies), or red (not suitable for this DRM based on current knowledge). The decision framework will rely on several information resources to inform the ultimate decision, including the ExMC Pharmacy Information Database, published literature, FDA/drug manufacturer monographs, and USP. The results of this framework will be used to classify the state of knowledge for pharmaceutical stability for any specified DRM and guide future research efforts accordingly. This presentation will provide an overview of how this decision framework was developed, detail the challenges and limitations of the pathways, and discuss how researchers can apply the lessons learned from this project to future work

S Kurian↗
DOE OSTI2024

From soil to sequence: filling the critical gap in genome-resolved metagenomics is essential to the future of soil microbial ecology

Abstract Soil microbiomes are heterogeneous, complex microbial communities. Metagenomic analysis is generating vast amounts of data, creating immense challenges in sequence assembly and analysis. Although advances in technology have resulted in the ability to easily collect large amounts of sequence data, soil samples containing thousands of unique taxa are often poorly characterized. These challenges reduce the usefulness of genome-resolved metagenomic (GRM) analysis seen in other fields of microbiology, such as the creation of high quality metagenomic assembled genomes and the adoption of genome scale modeling approaches. The absence of these resources restricts the scale of future research, limiting hypothesis generation and the predictive modeling of microbial communities. Creating publicly available databases of soil MAGs, similar to databases produced for other microbiomes, has the potential to transform scientific insights about soil microbiomes without requiring the computational resources and domain expertise for assembly and binning.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

DIPS-Plus: The enhanced database of interacting protein structures for interface prediction

Abstract In this work, we expand on a dataset recently introduced for protein interface prediction (PIP), the Database of Interacting Protein Structures (DIPS), to present DIPS-Plus, an enhanced, feature-rich dataset of 42,112 complexes for machine learning of protein interfaces. While the original DIPS dataset contains only the Cartesian coordinates for atoms contained in the protein complex along with their types, DIPS-Plus contains multiple residue-level features including surface proximities, half-sphere amino acid compositions, and new profile hidden Markov model (HMM)-based sequence features for each amino acid, providing researchers a curated feature bank for training protein interface prediction methods. We demonstrate through rigorous benchmarks that training an existing state-of-the-art (SOTA) model for PIP on DIPS-Plus yields new SOTA results, surpassing the performance of some of the latest models trained on residue-level and atom-level encodings of protein complexes to date.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1998

An Operational Concept for Flying FMS Trajectories in Center and TRACON Airspace

Current Flight Management Systems (FMS) do a good job of constructing and flying an optimal trajectory for a single aircraft. Unfortunately, flight crews are often unable to fly these FMS routes during arrivals at busy airports. The Center TRACON Automation System (CTAS) has been designed to aid Center and TRACON (Terminal Radar Approach Control) controllers in assigning runways, sequencing and vectoring all classes of aircraft. CTAS bases its advisories on trajectory predictions for arriving aircraft using algorithms very similar to those in airborne FMS systems. This paper presents near and far term operational concepts for how a ground ATM (air traffic management) automation system like CTAS could work more effectively with the airborne automation in FMS equipped aircraft. The concepts for a more compatible air-ground system include: 1) a common route databases for both CTAS and FMS; 2) datalink to downlink information on aircraft weight, final approach speed and trajectory intent and to uplink wind information; 3) new FMS functions to allow flight crews to easily update their FMS trajectory to match the trajectory suggested by the ground automation with voice clearances, and 4) in the far term, datalink to downlink user preferred trajectories and to uplink trajectory clearances in the terminal area. The paper analyses some of the human factors issues that may result in allowing aircraft to fly FMS routes during enroute descent and in the terminal area. A series of linked human in the loop flight deck and air traffic control simulations and a field test with the NASA 757 are being conducted at NASA's Ames and Langley Research Centers to address these issues and to evaluate the operational feasibility of these approaches to more efficient flight and increased airport throughput.

