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Overview of the NASA Earth Action Strategies Wildland Fire Initiative

As part of NASA’s new Earth Action strategy, the Wildland Fire initiative was established, which includes both the NASA Wildland Fire Program (WFP) and the FireSense project. NASA has over 50 years of experience generating data and technology to enhance fire science and operational management. The WFP’s mission is threefold: 1) assemble communities of practice through collaborative efforts with government, academia, and the private sector; 2) co-develop knowledge and applications with relevant partners and stakeholders in the wildfire community; and 3) improve wildland fire management through the transitioning of NASA data, technology, tools, and science to stakeholder organizations. The WFP is focusing on supporting proactive fire management, including situational awareness, preparedness, and risk mitigation. This will be accomplished through selected projects that identify management challenges, relevant to partners and end users, and the NASA data that will be utilized to deliver innovative solutions to enhance the management of wildland fires. Examples include: i) investigation of evaporative stress from OpenET to help predict the risk of wildfire occurrence in watersheds; ii) incorporation of space based LiDAR for the generation of 3-dimensional forest fuel metrics, used to improve wildfire risk and behavior models; iii) integration of global, multi-platform geostationary active-fire data in near-real-time into NASA’s Fire Information for Resource Management System (FIRMS); and iv) identification of post-fire ecohydrological conditions using thermal, multispectral, synthetic aperture radar (SAR), and hyperspectral remotely-sensed data to improve flood hazard forecast models. The FireSense project is a US-focused 5-year project that will focus on delivering NASA’s unique Earth science and technological capabilities to operational agencies, striving towards enhancing fire fighting and air quality management. The project will include airborne campaigns and new technology that will likely have global implications. Initial stakeholder engagement led FireSense to focus on four use-cases focused on the characterization and measurement of: (i) pre-fire fuels conditions, (ii) active fire-dynamics; (iii) post-fire impact and threats; and iv) air quality impacts and forecasting, each-developed with identified stakeholders.

Wildland Fire program↗

NASA NTRS2004

An Ontology for Requesting Distant Robotic Action: A Case Study in Naming and Action Identification for Planning on the Mars Exploration Rover Mission

This paper focuses on the development and use of the abbreviated names as well as an emergent ontology associated with making requests for action of a distant robotic rover during the 2003-2004 NASA Mars Exploration Rover (MER) mission, run by the Jet Propulsion Laboratory. The infancy of the domain of Martian telerobotic science, in which specialists request work from a rover moving through the landscape, as well as the need to consider the interdisciplinary teams involved in the work required an empirical approach. The formulation of this ontology is grounded in human behavior and work practice. The purpose of this paper is to identify general issues for an ontology of action (specifically for requests for action), while maintaining sensitivity to the users, tools and the work system within a specific technical domain. We found that this ontology of action must take into account a dynamic environment, changing in response to the movement of the rover, changes on the rover itself, as well as be responsive to the purposeful intent of the science requestors. Analysis of MER mission events demonstrates that the work practice and even robotic tool usage changes over time. Therefore, an ontology must adapt and represent both incremental change and revolutionary change, and the ontology can never be more than a partial agreement on the conceptualizations involved. Although examined in a rather unique technical domain, the general issues pertain to the control of any complex, distributed work system as well as the archival record of its accomplishments.

Wales, Roxana C.↗

DOE OSTI2013

A common intermediate for N2 formation in enzymes and zeolites: side-on Cu-nitrosyl complexes

