SPANG: a SPARQL client supporting generation and reuse of queries for distributed RDF databases.

PubMed

Chiba, Hirokazu; Uchiyama, Ikuo

2017-02-08

Toward improved interoperability of distributed biological databases, an increasing number of datasets have been published in the standardized Resource Description Framework (RDF). Although the powerful SPARQL Protocol and RDF Query Language (SPARQL) provides a basis for exploiting RDF databases, writing SPARQL code is burdensome for users including bioinformaticians. Thus, an easy-to-use interface is necessary. We developed SPANG, a SPARQL client that has unique features for querying RDF datasets. SPANG dynamically generates typical SPARQL queries according to specified arguments. It can also call SPARQL template libraries constructed in a local system or published on the Web. Further, it enables combinatorial execution of multiple queries, each with a distinct target database. These features facilitate easy and effective access to RDF datasets and integrative analysis of distributed data. SPANG helps users to exploit RDF datasets by generation and reuse of SPARQL queries through a simple interface. This client will enhance integrative exploitation of biological RDF datasets distributed across the Web. This software package is freely available at http://purl.org/net/spang .

Querying XML Data with SPARQL

NASA Astrophysics Data System (ADS)

Bikakis, Nikos; Gioldasis, Nektarios; Tsinaraki, Chrisa; Christodoulakis, Stavros

SPARQL is today the standard access language for Semantic Web data. In the recent years XML databases have also acquired industrial importance due to the widespread applicability of XML in the Web. In this paper we present a framework that bridges the heterogeneity gap and creates an interoperable environment where SPARQL queries are used to access XML databases. Our approach assumes that fairly generic mappings between ontology constructs and XML Schema constructs have been automatically derived or manually specified. The mappings are used to automatically translate SPARQL queries to semantically equivalent XQuery queries which are used to access the XML databases. We present the algorithms and the implementation of SPARQL2XQuery framework, which is used for answering SPARQL queries over XML databases.

SpEnD: Linked Data SPARQL Endpoints Discovery Using Search Engines

NASA Astrophysics Data System (ADS)

Yumusak, Semih; Dogdu, Erdogan; Kodaz, Halife; Kamilaris, Andreas; Vandenbussche, Pierre-Yves

In this study, a novel metacrawling method is proposed for discovering and monitoring linked data sources on the Web. We implemented the method in a prototype system, named SPARQL Endpoints Discovery (SpEnD). SpEnD starts with a "search keyword" discovery process for finding relevant keywords for the linked data domain and specifically SPARQL endpoints. Then, these search keywords are utilized to find linked data sources via popular search engines (Google, Bing, Yahoo, Yandex). By using this method, most of the currently listed SPARQL endpoints in existing endpoint repositories, as well as a significant number of new SPARQL endpoints, have been discovered. Finally, we have developed a new SPARQL endpoint crawler (SpEC) for crawling and link analysis.

Efficient Synthesis of Graph Methods: a Dynamically Scheduled Architecture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Minutoli, Marco; Castellana, Vito G.; Tumeo, Antonino

RDF databases naturally map to a graph representation and employ languages, such as SPARQL, that implements queries as graph pattern matching routines. Graph methods exhibit an irregular behavior: they present unpredictable, fine-grained data accesses, and are synchronization inten- sive. Graph data structures expose large amounts of dy- namic parallelism, but are difficult to partition without gen- erating load unbalance. In this paper, we present a novel ar- chitecture to improve the synthesis of graph methods. Our design addresses the issues of these algorithms with two com- ponents: a Dynamic Task Scheduler (DTS), which reduces load unbalance and maximize resource utilization,more » and a Hi- erarchical Memory Interface controller (HMI), which pro- vides support for concurrent memory operations on multi- ported/multi-banked shared memories. We evaluate our ap- proach by generating the accelerators for a set of SPARQL queries from the Lehigh University Benchmark (LUBM). We first analyze the load unbalance of these queries, showing that execution time among tasks can differ even of order of magnitudes. We then synthesize the queries and com- pare the performance of the resulting accelerators against the current state of the art. Experimental results show that our solution provides a speedup over the serial implementa- tion close to the theoretical maximum and a speedup up to 3.45 over a baseline parallel implementation. We conclude our study by exploring the design space to achieve maximum memory channels utilization. The best design used at least three of the four memory channels for more than 90% of the execution time.« less

RDF-GL: A SPARQL-Based Graphical Query Language for RDF

NASA Astrophysics Data System (ADS)

Hogenboom, Frederik; Milea, Viorel; Frasincar, Flavius; Kaymak, Uzay

This chapter presents RDF-GL, a graphical query language (GQL) for RDF. The GQL is based on the textual query language SPARQL and mainly focuses on SPARQL SELECT queries. The advantage of a GQL over textual query languages is that complexity is hidden through the use of graphical symbols. RDF-GL is supported by a Java-based editor, SPARQLinG, which is presented as well. The editor does not only allow for RDF-GL query creation, but also converts RDF-GL queries to SPARQL queries and is able to subsequently execute these. Experiments show that using the GQL in combination with the editor makes RDF querying more accessible for end users.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madduri, Kamesh; Wu, Kesheng

The Resource Description Framework (RDF) is a popular data model for representing linked data sets arising from the web, as well as large scienti c data repositories such as UniProt. RDF data intrinsically represents a labeled and directed multi-graph. SPARQL is a query language for RDF that expresses subgraph pattern- nding queries on this implicit multigraph in a SQL- like syntax. SPARQL queries generate complex intermediate join queries; to compute these joins e ciently, we propose a new strategy based on bitmap indexes. We store the RDF data in column-oriented structures as compressed bitmaps along with two dictionaries. This papermore » makes three new contributions. (i) We present an e cient parallel strategy for parsing the raw RDF data, building dictionaries of unique entities, and creating compressed bitmap indexes of the data. (ii) We utilize the constructed bitmap indexes to e ciently answer SPARQL queries, simplifying the join evaluations. (iii) To quantify the performance impact of using bitmap indexes, we compare our approach to the state-of-the-art triple-store RDF-3X. We nd that our bitmap index-based approach to answering queries is up to an order of magnitude faster for a variety of SPARQL queries, on gigascale RDF data sets.« less

Toward a Data Scalable Solution for Facilitating Discovery of Science Resources

DOE Office of Scientific and Technical Information (OSTI.GOV)

Weaver, Jesse R.; Castellana, Vito G.; Morari, Alessandro

Science is increasingly motivated by the need to process larger quantities of data. It is facing severe challenges in data collection, management, and processing, so much so that the computational demands of “data scaling” are competing with, and in many fields surpassing, the traditional objective of decreasing processing time. Example domains with large datasets include astronomy, biology, genomics, climate/weather, and material sciences. This paper presents a real-world use case in which we wish to answer queries pro- vided by domain scientists in order to facilitate discovery of relevant science resources. The problem is that the metadata for these science resourcesmore » is very large and is growing quickly, rapidly increasing the need for a data scaling solution. We propose a system – SGEM – designed for answering graph-based queries over large datasets on cluster architectures, and we re- port performance results for queries on the current RDESC dataset of nearly 1.4 billion triples, and on the well-known BSBM SPARQL query benchmark.« less

SPARQL-enabled identifier conversion with Identifiers.org

PubMed Central

Wimalaratne, Sarala M.; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-01-01

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. Contact: sarala@ebi.ac.uk PMID:25638809

SPARQL-enabled identifier conversion with Identifiers.org.

PubMed

Wimalaratne, Sarala M; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-06-01

On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. © The Author 2015. Published by Oxford University Press.

On the Semantics of SPARQL

NASA Astrophysics Data System (ADS)

Arenas, Marcelo; Gutierrez, Claudio; Pérez, Jorge

The Resource Description Framework (RDF) is the standard data model for representing information about World Wide Web resources. In January 2008, it was released the recommendation of the W3C for querying RDF data, a query language called SPARQL. In this chapter, we give a detailed description of the semantics of this language. We start by focusing on the definition of a formal semantics for the core part of SPARQL, and then move to the definition for the entire language, including all the features in the specification of SPARQL by the W3C such as blank nodes in graph patterns and bag semantics for solutions.

Exposing the cancer genome atlas as a SPARQL endpoint

PubMed Central

Deus, Helena F.; Veiga, Diogo F.; Freire, Pablo R.; Weinstein, John N.; Mills, Gordon B.; Almeida, Jonas S.

2011-01-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. PMID:20851208

Active Wiki Knowledge Repository

DTIC Science & Technology

2012-10-01

data using SPARQL queries or RESTful web-services; ‘gardening’ tools for examining the semantically tagged content in the wiki; high-level language tool...Tagging & RDF triple-store Fusion and inferences for collaboration Tools for Consuming Data SPARQL queries or RESTful WS Inference & Gardening tools...other stores using AW SPARQL queries and rendering templates; and 4) Interactively share maps and other content using annotation tools to post notes

SPARQL Assist language-neutral query composer

PubMed Central

2012-01-01

Background SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. Results We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. Conclusions To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources. PMID:22373327

Foundations of RDF Databases

NASA Astrophysics Data System (ADS)

Arenas, Marcelo; Gutierrez, Claudio; Pérez, Jorge

The goal of this paper is to give an overview of the basics of the theory of RDF databases. We provide a formal definition of RDF that includes the features that distinguish this model from other graph data models. We then move into the fundamental issue of querying RDF data. We start by considering the RDF query language SPARQL, which is a W3C Recommendation since January 2008. We provide an algebraic syntax and a compositional semantics for this language, study the complexity of the evaluation problem for different fragments of SPARQL, and consider the problem of optimizing the evaluation of SPARQL queries, showing that a natural fragment of this language has some good properties in this respect. We furthermore study the expressive power of SPARQL, by comparing it with some well-known query languages such as relational algebra. We conclude by considering the issue of querying RDF data in the presence of RDFS vocabulary. In particular, we present a recently proposed extension of SPARQL with navigational capabilities.

SPARQL assist language-neutral query composer.

PubMed

McCarthy, Luke; Vandervalk, Ben; Wilkinson, Mark

2012-01-25

SPARQL query composition is difficult for the lay-person, and even the experienced bioinformatician in cases where the data model is unfamiliar. Moreover, established best-practices and internationalization concerns dictate that the identifiers for ontological terms should be opaque rather than human-readable, which further complicates the task of synthesizing queries manually. We present SPARQL Assist: a Web application that addresses these issues by providing context-sensitive type-ahead completion during SPARQL query construction. Ontological terms are suggested using their multi-lingual labels and descriptions, leveraging existing support for internationalization and language-neutrality. Moreover, the system utilizes the semantics embedded in ontologies, and within the query itself, to help prioritize the most likely suggestions. To ensure success, the Semantic Web must be easily available to all users, regardless of locale, training, or preferred language. By enhancing support for internationalization, and moreover by simplifying the manual construction of SPARQL queries through the use of controlled-natural-language interfaces, we believe we have made some early steps towards simplifying access to Semantic Web resources.

Exposing the cancer genome atlas as a SPARQL endpoint.

PubMed

Deus, Helena F; Veiga, Diogo F; Freire, Pablo R; Weinstein, John N; Mills, Gordon B; Almeida, Jonas S

2010-12-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. Copyright © 2010 Elsevier Inc. All rights reserved.

A Framework for Building and Reasoning with Adaptive and Interoperable PMESII Models

DTIC Science & Technology

2007-11-01

Description Logic SOA Service Oriented Architecture SPARQL Simple Protocol And RDF Query Language SQL Standard Query Language SROM Stability and...another by providing a more expressive ontological structure for one of the models, e.g., semantic networks can be mapped to first- order logical...Pellet is an open-source reasoner that works with OWL-DL. It accepts the SPARQL protocol and RDF query language ( SPARQL ) and provides a Java API to

Querying clinical data in HL7 RIM based relational model with morph-RDB.

PubMed

Priyatna, Freddy; Alonso-Calvo, Raul; Paraiso-Medina, Sergio; Corcho, Oscar

2017-10-05

Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources. Our previous efforts involved materialized RDF datasets, hence losing data freshness. In this paper we present a solution that uses an ontology based on the HL7 v3 Reference Information Model and a set of R2RML mappings that relate this ontology to an underlying relational database implementation, and where morph-RDB is used to expose a virtual, non-materialized SPARQL endpoint over the data. By applying a set of optimization techniques on the SPARQL-to-SQL query translation algorithm, we can now issue SPARQL queries to the underlying relational data with generally acceptable performance.

Processing SPARQL queries with regular expressions in RDF databases

PubMed Central

2011-01-01

Background As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users’ requests for extracting information from the RDF data as well as the lack of users’ knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. Results In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Conclusions Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns. PMID:21489225

Processing SPARQL queries with regular expressions in RDF databases.

PubMed

Lee, Jinsoo; Pham, Minh-Duc; Lee, Jihwan; Han, Wook-Shin; Cho, Hune; Yu, Hwanjo; Lee, Jeong-Hoon

2011-03-29

As the Resource Description Framework (RDF) data model is widely used for modeling and sharing a lot of online bioinformatics resources such as Uniprot (dev.isb-sib.ch/projects/uniprot-rdf) or Bio2RDF (bio2rdf.org), SPARQL - a W3C recommendation query for RDF databases - has become an important query language for querying the bioinformatics knowledge bases. Moreover, due to the diversity of users' requests for extracting information from the RDF data as well as the lack of users' knowledge about the exact value of each fact in the RDF databases, it is desirable to use the SPARQL query with regular expression patterns for querying the RDF data. To the best of our knowledge, there is currently no work that efficiently supports regular expression processing in SPARQL over RDF databases. Most of the existing techniques for processing regular expressions are designed for querying a text corpus, or only for supporting the matching over the paths in an RDF graph. In this paper, we propose a novel framework for supporting regular expression processing in SPARQL query. Our contributions can be summarized as follows. 1) We propose an efficient framework for processing SPARQL queries with regular expression patterns in RDF databases. 2) We propose a cost model in order to adapt the proposed framework in the existing query optimizers. 3) We build a prototype for the proposed framework in C++ and conduct extensive experiments demonstrating the efficiency and effectiveness of our technique. Experiments with a full-blown RDF engine show that our framework outperforms the existing ones by up to two orders of magnitude in processing SPARQL queries with regular expression patterns.

NCBI2RDF: enabling full RDF-based access to NCBI databases.

PubMed

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments.

Query Results Clustering by Extending SPARQL with CLUSTER BY

NASA Astrophysics Data System (ADS)

Ławrynowicz, Agnieszka

The task of dynamic clustering of the search results proved to be useful in the Web context, where the user often does not know the granularity of the search results in advance. The goal of this paper is to provide a declarative way for invoking dynamic clustering of the results of queries submitted over Semantic Web data. To achieve this goal the paper proposes an approach that extends SPARQL by clustering abilities. The approach introduces a new statement, CLUSTER BY, into the SPARQL grammar and proposes semantics for such extension.

NCBI2RDF: Enabling Full RDF-Based Access to NCBI Databases

PubMed Central

Anguita, Alberto; García-Remesal, Miguel; de la Iglesia, Diana; Maojo, Victor

2013-01-01

RDF has become the standard technology for enabling interoperability among heterogeneous biomedical databases. The NCBI provides access to a large set of life sciences databases through a common interface called Entrez. However, the latter does not provide RDF-based access to such databases, and, therefore, they cannot be integrated with other RDF-compliant databases and accessed via SPARQL query interfaces. This paper presents the NCBI2RDF system, aimed at providing RDF-based access to the complete NCBI data repository. This API creates a virtual endpoint for servicing SPARQL queries over different NCBI repositories and presenting to users the query results in SPARQL results format, thus enabling this data to be integrated and/or stored with other RDF-compliant repositories. SPARQL queries are dynamically resolved, decomposed, and forwarded to the NCBI-provided E-utilities programmatic interface to access the NCBI data. Furthermore, we show how our approach increases the expressiveness of the native NCBI querying system, allowing several databases to be accessed simultaneously. This feature significantly boosts productivity when working with complex queries and saves time and effort to biomedical researchers. Our approach has been validated with a large number of SPARQL queries, thus proving its reliability and enhanced capabilities in biomedical environments. PMID:23984425

Research on Extension of Sparql Ontology Query Language Considering the Computation of Indoor Spatial Relations

NASA Astrophysics Data System (ADS)

Li, C.; Zhu, X.; Guo, W.; Liu, Y.; Huang, H.

