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EMSL-Computing/fticRanalysis
fticRanalysis - a package to hand data formatting and storage of Fourier-transform ion cyclotron resonance (FTICR) data in a generalizable way. Additional functionality is available for manipulating and transforming the data, filtering the data based on different criteria, creating summary plots (e.g. Van Krevelen plots, Kendrick plots, etc.), summarizing group-level data, comparing treatment groups, and making complementary plotting functionality
Processing system
To implement the analysis techniques and to provide end-to-end processing, a system was designed with the following capabilities: receive and catalog data from many sources; organize the data on mass storage for rapid access; edit for reasonableness; create new data sets by sorting on parameter, averaging and merging; provide statistical analysis and display tools; and distribute data on demand. Consideration was given to developing a flexible system that could meet immediate workshop needs and respond to future requirements. System architecture and data set details implemented are discussed.
A pattern recognition system for locating small volvanoes in Magellan SAR images of Venus
The Magellan data set constitutes an example of the large volumes of data that today's instruments can collect, providing more detail of Venus than was previously available from Pioneer Venus, Venera 15/16, or ground-based radar observations put together. However, data analysis technology has not kept pace with data collection and storage technology. Due to the sheer size of the data, complete and comprehensive scientific analysis of such large volumes of image data is no longer feasible without the use of computational aids. Our progress towards developing a pattern recognition system for aiding in the detection and cataloging of small-scale natural features in large collections of images is reported. Combining classical image processing, machine learning, and a graphical user interface, the detection of the 'small-shield' volcanoes (less than 15km in diameter) that constitute the most abundant visible geologic feature in the more that 30,000 synthetic aperture radar (SAR) images of the surface of Venus are initially targeted. Our eventual goal is to provide a general, trainable tool for locating small-scale features where scientists specify what to look for simply by providing examples and attributes of interest to measure. This contrasts with the traditional approach of developing problem specific programs for detecting Specific patterns. The approach and initial results in the specific context of locating small volcanoes is reported. It is estimated, based on extrapolating from previous studies and knowledge of the underlying geologic processes, that there should be on the order of 10(exp 5) to 10(exp 6) of these volcanoes visible in the Magellan data. Identifying and studying these volcanoes is fundamental to a proper understanding of the geologic evolution of Venus. However, locating and parameterizing them in a manual manner is forbiddingly time-consuming. Hence, the development of techniques to partially automate this task were undertaken. The primary constraints for this particular problem are that the method must be reasonably robust and fast. Unlike most geological features, the small volcanoes of Venus can be ascribed to a basic process that produces features with a short list of readily defined characteristics differing significantly from other surface features on Venus. For pattern recognition purposes the relevant criteria include (1) a circular planimetric outline, (2) known diameter frequency distribution from preliminary studies, (3) a limited number of basic morphological shapes, and (4) the common occurrence of a single, circular summit pit at the center of the edifice.
Countermeasure Evaluation and Validation Project (CEVP) Database Requirement Documentation
The initial focus of the project by the JSC laboratories will be to develop, test and implement a standardized complement of integrated physiological test (Integrated Testing Regimen, ITR) that will examine both system and intersystem function, and will be used to validate and certify candidate countermeasures. The ITR will consist of medical requirements (MRs) and non-MR core ITR tests, and countermeasure-specific testing. Non-MR and countermeasure-specific test data will be archived in a database specific to the CEVP. Development of a CEVP Database will be critical to documenting the progress of candidate countermeasures. The goal of this work is a fully functional software system that will integrate computer-based data collection and storage with secure, efficient, and practical distribution of that data over the Internet. This system will provide the foundation of a new level of interagency and international cooperation for scientific experimentation and research, providing intramural, international, and extramural collaboration through management and distribution of the CEVP data. The research performed this summer includes the first phase of the project. The first phase of the project is a requirements analysis. This analysis will identify the expected behavior of the system under normal conditions and abnormal conditions; that could affect the system's ability to produce this behavior; and the internal features in the system needed to reduce the risk of unexpected or unwanted behaviors. The second phase of this project have also performed in this summer. The second phase of project is the design of data entry screen and data retrieval screen for a working model of the Ground Data Database. The final report provided the requirements for the CEVP system in a variety of ways, so that both the development team and JSC technical management have a thorough understanding of how the system is expected to behave.