Palmer, Everett↗
NASA NTRS2023

Heat Transfer and Interfacial Flow Physics of Microgravity Flow Boiling in Single-Side-Heated Rectangular Channel with Subcooled Inlet Conditions – Experiments Onboard the International Space Station

This study is the culmination of a long-term collaborative effort between researchers from the Purdue University Boiling and Two-Phase Flow Laboratory (PU-BTPFL) and the NASA Glenn Research Center to investigate gravitational effects on flow boiling and flow condensation. The science and design concepts for this large-scale effort were initiated in 2011 and included several studies detailing various aspects of two-phase fluid physics in both Earth gravity and microgravity, culminating in construction of the large-scale experimental facility named “Flow Boiling and Condensation Experiment (FBCE)”. The experiment was launched to the International Space Station (ISS) in August 2021. Following the successful installation of FBCE, equipped with the Flow Boiling Module (FBM), onboard the ISS and completion of several safety checks, flow boiling experiments were performed for five months from February 2022 until July 2022. This resulted in a large flow boiling database covering broad ranges of operating parameters and heating configurations spanning several research objectives. This study investigates microgravity flow boiling of n-perfluorohexane with subcooled inlet in a single-side-heated rectangular channel of dimensions 114.6-mm heated length, 2.5-mm heated width, and 5.0-mm height. Key operating parameters investigated are mass velocity (199.90 – 3200.13 kg/m 2 s), inlet subcooling (0.10 – 45.76°C), and inlet pressure (113.30 – 164.29 kPa). Images and image sequences acquired via high-speed-video are presented to elucidate the interfacial flow physics. To analyze and explain the effects of various parameters in microgravity, heat transfer results are presented as flow boiling curves, streamwise profiles of wall temperature and heat transfer coefficient, and parametric trends of local and averaged heat transfer coefficient. Mass velocity and inlet subcooling significantly influenced most of the aforementioned aspects of flow boiling, whereas effects of inlet pressure were comparatively insignificant. Although the data and observed flow physics might be different, the parametric effects and trends in microgravity are similar to vertical upflow in Earth gravity. Some cases, especially low mass velocities, high heat fluxes, and large degrees of inlet subcooling, experienced temporally anomalous flow behaviors caused by two-phase flow instabilities manifesting as flow reversals and resulted in deviations in overall trends. Severe thermodynamic non-equilibrium is observed throughout the channel. Overall, FBCE’s ISS experiments were successful for subcooled inlet with single-sided heating of rectangular channel, and the collected data well established the various effects on flow boiling physics in highly controlled long-term microgravity conditions.

flow boiling↗
NASA NTRS1981

An application of computer aided requirements analysis to a real time deep space system

The entire procedure of incorporating the requirements and goals of a space flight project into integrated, time ordered sequences of spacecraft commands, is called the uplink process. The Uplink Process Control Task (UPCT) was created to examine the uplink process and determine ways to improve it. The Problem Statement Language/Problem Statement Analyzer (PSL/PSA) designed to assist the designer/analyst/engineer in the preparation of specifications of an information system is used as a supporting tool to aid in the analysis. Attention is given to a definition of the uplink process, the definition of PSL/PSA, the construction of a PSA database, the value of analysis to the study of the uplink process, and the PSL/PSA lessons learned.

Farny, A. M.↗
DOE OSTI2024

APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics

The prediction of protein 3D structure from amino acid sequence is a computational grand challenge in biophysics and plays a key role in robust protein structure prediction algorithms, from drug discovery to genome interpretation. The advent of AI models, such as AlphaFold, is revolutionizing applications that depend on robust protein structure prediction algorithms. To maximize the impact, and ease the usability, of these AI tools we introduce APACE, AlphaFold2 and advanced computing as a service, a computational framework that effectively handles this AI model and its TB-size database to conduct accelerated protein structure prediction analyses in modern supercomputing environments. We deployed APACE in the Delta and Polaris supercomputers and quantified its performance for accurate protein structure predictions using four exemplar proteins: 6AWO, 6OAN, 7MEZ, and 6D6U. Using up to 300 ensembles, distributed across 200 NVIDIA A100 GPUs, we found that APACE is up to two orders of magnitude faster than off-the-self AlphaFold2 implementations, reducing time-to-solution from weeks to minutes. This computational approach may be readily linked with robotics laboratories to automate and accelerate scientific discovery.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Discovery of 15 A-F Main Sequence Pulsating Star Candidates