2015-05-01

A method suitable for indoor complex semantic query considering the computation of indoor spatial relations is provided According to the characteristics of indoor space. This paper designs ontology model describing the space related information of humans, events and Indoor space objects (e.g. Storey and Room) as well as their relations to meet the indoor semantic query. The ontology concepts are used in IndoorSPARQL query language which extends SPARQL syntax for representing and querying indoor space. And four types specific primitives for indoor query, "Adjacent", "Opposite", "Vertical" and "Contain", are defined as query functions in IndoorSPARQL used to support quantitative spatial computations. Also a method is proposed to analysis the query language. Finally this paper adopts this method to realize indoor semantic query on the study area through constructing the ontology model for the study building. The experimental results show that the method proposed in this paper can effectively support complex indoor space semantic query.

PIBAS FedSPARQL: a web-based platform for integration and exploration of bioinformatics datasets.

PubMed

Djokic-Petrovic, Marija; Cvjetkovic, Vladimir; Yang, Jeremy; Zivanovic, Marko; Wild, David J

2017-09-20

There are a huge variety of data sources relevant to chemical, biological and pharmacological research, but these data sources are highly siloed and cannot be queried together in a straightforward way. Semantic technologies offer the ability to create links and mappings across datasets and manage them as a single, linked network so that searching can be carried out across datasets, independently of the source. We have developed an application called PIBAS FedSPARQL that uses semantic technologies to allow researchers to carry out such searching across a vast array of data sources. PIBAS FedSPARQL is a web-based query builder and result set visualizer of bioinformatics data. As an advanced feature, our system can detect similar data items identified by different Uniform Resource Identifiers (URIs), using a text-mining algorithm based on the processing of named entities to be used in Vector Space Model and Cosine Similarity Measures. According to our knowledge, PIBAS FedSPARQL was unique among the systems that we found in that it allows detecting of similar data items. As a query builder, our system allows researchers to intuitively construct and run Federated SPARQL queries across multiple data sources, including global initiatives, such as Bio2RDF, Chem2Bio2RDF, EMBL-EBI, and one local initiative called CPCTAS, as well as additional user-specified data source. From the input topic, subtopic, template and keyword, a corresponding initial Federated SPARQL query is created and executed. Based on the data obtained, end users have the ability to choose the most appropriate data sources in their area of interest and exploit their Resource Description Framework (RDF) structure, which allows users to select certain properties of data to enhance query results. The developed system is flexible and allows intuitive creation and execution of queries for an extensive range of bioinformatics topics. Also, the novel "similar data items detection" algorithm can be particularly useful for suggesting new data sources and cost optimization for new experiments. PIBAS FedSPARQL can be expanded with new topics, subtopics and templates on demand, rendering information retrieval more robust.

Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins.

PubMed

Yokochi, Masashi; Kobayashi, Naohiro; Ulrich, Eldon L; Kinjo, Akira R; Iwata, Takeshi; Ioannidis, Yannis E; Livny, Miron; Markley, John L; Nakamura, Haruki; Kojima, Chojiro; Fujiwara, Toshimichi

2016-05-05

The nuclear magnetic resonance (NMR) spectroscopic data for biological macromolecules archived at the BioMagResBank (BMRB) provide a rich resource of biophysical information at atomic resolution. The NMR data archived in NMR-STAR ASCII format have been implemented in a relational database. However, it is still fairly difficult for users to retrieve data from the NMR-STAR files or the relational database in association with data from other biological databases. To enhance the interoperability of the BMRB database, we present a full conversion of BMRB entries to two standard structured data formats, XML and RDF, as common open representations of the NMR-STAR data. Moreover, a SPARQL endpoint has been deployed. The described case study demonstrates that a simple query of the SPARQL endpoints of the BMRB, UniProt, and Online Mendelian Inheritance in Man (OMIM), can be used in NMR and structure-based analysis of proteins combined with information of single nucleotide polymorphisms (SNPs) and their phenotypes. We have developed BMRB/XML and BMRB/RDF and demonstrate their use in performing a federated SPARQL query linking the BMRB to other databases through standard semantic web technologies. This will facilitate data exchange across diverse information resources.

SPARK: Adapting Keyword Query to Semantic Search

NASA Astrophysics Data System (ADS)

Zhou, Qi; Wang, Chong; Xiong, Miao; Wang, Haofen; Yu, Yong

Semantic search promises to provide more accurate result than present-day keyword search. However, progress with semantic search has been delayed due to the complexity of its query languages. In this paper, we explore a novel approach of adapting keywords to querying the semantic web: the approach automatically translates keyword queries into formal logic queries so that end users can use familiar keywords to perform semantic search. A prototype system named 'SPARK' has been implemented in light of this approach. Given a keyword query, SPARK outputs a ranked list of SPARQL queries as the translation result. The translation in SPARK consists of three major steps: term mapping, query graph construction and query ranking. Specifically, a probabilistic query ranking model is proposed to select the most likely SPARQL query. In the experiment, SPARK achieved an encouraging translation result.

BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data

PubMed Central

2014-01-01

Background Biological databases vary enormously in size and data complexity, from small databases that contain a few million Resource Description Framework (RDF) triples to large databases that contain billions of triples. In this paper, we evaluate whether RDF native stores can be used to meet the needs of a biological database provider. Prior evaluations have used synthetic data with a limited database size. For example, the largest BSBM benchmark uses 1 billion synthetic e-commerce knowledge RDF triples on a single node. However, real world biological data differs from the simple synthetic data much. It is difficult to determine whether the synthetic e-commerce data is efficient enough to represent biological databases. Therefore, for this evaluation, we used five real data sets from biological databases. Results We evaluated five triple stores, 4store, Bigdata, Mulgara, Virtuoso, and OWLIM-SE, with five biological data sets, Cell Cycle Ontology, Allie, PDBj, UniProt, and DDBJ, ranging in size from approximately 10 million to 8 billion triples. For each database, we loaded all the data into our single node and prepared the database for use in a classical data warehouse scenario. Then, we ran a series of SPARQL queries against each endpoint and recorded the execution time and the accuracy of the query response. Conclusions Our paper shows that with appropriate configuration Virtuoso and OWLIM-SE can satisfy the basic requirements to load and query biological data less than 8 billion or so on a single node, for the simultaneous access of 64 clients. OWLIM-SE performs best for databases with approximately 11 million triples; For data sets that contain 94 million and 590 million triples, OWLIM-SE and Virtuoso perform best. They do not show overwhelming advantage over each other; For data over 4 billion Virtuoso works best. 4store performs well on small data sets with limited features when the number of triples is less than 100 million, and our test shows its scalability is poor; Bigdata demonstrates average performance and is a good open source triple store for middle-sized (500 million or so) data set; Mulgara shows a little of fragility. PMID:25089180

BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data.

PubMed

Wu, Hongyan; Fujiwara, Toyofumi; Yamamoto, Yasunori; Bolleman, Jerven; Yamaguchi, Atsuko

2014-01-01

Biological databases vary enormously in size and data complexity, from small databases that contain a few million Resource Description Framework (RDF) triples to large databases that contain billions of triples. In this paper, we evaluate whether RDF native stores can be used to meet the needs of a biological database provider. Prior evaluations have used synthetic data with a limited database size. For example, the largest BSBM benchmark uses 1 billion synthetic e-commerce knowledge RDF triples on a single node. However, real world biological data differs from the simple synthetic data much. It is difficult to determine whether the synthetic e-commerce data is efficient enough to represent biological databases. Therefore, for this evaluation, we used five real data sets from biological databases. We evaluated five triple stores, 4store, Bigdata, Mulgara, Virtuoso, and OWLIM-SE, with five biological data sets, Cell Cycle Ontology, Allie, PDBj, UniProt, and DDBJ, ranging in size from approximately 10 million to 8 billion triples. For each database, we loaded all the data into our single node and prepared the database for use in a classical data warehouse scenario. Then, we ran a series of SPARQL queries against each endpoint and recorded the execution time and the accuracy of the query response. Our paper shows that with appropriate configuration Virtuoso and OWLIM-SE can satisfy the basic requirements to load and query biological data less than 8 billion or so on a single node, for the simultaneous access of 64 clients. OWLIM-SE performs best for databases with approximately 11 million triples; For data sets that contain 94 million and 590 million triples, OWLIM-SE and Virtuoso perform best. They do not show overwhelming advantage over each other; For data over 4 billion Virtuoso works best. 4store performs well on small data sets with limited features when the number of triples is less than 100 million, and our test shows its scalability is poor; Bigdata demonstrates average performance and is a good open source triple store for middle-sized (500 million or so) data set; Mulgara shows a little of fragility.

Graph Visualization for RDF Graphs with SPARQL-EndPoints

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sukumar, Sreenivas R; Bond, Nathaniel

2014-07-11

RDF graphs are hard to visualize as triples. This software module is a web interface that connects to a SPARQL endpoint and retrieves graph data that the user can explore interactively and seamlessly. The software written in python and JavaScript has been tested to work on screens as little as the smart phones to large screens such as EVEREST.

Advanced SPARQL querying in small molecule databases.

PubMed

Galgonek, Jakub; Hurt, Tomáš; Michlíková, Vendula; Onderka, Petr; Schwarz, Jan; Vondrášek, Jiří

2016-01-01

In recent years, the Resource Description Framework (RDF) and the SPARQL query language have become more widely used in the area of cheminformatics and bioinformatics databases. These technologies allow better interoperability of various data sources and powerful searching facilities. However, we identified several deficiencies that make usage of such RDF databases restrictive or challenging for common users. We extended a SPARQL engine to be able to use special procedures inside SPARQL queries. This allows the user to work with data that cannot be simply precomputed and thus cannot be directly stored in the database. We designed an algorithm that checks a query against data ontology to identify possible user errors. This greatly improves query debugging. We also introduced an approach to visualize retrieved data in a user-friendly way, based on templates describing visualizations of resource classes. To integrate all of our approaches, we developed a simple web application. Our system was implemented successfully, and we demonstrated its usability on the ChEBI database transformed into RDF form. To demonstrate procedure call functions, we employed compound similarity searching based on OrChem. The application is publicly available at https://bioinfo.uochb.cas.cz/projects/chemRDF.

Generating and Executing Complex Natural Language Queries across Linked Data.

PubMed

Hamon, Thierry; Mougin, Fleur; Grabar, Natalia

2015-01-01

With the recent and intensive research in the biomedical area, the knowledge accumulated is disseminated through various knowledge bases. Links between these knowledge bases are needed in order to use them jointly. Linked Data, SPARQL language, and interfaces in Natural Language question-answering provide interesting solutions for querying such knowledge bases. We propose a method for translating natural language questions in SPARQL queries. We use Natural Language Processing tools, semantic resources, and the RDF triples description. The method is designed on 50 questions over 3 biomedical knowledge bases, and evaluated on 27 questions. It achieves 0.78 F-measure on the test set. The method for translating natural language questions into SPARQL queries is implemented as Perl module available at http://search.cpan.org/ thhamon/RDF-NLP-SPARQLQuery.

Enabling Graph Appliance for Genome Assembly

DOE Office of Scientific and Technical Information (OSTI.GOV)

Singh, Rina; Graves, Jeffrey A; Lee, Sangkeun

2015-01-01

In recent years, there has been a huge growth in the amount of genomic data available as reads generated from various genome sequencers. The number of reads generated can be huge, ranging from hundreds to billions of nucleotide, each varying in size. Assembling such large amounts of data is one of the challenging computational problems for both biomedical and data scientists. Most of the genome assemblers developed have used de Bruijn graph techniques. A de Bruijn graph represents a collection of read sequences by billions of vertices and edges, which require large amounts of memory and computational power to storemore » and process. This is the major drawback to de Bruijn graph assembly. Massively parallel, multi-threaded, shared memory systems can be leveraged to overcome some of these issues. The objective of our research is to investigate the feasibility and scalability issues of de Bruijn graph assembly on Cray s Urika-GD system; Urika-GD is a high performance graph appliance with a large shared memory and massively multithreaded custom processor designed for executing SPARQL queries over large-scale RDF data sets. However, to the best of our knowledge, there is no research on representing a de Bruijn graph as an RDF graph or finding Eulerian paths in RDF graphs using SPARQL for potential genome discovery. In this paper, we address the issues involved in representing a de Bruin graphs as RDF graphs and propose an iterative querying approach for finding Eulerian paths in large RDF graphs. We evaluate the performance of our implementation on real world ebola genome datasets and illustrate how genome assembly can be accomplished with Urika-GD using iterative SPARQL queries.« less

Agent-Based Computing Integration and Testing

DTIC Science & Technology

2006-12-01

Query Language (DQL). Regrettably, DQL never became a W3C Member Submission itself, but likely had some influence on the SPARQL Protocol And RDF... Query Language ( SPARQL ) subsequently produced by the W3C Data Access Working Group (DAWG) as that working group also contained members from the DAML...Sponsored by Defense Advanced Research Projects Agency DARPA Order No. K536 APPROVED FOR PUBLIC RELEASE

Automatically exposing OpenLifeData via SADI semantic Web Services.

PubMed

González, Alejandro Rodríguez; Callahan, Alison; Cruz-Toledo, José; Garcia, Adrian; Egaña Aranguren, Mikel; Dumontier, Michel; Wilkinson, Mark D

2014-01-01

Two distinct trends are emerging with respect to how data is shared, collected, and analyzed within the bioinformatics community. First, Linked Data, exposed as SPARQL endpoints, promises to make data easier to collect and integrate by moving towards the harmonization of data syntax, descriptive vocabularies, and identifiers, as well as providing a standardized mechanism for data access. Second, Web Services, often linked together into workflows, normalize data access and create transparent, reproducible scientific methodologies that can, in principle, be re-used and customized to suit new scientific questions. Constructing queries that traverse semantically-rich Linked Data requires substantial expertise, yet traditional RESTful or SOAP Web Services cannot adequately describe the content of a SPARQL endpoint. We propose that content-driven Semantic Web Services can enable facile discovery of Linked Data, independent of their location. We use a well-curated Linked Dataset - OpenLifeData - and utilize its descriptive metadata to automatically configure a series of more than 22,000 Semantic Web Services that expose all of its content via the SADI set of design principles. The OpenLifeData SADI services are discoverable via queries to the SHARE registry and easy to integrate into new or existing bioinformatics workflows and analytical pipelines. We demonstrate the utility of this system through comparison of Web Service-mediated data access with traditional SPARQL, and note that this approach not only simplifies data retrieval, but simultaneously provides protection against resource-intensive queries. We show, through a variety of different clients and examples of varying complexity, that data from the myriad OpenLifeData can be recovered without any need for prior-knowledge of the content or structure of the SPARQL endpoints. We also demonstrate that, via clients such as SHARE, the complexity of federated SPARQL queries is dramatically reduced.

Generation of Test Questions from RDF Files Using PYTHON and SPARQL

NASA Astrophysics Data System (ADS)

Omarbekova, Assel; Sharipbay, Altynbek; Barlybaev, Alibek

2017-02-01

This article describes the development of the system for the automatic generation of test questions based on the knowledge base. This work has an applicable nature and provides detailed examples of the development of ontology and implementation the SPARQL queries in RDF-documents. Also it describes implementation of the program generating questions in the Python programming language including the necessary libraries while working with RDF-files.