The UCLA Cosmochemistry Database
The UCLA Cosmochemistry Database was initiated as part of a data-rescue and -storage project aimed at archiving a variety of cosmochemical data acquired at University of California, Los Angeles (UCLA). The data collection includes elemental compositions of extraterrestrial materials analyzed by UCLA cosmochemists over the last five decades. The analytical techniques include atomic absorption spectrometry (AAS) and neutron activation analysis (NAA) at UCLA. The data collection is stored on the Astromaterials Data System (Astromat). We provide both interactive tables and downloadable datasheets for users to access all data. The UCLA Cosmochemistry Database archives cosmochemical data that are essential tools for increasing our understanding of the nature and origin of extraterrestrial materials. Future studies can reference the data collection in the examination, analysis, and classification of newly acquired extraterrestrial samples.
System and method for performing SRAM write assist
A method and a system are provided for performing write assist. Write assist circuitry is initialized and voltage collapse is initiated to reduce a column supply voltage provided to a storage cell. A bitline of the storage cell is boosted to a boosted voltage level that is below a low supply voltage provided to the storage cell and data encoded by the bitline is written to the storage cell.
Remote Sensing of Groundwater Storage Changes in Illinois using the Gravity Recovery and Climate Experiment (GRACE)
Regional groundwater storage changes in Illinois are estimated from monthly GRACE total water storage change (TWSC) data and in situ measurements of soil moisture for the period 2002-2005. Groundwater storage change estimates are compared to those derived from the soil moisture and available well level data. The seasonal pattern and amplitude of GRACE-estimated groundwater storage changes track those of the in situ measurements reasonably well, although substantial differences exist in month-to-month variations. The seasonal cycle of GRACE TWSC agrees well with observations (correlation coefficient = 0.83), while the seasonal cycle of GRACE-based estimates of groundwater storage changes beneath 2 m depth agrees with observations with a correlation coefficient of 0.63. We conclude that the GRACE-based method of estimating monthly to seasonal groundwater storage changes performs reasonably well at the 200,000 sq km scale of Illinois.
Software Defined Cyberinfrastructure
Within and across thousands of science labs, researchers and students struggle to manage data produced in experiments, simulations, and analyses. Largely manual research data lifecycle management processes mean that much time is wasted, research results are often irreproducible, and data sharing and reuse remain rare. In response, we propose a new approach to data lifecycle management in which researchers are empowered to define the actions to be performed at individual storage systems when data are created or modified: actions such as analysis, transformation, copying, and publication. We term this approach software-defined cyberinfrastructure because users can implement powerful data management policies by deploying rules to local storage systems, much as software-defined networking allows users to configure networks by deploying rules to switches.We argue that this approach can enable a new class of responsive distributed storage infrastructure that will accelerate research innovation by allowing any researcher to associate data workflows with data sources, whether local or remote, for such purposes as data ingest, characterization, indexing, and sharing. We report on early experiments with this approach in the context of experimental science, in which a simple if-trigger-then-action (IFTA) notation is used to define rules.
External insulation systems for cryogenic storage systems - Bibliography/synopsis and category report /type 2 data/
Bibliography synopsis of external insulation materials and techniques for cryogenic storage systems
The Stability of Bioactive Compounds in Spaceflight Foods
The status and stability of bioactive compounds in the processed and shelf-stable spaceflight food system have not previously been investigated though the presence of such compounds in aged space foods could have health significance for crews on long duration exploration missions. Over forty foods - either existing International Space Station (ISS) food provisioning items, newly developed foods for spaceflight, or commercially-available ready-to-eat foods - that were predicted to have a relatively high concentrations of one or more bioactive compounds (lycopene, lutein, omega-3 fatty acids, phenolics, sterols, and/or flavonoids) were selected for the study. Food samples were sent overnight to the Food Composition Laboratory of the Linus Pauling Institute at Oregon State University (Corvallis, OR) for bioactive compound analysis. Three packages of each product were blended together for the analysis to reduce package-to-package variability. All ISS food items and commercial foods were analyzed initially and after 12 and 24 months of 21degC storage. Food development occurred in a staggered fashion, so data collection for the newly developed foods continues. Lastly, sensory evaluation and additional temperature storage data (4degC, 35degC) for select foods were collected to establish additional stability parameters. Efficacious concentrations of lycopene, lutein, and omega-3 fatty acids were measured in limited spaceflight foods; two grams of sterols a day may be difficult to achieve with the current space diet. Total polyphenol delivery appears stable and adequate, but individual phenolic compounds vary in stability and were not specifically evaluated in this study. The data suggests that some bioactive compounds, like lycopene and lutein, degrade and then plateau at some equilibrium concentration. The anthocyanin stability appears to be related to storage temperature and food matrix, and lutein stability in leafy vegetables may be impacted by storage temperature. Because of the limited number of foods with high concentrations of the bioactive compounds, additional menu variety, formulation optimization, and reduced temperature storage will be required to ensure delivery of several bioactive compounds in the space food system. Validation of stability to five years will enable provisioning of these functional foods within the space food system for a mission to Mars.