Understanding the mechanisms of catalytic processes requires the identification of reaction centers and key intermediates, both of which are often achieved by the use of spectroscopic characterization tools. Due to the heterogeneity of active centers in heterogeneous catalysts, it is frequently difficult to identify the specific sites that are responsible for the overall activity. Furthermore, the simultaneous presence of a large number of surface species on the catalyst surface often poses a great challenge for the unambiguous determination of the relevant species in the reaction mechanism. In contrast, enzymes possess catalytically active centers with precisely defined coordination environments that are only able to accommodate intermediates relevant to the specific catalytic process. Here we show that side-on Cu+-NO+ complexes characterized by high magnetic field solid state magic angle spinning nuclear magnetic resonance (NMR) and Fourier transform infrared (FTIR) spectroscopies are the key intermediates in the selective catalytic reduction of NO over Cu-SSZ-13 zeolite catalysts. Analogous intermediates have been observed and characterized in nitrite reductase enzymes, and shown to be the critical intermediates in the formation of N2 for anaerobic ammonium oxidation reactions.[1] The identification of this key reaction intermediate, combined with the results of our prior kinetic studies, allows us to propose a new reaction mechanism for the selective catalytic reduction of NO with NH3 under oxygen-rich environments over Cu-SSZ-13 zeolites, a key reaction in automotive emission control. The authors acknowledge the US Department of Energy (DOE), Office of Energy Efficiency and Renewable Energy/Vehicle Technologies Program for the support of this work. The research described in this paper was performed at the Environmental Molecular Sciences Laboratory (EMSL), a national scientific user facility sponsored by the DOE’s Office of Biological and Environmental Research and located at Pacific Northwest National Laboratory (PNNL). PNNL is operated for the US DOE by Battelle Memorial Institute.

Environmental Molecular Sciences Laboratory↗

DOE OSTI2018

Uncertainty in master-equation-based rate coefficient calculations

Rate coefficients are key quantities in gas phase kinetics and can be determined theoretically via master equation (ME) calculations. Rate coefficients characterize how fast a certain chemical species reacts away due to collisions into a specific product. Some of these collisions are simply transferring energy between the colliding partners, in which case the initial chemical species can undergo a unimolecular reaction: dissociation or isomerization. Other collisions are reactive, and the colliding partners either exchange atoms, these are direct reactions, or form complexes that can themselves react further or get stabilized by deactivating collisions with a bath gas. The input of MEs are molecular parameters: geometries, energies, and frequencies determined from ab initio calculations. While the calculation of these rate coefficients using ab initio data is becoming routine in many cases, the determination of the uncertainties of the rate coefficients are often ignored, sometimes crudely assessed by varying independently just a few of the numerous parameters, and only occasionally studied in detail. In this study, molecular frequencies, barrier heights, well depths, and imaginary frequencies (needed to calculate quantum mechanical tunneling) were automatically perturbed in an uncorrelated fashion. Our Python tool, MEUQ, takes user requests to change all or specified well, barrier, or bimolecular product parameters for a reaction. We propagate the uncertainty in these input parameters and perform global sensitivity analysis in the rate coefficients for the ethyl + O 2 system using state-of-the-art uncertainty quantification (UQ) techniques via Python interface to UQ Toolkit (www . sandia.gov/uqtoolkit). A total of 10,000 sets of rate coefficients were collected after perturbing 240 molecular parameters. With our methodology, sensitive mechanistic steps can be revealed to a modeler in a straightforward manner for identification of significant and negligible influences in bimolecular reactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

NASA NTRS1983

User manual of the CATSS system (version 1.0) communication analysis tool for space station

The Communication Analysis Tool for the Space Station (CATSS) is a FORTRAN language software package capable of predicting the communications links performance for the Space Station (SS) communication and tracking (C & T) system. An interactive software package was currently developed to run on the DEC/VAX computers. The CATSS models and evaluates the various C & T links of the SS, which includes the modulation schemes such as Binary-Phase-Shift-Keying (BPSK), BPSK with Direct Sequence Spread Spectrum (PN/BPSK), and M-ary Frequency-Shift-Keying with Frequency Hopping (FH/MFSK). Optical Space Communication link is also included. CATSS is a C & T system engineering tool used to predict and analyze the system performance for different link environment. Identification of system weaknesses is achieved through evaluation of performance with varying system parameters. System tradeoff for different values of system parameters are made based on the performance prediction.