Applying Semantic Web Concepts to Support Net-Centric Warfare Using the Tactical Assessment Markup Language (TAML)

DTIC Science & Technology

2006-06-01

SPARQL SPARQL Protocol and RDF Query Language SQL Structured Query Language SUMO Suggested Upper Merged Ontology SW... Query optimization algorithms are implemented in the Pellet reasoner in order to ensure querying a knowledge base is efficient . These algorithms...memory as a treelike structure in order for the data to be queried . XML Query (XQuery) is the standard language used when querying XML

EAGLE: 'EAGLE'Is an' Algorithmic Graph Library for Exploration

DOE Office of Scientific and Technical Information (OSTI.GOV)

2015-01-16

The Resource Description Framework (RDF) and SPARQL Protocol and RDF Query Language (SPARQL) were introduced about a decade ago to enable flexible schema-free data interchange on the Semantic Web. Today data scientists use the framework as a scalable graph representation for integrating, querying, exploring and analyzing data sets hosted at different sources. With increasing adoption, the need for graph mining capabilities for the Semantic Web has emerged. Today there is no tools to conduct "graph mining" on RDF standard data sets. We address that need through implementation of popular iterative Graph Mining algorithms (Triangle count, Connected component analysis, degree distribution,more » diversity degree, PageRank, etc.). We implement these algorithms as SPARQL queries, wrapped within Python scripts and call our software tool as EAGLE. In RDF style, EAGLE stands for "EAGLE 'Is an' algorithmic graph library for exploration. EAGLE is like 'MATLAB' for 'Linked Data.'« less

Regular paths in SparQL: querying the NCI Thesaurus.

PubMed

Detwiler, Landon T; Suciu, Dan; Brinkley, James F

2008-11-06

OWL, the Web Ontology Language, provides syntax and semantics for representing knowledge for the semantic web. Many of the constructs of OWL have a basis in the field of description logics. While the formal underpinnings of description logics have lead to a highly computable language, it has come at a cognitive cost. OWL ontologies are often unintuitive to readers lacking a strong logic background. In this work we describe GLEEN, a regular path expression library, which extends the RDF query language SparQL to support complex path expressions over OWL and other RDF-based ontologies. We illustrate the utility of GLEEN by showing how it can be used in a query-based approach to defining simpler, more intuitive views of OWL ontologies. In particular we show how relatively simple GLEEN-enhanced SparQL queries can create views of the OWL version of the NCI Thesaurus that match the views generated by the web-based NCI browser.

BioCarian: search engine for exploratory searches in heterogeneous biological databases.

PubMed

Zaki, Nazar; Tennakoon, Chandana

2017-10-02

There are a large number of biological databases publicly available for scientists in the web. Also, there are many private databases generated in the course of research projects. These databases are in a wide variety of formats. Web standards have evolved in the recent times and semantic web technologies are now available to interconnect diverse and heterogeneous sources of data. Therefore, integration and querying of biological databases can be facilitated by techniques used in semantic web. Heterogeneous databases can be converted into Resource Description Format (RDF) and queried using SPARQL language. Searching for exact queries in these databases is trivial. However, exploratory searches need customized solutions, especially when multiple databases are involved. This process is cumbersome and time consuming for those without a sufficient background in computer science. In this context, a search engine facilitating exploratory searches of databases would be of great help to the scientific community. We present BioCarian, an efficient and user-friendly search engine for performing exploratory searches on biological databases. The search engine is an interface for SPARQL queries over RDF databases. We note that many of the databases can be converted to tabular form. We first convert the tabular databases to RDF. The search engine provides a graphical interface based on facets to explore the converted databases. The facet interface is more advanced than conventional facets. It allows complex queries to be constructed, and have additional features like ranking of facet values based on several criteria, visually indicating the relevance of a facet value and presenting the most important facet values when a large number of choices are available. For the advanced users, SPARQL queries can be run directly on the databases. Using this feature, users will be able to incorporate federated searches of SPARQL endpoints. We used the search engine to do an exploratory search on previously published viral integration data and were able to deduce the main conclusions of the original publication. BioCarian is accessible via http://www.biocarian.com . We have developed a search engine to explore RDF databases that can be used by both novice and advanced users.

Semantically enabled and statistically supported biological hypothesis testing with tissue microarray databases

PubMed Central

2011-01-01

Background Although many biological databases are applying semantic web technologies, meaningful biological hypothesis testing cannot be easily achieved. Database-driven high throughput genomic hypothesis testing requires both of the capabilities of obtaining semantically relevant experimental data and of performing relevant statistical testing for the retrieved data. Tissue Microarray (TMA) data are semantically rich and contains many biologically important hypotheses waiting for high throughput conclusions. Methods An application-specific ontology was developed for managing TMA and DNA microarray databases by semantic web technologies. Data were represented as Resource Description Framework (RDF) according to the framework of the ontology. Applications for hypothesis testing (Xperanto-RDF) for TMA data were designed and implemented by (1) formulating the syntactic and semantic structures of the hypotheses derived from TMA experiments, (2) formulating SPARQLs to reflect the semantic structures of the hypotheses, and (3) performing statistical test with the result sets returned by the SPARQLs. Results When a user designs a hypothesis in Xperanto-RDF and submits it, the hypothesis can be tested against TMA experimental data stored in Xperanto-RDF. When we evaluated four previously validated hypotheses as an illustration, all the hypotheses were supported by Xperanto-RDF. Conclusions We demonstrated the utility of high throughput biological hypothesis testing. We believe that preliminary investigation before performing highly controlled experiment can be benefited. PMID:21342584

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hasan, S. M. Shamimul; Fox, Edward A.; Bisset, Keith

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. Asmore » a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK—a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.« less

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

DOE PAGES

Hasan, S. M. Shamimul; Fox, Edward A.; Bisset, Keith; ...

2017-11-06

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. Asmore » a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK—a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.« less

TopFed: TCGA tailored federated query processing and linking to LOD.

PubMed

Saleem, Muhammad; Padmanabhuni, Shanmukha S; Ngomo, Axel-Cyrille Ngonga; Iqbal, Aftab; Almeida, Jonas S; Decker, Stefan; Deus, Helena F

2014-01-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to catalogue genetic mutations responsible for cancer using genome analysis techniques. One of the aims of this project is to create a comprehensive and open repository of cancer related molecular analysis, to be exploited by bioinformaticians towards advancing cancer knowledge. However, devising bioinformatics applications to analyse such large dataset is still challenging, as it often requires downloading large archives and parsing the relevant text files. Therefore, it is making it difficult to enable virtual data integration in order to collect the critical co-variates necessary for analysis. We address these issues by transforming the TCGA data into the Semantic Web standard Resource Description Format (RDF), link it to relevant datasets in the Linked Open Data (LOD) cloud and further propose an efficient data distribution strategy to host the resulting 20.4 billion triples data via several SPARQL endpoints. Having the TCGA data distributed across multiple SPARQL endpoints, we enable biomedical scientists to query and retrieve information from these SPARQL endpoints by proposing a TCGA tailored federated SPARQL query processing engine named TopFed. We compare TopFed with a well established federation engine FedX in terms of source selection and query execution time by using 10 different federated SPARQL queries with varying requirements. Our evaluation results show that TopFed selects on average less than half of the sources (with 100% recall) with query execution time equal to one third to that of FedX. With TopFed, we aim to offer biomedical scientists a single-point-of-access through which distributed TCGA data can be accessed in unison. We believe the proposed system can greatly help researchers in the biomedical domain to carry out their research effectively with TCGA as the amount and diversity of data exceeds the ability of local resources to handle its retrieval and parsing.

OpenFlyData: an exemplar data web integrating gene expression data on the fruit fly Drosophila melanogaster.

PubMed

Miles, Alistair; Zhao, Jun; Klyne, Graham; White-Cooper, Helen; Shotton, David

2010-10-01

Integrating heterogeneous data across distributed sources is a major requirement for in silico bioinformatics supporting translational research. For example, genome-scale data on patterns of gene expression in the fruit fly Drosophila melanogaster are widely used in functional genomic studies in many organisms to inform candidate gene selection and validate experimental results. However, current data integration solutions tend to be heavy weight, and require significant initial and ongoing investment of effort. Development of a common Web-based data integration infrastructure (a.k.a. data web), using Semantic Web standards, promises to alleviate these difficulties, but little is known about the feasibility, costs, risks or practical means of migrating to such an infrastructure. We describe the development of OpenFlyData, a proof-of-concept system integrating gene expression data on D. melanogaster, combining Semantic Web standards with light-weight approaches to Web programming based on Web 2.0 design patterns. To support researchers designing and validating functional genomic studies, OpenFlyData includes user-facing search applications providing intuitive access to and comparison of gene expression data from FlyAtlas, the BDGP in situ database, and FlyTED, using data from FlyBase to expand and disambiguate gene names. OpenFlyData's services are also openly accessible, and are available for reuse by other bioinformaticians and application developers. Semi-automated methods and tools were developed to support labour- and knowledge-intensive tasks involved in deploying SPARQL services. These include methods for generating ontologies and relational-to-RDF mappings for relational databases, which we illustrate using the FlyBase Chado database schema; and methods for mapping gene identifiers between databases. The advantages of using Semantic Web standards for biomedical data integration are discussed, as are open issues. In particular, although the performance of open source SPARQL implementations is sufficient to query gene expression data directly from user-facing applications such as Web-based data fusions (a.k.a. mashups), we found open SPARQL endpoints to be vulnerable to denial-of-service-type problems, which must be mitigated to ensure reliability of services based on this standard. These results are relevant to data integration activities in translational bioinformatics. The gene expression search applications and SPARQL endpoints developed for OpenFlyData are deployed at http://openflydata.org. FlyUI, a library of JavaScript widgets providing re-usable user-interface components for Drosophila gene expression data, is available at http://flyui.googlecode.com. Software and ontologies to support transformation of data from FlyBase, FlyAtlas, BDGP and FlyTED to RDF are available at http://openflydata.googlecode.com. SPARQLite, an implementation of the SPARQL protocol, is available at http://sparqlite.googlecode.com. All software is provided under the GPL version 3 open source license.

U.S. Army Research Laboratory Fiscal Year 2010 Status Report for the Advanced, All-Source, Fusion Technology Program Annex

DTIC Science & Technology

2011-03-01

9 Figure 7. RDS preferences widget after loading an unusual font (left) and RDS SPARQL query widget (right...Entered By Individual: SGT Juan Gonzalez DOI: 2007-01-06 13:00:00 Date Entered: 2007-01-06 23:32:03 Subject: Al-Qaeda Reading Material Source...preferences widget after loading an unusual font (left) and RDS SPARQL query widget (right). NetKernel and RDS-specific modules are specified with a URL

SemantGeo: Powering Ecological and Environment Data Discovery and Search with Standards-Based Geospatial Reasoning

NASA Astrophysics Data System (ADS)

Seyed, P.; Ashby, B.; Khan, I.; Patton, E. W.; McGuinness, D. L.

2013-12-01

Recent efforts to create and leverage standards for geospatial data specification and inference include the GeoSPARQL standard, Geospatial OWL ontologies (e.g., GAZ, Geonames), and RDF triple stores that support GeoSPARQL (e.g., AllegroGraph, Parliament) that use RDF instance data for geospatial features of interest. However, there remains a gap on how best to fuse software engineering best practices and GeoSPARQL within semantic web applications to enable flexible search driven by geospatial reasoning. In this abstract we introduce the SemantGeo module for the SemantEco framework that helps fill this gap, enabling scientists find data using geospatial semantics and reasoning. SemantGeo provides multiple types of geospatial reasoning for SemantEco modules. The server side implementation uses the Parliament SPARQL Endpoint accessed via a Tomcat servlet. SemantGeo uses the Google Maps API for user-specified polygon construction and JsTree for providing containment and categorical hierarchies for search. SemantGeo uses GeoSPARQL for spatial reasoning alone and in concert with RDFS/OWL reasoning capabilities to determine, e.g., what geofeatures are within, partially overlap with, or within a certain distance from, a given polygon. We also leverage qualitative relationships defined by the Gazetteer ontology that are composites of spatial relationships as well as administrative designations or geophysical phenomena. We provide multiple mechanisms for exploring data, such as polygon (map-based) and named-feature (hierarchy-based) selection, that enable flexible search constraints using boolean combination of selections. JsTree-based hierarchical search facets present named features and include a 'part of' hierarchy (e.g., measurement-site-01, Lake George, Adirondack Region, NY State) and type hierarchies (e.g., nodes in the hierarchy for WaterBody, Park, MeasurementSite), depending on the ';axis of choice' option selected. Using GeoSPARQL and aforementioned ontology, these hierarchies are constrained based on polygon selection, where the corresponding polygons of the contained features are visually rendered to assist exploration. Once measurement sites are plotted based on initial search, subsequent searches using JsTree selections can extend the previous based on nearby waterbodies in some semantic relationship of interest. For example, ';tributary of' captures water bodies that flow into the current one, and extending the original search to include tributaries of the observed water body is useful to environmental scientists for isolating the source of characteristic levels, including pollutants. Ultimately any SemantEco module can leverage SemantGeo's underlying APIs, leveraged in a deployment of SemantEco that combines EPA and USGS water quality data, and one customized for searching data available from the Darrin Freshwater Institute. Future work will address generating RDF geometry data from shape files, aligning RDF data sources to better leverage qualitative and spatial relationships, and validating newly generated RDF data adhering to the GeoSPARQL standard.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

PubMed Central

Waagmeester, Andra; Pico, Alexander R.

2016-01-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web. PMID:27336457

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources.

PubMed

Waagmeester, Andra; Kutmon, Martina; Riutta, Anders; Miller, Ryan; Willighagen, Egon L; Evelo, Chris T; Pico, Alexander R

2016-06-01

The diversity of online resources storing biological data in different formats provides a challenge for bioinformaticians to integrate and analyse their biological data. The semantic web provides a standard to facilitate knowledge integration using statements built as triples describing a relation between two objects. WikiPathways, an online collaborative pathway resource, is now available in the semantic web through a SPARQL endpoint at http://sparql.wikipathways.org. Having biological pathways in the semantic web allows rapid integration with data from other resources that contain information about elements present in pathways using SPARQL queries. In order to convert WikiPathways content into meaningful triples we developed two new vocabularies that capture the graphical representation and the pathway logic, respectively. Each gene, protein, and metabolite in a given pathway is defined with a standard set of identifiers to support linking to several other biological resources in the semantic web. WikiPathways triples were loaded into the Open PHACTS discovery platform and are available through its Web API (https://dev.openphacts.org/docs) to be used in various tools for drug development. We combined various semantic web resources with the newly converted WikiPathways content using a variety of SPARQL query types and third-party resources, such as the Open PHACTS API. The ability to use pathway information to form new links across diverse biological data highlights the utility of integrating WikiPathways in the semantic web.

Provenance Storage, Querying, and Visualization in PBase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kianmajd, Parisa; Ludascher, Bertram; Missier, Paolo

2015-01-01

We present PBase, a repository for scientific workflows and their corresponding provenance information that facilitates the sharing of experiments among the scientific community. PBase is interoperable since it uses ProvONE, a standard provenance model for scientific workflows. Workflows and traces are stored in RDF, and with the support of SPARQL and the tree cover encoding, the repository provides a scalable infrastructure for querying the provenance data. Furthermore, through its user interface, it is possible to: visualize workflows and execution traces; visualize reachability relations within these traces; issue SPARQL queries; and visualize query results.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases.

PubMed

Wollbrett, Julien; Larmande, Pierre; de Lamotte, Frédéric; Ruiz, Manuel

2013-04-15

In recent years, a large amount of "-omics" data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic.

Clever generation of rich SPARQL queries from annotated relational schema: application to Semantic Web Service creation for biological databases

PubMed Central

2013-01-01

Background In recent years, a large amount of “-omics” data have been produced. However, these data are stored in many different species-specific databases that are managed by different institutes and laboratories. Biologists often need to find and assemble data from disparate sources to perform certain analyses. Searching for these data and assembling them is a time-consuming task. The Semantic Web helps to facilitate interoperability across databases. A common approach involves the development of wrapper systems that map a relational database schema onto existing domain ontologies. However, few attempts have been made to automate the creation of such wrappers. Results We developed a framework, named BioSemantic, for the creation of Semantic Web Services that are applicable to relational biological databases. This framework makes use of both Semantic Web and Web Services technologies and can be divided into two main parts: (i) the generation and semi-automatic annotation of an RDF view; and (ii) the automatic generation of SPARQL queries and their integration into Semantic Web Services backbones. We have used our framework to integrate genomic data from different plant databases. Conclusions BioSemantic is a framework that was designed to speed integration of relational databases. We present how it can be used to speed the development of Semantic Web Services for existing relational biological databases. Currently, it creates and annotates RDF views that enable the automatic generation of SPARQL queries. Web Services are also created and deployed automatically, and the semantic annotations of our Web Services are added automatically using SAWSDL attributes. BioSemantic is downloadable at http://southgreen.cirad.fr/?q=content/Biosemantic. PMID:23586394

A journey to Semantic Web query federation in the life sciences.