Delta Scuti stars, spanning spectral types A to F with masses between 1.5 and 2.5 solar masses, exhibit a complex mix of radial and non-radial pressure modes. This study focuses on 15 Delta Scuti, Gamma Doradus, and Hybrid candidate stars using TESS satellite photometry data with a time series of exposures ranging from 20 to 600 seconds across different sky regions. Employing the prewhitening technique via fast Fourier transforms, significant frequencies are extracted from light curves. Three approximation methods are used to estimate critical stellar parameters such as density, radius, and mass. This research also verifies the variability of these stars, which are currently not classified as variable in databases like SIMBAD.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Kraken2 Metagenomic Virus Database

The Database: Kraken2 [1] database built from a classification tree containing over 700k metagenomic viruses from JGI IMG/VR [2]. (1) Wood, D. E., Lu, J., and Langmead, B. (2019). Improved metagenomic analysis with Kraken 2. Genome Biol., 20(1), 1–13. doi: 10.1186/s13059-019-1891-0 (2) Paez-Espino D, Chen I-MA, Palaniappan K, Ratner A, Chu K, Szeto E, et al. IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses. Nucleic Acids Res. 2017;45:D457-65. For Paper: Title: A k-mer based approach for virus classification in metatranscriptomic and metagenomic samples identifies viral associations in the Populus phytobiome and autism brains Abstract Background Viruses are an underrepresented taxa in the study and identification of microbiome constituents; however, they play an important role in health, microbiome regulation, and transfer of genetic material. Only a few thousand viruses have been isolated, sequenced, and assigned a taxonomy, which further limits the ability to identify and quantify viruses in the microbiome. Additionally, the vast diversity of viruses represents a challenge for classification, not only in constructing a viral taxonomy, but also in identifying similarities between a virus' genotype and its phenotype. However, the diversity of viral sequences can be leveraged to classify their sequences in metagenomic and metatranscriptomic samples. Methods To identify viruses in transcriptomic and genomic samples, we developed a dynamic programming algorithm for creating a classification tree out of 715,672 metagenome viruses. To create the classification tree, we clustered proportional similarity scores generated from the k-mer profiles of each of the metagenome viruses. We then integrated the viral classification tree with the NCBI taxonomy for use with ParaKraken, a metagenomic/transcriptomic classifier. Results To illustrate the breadth of our utility for classifying viruses with ParaKraken, we analyzed data from a plant metagenome study identifying the differences between two Populus genotypes in three different compartments and on a human metatranscriptome study identifying the differences between Autism Spectrum Disorder patients and controls in post mortem brain biopsies. In the Populus study, we identified genotype and compartment specific viral signatures, while in the Autism study we identified a significant increased abundance of eight viral sequences in Autism brain biopsies. Conclusion Viruses represent an important aspect of the microbiome. The ability to classify viruses represents the first step in being able to better understand their role in the microbiome. The viral classification method presented here allows for more complete identification of viral sequences for use in identifying associations between viruses and the host and viruses and other microbiome members. Acknowledgements and Funding This research used resources of the Oak Ridge Leadership Computing Facility at the Oak Ridge National Laboratory, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC05-00OR22725. This research was also supported by the Plant-Microbe Interfaces Scientific Focus Area in the Genomic Science Program, the Office of Biological and Environmental Research (BER) in the U.S. Department of Energy Office of Science, and by the Department of Energy, Laboratory Directed Research and Development funding (ProjectID 8321), at the Oak Ridge National Laboratory. Oak Ridge National Laboratory is managed by UT-Battelle, LLC, for the US DOE under contract DE-AC05-00OR22725. This research used resources of the Compute and Data Environment for Science (CADES).