Tsang, C. S.↗

NASA NTRS2008

Services, Perspective and Directions of the Space Physics Data Facility

The multi-mission data and orbit services of NASA's Space Physics Data Facility (SPDF) project offer unique capabilities supporting science of the Heliophysics Great Observatory and that are highly complementary to other services now evolving in the international heliophysics data environment. The VSPO (Virtual Space Physics Observatory) service is an active portal to a wide rage of distributed data sources. CDAWeb (Coordinated Data Analysis Web) offers plots, listings and file downloads for current data from many missions across the boundaries of missions and instrument types. CDAWeb now includes extensive new data from STEREO and THEMIS, plus new ROCSAT IPEI data, the latest data from all four TIMED instruments and high-resolution data from all DE-2 experiments. SSCWeb, Helioweb and out 3D Animated Orbit Viewer (TIPSOD) provide position data and identification of spacecraft and ground conjunctions. OMNI Web, with its new extension to 1- and 5-minute resolution, provides interplanetary parameters at the Earth's bow shock. SPDF maintains NASA's CDF (Common Data Format) standard and a range of associated tools including format translation services. These capabilities are all now available through web services based APIs, one element in SPDF's ongoing work to enable heliophysics community development of Virtual discipline Observatories (e.g. VITMO). We will demonstrate out latest data and capabilities, review the lessons we continue to learn in what science users need and value in this class of services, and discuss out current thinking to the future role and appropriate focus of the SPDF effort in the evolving and increasingly distributed heliophysics data environment.

McGuire, Robert E.↗

DOE OSTI2025

Automated tabletop exfoliation and identification of monolayer graphene flakes

Over the past two decades, graphene has been intensively studied because of its remarkable mechanical, optical, and electronic properties. Initial studies were enabled by manual “Scotch Tape” exfoliation; nearly two decades later, this method is still widely used to obtain chemically pristine flakes of graphene and other 2D van der Waals materials. Unfortunately, the yield of large, pristine flakes with uniform thickness is inconsistent. Thus, significant time and effort are required to exfoliate and locate flakes suitable for fabricating multilayer van der Waals heterostructures. Here, we describe a relatively affordable tabletop device (the “eXfoliator”) that can reproducibly control key parameters and largely automate the exfoliation process. In a typical exfoliation run, the eXfoliator produces 3 or more large (≥ 400 μm 2 ) high-quality graphene monolayer flakes, allowing new users to produce such flakes at a rate comparable to manual exfoliation by an experienced user. Furthermore, we use an automated mapping system and a computer vision algorithm to locate candidate flakes. Our results provide a starting point for future research efforts to identify more precisely which parameters matter for the success of exfoliation and to optimize them.

47 OTHER INSTRUMENTATION↗

NASA NTRS2012

Social Semantics for an Effective Enterprise

An evolution of the Semantic Web, the Social Semantic Web (s2w), facilitates knowledge sharing with "useful information based on human contributions, which gets better as more people participate." The s2w reaches beyond the search box to move us from a collection of hyperlinked facts, to meaningful, real time context. When focused through the lens of Enterprise Search, the Social Semantic Web facilitates the fluid transition of meaningful business information from the source to the user. It is the confluence of human thought and computer processing structured with the iterative application of taxonomies, folksonomies, ontologies, and metadata schemas. The importance and nuances of human interaction are often deemphasized when focusing on automatic generation of semantic markup, which results in dissatisfied users and unrealized return on investment. Users consistently qualify the value of information sets through the act of selection, making them the de facto stakeholders of the Social Semantic Web. Employers are the ultimate beneficiaries of s2w utilization with a better informed, more decisive workforce; one not achieved with an IT miracle technology, but by improved human-computer interactions. Johnson Space Center Taxonomist Sarah Berndt and Mike Doane, principal owner of Term Management, LLC discuss the planning, development, and maintenance stages for components of a semantic system while emphasizing the necessity of a Social Semantic Web for the Enterprise. Identification of risks and variables associated with layering the successful implementation of a semantic system are also modeled.