PubMed

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-10-01

As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community.

A journey to Semantic Web query federation in the life sciences

PubMed Central

Cheung, Kei-Hoi; Frost, H Robert; Marshall, M Scott; Prud'hommeaux, Eric; Samwald, Matthias; Zhao, Jun; Paschke, Adrian

2009-01-01

Background As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technologies, SPARQL endpoints, Linked Data, and Vocabulary of Interlinked Datasets have emerged in recent years. In addition to the data warehouse construction, these technological approaches can be used to support dynamic query federation. As a community effort, the BioRDF task force, within the Semantic Web for Health Care and Life Sciences Interest Group, is exploring how these emerging approaches can be utilized to execute distributed queries across different neuroscience data sources. Methods and results We have created two health care and life science knowledge bases. We have explored a variety of Semantic Web approaches to describe, map, and dynamically query multiple datasets. We have demonstrated several federation approaches that integrate diverse types of information about neurons and receptors that play an important role in basic, clinical, and translational neuroscience research. Particularly, we have created a prototype receptor explorer which uses OWL mappings to provide an integrated list of receptors and executes individual queries against different SPARQL endpoints. We have also employed the AIDA Toolkit, which is directed at groups of knowledge workers who cooperatively search, annotate, interpret, and enrich large collections of heterogeneous documents from diverse locations. We have explored a tool called "FeDeRate", which enables a global SPARQL query to be decomposed into subqueries against the remote databases offering either SPARQL or SQL query interfaces. Finally, we have explored how to use the vocabulary of interlinked Datasets (voiD) to create metadata for describing datasets exposed as Linked Data URIs or SPARQL endpoints. Conclusion We have demonstrated the use of a set of novel and state-of-the-art Semantic Web technologies in support of a neuroscience query federation scenario. We have identified both the strengths and weaknesses of these technologies. While Semantic Web offers a global data model including the use of Uniform Resource Identifiers (URI's), the proliferation of semantically-equivalent URI's hinders large scale data integration. Our work helps direct research and tool development, which will be of benefit to this community. PMID:19796394

vSPARQL: A View Definition Language for the Semantic Web

PubMed Central

Shaw, Marianne; Detwiler, Landon T.; Noy, Natalya; Brinkley, James; Suciu, Dan

2010-01-01

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages. PMID:20800106

vSPARQL: a view definition language for the semantic web.

PubMed

Shaw, Marianne; Detwiler, Landon T; Noy, Natalya; Brinkley, James; Suciu, Dan

2011-02-01

Translational medicine applications would like to leverage the biological and biomedical ontologies, vocabularies, and data sets available on the semantic web. We present a general solution for RDF information set reuse inspired by database views. Our view definition language, vSPARQL, allows applications to specify the exact content that they are interested in and how that content should be restructured or modified. Applications can access relevant content by querying against these view definitions. We evaluate the expressivity of our approach by defining views for practical use cases and comparing our view definition language to existing query languages. Copyright © 2010 Elsevier Inc. All rights reserved.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.

PubMed

Bolleman, Jerven T; Mungall, Christopher J; Strozzi, Francesco; Baran, Joachim; Dumontier, Michel; Bonnal, Raoul J P; Buels, Robert; Hoehndorf, Robert; Fujisawa, Takatomo; Katayama, Toshiaki; Cock, Peter J A

2016-06-13

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. We have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned "omics" areas. Using the same data format to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe - and potentially merge - sequence annotations from multiple sources. Data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.

Towards Linked Open Services and Processes

NASA Astrophysics Data System (ADS)

Krummenacher, Reto; Norton, Barry; Marte, Adrian

The combination of semantic technology and Web services in form of 'Semantic Web Services' has until now been oriented towards extension of the WS-* stack with ontology-based descriptions. The same time, there is a strong movement away from this stack - for which the 'Web' part is little more than branding - towards RESTful services. The Linked Open Data initiative is a keen adopter of this approach and exposes many datasets via SPARQL endpoints and RESTful services. Our developing approach of 'Linked Open Services', whose current state is described in this paper, accommodates such Linked Data endpoints and general RESTful services alongside WS-* stack-based services with descriptions based on RDF and SPARQL. This capitalises on the Linked Data Cloud and makes service description and comprehension more easy and direct to the growing Linked Data community. Along the way, we show how the existing link between service messaging and the semantic viewpoint, commonly called 'lifting and lowering', is usually unduly restricted to ontology-based classification and misses how the effect of a service contributes to the knowledge of its consumer. Our SPARQL-based approach helps also in the composition of services as knowledge-centric processes, and encourages the development and exposure of services that communicate RDF.

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

DOE PAGES

Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco; ...

2016-06-13

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. In this paper, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data formatmore » to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Finally, data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bolleman, Jerven T.; Mungall, Christopher J.; Strozzi, Francesco

Nucleotide and protein sequence feature annotations are essential to understand biology on the genomic, transcriptomic, and proteomic level. Using Semantic Web technologies to query biological annotations, there was no standard that described this potentially complex location information as subject-predicate-object triples. In this paper, we have developed an ontology, the Feature Annotation Location Description Ontology (FALDO), to describe the positions of annotated features on linear and circular sequences. FALDO can be used to describe nucleotide features in sequence records, protein annotations, and glycan binding sites, among other features in coordinate systems of the aforementioned “omics” areas. Using the same data formatmore » to represent sequence positions that are independent of file formats allows us to integrate sequence data from multiple sources and data types. The genome browser JBrowse is used to demonstrate accessing multiple SPARQL endpoints to display genomic feature annotations, as well as protein annotations from UniProt mapped to genomic locations. Our ontology allows users to uniformly describe – and potentially merge – sequence annotations from multiple sources. Finally, data sources using FALDO can prospectively be retrieved using federalised SPARQL queries against public SPARQL endpoints and/or local private triple stores.« less

Moving Controlled Vocabularies into the Semantic Web

NASA Astrophysics Data System (ADS)

Thomas, R.; Lowry, R. K.; Kokkinaki, A.

2015-12-01

One of the issues with legacy oceanographic data formats is that the only tool available for describing what a measurement is and how it was made is a single metadata tag known as the parameter code. The British Oceanographic Data Centre (BODC) has been supporting the international oceanographic community gain maximum benefit from this through a controlled vocabulary known as the BODC Parameter Usage Vocabulary (PUV). Over time this has grown to over 34,000 entries some of which have preferred labels with over 400 bytes of descriptive information detailing what was measured and how. A decade ago the BODC pioneered making this information available in a more useful form with the implementation of a prototype vocabulary server (NVS) that referenced each 'parameter code' as a URL. This developed into the current server (NVS V2) in which the parameter URL resolves into an RDF document based on the SKOS data model which includes a list of resource URLs mapped to the 'parameter'. For example the parameter code for a contaminant in biota, such as 'cadmium in Mytilus edulis', carries RDF triples leading to the entry for Mytilus edulis in the WoRMS and for cadmium in the ChEBI ontologies. By providing links into these external ontologies the information captured in a 1980s parameter code now conforms to the Linked Data paradigm of the Semantic Web, vastly increasing the descriptive information accessible to a user. This presentation will describe the next steps along the road to the Semantic Web with the development of a SPARQL end point1 to expose the PUV plus the 190 other controlled vocabularies held in NVS. Whilst this is ideal for those fluent in SPARQL, most users require something a little more user-friendly and so the NVS browser2 was developed over the end point to allow less technical users to query the vocabularies and navigate the NVS ontology. This tool integrates into an editor that allows vocabulary content to be manipulated by authorised users outside BODC. Having placed Linked Data tooling over a single SPARQL end point the obvious future development for this system is to support semantic interoperability outside NVS by the incorporation of federated SPARQL end points in the USA and Australia during the ODIP II project. 1https://vocab.nerc.ac.uk/sparql 2 https://www.bodc.ac.uk/data/codes_and_formats/vocabulary_search/

Time-related patient data retrieval for the case studies from the pharmacogenomics research network

PubMed Central

Zhu, Qian; Tao, Cui; Ding, Ying; Chute, Christopher G.

2012-01-01

There are lots of question-based data elements from the pharmacogenomics research network (PGRN) studies. Many data elements contain temporal information. To semantically represent these elements so that they can be machine processiable is a challenging problem for the following reasons: (1) the designers of these studies usually do not have the knowledge of any computer modeling and query languages, so that the original data elements usually are represented in spreadsheets in human languages; and (2) the time aspects in these data elements can be too complex to be represented faithfully in a machine-understandable way. In this paper, we introduce our efforts on representing these data elements using semantic web technologies. We have developed an ontology, CNTRO, for representing clinical events and their temporal relations in the web ontology language (OWL). Here we use CNTRO to represent the time aspects in the data elements. We have evaluated 720 time-related data elements from PGRN studies. We adapted and extended the knowledge representation requirements for EliXR-TIME to categorize our data elements. A CNTRO-based SPARQL query builder has been developed to customize users’ own SPARQL queries for each knowledge representation requirement. The SPARQL query builder has been evaluated with a simulated EHR triple store to ensure its functionalities. PMID:23076712

Time-related patient data retrieval for the case studies from the pharmacogenomics research network.

PubMed

Zhu, Qian; Tao, Cui; Ding, Ying; Chute, Christopher G

2012-11-01

There are lots of question-based data elements from the pharmacogenomics research network (PGRN) studies. Many data elements contain temporal information. To semantically represent these elements so that they can be machine processiable is a challenging problem for the following reasons: (1) the designers of these studies usually do not have the knowledge of any computer modeling and query languages, so that the original data elements usually are represented in spreadsheets in human languages; and (2) the time aspects in these data elements can be too complex to be represented faithfully in a machine-understandable way. In this paper, we introduce our efforts on representing these data elements using semantic web technologies. We have developed an ontology, CNTRO, for representing clinical events and their temporal relations in the web ontology language (OWL). Here we use CNTRO to represent the time aspects in the data elements. We have evaluated 720 time-related data elements from PGRN studies. We adapted and extended the knowledge representation requirements for EliXR-TIME to categorize our data elements. A CNTRO-based SPARQL query builder has been developed to customize users' own SPARQL queries for each knowledge representation requirement. The SPARQL query builder has been evaluated with a simulated EHR triple store to ensure its functionalities.

Semantic Web repositories for genomics data using the eXframe platform.

PubMed

Merrill, Emily; Corlosquet, Stéphane; Ciccarese, Paolo; Clark, Tim; Das, Sudeshna

2014-01-01

With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Guo Qiang; Luo, Lingyun; Ogbuji, Chime

The interaction of multiple types of relationships among anatomical classes in the Foundational Model of Anatomy (FMA) can provide inferred information valuable for quality assurance. This paper introduces a method called Motif Checking (MOCH) to study the effects of such multi-relation type interactions. MOCH represents patterns of multitype interaction as small labeled sub-graph motifs, whose nodes represent class variables, and labeled edges represent relational types. By representing FMA as an RDF graph and motifs as SPARQL queries, fragments of FMA are automatically obtained as auditing candidates. Leveraging the scalability and reconfigurability of Semantic Web Technology (OWL, RDF and SPARQL) andmore » Virtuoso, we performed exhaustive analyses of three 2-node motifs, resulting in 638 matching FMA configurations; twelve 3-node motifs, resulting in 202,960 configurations. Using the Principal Ideal Explorer (PIE) methodology as an extension of MOCH, we were able to identify 755 root nodes with 4,100 respective descendants with opposing antonyms in their class names for arbitrary-length motifs. With possible disjointness implied by antonyms, we performed manual inspection of a subset of the resulting FMA fragments and tracked down a source of abnormal inferred conclusions (captured by the motifs), coming from a gender-neutral class being modeled as a part of gender-specific class, such as “Urinary system” is a part of “Female human body.” Our results demonstrate that MOCH and PIE provide a unique source of valuable information for quality assurance. Since our approach is general, it is applicable to any ontological system with an OWL representation.« less

In-Memory Graph Databases for Web-Scale Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castellana, Vito G.; Morari, Alessandro; Weaver, Jesse R.

RDF databases have emerged as one of the most relevant way for organizing, integrating, and managing expo- nentially growing, often heterogeneous, and not rigidly structured data for a variety of scientific and commercial fields. In this paper we discuss the solutions integrated in GEMS (Graph database Engine for Multithreaded Systems), a software framework for implementing RDF databases on commodity, distributed-memory high-performance clusters. Unlike the majority of current RDF databases, GEMS has been designed from the ground up to primarily employ graph-based methods. This is reflected in all the layers of its stack. The GEMS framework is composed of: a SPARQL-to-C++more » compiler, a library of data structures and related methods to access and modify them, and a custom runtime providing lightweight software multithreading, network messages aggregation and a partitioned global address space. We provide an overview of the framework, detailing its component and how they have been closely designed and customized to address issues of graph methods applied to large-scale datasets on clusters. We discuss in details the principles that enable automatic translation of the queries (expressed in SPARQL, the query language of choice for RDF databases) to graph methods, and identify differences with respect to other RDF databases.« less

Investigating Geosparql Requirements for Participatory Urban Planning

NASA Astrophysics Data System (ADS)

Mohammadi, E.; Hunter, A. J. S.

2015-06-01

We propose that participatory GIS (PGIS) activities including participatory urban planning can be made more efficient and effective if spatial reasoning rules are integrated with PGIS tools to simplify engagement for public contributors. Spatial reasoning is used to describe relationships between spatial entities. These relationships can be evaluated quantitatively or qualitatively using geometrical algorithms, ontological relations, and topological methods. Semantic web services utilize tools and methods that can facilitate spatial reasoning. GeoSPARQL, introduced by OGC, is a spatial reasoning standard used to make declarations about entities (graphical contributions) that take the form of a subject-predicate-object triple or statement. GeoSPARQL uses three basic methods to infer topological relationships between spatial entities, including: OGC's simple feature topology, RCC8, and the DE-9IM model. While these methods are comprehensive in their ability to define topological relationships between spatial entities, they are often inadequate for defining complex relationships that exist in the spatial realm. Particularly relationships between urban entities, such as those between a bus route, the collection of associated bus stops and their overall surroundings as an urban planning pattern. In this paper we investigate common qualitative spatial reasoning methods as a preliminary step to enhancing the capabilities of GeoSPARQL in an online participatory GIS framework in which reasoning is used to validate plans based on standard patterns that can be found in an efficient/effective urban environment.

SPARQLog: SPARQL with Rules and Quantification

NASA Astrophysics Data System (ADS)

Bry, François; Furche, Tim; Marnette, Bruno; Ley, Clemens; Linse, Benedikt; Poppe, Olga

SPARQL has become the gold-standard for RDF query languages. Nevertheless, we believe there is further room for improving RDF query languages. In this chapter, we investigate the addition of rules and quantifier alternation to SPARQL. That extension, called SPARQLog, extends previous RDF query languages by arbitrary quantifier alternation: blank nodes may occur in the scope of all, some, or none of the universal variables of a rule. In addition, SPARQLog is aware of important RDF features such as the distinction between blank nodes, literals and IRIs or the RDFS vocabulary. The semantics of SPARQLog is closed (every answer is an RDF graph), but lifts RDF's restrictions on literal and blank node occurrences for intermediary data. We show how to define a sound and complete operational semantics that can be implemented using existing logic programming techniques. While SPARQLog is Turing complete, we identify a decidable (in fact, polynomial time) fragment SwARQLog ensuring polynomial data-complexity inspired from the notion of super-weak acyclicity in data exchange. Furthermore, we prove that SPARQLog with no universal quantifiers in the scope of existential ones (∀ ∃ fragment) is equivalent to full SPARQLog in presence of graph projection. Thus, the convenience of arbitrary quantifier alternation comes, in fact, for free. These results, though here presented in the context of RDF querying, apply similarly also in the more general setting of data exchange.