Deriving Simulation Parameters for Storage-Type Water Heaters Using Ratings Data Produced from the Uniform Energy Factor Test Procedure: Preprint
Building energy modeling (BEM) is commonly used to estimate the energy usage of residential buildings. Uses for BEM include calculating home energy ratings, demonstrating compliance with performance-based energy codes, and establishing whether designs meet voluntary program requirements, such as ENERGY STAR® qualified homes. BEM requires simulating subsystems within the building, including storage-type water heaters. To properly simulate the in-situ performance of residential storage water heaters, it is necessary to determine key water heater parameters, including the overall heat loss coefficient (UA) and conversion efficiency (?c) of the water heater, based on the rated efficiency of the water heater. The testing procedure and rating standard for residential water heaters have recently changed: the new rating standard provides a Uniform Energy Factor (UEF) rather than the Energy Factor (EF) used previously. This paper discusses how to derive the necessary model parameters from the ratings data produced from the latest test procedure.
Goddard Conference on Mass Storage Systems and Technologies, volume 2
Papers and viewgraphs from the conference are presented. Discussion topics include the IEEE Mass Storage System Reference Model, data archiving standards, high-performance storage devices, magnetic and magneto-optic storage systems, magnetic and optical recording technologies, high-performance helical scan recording systems, and low end helical scan tape drives. Additional discussion topics addressed the evolution of the identifiable unit for processing (file, granule, data set, or some similar object) as data ingestion rates increase dramatically, and the present state of the art in mass storage technology.
Conceptual Study of Intelligent Data Archives of the Future
A conceptual architecture study is under way to address the problem of getting the most scientific value from the large volumes of Earth and space science data that NASA expects to accumulate in the future. This involves efficient storage and access, but goes beyond that to facilitate intelligent data understanding and utilization through modeling realistic virtual entities with predictive capabilities. The objective of the study is to formulate ideas and concepts and to provide recommendations that lead to prototyping and implementation in the period from 2010 to 2020. The approach consists of the definition of future scenarios and needs for data usage in applications (in consultation with scientific and applications users), projection of advances in technologies, and an abstraction of an intelligent archive architecture. Strategic evolution is considered in various areas such as storage, data, information and knowledge management, data ingest and mining, user interfaces, and advances in intelligent data understanding algorithms.
Using Xrootd to federate regional storage
While the LHC data movement systems have demonstrated the ability to move data at the necessary throughput, we have identified two weaknesses: the latency for physicists to access data and the complexity of the tools involved. To address these, both ATLAS and CMS have begun to federate regional storage systems using Xrootd. Xrootd, referring to a protocol and implementation, allows us to provide data access to all disk-resident data from a single virtual endpoint. This redirector discovers the actual location of the data and redirects the client to the appropriate site. The approach is particularly advantageous since typically the redirection requires much less than 500 milliseconds and the Xrootd client is conveniently built into LHC physicists analysis tools. Currently, there are three regional storage federations - a US ATLAS region, a European CMS region, and a US CMS region. The US ATLAS and US CMS regions include their respective Tier 1, Tier 2 and some Tier 3 facilities, a large percentage of experimental data is available via the federation. Additionally, US ATLAS has begun studying low-latency regional federations of close-by sites. From the base idea of federating storage behind an endpoint, the implementations and use cases diverge. The CMS software framework is capable of efficiently processing data over high-latency links, so using the remote site directly is comparable to accessing local data. The ATLAS processing model allows a broad spectrum of user applications with varying degrees of performance with regard to latency, a particular focus has been optimizing n-tuple analysis. Both VOs use GSI security. ATLAS has developed a mapping of VOMS roles to specific file system authorizations, while CMS has developed callouts to the site's mapping service. Each federation presents a global namespace to users. For ATLAS, the global-to-local mapping is based on a heuristic-based lookup from the site's local file catalog, while CMS does the mapping based on translations given in a configuration file. We will also cover the latest usage statistics and interesting use cases that have developed over the previous 18 months.