Berndt, Sarah↗

DOE OSTI2018

Study of Data-Driven Mesh-Model Optimization in System Thermal-Hydraulic Simulation

Quantification of nuclear power plant safety risk requires a systematic and yet practical approach to identification of accident scenarios, assessment of their likelihood and consequences. Instrumental to this goal is risk-informed safety margin characterization (RISMC) framework, whose realization requires computationally robust and affordable methods for sufficiently accurate simulation of complex multi-dimensional physical phenomena, such as turbulent and multi-phase flow. The CFD-like correlation-based codes with 3D simulation capability (e.g., GOTHIC) ensure computational efficiency using coarse mesh size and the sub-grid phenomena in the boundary layer that can be captured by adequate constitutive correlations. However, the error sources and user effects on the selection of mesh size and models lead to unpredictable simulation error, while rich High-Fidelity (HF) data from experiments and numerical simulation using validated code or DNS are not fully explored. It would be useful to have a “smart” data-driven multi-scale framework in which the low-resolution models can be “taught” to emulate high-resolution models. The objective of this work is to develop and evaluate a physical-based data-driven mesh-model optimization approach (Optimized Mesh/Model Information System, OMIS) to estimate the simulation error and give advice on the optimized selection of coarse mesh size and Low-Fidelity (LF) models for System Thermal Hydraulic (STH) simulation to achieve accuracy comparable to that of HF models. This approach takes advantages of computational efficiency of coarse-mesh simulation and application of Machine Learning (ML) algorithms.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2018

Developing a Community of Practice for Applied Uses of Future PACE Data to Address Food Security Challenges

Ocean color satellite measurements have yielded valuable information about the base of the marine food web for over 20 years. The Plankton, Aerosol, Cloud, ocean Ecosystem (PACE) mission is building an advanced spectrometer to further refine ecosystem monitoring. Higher spectral resolution data from PACE will enable identification of additional marine biological indicators and their response to multiple stressors to guide sustainable management. Seafood is an important source of protein for a significant number of people. Wild catches cannot match increasing demand and their sustainability is in question. Aquaculture is an ever more important industry to feed the world's population. We share early efforts to engage a community of practice around food security to increase satellite data product use in support of resource management, business decisions, and policy analysis. Understanding the needs of applied scientists as well as non-traditional users of satellite data early in the PACE mission process will improve planning and preparation for a broader user base and hopefully help to mitigate food insecurity.

Schollaert Uz, Stephanie↗

DOE OSTI2025

FIRM image analysis: A machine learning workflow for quantifying extracellular matrix components from electron microscopy images

The extracellular matrix (ECM) is a complex network of biomolecules that plays an integral role in the structure, processes, and signaling mechanisms of cells and tissues. Identifying and quantifying changes in these matrix components provides insight into the mechanisms behind specific tissue remodeling processes; however, quantifying these changes is challenging due to difficult imaging conditions, complexity of the ECM, and the subtlety of these changes. Current imaging techniques allow us to visualize these critical remodeling events and developments in image analysis have employed a combination of analysis software and machine learning techniques to improve the efficiency and accuracy with which features are measured. Although image analysis has seen much improvement in recent years, there has been no technique developed to address ambiguity in feature edges in electron microscopy images. Presented here is a new machine learning-based workflow for the analysis of microscopy images named FIRM (Feature Identification from Raw Microscopy) that uses a random forest classifier to identify ECM features of interest and generate binary segmentation masks for quantification with ImageJ-FIJI. FIRM performed with an F1 score of 0.794 and greater than 80% accuracy for number and size of features detected. FIRM had similar deviation from the ground truth in the number of identified fibrils, fibril size, and size distributions when compared to human analyses. The results suggest that FIRM performs as well as manual analysis and requires a fraction of the time. This analysis technique is more efficient, eliminates user bias, and can be easily optimized to identify a variety of features, making it useful for any discipline requiring image analysis.