Semantic Web repositories for genomics data using the eXframe platform

PubMed Central

2014-01-01

Background With the advent of inexpensive assay technologies, there has been an unprecedented growth in genomics data as well as the number of databases in which it is stored. In these databases, sample annotation using ontologies and controlled vocabularies is becoming more common. However, the annotation is rarely available as Linked Data, in a machine-readable format, or for standardized queries using SPARQL. This makes large-scale reuse, or integration with other knowledge bases very difficult. Methods To address this challenge, we have developed the second generation of our eXframe platform, a reusable framework for creating online repositories of genomics experiments. This second generation model now publishes Semantic Web data. To accomplish this, we created an experiment model that covers provenance, citations, external links, assays, biomaterials used in the experiment, and the data collected during the process. The elements of our model are mapped to classes and properties from various established biomedical ontologies. Resource Description Framework (RDF) data is automatically produced using these mappings and indexed in an RDF store with a built-in Sparql Protocol and RDF Query Language (SPARQL) endpoint. Conclusions Using the open-source eXframe software, institutions and laboratories can create Semantic Web repositories of their experiments, integrate it with heterogeneous resources and make it interoperable with the vast Semantic Web of biomedical knowledge. PMID:25093072

Connecting geoscience systems and data using Linked Open Data in the Web of Data

NASA Astrophysics Data System (ADS)

Ritschel, Bernd; Neher, Günther; Iyemori, Toshihiko; Koyama, Yukinobu; Yatagai, Akiyo; Murayama, Yasuhiro; Galkin, Ivan; King, Todd; Fung, Shing F.; Hughes, Steve; Habermann, Ted; Hapgood, Mike; Belehaki, Anna

2014-05-01

Linked Data or Linked Open Data (LOD) in the realm of free and publically accessible data is one of the most promising and most used semantic Web frameworks connecting various types of data and vocabularies including geoscience and related domains. The semantic Web extension to the commonly existing and used World Wide Web is based on the meaning of entities and relationships or in different words classes and properties used for data in a global data and information space, the Web of Data. LOD data is referenced and mash-uped by URIs and is retrievable using simple parameter controlled HTTP-requests leading to a result which is human-understandable or machine-readable. Furthermore the publishing and mash-up of data in the semantic Web realm is realized by specific Web standards, such as RDF, RDFS, OWL and SPARQL defined for the Web of Data. Semantic Web based mash-up is the Web method to aggregate and reuse various contents from different sources, such as e.g. using FOAF as a model and vocabulary for the description of persons and organizations -in our case- related to geoscience projects, instruments, observations, data and so on. On the example of three different geoscience data and information management systems, such as ESPAS, IUGONET and GFZ ISDC and the associated science data and related metadata or better called context data, the concept of the mash-up of systems and data using the semantic Web approach and the Linked Open Data framework is described in this publication. Because the three systems are based on different data models, data storage structures and technical implementations an extra semantic Web layer upon the existing interfaces is used for mash-up solutions. In order to satisfy the semantic Web standards, data transition processes, such as the transfer of content stored in relational databases or mapped in XML documents into SPARQL capable databases or endpoints using D2R or XSLT is necessary. In addition, the use of mapped and/or merged domain specific and cross-domain vocabularies in the sense of terminological ontologies are the foundation for a virtually unified data retrieval and access in IUGONET, ESPAS and GFZ ISDC data management systems. SPARQL endpoints realized either by originally RDF databases, e.g. Virtuoso or by virtual SPARQL endpoints, e.g. D2R services enable an only upon Web standard-based mash-up of domain-specific systems and data, such as in this case the space weather and geomagnetic domain but also cross-domain connection to data and vocabularies, e.g. related to NASA's VxOs, particularly VWO or NASA's PDS data system within LOD. LOD - Linked Open Data RDF - Resource Description Framework RDFS - RDF Schema OWL - Ontology Web Language SPARQL - SPARQL Protocol and RDF Query Language FOAF - Friends of a Friend ontology ESPAS - Near Earth Space Data Infrastructure for e-Science (Project) IUGONET - Inter-university Upper Atmosphere Global Observation Network (Project) GFZ ISDC - German Research Centre for Geosciences Information System and Data Center XML - Extensible Mark-up Language D2R - (Relational) Database to RDF (Transformation) XSLT - Extensible Stylesheet Language Transformation Virtuoso - OpenLink Virtuoso Universal Server (including RDF data management) NASA - National Aeronautics and Space Administration VOx - Virtual Observatories VWO - Virtual Wave Observatory PDS - Planetary Data System

High Performance Semantic Factoring of Giga-Scale Semantic Graph Databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joslyn, Cliff A.; Adolf, Robert D.; Al-Saffar, Sinan

2010-10-04

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors.« less

RDFBuilder: a tool to automatically build RDF-based interfaces for MAGE-OM microarray data sources.

PubMed

Anguita, Alberto; Martin, Luis; Garcia-Remesal, Miguel; Maojo, Victor

2013-07-01

This paper presents RDFBuilder, a tool that enables RDF-based access to MAGE-ML-compliant microarray databases. We have developed a system that automatically transforms the MAGE-OM model and microarray data stored in the ArrayExpress database into RDF format. Additionally, the system automatically enables a SPARQL endpoint. This allows users to execute SPARQL queries for retrieving microarray data, either from specific experiments or from more than one experiment at a time. Our system optimizes response times by caching and reusing information from previous queries. In this paper, we describe our methods for achieving this transformation. We show that our approach is complementary to other existing initiatives, such as Bio2RDF, for accessing and retrieving data from the ArrayExpress database. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

High performance semantic factoring of giga-scale semantic graph databases.

DOE Office of Scientific and Technical Information (OSTI.GOV)

al-Saffar, Sinan; Adolf, Bob; Haglin, David

2010-10-01

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to bring high performance computational resources to bear on their analysis, interpretation, and visualization, especially with respect to their innate semantic structure. Our research group built a novel high performance hybrid system comprising computational capability for semantic graph database processing utilizing the large multithreaded architecture of the Cray XMT platform, conventional clusters, and large data stores. In this paper we describe that architecture, and present the results of our deployingmore » that for the analysis of the Billion Triple dataset with respect to its semantic factors, including basic properties, connected components, namespace interaction, and typed paths.« less

Benchmarking and Performance Measurement.

ERIC Educational Resources Information Center

Town, J. Stephen

This paper defines benchmarking and its relationship to quality management, describes a project which applied the technique in a library context, and explores the relationship between performance measurement and benchmarking. Numerous benchmarking methods contain similar elements: deciding what to benchmark; identifying partners; gathering…

Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong

The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existingmore » graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.« less

Enabling Graph Mining in RDF Triplestores using SPARQL for Holistic In-situ Graph Analysis

DOE PAGES

Lee, Sangkeun; Sukumar, Sreenivas R; Hong, Seokyong; ...

2016-01-01

The graph analysis is now considered as a promising technique to discover useful knowledge in data with a new perspective. We envi- sion that there are two dimensions of graph analysis: OnLine Graph Analytic Processing (OLGAP) and Graph Mining (GM) where each respectively focuses on subgraph pattern matching and automatic knowledge discovery in graph. Moreover, as these two dimensions aim to complementarily solve complex problems, holistic in-situ graph analysis which covers both OLGAP and GM in a single system is critical for minimizing the burdens of operating multiple graph systems and transferring intermediate result-sets between those systems. Nevertheless, most existingmore » graph analysis systems are only capable of one dimension of graph analysis. In this work, we take an approach to enabling GM capabilities (e.g., PageRank, connected-component analysis, node eccentricity, etc.) in RDF triplestores, which are originally developed to store RDF datasets and provide OLGAP capability. More specifically, to achieve our goal, we implemented six representative graph mining algorithms using SPARQL. The approach allows a wide range of available RDF data sets directly applicable for holistic graph analysis within a system. For validation of our approach, we evaluate performance of our implementations with nine real-world datasets and three different computing environments - a laptop computer, an Amazon EC2 instance, and a shared-memory Cray XMT2 URIKA-GD graph-processing appliance. The experimen- tal results show that our implementation can provide promising and scalable performance for real world graph analysis in all tested environments. The developed software is publicly available in an open-source project that we initiated.« less

How to achieve and prove performance improvement - 15 years of experience in German wastewater benchmarking.

PubMed

Bertzbach, F; Franz, T; Möller, K

2012-01-01

This paper shows the results of performance improvement, which have been achieved in benchmarking projects in the wastewater industry in Germany over the last 15 years. A huge number of changes in operational practice and also in achieved annual savings can be shown, induced in particular by benchmarking at process level. Investigation of this question produces some general findings for the inclusion of performance improvement in a benchmarking project and for the communication of its results. Thus, we elaborate on the concept of benchmarking at both utility and process level, which is still a necessary distinction for the integration of performance improvement into our benchmarking approach. To achieve performance improvement via benchmarking it should be made quite clear that this outcome depends, on one hand, on a well conducted benchmarking programme and, on the other, on the individual situation within each participating utility.

Developing integrated benchmarks for DOE performance measurement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Barancik, J.I.; Kramer, C.F.; Thode, Jr. H.C.

1992-09-30

The objectives of this task were to describe and evaluate selected existing sources of information on occupational safety and health with emphasis on hazard and exposure assessment, abatement, training, reporting, and control identifying for exposure and outcome in preparation for developing DOE performance benchmarks. Existing resources and methodologies were assessed for their potential use as practical performance benchmarks. Strengths and limitations of current data resources were identified. Guidelines were outlined for developing new or improved performance factors, which then could become the basis for selecting performance benchmarks. Data bases for non-DOE comparison populations were identified so that DOE performance couldmore » be assessed relative to non-DOE occupational and industrial groups. Systems approaches were described which can be used to link hazards and exposure, event occurrence, and adverse outcome factors, as needed to generate valid, reliable, and predictive performance benchmarks. Data bases were identified which contain information relevant to one or more performance assessment categories . A list of 72 potential performance benchmarks was prepared to illustrate the kinds of information that can be produced through a benchmark development program. Current information resources which may be used to develop potential performance benchmarks are limited. There is need to develop an occupational safety and health information and data system in DOE, which is capable of incorporating demonstrated and documented performance benchmarks prior to, or concurrent with the development of hardware and software. A key to the success of this systems approach is rigorous development and demonstration of performance benchmark equivalents to users of such data before system hardware and software commitments are institutionalized.« less

A Querying Method over RDF-ized Health Level Seven v2.5 Messages Using Life Science Knowledge Resources.

PubMed

Kawazoe, Yoshimasa; Imai, Takeshi; Ohe, Kazuhiko

2016-04-05

Health level seven version 2.5 (HL7 v2.5) is a widespread messaging standard for information exchange between clinical information systems. By applying Semantic Web technologies for handling HL7 v2.5 messages, it is possible to integrate large-scale clinical data with life science knowledge resources. Showing feasibility of a querying method over large-scale resource description framework (RDF)-ized HL7 v2.5 messages using publicly available drug databases. We developed a method to convert HL7 v2.5 messages into the RDF. We also converted five kinds of drug databases into RDF and provided explicit links between the corresponding items among them. With those linked drug data, we then developed a method for query expansion to search the clinical data using semantic information on drug classes along with four types of temporal patterns. For evaluation purpose, medication orders and laboratory test results for a 3-year period at the University of Tokyo Hospital were used, and the query execution times were measured. Approximately 650 million RDF triples for medication orders and 790 million RDF triples for laboratory test results were converted. Taking three types of query in use cases for detecting adverse events of drugs as an example, we confirmed these queries were represented in SPARQL Protocol and RDF Query Language (SPARQL) using our methods and comparison with conventional query expressions were performed. The measurement results confirm that the query time is feasible and increases logarithmically or linearly with the amount of data and without diverging. The proposed methods enabled query expressions that separate knowledge resources and clinical data, thereby suggesting the feasibility for improving the usability of clinical data by enhancing the knowledge resources. We also demonstrate that when HL7 v2.5 messages are automatically converted into RDF, searches are still possible through SPARQL without modifying the structure. As such, the proposed method benefits not only our hospitals, but also numerous hospitals that handle HL7 v2.5 messages. Our approach highlights a potential of large-scale data federation techniques to retrieve clinical information, which could be applied as applications of clinical intelligence to improve clinical practices, such as adverse drug event monitoring and cohort selection for a clinical study as well as discovering new knowledge from clinical information.

PDS: A Performance Database Server

DOE PAGES

Berry, Michael W.; Dongarra, Jack J.; Larose, Brian H.; ...

1994-01-01

The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS) that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib) to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallelmore » benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry) of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.« less

Browsing and Visualization of Linked Environmental Data

NASA Astrophysics Data System (ADS)

Nikolaou, Charalampos; Kyzirakos, Kostis; Bereta, Konstantina; Dogani, Kallirroi; Koubarakis, Manolis

2014-05-01

Linked environmental data has started to appear on the Web as environmental researchers make use of technologies such as ontologies, RDF, and SPARQL. Many of these datasets have an important geospatial and temporal dimension. The same is true also for the Web of data that is being rapidly populated not only with geospatial information, but also with temporal information. As the real-world entities represented in linked geospatial datasets evolve over time, the datasets themselves get updated and both the spatial and the temporal dimension of data become significant for users. For example, in the Earth Observation and Environment domains, data is constantly produced by satellite sensors and is associated with metadata containing, among others, temporal attributes, such as the time that an image was acquired. In addition, the acquisitions are considered to be valid for specific periods of time, for example until they get updated by new acquisitions. Satellite acquisitions might be utilized in applications such as the CORINE Land Cover programme operated by the European Environment Agency that makes available as a cartographic product the land cover of European areas. Periodically CORINE publishes the changes in the land cover of these areas in the form of changesets. Tools for exploiting the abundance of geospatial information have also started to emerge. However, these tools are designed for browsing a single data source, while in addition they cannot represent the temporal dimension. This is for two reasons: a) the lack of an implementation of a data model and a query language with temporal features covering the various semantics associated with the representation of time (e.g., valid and user-defined), and b) the lack of a standard temporal extension of RDF that would allow practitioners to utilize when publishing RDF data. Recently, we presented the temporal features of the data model stRDF, the query language stSPARQL, and their implementation in the geospatial RDF store Strabon (http://www.strabon.di.uoa.gr/) which, apart from querying geospatial information, can also be used to query both the valid time of a triple and user-defined time. With the aim of filling the aforementioned gaps and going beyond data exploration to map creation and sharing, we have designed and developed SexTant (http://sextant.di.uoa.gr/). SexTant can be used to produce thematic maps by layering spatiotemporal information which exists in a number of data sources ranging from standard SPARQL endpoints, to SPARQL endpoints following the standard GeoSPARQL defined by the Open Geospatial Consortium (OGC) for the modelling and querying of geospatial information, and other well-adopted geospatial file formats, such as KML and GeoJSON. In this work, we pick some real use cases from the environment domain to showcase the usefulness of SexTant to the environmental studies of a domain expert by presenting its browsing and visualization capabilities using a number of environmental datasets that we have published as linked data and also other geospatial data sources publicly available on the Web, such as KML files.

Benchmarking: your performance measurement and improvement tool.

PubMed

Senn, G F

2000-01-01

Many respected professional healthcare organizations and societies today are seeking to establish data-driven performance measurement strategies such as benchmarking. Clinicians are, however, resistant to "benchmarking" that is based on financial data alone, concerned that it may be adverse to the patients' best interests. Benchmarking of clinical procedures that uses physician's codes such as Current Procedural Terminology (CPTs) has greater credibility with practitioners. Better Performers, organizations that can perform procedures successfully at lower cost and in less time, become the "benchmark" against which other organizations can measure themselves. The Better Performers' strategies can be adopted by other facilities to save time or money while maintaining quality patient care.

An ontology-driven semantic mash-up of gene and biological pathway information: Application to the domain of nicotine dependence

PubMed Central

Sahoo, Satya S.; Bodenreider, Olivier; Rutter, Joni L.; Skinner, Karen J.; Sheth, Amit P.