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

Abstract The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA’s versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria

The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host taxonomy at the genus rank for a broad range of viruses infecting bacteria and archaea, while retaining a low false discovery rate. Based on a large dataset of metagenome-derived virus genomes from the IMG/VR database, we illustrate how iPHoP can provide extensive host prediction and guide further characterization of uncultivated viruses.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS1997

Boron Abundances in A and B-type Stars

Boron abundances in A- and B-type stars may be a successful way to track evolutionary effects in these hot stars. The light elements - Li, Be, and B - are tracers of exposure to temperatures more moderate than those in which the H-burning CN-cycle operates. Thus, any exposure of surface stellar layers to deeper layers will affect these light element abundances. Li and Be are used in this role in investigations of evolutionary processes in cool stars, but are not observable in hotter stars. An investigation of boron, however, is possible through the B II 1362 A resonance line. We have gathered high resolution spectra from the IUE database of A- and B-type stars near 10 solar mass for which nitrogen abundances have been determined. The B II 1362 A line is blended throughout; the temperature range of this program, requiring spectrum syntheses to recover the boron abundances. For no star could we synthesize the 1362 A region using the meteoritic/solar boron abundance of log e (B) = 2.88; a lower boron abundance was necessary which may reflect evolutionary effects (e.g., mass loss or mixing near the main-sequence), the natal composition of the star forming regions, or a systematic error in the analyses (e.g., non-LTE effects). Regardless of the initial boron abundance, and despite the possibility of non-LTE effects, it seems clear that boron is severely depleted in some stars. It may be that the nitrogen and boron abundances are anticorrelated, as would be expected from mixing between the H-burning and outer stellar layers. If, as we suspect, a residue of boron is present in the A-type supergiants, we may exclude a scenario in which mixing occurs continuously between the surface and the deep layers operating the CN-cycle. Further exploitation of the B II 1362 A line as an indicator of the evolutionary status of A- and B-type stars will require a larger stellar sample to be observed with higher signal-to-noise as attainable with the Hubble Space Telescope.

Lambert, David L.↗
DOE OSTI2023

CasPEDIA Database: a functional classification system for class 2 CRISPR-Cas enzymes

Abstract CRISPR-Cas enzymes enable RNA-guided bacterial immunity and are widely used for biotechnological applications including genome editing. In particular, the Class 2 CRISPR-associated enzymes (Cas9, Cas12 and Cas13 families), have been deployed for numerous research, clinical and agricultural applications. However, the immense genetic and biochemical diversity of these proteins in the public domain poses a barrier for researchers seeking to leverage their activities. We present CasPEDIA (http://caspedia.org), the Cas Protein Effector Database of Information and Assessment, a curated encyclopedia that integrates enzymatic classification for hundreds of different Cas enzymes across 27 phylogenetic groups spanning the Cas9, Cas12 and Cas13 families, as well as evolutionarily related IscB and TnpB proteins. All enzymes in CasPEDIA were annotated with a standard workflow based on their primary nuclease activity, target requirements and guide-RNA design constraints. Our functional classification scheme, CasID, is described alongside current phylogenetic classification, allowing users to search related orthologs by enzymatic function and sequence similarity. CasPEDIA is a comprehensive data portal that summarizes and contextualizes enzymatic properties of widely used Cas enzymes, equipping users with valuable resources to foster biotechnological development. CasPEDIA complements phylogenetic Cas nomenclature and enables researchers to leverage the multi-faceted nucleic-acid targeting rules of diverse Class 2 Cas enzymes.

59 BASIC BIOLOGICAL SCIENCES↗