Closing the Gap between FAIR Data Repositories and Hierarchical Data Formats
Many in the scientific community, particularly in publicly funded research, are pushing to adhere to more accessible data standards to maximize the findability, accessibility, interoperability, and reusability (FAIR) of scientific data, especially with the growing prevalence of machine learning augmented research. Online FAIR data repositories, such as the Open Science Framework (OSF), help facilitate the adoption of these standards by providing frameworks for storage, access, search, APIs, and other features that create organized hubs of scientific data. However, the wider acceptance of such repositories is hindered by the lack of support of hierarchical data formats, such as Technical Data Management Streaming (TDMS) and Hierarchical Data Format 5 (HDF5), that many researchers rely on to organize their datasets. Various tools and strategies should be used to allow hierarchical data formats, FAIR data repositories, and scientific organizations to work more seamlessly together. A pilot project at Los Alamos National Laboratory (LANL) addresses the disconnect between them by integrating the OSF FAIR data repository with hierarchical data renderers, extending support for additional file types in their framework. The multifaceted interactive renderer displays a tree of metadata alongside a table and plot of the data channels in the file. This allows users to quickly and efficiently load large and complex data files directly in the OSF webapp. Users who are browsing files can quickly and intuitively see the files in the way they or their colleagues structured the hierarchical form and immediately grasp their contents. This solution helps bridge the gap between hierarchical data storage techniques and FAIR data repositories, making both of them more viable options for scientific institutions like LANL which have been put off by the lack of integration between them.
Pooling the resources of the CMS Tier-1 sites
The CMS experiment at the LHC relies on 7 Tier-1 centres of the WLCG to perform the majority of its bulk processing activity, and to archive its data. During the first run of the LHC, these two functions were tightly coupled as each Tier-1 was constrained to process only the data archived on its hierarchical storage. This lack of flexibility in the assignment of processing workflows occasionally resulted in uneven resource utilisation and in an increased latency in the delivery of the results to the physics community.The long shutdown of the LHC in 2013-2014 was an opportunity to revisit this mode of operations, disentangling the processing and archive functionalities of the Tier-1 centres. The storage services at the Tier-1s were redeployed breaking the traditional hierarchical model: each site now provides a large disk storage to host input and output data for processing, and an independent tape storage used exclusively for archiving. Movement of data between the tape and disk endpoints is not automated, but triggered externally through the WLCG transfer management systems.With this new setup, CMS operations actively controls at any time which data is available on disk for processing and which data should be sent to archive. Thanks to the high-bandwidth connectivity guaranteed by the LHCOPN, input data can be freely transferred between disk endpoints as needed to take advantage of free CPU, turning the Tier-1s into a large pool of shared resources. The output data can be validated before archiving them permanently, and temporary data formats can be produced without wasting valuable tape resources. Lastly, the data hosted on disk at Tier-1s can now be made available also for user analysis since there is no risk any longer of triggering chaotic staging from tape.In this contribution, we describe the technical solutions adopted for the new disk and tape endpoints at the sites, and we report on the commissioning and scale testing of the service. We detail the procedures implemented by CMS computing operations to actively manage data on disk at Tier-1 sites, and we give examples of the benefits brought to CMS workflows by the additional flexibility of the new system.
Platform for efficient large-scale storage and analysis of multi-omics data in plant and microbial systems (Final Technical Report)
Genomic variation at the sequence level fundamentally affects the phenotypic state of all organisms at all stages of development, while dynamic processes such as changes in the epigenome (e.g. DNA methylation state) and transcriptome regulate the specific phenotype expressed at any given state of development based upon that genomic variation. In plants, DNA methylation is a particularly important mechanism for both regulating transcriptomic expression and for management of genomic variations that could be deleterious to the organism due to the presence of active retrotransposons in plant genomes. While DNA methylation is heritable, it is also dynamic through a given plant’s development and life cycle, particularly during the development from seed to mature specimen suggesting variations in DNA methylation could be critical regulators of biologically and commercially important phenotypes such as time to flowering; in addition, plant DNA methylation is more complex than that of animals, with methylation of CHG and CHH trinucleotides evident in addition to the better-known CG methylation. The complexity of plant DNA methylation and its interplay with genomic sequence variation, transcriptomics and other epigenomic factors demand a storage and analysis framework that can cope with the complexity both within a single specimen and with analyses that span many individuals and even many species, such as attempts to extend models from model organisms to commercially relevant species. In addition to complexity, the rapid development and proliferation of sequencing technology has led to an explosion of data volume that conventional storage and analysis solutions will likely be unable to cope with in the long run. We proposed to study these with suitable distributed storage and computation and therefore for the application of cloud computing to biological analyses; integrate with existing data sources and compatible with virtually any interface use case, from fully automated shell scripts to notebooks and do all these at scale in this STTR grant.