2008-01-01

Objectives This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. Methods We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Results Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Conclusion Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. Resource page http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/ PMID:18395495

An ontology-driven semantic mashup of gene and biological pathway information: application to the domain of nicotine dependence.

PubMed

Sahoo, Satya S; Bodenreider, Olivier; Rutter, Joni L; Skinner, Karen J; Sheth, Amit P

2008-10-01

This paper illustrates how Semantic Web technologies (especially RDF, OWL, and SPARQL) can support information integration and make it easy to create semantic mashups (semantically integrated resources). In the context of understanding the genetic basis of nicotine dependence, we integrate gene and pathway information and show how three complex biological queries can be answered by the integrated knowledge base. We use an ontology-driven approach to integrate two gene resources (Entrez Gene and HomoloGene) and three pathway resources (KEGG, Reactome and BioCyc), for five organisms, including humans. We created the Entrez Knowledge Model (EKoM), an information model in OWL for the gene resources, and integrated it with the extant BioPAX ontology designed for pathway resources. The integrated schema is populated with data from the pathway resources, publicly available in BioPAX-compatible format, and gene resources for which a population procedure was created. The SPARQL query language is used to formulate queries over the integrated knowledge base to answer the three biological queries. Simple SPARQL queries could easily identify hub genes, i.e., those genes whose gene products participate in many pathways or interact with many other gene products. The identification of the genes expressed in the brain turned out to be more difficult, due to the lack of a common identification scheme for proteins. Semantic Web technologies provide a valid framework for information integration in the life sciences. Ontology-driven integration represents a flexible, sustainable and extensible solution to the integration of large volumes of information. Additional resources, which enable the creation of mappings between information sources, are required to compensate for heterogeneity across namespaces. RESOURCE PAGE: http://knoesis.wright.edu/research/lifesci/integration/structured_data/JBI-2008/

Benchmarking reference services: an introduction.

PubMed

Marshall, J G; Buchanan, H S

1995-01-01

Benchmarking is based on the common sense idea that someone else, either inside or outside of libraries, has found a better way of doing certain things and that your own library's performance can be improved by finding out how others do things and adopting the best practices you find. Benchmarking is one of the tools used for achieving continuous improvement in Total Quality Management (TQM) programs. Although benchmarking can be done on an informal basis, TQM puts considerable emphasis on formal data collection and performance measurement. Used to its full potential, benchmarking can provide a common measuring stick to evaluate process performance. This article introduces the general concept of benchmarking, linking it whenever possible to reference services in health sciences libraries. Data collection instruments that have potential application in benchmarking studies are discussed and the need to develop common measurement tools to facilitate benchmarking is emphasized.

Transaction Processing Performance Council (TPC): State of the Council 2010

NASA Astrophysics Data System (ADS)

Nambiar, Raghunath; Wakou, Nicholas; Carman, Forrest; Majdalany, Michael

The Transaction Processing Performance Council (TPC) is a non-profit corporation founded to define transaction processing and database benchmarks and to disseminate objective, verifiable performance data to the industry. Established in August 1988, the TPC has been integral in shaping the landscape of modern transaction processing and database benchmarks over the past twenty-two years. This paper provides an overview of the TPC's existing benchmark standards and specifications, introduces two new TPC benchmarks under development, and examines the TPC's active involvement in the early creation of additional future benchmarks.

A review on the benchmarking concept in Malaysian construction safety performance

NASA Astrophysics Data System (ADS)

Ishak, Nurfadzillah; Azizan, Muhammad Azizi

2018-02-01

Construction industry is one of the major industries that propels Malaysia's economy in highly contributes to our nation's GDP growth, yet the high fatality rates on construction sites have caused concern among safety practitioners and the stakeholders. Hence, there is a need of benchmarking in performance of Malaysia's construction industry especially in terms of safety. This concept can create a fertile ground for ideas, but only in a receptive environment, organization that share good practices and compare their safety performance against other benefit most to establish improvement in safety culture. This research was conducted to study the awareness important, evaluate current practice and improvement, and also identify the constraint in implement of benchmarking on safety performance in our industry. Additionally, interviews with construction professionals were come out with different views on this concept. Comparison has been done to show the different understanding of benchmarking approach and how safety performance can be benchmarked. But, it's viewed as one mission, which to evaluate objectives identified through benchmarking that will improve the organization's safety performance. Finally, the expected result from this research is to help Malaysia's construction industry implement best practice in safety performance management through the concept of benchmarking.

Using a linked data approach to aid development of a metadata portal to support Marine Strategy Framework Directive (MSFD) implementation

NASA Astrophysics Data System (ADS)

Wood, Chris

2016-04-01

Under the Marine Strategy Framework Directive (MSFD), EU Member States are mandated to achieve or maintain 'Good Environmental Status' (GES) in their marine areas by 2020, through a series of Programme of Measures (PoMs). The Celtic Seas Partnership (CSP), an EU LIFE+ project, aims to support policy makers, special-interest groups, users of the marine environment, and other interested stakeholders on MSFD implementation in the Celtic Seas geographical area. As part of this support, a metadata portal has been built to provide a signposting service to datasets that are relevant to MSFD within the Celtic Seas. To ensure that the metadata has the widest possible reach, a linked data approach was employed to construct the database. Although the metadata are stored in a traditional RDBS, the metadata are exposed as linked data via the D2RQ platform, allowing virtual RDF graphs to be generated. SPARQL queries can be executed against the end-point allowing any user to manipulate the metadata. D2RQ's mapping language, based on turtle, was used to map a wide range of relevant ontologies to the metadata (e.g. The Provenance Ontology (prov-o), Ocean Data Ontology (odo), Dublin Core Elements and Terms (dc & dcterms), Friend of a Friend (foaf), and Geospatial ontologies (geo)) allowing users to browse the metadata, either via SPARQL queries or by using D2RQ's HTML interface. The metadata were further enhanced by mapping relevant parameters to the NERC Vocabulary Server, itself built on a SPARQL endpoint. Additionally, a custom web front-end was built to enable users to browse the metadata and express queries through an intuitive graphical user interface that requires no prior knowledge of SPARQL. As well as providing means to browse the data via MSFD-related parameters (Descriptor, Criteria, and Indicator), the metadata records include the dataset's country of origin, the list of organisations involved in the management of the data, and links to any relevant INSPIRE-compliant services relating to the dataset. The web front-end therefore enables users to effectively filter, sort, or search the metadata. As the MSFD timeline requires Member States to review their progress on achieving or maintaining GES every six years, the timely development of this metadata portal will not only aid interested stakeholders in understanding how member states are meeting their targets, but also shows how linked data can be used effectively to support policy makers and associated legislative bodies.

Proposed biopsy performance benchmarks for MRI based on an audit of a large academic center.

PubMed

Sedora Román, Neda I; Mehta, Tejas S; Sharpe, Richard E; Slanetz, Priscilla J; Venkataraman, Shambhavi; Fein-Zachary, Valerie; Dialani, Vandana

2018-05-01

Performance benchmarks exist for mammography (MG); however, performance benchmarks for magnetic resonance imaging (MRI) are not yet fully developed. The purpose of our study was to perform an MRI audit based on established MG and screening MRI benchmarks and to review whether these benchmarks can be applied to an MRI practice. An IRB approved retrospective review of breast MRIs was performed at our center from 1/1/2011 through 12/31/13. For patients with biopsy recommendation, core biopsy and surgical pathology results were reviewed. The data were used to derive mean performance parameter values, including abnormal interpretation rate (AIR), positive predictive value (PPV), cancer detection rate (CDR), percentage of minimal cancers and axillary node negative cancers and compared with MG and screening MRI benchmarks. MRIs were also divided by screening and diagnostic indications to assess for differences in performance benchmarks amongst these two groups. Of the 2455 MRIs performed over 3-years, 1563 were performed for screening indications and 892 for diagnostic indications. With the exception of PPV2 for screening breast MRIs from 2011 to 2013, PPVs were met for our screening and diagnostic populations when compared to the MRI screening benchmarks established by the Breast Imaging Reporting and Data System (BI-RADS) 5 Atlas ® . AIR and CDR were lower for screening indications as compared to diagnostic indications. New MRI screening benchmarks can be used for screening MRI audits while the American College of Radiology (ACR) desirable goals for diagnostic MG can be used for diagnostic MRI audits. Our study corroborates established findings regarding differences in AIR and CDR amongst screening versus diagnostic indications. © 2017 Wiley Periodicals, Inc.

How to Advance TPC Benchmarks with Dependability Aspects

NASA Astrophysics Data System (ADS)

Almeida, Raquel; Poess, Meikel; Nambiar, Raghunath; Patil, Indira; Vieira, Marco

Transactional systems are the core of the information systems of most organizations. Although there is general acknowledgement that failures in these systems often entail significant impact both on the proceeds and reputation of companies, the benchmarks developed and managed by the Transaction Processing Performance Council (TPC) still maintain their focus on reporting bare performance. Each TPC benchmark has to pass a list of dependability-related tests (to verify ACID properties), but not all benchmarks require measuring their performances. While TPC-E measures the recovery time of some system failures, TPC-H and TPC-C only require functional correctness of such recovery. Consequently, systems used in TPC benchmarks are tuned mostly for performance. In this paper we argue that nowadays systems should be tuned for a more comprehensive suite of dependability tests, and that a dependability metric should be part of TPC benchmark publications. The paper discusses WHY and HOW this can be achieved. Two approaches are introduced and discussed: augmenting each TPC benchmark in a customized way, by extending each specification individually; and pursuing a more unified approach, defining a generic specification that could be adjoined to any TPC benchmark.

Statistical Analysis of NAS Parallel Benchmarks and LINPACK Results

NASA Technical Reports Server (NTRS)

Meuer, Hans-Werner; Simon, Horst D.; Strohmeier, Erich; Lasinski, T. A. (Technical Monitor)

1994-01-01

In the last three years extensive performance data have been reported for parallel machines both based on the NAS Parallel Benchmarks, and on LINPACK. In this study we have used the reported benchmark results and performed a number of statistical experiments using factor, cluster, and regression analyses. In addition to the performance results of LINPACK and the eight NAS parallel benchmarks, we have also included peak performance of the machine, and the LINPACK n and n(sub 1/2) values. Some of the results and observations can be summarized as follows: 1) All benchmarks are strongly correlated with peak performance. 2) LINPACK and EP have each a unique signature. 3) The remaining NPB can grouped into three groups as follows: (CG and IS), (LU and SP), and (MG, FT, and BT). Hence three (or four with EP) benchmarks are sufficient to characterize the overall NPB performance. Our poster presentation will follow a standard poster format, and will present the data of our statistical analysis in detail.

Performance analysis of fusion nuclear-data benchmark experiments for light to heavy materials in MeV energy region with a neutron spectrum shifter

NASA Astrophysics Data System (ADS)

Murata, Isao; Ohta, Masayuki; Miyamaru, Hiroyuki; Kondo, Keitaro; Yoshida, Shigeo; Iida, Toshiyuki; Ochiai, Kentaro; Konno, Chikara

2011-10-01

Nuclear data are indispensable for development of fusion reactor candidate materials. However, benchmarking of the nuclear data in MeV energy region is not yet adequate. In the present study, benchmark performance in the MeV energy region was investigated theoretically for experiments by using a 14 MeV neutron source. We carried out a systematical analysis for light to heavy materials. As a result, the benchmark performance for the neutron spectrum was confirmed to be acceptable, while for gamma-rays it was not sufficiently accurate. Consequently, a spectrum shifter has to be applied. Beryllium had the best performance as a shifter. Moreover, a preliminary examination of whether it is really acceptable that only the spectrum before the last collision is considered in the benchmark performance analysis. It was pointed out that not only the last collision but also earlier collisions should be considered equally in the benchmark performance analysis.

Research on computer systems benchmarking

NASA Technical Reports Server (NTRS)

Smith, Alan Jay (Principal Investigator)

1996-01-01

This grant addresses the topic of research on computer systems benchmarking and is more generally concerned with performance issues in computer systems. This report reviews work in those areas during the period of NASA support under this grant. The bulk of the work performed concerned benchmarking and analysis of CPUs, compilers, caches, and benchmark programs. The first part of this work concerned the issue of benchmark performance prediction. A new approach to benchmarking and machine characterization was reported, using a machine characterizer that measures the performance of a given system in terms of a Fortran abstract machine. Another report focused on analyzing compiler performance. The performance impact of optimization in the context of our methodology for CPU performance characterization was based on the abstract machine model. Benchmark programs are analyzed in another paper. A machine-independent model of program execution was developed to characterize both machine performance and program execution. By merging these machine and program characterizations, execution time can be estimated for arbitrary machine/program combinations. The work was continued into the domain of parallel and vector machines, including the issue of caches in vector processors and multiprocessors. All of the afore-mentioned accomplishments are more specifically summarized in this report, as well as those smaller in magnitude supported by this grant.

Method and system for benchmarking computers

DOEpatents

Gustafson, John L.

1993-09-14

A testing system and method for benchmarking computer systems. The system includes a store containing a scalable set of tasks to be performed to produce a solution in ever-increasing degrees of resolution as a larger number of the tasks are performed. A timing and control module allots to each computer a fixed benchmarking interval in which to perform the stored tasks. Means are provided for determining, after completion of the benchmarking interval, the degree of progress through the scalable set of tasks and for producing a benchmarking rating relating to the degree of progress for each computer.

Performance Evaluation of Supercomputers using HPCC and IMB Benchmarks

NASA Technical Reports Server (NTRS)

Saini, Subhash; Ciotti, Robert; Gunney, Brian T. N.; Spelce, Thomas E.; Koniges, Alice; Dossa, Don; Adamidis, Panagiotis; Rabenseifner, Rolf; Tiyyagura, Sunil R.; Mueller, Matthias;

Electric-Drive Vehicle Thermal Performance Benchmarking | Transportation

Science.gov Websites

studies are as follows: Characterize the thermal resistance and conductivity of various layers in the Research | NREL Electric-Drive Vehicle Thermal Performance Benchmarking Electric-Drive Vehicle Thermal Performance Benchmarking A photo of the internal components of an automotive inverter. NREL

Combining Phase Identification and Statistic Modeling for Automated Parallel Benchmark Generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Ye; Ma, Xiaosong; Liu, Qing Gary

2015-01-01

Parallel application benchmarks are indispensable for evaluating/optimizing HPC software and hardware. However, it is very challenging and costly to obtain high-fidelity benchmarks reflecting the scale and complexity of state-of-the-art parallel applications. Hand-extracted synthetic benchmarks are time-and labor-intensive to create. Real applications themselves, while offering most accurate performance evaluation, are expensive to compile, port, reconfigure, and often plainly inaccessible due to security or ownership concerns. This work contributes APPRIME, a novel tool for trace-based automatic parallel benchmark generation. Taking as input standard communication-I/O traces of an application's execution, it couples accurate automatic phase identification with statistical regeneration of event parameters tomore » create compact, portable, and to some degree reconfigurable parallel application benchmarks. Experiments with four NAS Parallel Benchmarks (NPB) and three real scientific simulation codes confirm the fidelity of APPRIME benchmarks. They retain the original applications' performance characteristics, in particular the relative performance across platforms.« less

Performance Against WELCOA's Worksite Health Promotion Benchmarks Across Years Among Selected US Organizations.

PubMed

Weaver, GracieLee M; Mendenhall, Brandon N; Hunnicutt, David; Picarella, Ryan; Leffelman, Brittanie; Perko, Michael; Bibeau, Daniel L

2018-05-01

The purpose of this study was to quantify the performance of organizations' worksite health promotion (WHP) activities against the benchmarking criteria included in the Well Workplace Checklist (WWC). The Wellness Council of America (WELCOA) developed a tool to assess WHP with its 100-item WWC, which represents WELCOA's 7 performance benchmarks. Workplaces. This study includes a convenience sample of organizations who completed the checklist from 2008 to 2015. The sample size was 4643 entries from US organizations. The WWC includes demographic questions, general questions about WHP programs, and scales to measure the performance against the WELCOA 7 benchmarks. Descriptive analyses of WWC items were completed separately for each year of the study period. The majority of the organizations represented each year were multisite, multishift, medium- to large-sized companies mostly in the services industry. Despite yearly changes in participating organizations, results across the WELCOA 7 benchmark scores were consistent year to year. Across all years, benchmarks that organizations performed the lowest were senior-level support, data collection, and programming; wellness teams and supportive environments were the highest scoring benchmarks. In an era marked with economic swings and health-care reform, it appears that organizations are staying consistent in their performance across these benchmarks. The WWC could be useful for organizations, practitioners, and researchers in assessing the quality of WHP programs.