Science & Technology - Other Topics↗

DOE OSTI2013

Distributed Dynamic State Estimator, Generator Parameter Estimation and Stability Monitoring Demonstration

This is the final report for this project that was performed in the period: October1, 2009 to June 30, 2013. In this project, a fully distributed high-fidelity dynamic state estimator (DSE) that continuously tracks the real time dynamic model of a wide area system with update rates better than 60 times per second is achieved. The proposed technology is based on GPS-synchronized measurements but also utilizes data from all available Intelligent Electronic Devices in the system (numerical relays, digital fault recorders, digital meters, etc.). The distributed state estimator provides the real time model of the system not only the voltage phasors. The proposed system provides the infrastructure for a variety of applications and two very important applications (a) a high fidelity generating unit parameters estimation and (b) an energy function based transient stability monitoring of a wide area electric power system with predictive capability. Also the dynamic distributed state estimation results are stored (the storage scheme includes data and coincidental model) enabling an automatic reconstruction and “play back” of a system wide disturbance. This approach enables complete play back capability with fidelity equal to that of real time with the advantage of “playing back” at a user selected speed. The proposed technologies were developed and tested in the lab during the first 18 months of the project and then demonstrated on two actual systems, the USVI Water and Power Administration system and the New York Power Authority’s Blenheim-Gilboa pumped hydro plant in the last 18 months of the project. The four main thrusts of this project, mentioned above, are extremely important to the industry. The DSE with the achieved update rates (more than 60 times per second) provides a superior solution to the “grid visibility” question. The generator parameter identification method fills an important and practical need of the industry. The “energy function” based transient stability monitoring opens up new ways to protect the power grid, better manage disturbances, confine their impact and in general improve the reliability and security of the system. Finally, as a by-product of the proposed research project, the developed system is able to “play back” disturbances by a click of a mouse. The importance of this by-product is evident by considering the tremendous effort exerted after the August 2003 blackout to piece together all the disturbance recordings, align them and recreate the sequence of events. This project has moved the state of art from fault recording by individual devices to system wide disturbance recording with “play back” capability.

24 POWER TRANSMISSION AND DISTRIBUTION↗

NASA NTRS2012

QuakeSim 2.0

QuakeSim 2.0 improves understanding of earthquake processes by providing modeling tools and integrating model applications and various heterogeneous data sources within a Web services environment. QuakeSim is a multisource, synergistic, data-intensive environment for modeling the behavior of earthquake faults individually, and as part of complex interacting systems. Remotely sensed geodetic data products may be explored, compared with faults and landscape features, mined by pattern analysis applications, and integrated with models and pattern analysis applications in a rich Web-based and visualization environment. Integration of heterogeneous data products with pattern informatics tools enables efficient development of models. Federated database components and visualization tools allow rapid exploration of large datasets, while pattern informatics enables identification of subtle, but important, features in large data sets. QuakeSim is valuable for earthquake investigations and modeling in its current state, and also serves as a prototype and nucleus for broader systems under development. The framework provides access to physics-based simulation tools that model the earthquake cycle and related crustal deformation. Spaceborne GPS and Inter ferometric Synthetic Aperture (InSAR) data provide information on near-term crustal deformation, while paleoseismic geologic data provide longerterm information on earthquake fault processes. These data sources are integrated into QuakeSim's QuakeTables database system, and are accessible by users or various model applications. UAVSAR repeat pass interferometry data products are added to the QuakeTables database, and are available through a browseable map interface or Representational State Transfer (REST) interfaces. Model applications can retrieve data from Quake Tables, or from third-party GPS velocity data services; alternatively, users can manually input parameters into the models. Pattern analysis of GPS and seismicity data has proved useful for mid-term forecasting of earthquakes, and for detecting subtle changes in crustal deformation. The GPS time series analysis has also proved useful as a data-quality tool, enabling the discovery of station anomalies and data processing and distribution errors. Improved visualization tools enable more efficient data exploration and understanding. Tools provide flexibility to science users for exploring data in new ways through download links, but also facilitate standard, intuitive, and routine uses for science users and end users such as emergency responders.

Donnellan, Andrea↗

DOE OSTI2016

The Nuclear Energy Knowledge and Validation Center – Summary of Activities Conducted in FY15

The Nuclear Energy Knowledge and Validation Center (NEKVaC) is a new initiative by the Department of Energy and the Idaho National Laboratory to coordinate and focus the resources and expertise that exist with the DOE Complex toward solving issues in modern nuclear code validation. In time, code owners, users, and developers will view the Center as a partner and essential resource for acquiring the best practices and latest techniques for validating codes, for guidance in planning and executing experiments, for facilitating access to, and maximizing the usefulness of, existing data, and for preserving knowledge for continual use by nuclear professionals and organizations for their own validation needs. The scope of the center covers many inter-related activities which will need to be cultivated carefully in the near-term and managed properly once the Center is fully functional. Three areas comprise the principal mission: 1) identification and prioritization of projects that extend the field of validation science and its application to modern codes, 2) adapt or develop best practices and guidelines for high fidelity multiphysics/multiscale analysis code development and associated experiment design, and 3) define protocols for data acquisition and knowledge preservation and provide a portal for access to databases currently scattered among numerous organizations. These mission areas, while each having a unique focus, are inter-dependent and complementary. Likewise, all activities supported by the NEKVaC, both near-term and long-term), must possess elements supporting all three. This cross-cutting nature is essential to ensuring that activities and supporting personnel do not become ‘stove-piped’, i.e. focused so much on a specific function that the activity itself becomes the objective rather than the achieving the larger vision. Achieving the broader vision will require a healthy and accountable level of activity in each of the areas. This will take time and significant DOE support. Growing too fast (budget-wise) will not allow ideas to mature, lessons to be learned, and taxpayer money to be spent responsibly. The process should be initiated with a small set of tasks, executed over a short but reasonable term, that will exercise most if not all aspects of the Center’s potential operation. The initial activities described in this report have a high potential for near-term success in demonstrating Center objectives but also to work out some of the issues in task execution, communication between functional elements, and the ability to raise awareness of the Center and cement stakeholder buy-in. This report begins with a description of the Mission areas; specifically the role played by each and the types of activities for which they are responsible. It then lists and describes the proposed near-term tasks upon which future efforts can build.

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

NASA NTRS1976

Evaluation of LANDSAT-1 image applications to geologic mapping, structural analysis and mineral resource inventory of South America with special emphasis on the Andes Mountain region

The author has identified the following significant results. The discovery of copper mineralization along a lineament mapped in Area 7 (La Paz) has lent credence to the use of LANDSAT 1 data as a basic step in mineral exploration. In Area 9 (Copiapo Region), a number of lineaments were found to be associated with the largest copper deposits of the region. In Area 12 (Magallanes), the identification of what is believed to be a tertiary basin from LANDSAT 1 data has resulted in a new area for petroleum exploration. Band 7 images, as black and white transparencies, were found to be the most useful for geologic interpretation in both tropical vegetated areas and desert regions. Color composites made by the diazochrome process, chromaline process, and from color additive viewers provided additional information. Mosaics of LANDSAT 1 data covering 4 x 6 degrees of latitude and longitude compiled at the 1:1,000,000 scale were found to be an ideal size and format for most users.

Carter, W. D.↗

DOE OSTI2023

IsoMatchMS : Open-Source Software for Automated Annotation and Visualization of High Resolution MALDI-MS Spectra

Due to its speed, accuracy, and adaptability to various sample types, matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) has become a popular method to identify molecular isotope profiles from biological samples. Often MALDI-MS data do not include tandem MS fragmentation data, and thus the identification of compounds in samples requires external databases so that the accurate mass of detected signals can be matched to known molecular compounds. Most relevant MALDI-MS software tools developed to confirm compound identifications are focused on small molecules (e.g., metabolites, lipids) and cannot be easily adapted to protein data due to their more complex isotopic distributions. Here, we present an R package called IsoMatchMS for the automated annotation of MALDI-MS data for multiple datatypes: intact proteins, peptides, and glycans. This tool accepts already derived molecular formulas or, for proteomics applications, can derive molecular formulas from a list of input peptides or proteins including proteins with post-translational modifications. In conclusion, visualization of all matched isotopic profiles is provided in a highly accessible HTML format called a trelliscope display, which allows users to filter and sort by several parameters such as match scores and the number of peaks matched. IsoMatchMS simplifies the annotation and visualization of MALDI-MS data for downstream analyses.

47 OTHER INSTRUMENTATION↗

DOE OSTI2020

Characterization and identification of HPC applications at leadership computing facility

High Performance Computing (HPC) is an important method for scientific discovery via large-scale simulation, data analysis, or artificial intelligence. Leadership-class supercomputers are expensive, but essential to run large HPC applications. The Petascale era of supercomputers began in 2008, with the first machines achieving performance in excess of one petaflops, and with the advent of new supercomputers in 2021 (e.g., Aurora, Frontier), the Exascale era will soon begin. However, the high theoretical computing capability (i.e., peak FLOPS) of a machine is not the only meaningful target when designing a supercomputer, as the resources demand of applications varies. A deep understanding of the characterization of applications that run on a leadership supercomputer is one of the most important ways for planning its design, development and operation. In order to improve our understanding of HPC applications, user demands and resource usage characteristics, we perform correlative analysis of various logs for different subsystems of a leadership supercomputer. This analysis reveals surprising, sometimes counter-intuitive patterns, which, in some cases, conflicts with existing assumptions, and have important implications for future system designs as well as supercomputer operations. For example, our analysis shows that while the applications spend significant time on MPI, most applications spend very little time on file I/O. Combined analysis of hardware event logs and task failure logs show that the probability of a hardware FATAL event causing task failure is low. Combined analysis of control system logs and file I/O logs reveals that pure POSIX I/O is used more widely than higher level parallel I/O. Based on holistic insights of the application gained through combined and co-analysis of multiple logs from different perspectives and general intuition, we engineer features to "fingerprint" HPC applications. We use t-SNE (a machine learning technique for dimensionality reduction) to validate the explainability of our features and finally train machine learning models to identify HPC applications or group those with similar characteristic. To the best of our knowledge, this is the first work that combines logs on file I/O, computing, and inter-node communication for insightful analysis of HPC applications in production.

Liu, Zhengchun↗

DOE OSTI2020

CasCollect: targeted assembly of CRISPR-associated operons from high-throughput sequencing data

Abstract CRISPR arrays and CRISPR-associated (Cas) proteins comprise a widespread adaptive immune system in bacteria and archaea. These systems function as a defense against exogenous parasitic mobile genetic elements that include bacteriophages, plasmids and foreign nucleic acids. With the continuous spread of antibiotic resistance, knowledge of pathogen susceptibility to bacteriophage therapy is becoming more critical. Additionally, gene-editing applications would benefit from the discovery of new cas genes with favorable properties. While next-generation sequencing has produced staggering quantities of data, transitioning from raw sequencing reads to the identification of CRISPR/Cas systems has remained challenging. This is especially true for metagenomic data, which has the highest potential for identifying novel cas genes. We report a comprehensive computational pipeline, CasCollect, for the targeted assembly and annotation of cas genes and CRISPR arrays—even isolated arrays—from raw sequencing reads. Benchmarking our targeted assembly pipeline demonstrates significantly improved timing by almost two orders of magnitude compared with conventional assembly and annotation, while retaining the ability to detect CRISPR arrays and cas genes. CasCollect is a highly versatile pipeline and can be used for targeted assembly of any specialty gene set, reconfigurable for user provided Hidden Markov Models and/or reference nucleotide sequences.

Podlevsky, Joshua D.↗