Cross-industry benchmarking: is it applicable to the operating room?

PubMed

Marco, A P; Hart, S

2001-01-01

The use of benchmarking has been growing in nonmedical industries. This concept is being increasingly applied to medicine as the industry strives to improve quality and improve financial performance. Benchmarks can be either internal (set by the institution) or external (use other's performance as a goal). In some industries, benchmarking has crossed industry lines to identify breakthroughs in thinking. In this article, we examine whether the airline industry can be used as a source of external process benchmarking for the operating room.

Evaluating the Effect of Labeled Benchmarks on Children’s Number Line Estimation Performance and Strategy Use

PubMed Central

Peeters, Dominique; Sekeris, Elke; Verschaffel, Lieven; Luwel, Koen

2017-01-01

Some authors argue that age-related improvements in number line estimation (NLE) performance result from changes in strategy use. More specifically, children’s strategy use develops from only using the origin of the number line, to using the origin and the endpoint, to eventually also relying on the midpoint of the number line. Recently, Peeters et al. (unpublished) investigated whether the provision of additional unlabeled benchmarks at 25, 50, and 75% of the number line, positively affects third and fifth graders’ NLE performance and benchmark-based strategy use. It was found that only the older children benefitted from the presence of these benchmarks at the quartiles of the number line (i.e., 25 and 75%), as they made more use of these benchmarks, leading to more accurate estimates. A possible explanation for this lack of improvement in third graders might be their inability to correctly link the presented benchmarks with their corresponding numerical values. In the present study, we investigated whether labeling these benchmarks with their corresponding numerical values, would have a positive effect on younger children’s NLE performance and quartile-based strategy use as well. Third and sixth graders were assigned to one of three conditions: (a) a control condition with an empty number line bounded by 0 at the origin and 1,000 at the endpoint, (b) an unlabeled condition with three additional external benchmarks without numerical labels at 25, 50, and 75% of the number line, and (c) a labeled condition in which these benchmarks were labeled with 250, 500, and 750, respectively. Results indicated that labeling the benchmarks has a positive effect on third graders’ NLE performance and quartile-based strategy use, whereas sixth graders already benefited from the mere provision of unlabeled benchmarks. These findings imply that children’s benchmark-based strategy use can be stimulated by adding additional externally provided benchmarks on the number line, but that, depending on children’s age and familiarity with the number range, these additional external benchmarks might need to be labeled. PMID:28713302

Evaluating the Effect of Labeled Benchmarks on Children's Number Line Estimation Performance and Strategy Use.

PubMed

Peeters, Dominique; Sekeris, Elke; Verschaffel, Lieven; Luwel, Koen

2017-01-01

Some authors argue that age-related improvements in number line estimation (NLE) performance result from changes in strategy use. More specifically, children's strategy use develops from only using the origin of the number line, to using the origin and the endpoint, to eventually also relying on the midpoint of the number line. Recently, Peeters et al. (unpublished) investigated whether the provision of additional unlabeled benchmarks at 25, 50, and 75% of the number line, positively affects third and fifth graders' NLE performance and benchmark-based strategy use. It was found that only the older children benefitted from the presence of these benchmarks at the quartiles of the number line (i.e., 25 and 75%), as they made more use of these benchmarks, leading to more accurate estimates. A possible explanation for this lack of improvement in third graders might be their inability to correctly link the presented benchmarks with their corresponding numerical values. In the present study, we investigated whether labeling these benchmarks with their corresponding numerical values, would have a positive effect on younger children's NLE performance and quartile-based strategy use as well. Third and sixth graders were assigned to one of three conditions: (a) a control condition with an empty number line bounded by 0 at the origin and 1,000 at the endpoint, (b) an unlabeled condition with three additional external benchmarks without numerical labels at 25, 50, and 75% of the number line, and (c) a labeled condition in which these benchmarks were labeled with 250, 500, and 750, respectively. Results indicated that labeling the benchmarks has a positive effect on third graders' NLE performance and quartile-based strategy use, whereas sixth graders already benefited from the mere provision of unlabeled benchmarks. These findings imply that children's benchmark-based strategy use can be stimulated by adding additional externally provided benchmarks on the number line, but that, depending on children's age and familiarity with the number range, these additional external benchmarks might need to be labeled.

Benchmarking child and adolescent mental health organizations.

PubMed

Brann, Peter; Walter, Garry; Coombs, Tim

2011-04-01

This paper describes aspects of the child and adolescent benchmarking forums that were part of the National Mental Health Benchmarking Project (NMHBP). These forums enabled participating child and adolescent mental health organizations to benchmark themselves against each other, with a view to understanding variability in performance against a range of key performance indicators (KPIs). Six child and adolescent mental health organizations took part in the NMHBP. Representatives from these organizations attended eight benchmarking forums at which they documented their performance against relevant KPIs. They also undertook two special projects designed to help them understand the variation in performance on given KPIs. There was considerable inter-organization variability on many of the KPIs. Even within organizations, there was often substantial variability over time. The variability in indicator data raised many questions for participants. This challenged participants to better understand and describe their local processes, prompted them to collect additional data, and stimulated them to make organizational comparisons. These activities fed into a process of reflection about their performance. Benchmarking has the potential to illuminate intra- and inter-organizational performance in the child and adolescent context.

Full Chain Benchmarking for Open Architecture Airborne ISR Systems: A Case Study for GMTI Radar Applications

DTIC Science & Technology

2015-09-15

middleware implementations via a common object-oriented software hierarchy, with library -specific implementations of the five GMTI benchmark ...Full-Chain Benchmarking for Open Architecture Airborne ISR Systems A Case Study for GMTI Radar Applications Matthias Beebe, Matthew Alexander...time performance, effective benchmarks are necessary to ensure that an ARP system can meet the mission constraints and performance requirements of

Key performance indicators to benchmark hospital information systems - a delphi study.

PubMed

Hübner-Bloder, G; Ammenwerth, E

2009-01-01

To identify the key performance indicators for hospital information systems (HIS) that can be used for HIS benchmarking. A Delphi survey with one qualitative and two quantitative rounds. Forty-four HIS experts from health care IT practice and academia participated in all three rounds. Seventy-seven performance indicators were identified and organized into eight categories: technical quality, software quality, architecture and interface quality, IT vendor quality, IT support and IT department quality, workflow support quality, IT outcome quality, and IT costs. The highest ranked indicators are related to clinical workflow support and user satisfaction. Isolated technical indicators or cost indicators were not seen as useful. The experts favored an interdisciplinary group of all the stakeholders, led by hospital management, to conduct the HIS benchmarking. They proposed benchmarking activities both in regular (annual) intervals as well as at defined events (for example after IT introduction). Most of the experts stated that in their institutions no HIS benchmarking activities are being performed at the moment. In the context of IT governance, IT benchmarking is gaining importance in the healthcare area. The found indicators reflect the view of health care IT professionals and researchers. Research is needed to further validate and operationalize key performance indicators, to provide an IT benchmarking framework, and to provide open repositories for a comparison of the HIS benchmarks of different hospitals.

DBpedia and the Live Extraction of Structured Data from Wikipedia

ERIC Educational Resources Information Center

Morsey, Mohamed; Lehmann, Jens; Auer, Soren; Stadler, Claus; Hellmann, Sebastian

2012-01-01

Purpose: DBpedia extracts structured information from Wikipedia, interlinks it with other knowledge bases and freely publishes the results on the web using Linked Data and SPARQL. However, the DBpedia release process is heavyweight and releases are sometimes based on several months old data. DBpedia-Live solves this problem by providing a live…

BioSearch: a semantic search engine for Bio2RDF

PubMed Central

Qiu, Honglei; Huang, Jiacheng

2017-01-01

Abstract Biomedical data are growing at an incredible pace and require substantial expertise to organize data in a manner that makes them easily findable, accessible, interoperable and reusable. Massive effort has been devoted to using Semantic Web standards and technologies to create a network of Linked Data for the life sciences, among others. However, while these data are accessible through programmatic means, effective user interfaces for non-experts to SPARQL endpoints are few and far between. Contributing to user frustrations is that data are not necessarily described using common vocabularies, thereby making it difficult to aggregate results, especially when distributed across multiple SPARQL endpoints. We propose BioSearch — a semantic search engine that uses ontologies to enhance federated query construction and organize search results. BioSearch also features a simplified query interface that allows users to optionally filter their keywords according to classes, properties and datasets. User evaluation demonstrated that BioSearch is more effective and usable than two state of the art search and browsing solutions. Database URL: http://ws.nju.edu.cn/biosearch/ PMID:29220451

A Methodology for Benchmarking Relational Database Machines,

DTIC Science & Technology

1984-01-01

user benchmarks is to compare the multiple users to the best-case performance The data for each query classification coll and the performance...called a benchmark. The term benchmark originates from the markers used by sur - veyors in establishing common reference points for their measure...formatted databases. In order to further simplify the problem, we restrict our study to those DBMs which support the relational model. A sur - vey

Evaluation of control strategies using an oxidation ditch benchmark.

PubMed

Abusam, A; Keesman, K J; Spanjers, H; van, Straten G; Meinema, K

2002-01-01

This paper presents validation and implementation results of a benchmark developed for a specific full-scale oxidation ditch wastewater treatment plant. A benchmark is a standard simulation procedure that can be used as a tool in evaluating various control strategies proposed for wastewater treatment plants. It is based on model and performance criteria development. Testing of this benchmark, by comparing benchmark predictions to real measurements of the electrical energy consumptions and amounts of disposed sludge for a specific oxidation ditch WWTP, has shown that it can (reasonably) be used for evaluating the performance of this WWTP. Subsequently, the validated benchmark was then used in evaluating some basic and advanced control strategies. Some of the interesting results obtained are the following: (i) influent flow splitting ratio, between the first and the fourth aerated compartments of the ditch, has no significant effect on the TN concentrations in the effluent, and (ii) for evaluation of long-term control strategies, future benchmarks need to be able to assess settlers' performance.

Bim-Gis Integrated Geospatial Information Model Using Semantic Web and Rdf Graphs

NASA Astrophysics Data System (ADS)

Hor, A.-H.; Jadidi, A.; Sohn, G.

2016-06-01

In recent years, 3D virtual indoor/outdoor urban modelling becomes a key spatial information framework for many civil and engineering applications such as evacuation planning, emergency and facility management. For accomplishing such sophisticate decision tasks, there is a large demands for building multi-scale and multi-sourced 3D urban models. Currently, Building Information Model (BIM) and Geographical Information Systems (GIS) are broadly used as the modelling sources. However, data sharing and exchanging information between two modelling domains is still a huge challenge; while the syntactic or semantic approaches do not fully provide exchanging of rich semantic and geometric information of BIM into GIS or vice-versa. This paper proposes a novel approach for integrating BIM and GIS using semantic web technologies and Resources Description Framework (RDF) graphs. The novelty of the proposed solution comes from the benefits of integrating BIM and GIS technologies into one unified model, so-called Integrated Geospatial Information Model (IGIM). The proposed approach consists of three main modules: BIM-RDF and GIS-RDF graphs construction, integrating of two RDF graphs, and query of information through IGIM-RDF graph using SPARQL. The IGIM generates queries from both the BIM and GIS RDF graphs resulting a semantically integrated model with entities representing both BIM classes and GIS feature objects with respect to the target-client application. The linkage between BIM-RDF and GIS-RDF is achieved through SPARQL endpoints and defined by a query using set of datasets and entity classes with complementary properties, relationships and geometries. To validate the proposed approach and its performance, a case study was also tested using IGIM system design.

Mashup of Geo and Space Science Data Provided via Relational Databases in the Semantic Web

NASA Astrophysics Data System (ADS)

Ritschel, B.; Seelus, C.; Neher, G.; Iyemori, T.; Koyama, Y.; Yatagai, A. I.; Murayama, Y.; King, T. A.; Hughes, J. S.; Fung, S. F.; Galkin, I. A.; Hapgood, M. A.; Belehaki, A.

2014-12-01

The use of RDBMS for the storage and management of geo and space science data and/or metadata is very common. Although the information stored in tables is based on a data model and therefore well organized and structured, a direct mashup with RDF based data stored in triple stores is not possible. One solution of the problem consists in the transformation of the whole content into RDF structures and storage in triple stores. Another interesting way is the use of a specific system/service, such as e.g. D2RQ, for the access to relational database content as virtual, read only RDF graphs. The Semantic Web based -proof of concept- GFZ ISDC uses the triple store Virtuoso for the storage of general context information/metadata to geo and space science satellite and ground station data. There is information about projects, platforms, instruments, persons, product types, etc. available but no detailed metadata about the data granuals itself. Such important information, as e.g. start or end time or the detailed spatial coverage of a single measurement is stored in RDBMS tables of the ISDC catalog system only. In order to provide a seamless access to all available information about the granuals/data products a mashup of the different data resources (triple store and RDBMS) is necessary. This paper describes the use of D2RQ for a Semantic Web/SPARQL based mashup of relational databases used for ISDC data server but also for the access to IUGONET and/or ESPAS and further geo and space science data resources. RDBMS Relational Database Management System RDF Resource Description Framework SPARQL SPARQL Protocol And RDF Query Language D2RQ Accessing Relational Databases as Virtual RDF Graphs GFZ ISDC German Research Centre for Geosciences Information System and Data Center IUGONET Inter-university Upper Atmosphere Global Observation Network (Japanese project) ESPAS Near earth space data infrastructure for e-science (European Union funded project)

Accumulo/Hadoop, MongoDB, and Elasticsearch Performance for Semi Structured Intrusion Detection (IDS) Data

DTIC Science & Technology

2016-11-01

iii Contents List of Figures v 1. Introduction 1 2. Background 1 3. Yahoo ! Cloud Serving Benchmark (YCSB) 2 3.1 Data Loading and Performance...transactional system. 3. Yahoo ! Cloud Serving Benchmark (YCSB) 3.1 Data Loading and Performance Testing Framework When originally setting out to perform the...that referred to a data loading and performance testing framework, Yahoo ! Cloud Serving Benchmark (YCSB).12 This framework is freely available and

Exposing SAMOS Data and Vocabularies within the Semantic Web

NASA Astrophysics Data System (ADS)

Dockery, Nkemdirim; Elya, Jocelyn; Smith, Shawn

2014-05-01

As part of the Ocean Data Interoperability Platform (ODIP), we at the Center for Ocean-Atmospheric Prediction Studies (COAPS) will present the development process for the exposure of quality-controlled data and core vocabularies managed by the Shipboard Automated Meteorological Oceanographic System (SAMOS) initiative using Semantic Web technologies. Participants in the SAMOS initiative collect continuous navigational (position, course, heading, speed), meteorological (winds, pressure, temperature, humidity, radiation), and near-surface oceanographic (sea temperature, salinity) parameters while at sea. One-minute interval observations are packaged and transmitted back to COAPS via daily emails, where they undergo standardized formatting and quality control. The authors will present methods used to expose these daily datasets. The Semantic Web, a vision of the World Wide Web Consortium, focuses on extending the principles of the web from connecting documents to connecting data. The creation of a web of Linked Data that can be used across different applications in a machine-readable way is the ultimate goal. The Resource Description Framework (RDF) is the standard language and format used in the Semantic Web. RDF pages may be queried using the SPARQL Protocol and RDF Query Language (SPARQL). The authors will showcase the development of RDF resources that map SAMOS vocabularies to internationally served vocabularies such as those found in the Natural Environment Research Council (NERC) Vocabulary Server. Each individual SAMOS vocabulary term (data parameter and quality control flag) will be described in an RDF resource page. These RDF resources will define each SAMOS vocabulary term and provide a link to the mapped vocabulary term (or multiple terms) served externally. Along with enhanced retrieval by parameter, time, and location, we will be able to add additional parameters with the confidence that they follow an international standard. The production of RDF resources that link daily SAMOS data to descriptors such as parameters, time and location information, quality assurance reports, and cruise tracks will also be described. The data is housed on a Thematic Real-time Environmental Distributed Data Services (THREDDS) data server, so these RDF resources will enable enhanced retrieval by any of the linked descriptors. We will showcase our collaboration with the Rolling Deck to Repository (R2R) program to develop SPARQL endpoints that distribute SAMOS content. R2R packages and transmits data on a per cruise basis, so an immediate result of the SAMOS exposure will be the narrowing of the gap between expedition type data (e.g. R2R cruises) and SAMOS observatory type data. The authors will present the development of RDF resources that will collectively expose shipboard data, vocabularies, and quality assurance reports in an overall structure which will serve as the basis for a COAPS SPARQL endpoint, enabling easier programmatic access to SAMOS data.

OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE - A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnis Judzis

2003-01-01

This document details the progress to date on the ''OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE -- A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING'' contract for the quarter starting October 2002 through December 2002. Even though we are awaiting the optimization portion of the testing program, accomplishments included the following: (1) Smith International participated in the DOE Mud Hammer program through full scale benchmarking testing during the week of 4 November 2003. (2) TerraTek acknowledges Smith International, BP America, PDVSA, and ConocoPhillips for cost-sharing the Smith benchmarking tests allowing extension of the contract to add to themore » benchmarking testing program. (3) Following the benchmark testing of the Smith International hammer, representatives from DOE/NETL, TerraTek, Smith International and PDVSA met at TerraTek in Salt Lake City to review observations, performance and views on the optimization step for 2003. (4) The December 2002 issue of Journal of Petroleum Technology (Society of Petroleum Engineers) highlighted the DOE fluid hammer testing program and reviewed last years paper on the benchmark performance of the SDS Digger and Novatek hammers. (5) TerraTek's Sid Green presented a technical review for DOE/NETL personnel in Morgantown on ''Impact Rock Breakage'' and its importance on improving fluid hammer performance. Much discussion has taken place on the issues surrounding mud hammer performance at depth conditions.« less

Benchmark for Strategic Performance Improvement.

ERIC Educational Resources Information Center

Gohlke, Annette

1997-01-01

Explains benchmarking, a total quality management tool used to measure and compare the work processes in a library with those in other libraries to increase library performance. Topics include the main groups of upper management, clients, and staff; critical success factors for each group; and benefits of benchmarking. (Author/LRW)

OWL2 benchmarking for the evaluation of knowledge based systems.

PubMed

Khan, Sher Afgun; Qadir, Muhammad Abdul; Abbas, Muhammad Azeem; Afzal, Muhammad Tanvir

2017-01-01

OWL2 semantics are becoming increasingly popular for the real domain applications like Gene engineering and health MIS. The present work identifies the research gap that negligible attention has been paid to the performance evaluation of Knowledge Base Systems (KBS) using OWL2 semantics. To fulfil this identified research gap, an OWL2 benchmark for the evaluation of KBS is proposed. The proposed benchmark addresses the foundational blocks of an ontology benchmark i.e. data schema, workload and performance metrics. The proposed benchmark is tested on memory based, file based, relational database and graph based KBS for performance and scalability measures. The results show that the proposed benchmark is able to evaluate the behaviour of different state of the art KBS on OWL2 semantics. On the basis of the results, the end users (i.e. domain expert) would be able to select a suitable KBS appropriate for his domain.

Benchmarking--Measuring and Comparing for Continuous Improvement.

ERIC Educational Resources Information Center

Henczel, Sue

2002-01-01

Discussion of benchmarking focuses on the use of internal and external benchmarking by special librarians. Highlights include defining types of benchmarking; historical development; benefits, including efficiency, improved performance, increased competitiveness, and better decision making; problems, including inappropriate adaptation; developing a…

Establishing Benchmarks for Outcome Indicators: A Statistical Approach to Developing Performance Standards.

ERIC Educational Resources Information Center

Henry, Gary T.; And Others

1992-01-01

A statistical technique is presented for developing performance standards based on benchmark groups. The benchmark groups are selected using a multivariate technique that relies on a squared Euclidean distance method. For each observation unit (a school district in the example), a unique comparison group is selected. (SLD)

Beyond Benchmarking: Value-Adding Metrics

ERIC Educational Resources Information Center

Fitz-enz, Jac

2007-01-01

HR metrics has grown up a bit over the past two decades, moving away from simple benchmarking practices and toward a more inclusive approach to measuring institutional performance and progress. In this article, the acknowledged "father" of human capital performance benchmarking provides an overview of several aspects of today's HR metrics…

The NAS kernel benchmark program

NASA Technical Reports Server (NTRS)

Bailey, D. H.; Barton, J. T.

1985-01-01

A collection of benchmark test kernels that measure supercomputer performance has been developed for the use of the NAS (Numerical Aerodynamic Simulation) program at the NASA Ames Research Center. This benchmark program is described in detail and the specific ground rules are given for running the program as a performance test.

High Performance Descriptive Semantic Analysis of Semantic Graph Databases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Joslyn, Cliff A.; Adolf, Robert D.; al-Saffar, Sinan

As semantic graph database technology grows to address components ranging from extant large triple stores to SPARQL endpoints over SQL-structured relational databases, it will become increasingly important to be able to understand their inherent semantic structure, whether codified in explicit ontologies or not. Our group is researching novel methods for what we call descriptive semantic analysis of RDF triplestores, to serve purposes of analysis, interpretation, visualization, and optimization. But data size and computational complexity makes it increasingly necessary to bring high performance computational resources to bear on this task. Our research group built a novel high performance hybrid system comprisingmore » computational capability for semantic graph database processing utilizing the large multi-threaded architecture of the Cray XMT platform, conventional servers, and large data stores. In this paper we describe that architecture and our methods, and present the results of our analyses of basic properties, connected components, namespace interaction, and typed paths such for the Billion Triple Challenge 2010 dataset.« less

LASL benchmark performance 1978. [CDC STAR-100, 6600, 7600, Cyber 73, and CRAY-1

DOE Office of Scientific and Technical Information (OSTI.GOV)

McKnight, A.L.

1979-08-01

This report presents the results of running several benchmark programs on a CDC STAR-100, a Cray Research CRAY-1, a CDC 6600, a CDC 7600, and a CDC Cyber 73. The benchmark effort included CRAY-1's at several installations running different operating systems and compilers. This benchmark is part of an ongoing program at Los Alamos Scientific Laboratory to collect performance data and monitor the development trend of supercomputers. 3 tables.

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, David (Editor); Barton, John (Editor); Lasinski, Thomas (Editor); Simon, Horst (Editor)

1993-01-01

A new set of benchmarks was developed for the performance evaluation of highly parallel supercomputers. These benchmarks consist of a set of kernels, the 'Parallel Kernels,' and a simulated application benchmark. Together they mimic the computation and data movement characteristics of large scale computational fluid dynamics (CFD) applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification - all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

Toward Scalable Benchmarks for Mass Storage Systems

NASA Technical Reports Server (NTRS)

Miller, Ethan L.

1996-01-01

This paper presents guidelines for the design of a mass storage system benchmark suite, along with preliminary suggestions for programs to be included. The benchmarks will measure both peak and sustained performance of the system as well as predicting both short- and long-term behavior. These benchmarks should be both portable and scalable so they may be used on storage systems from tens of gigabytes to petabytes or more. By developing a standard set of benchmarks that reflect real user workload, we hope to encourage system designers and users to publish performance figures that can be compared with those of other systems. This will allow users to choose the system that best meets their needs and give designers a tool with which they can measure the performance effects of improvements to their systems.

Determining the sample size required to establish whether a medical device is non-inferior to an external benchmark.

PubMed

Sayers, Adrian; Crowther, Michael J; Judge, Andrew; Whitehouse, Michael R; Blom, Ashley W

2017-08-28

The use of benchmarks to assess the performance of implants such as those used in arthroplasty surgery is a widespread practice. It provides surgeons, patients and regulatory authorities with the reassurance that implants used are safe and effective. However, it is not currently clear how or how many implants should be statistically compared with a benchmark to assess whether or not that implant is superior, equivalent, non-inferior or inferior to the performance benchmark of interest.We aim to describe the methods and sample size required to conduct a one-sample non-inferiority study of a medical device for the purposes of benchmarking. Simulation study. Simulation study of a national register of medical devices. We simulated data, with and without a non-informative competing risk, to represent an arthroplasty population and describe three methods of analysis (z-test, 1-Kaplan-Meier and competing risks) commonly used in surgical research. We evaluate the performance of each method using power, bias, root-mean-square error, coverage and CI width. 1-Kaplan-Meier provides an unbiased estimate of implant net failure, which can be used to assess if a surgical device is non-inferior to an external benchmark. Small non-inferiority margins require significantly more individuals to be at risk compared with current benchmarking standards. A non-inferiority testing paradigm provides a useful framework for determining if an implant meets the required performance defined by an external benchmark. Current contemporary benchmarking standards have limited power to detect non-inferiority, and substantially larger samples sizes, in excess of 3200 procedures, are required to achieve a power greater than 60%. It is clear when benchmarking implant performance, net failure estimated using 1-KM is preferential to crude failure estimated by competing risk models. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

The Isprs Benchmark on Indoor Modelling

NASA Astrophysics Data System (ADS)

Khoshelham, K.; Díaz Vilariño, L.; Peter, M.; Kang, Z.; Acharya, D.

2017-09-01

Automated generation of 3D indoor models from point cloud data has been a topic of intensive research in recent years. While results on various datasets have been reported in literature, a comparison of the performance of different methods has not been possible due to the lack of benchmark datasets and a common evaluation framework. The ISPRS benchmark on indoor modelling aims to address this issue by providing a public benchmark dataset and an evaluation framework for performance comparison of indoor modelling methods. In this paper, we present the benchmark dataset comprising several point clouds of indoor environments captured by different sensors. We also discuss the evaluation and comparison of indoor modelling methods based on manually created reference models and appropriate quality evaluation criteria. The benchmark dataset is available for download at: http://www2.isprs.org/commissions/comm4/wg5/benchmark-on-indoor-modelling.html.

Benchmarking Using Basic DBMS Operations

NASA Astrophysics Data System (ADS)

Crolotte, Alain; Ghazal, Ahmad

The TPC-H benchmark proved to be successful in the decision support area. Many commercial database vendors and their related hardware vendors used these benchmarks to show the superiority and competitive edge of their products. However, over time, the TPC-H became less representative of industry trends as vendors keep tuning their database to this benchmark-specific workload. In this paper, we present XMarq, a simple benchmark framework that can be used to compare various software/hardware combinations. Our benchmark model is currently composed of 25 queries that measure the performance of basic operations such as scans, aggregations, joins and index access. This benchmark model is based on the TPC-H data model due to its maturity and well-understood data generation capability. We also propose metrics to evaluate single-system performance and compare two systems. Finally we illustrate the effectiveness of this model by showing experimental results comparing two systems under different conditions.

Benchmarks--Standards Comparisons. Math Competencies: EFF Benchmarks Comparison [and] Reading Competencies: EFF Benchmarks Comparison [and] Writing Competencies: EFF Benchmarks Comparison.

ERIC Educational Resources Information Center

Kent State Univ., OH. Ohio Literacy Resource Center.

This document is intended to show the relationship between Ohio's Standards and Competencies, Equipped for the Future's (EFF's) Standards and Components of Performance, and Ohio's Revised Benchmarks. The document is divided into three parts, with Part 1 covering mathematics instruction, Part 2 covering reading instruction, and Part 3 covering…

Benchmarking can add up for healthcare accounting.

PubMed

Czarnecki, M T

1994-09-01

In 1993, a healthcare accounting and finance benchmarking survey of hospital and nonhospital organizations gathered statistics about key common performance areas. A low response did not allow for statistically significant findings, but the survey identified performance measures that can be used in healthcare financial management settings. This article explains the benchmarking process and examines some of the 1993 study's findings.

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, D. H.; Barszcz, E.; Barton, J. T.; Carter, R. L.; Lasinski, T. A.; Browning, D. S.; Dagum, L.; Fatoohi, R. A.; Frederickson, P. O.; Schreiber, R. S.

1991-01-01

A new set of benchmarks has been developed for the performance evaluation of highly parallel supercomputers in the framework of the NASA Ames Numerical Aerodynamic Simulation (NAS) Program. These consist of five 'parallel kernel' benchmarks and three 'simulated application' benchmarks. Together they mimic the computation and data movement characteristics of large-scale computational fluid dynamics applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification-all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

An RDF version of the VO Registry Version 1.00

NASA Astrophysics Data System (ADS)

Gray, Norman; Gray, Norman

2007-09-01

We describe the initial implementation of an RDF version of the IVOA Resource Registry, serving the registry data via a SPARQL query endpoint, including the creation of the ontology analogues of an important subset of the relevant XML Schemas, and the mechanics of the conversion process. The result is an experimental service, and this is an interim document.

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.

PubMed

Kawano, Shin; Watanabe, Tsutomu; Mizuguchi, Sohei; Araki, Norie; Katayama, Toshiaki; Yamaguchi, Atsuko

2014-07-01

TogoTable (http://togotable.dbcls.jp/) is a web tool that adds user-specified annotations to a table that a user uploads. Annotations are drawn from several biological databases that use the Resource Description Framework (RDF) data model. TogoTable uses database identifiers (IDs) in the table as a query key for searching. RDF data, which form a network called Linked Open Data (LOD), can be searched from SPARQL endpoints using a SPARQL query language. Because TogoTable uses RDF, it can integrate annotations from not only the reference database to which the IDs originally belong, but also externally linked databases via the LOD network. For example, annotations in the Protein Data Bank can be retrieved using GeneID through links provided by the UniProt RDF. Because RDF has been standardized by the World Wide Web Consortium, any database with annotations based on the RDF data model can be easily incorporated into this tool. We believe that TogoTable is a valuable Web tool, particularly for experimental biologists who need to process huge amounts of data such as high-throughput experimental output. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

Executing SPARQL Queries over the Web of Linked Data

NASA Astrophysics Data System (ADS)

Hartig, Olaf; Bizer, Christian; Freytag, Johann-Christoph

The Web of Linked Data forms a single, globally distributed dataspace. Due to the openness of this dataspace, it is not possible to know in advance all data sources that might be relevant for query answering. This openness poses a new challenge that is not addressed by traditional research on federated query processing. In this paper we present an approach to execute SPARQL queries over the Web of Linked Data. The main idea of our approach is to discover data that might be relevant for answering a query during the query execution itself. This discovery is driven by following RDF links between data sources based on URIs in the query and in partial results. The URIs are resolved over the HTTP protocol into RDF data which is continuously added to the queried dataset. This paper describes concepts and algorithms to implement our approach using an iterator-based pipeline. We introduce a formalization of the pipelining approach and show that classical iterators may cause blocking due to the latency of HTTP requests. To avoid blocking, we propose an extension of the iterator paradigm. The evaluation of our approach shows its strengths as well as the still existing challenges.

Produce and Consume Linked Data with Drupal!

NASA Astrophysics Data System (ADS)

Corlosquet, Stéphane; Delbru, Renaud; Clark, Tim; Polleres, Axel; Decker, Stefan

Currently a large number of Web sites are driven by Content Management Systems (CMS) which manage textual and multimedia content but also - inherently - carry valuable information about a site's structure and content model. Exposing this structured information to the Web of Data has so far required considerable expertise in RDF and OWL modelling and additional programming effort. In this paper we tackle one of the most popular CMS: Drupal. We enable site administrators to export their site content model and data to the Web of Data without requiring extensive knowledge on Semantic Web technologies. Our modules create RDFa annotations and - optionally - a SPARQL endpoint for any Drupal site out of the box. Likewise, we add the means to map the site data to existing ontologies on the Web with a search interface to find commonly used ontology terms. We also allow a Drupal site administrator to include existing RDF data from remote SPARQL endpoints on the Web in the site. When brought together, these features allow networked RDF Drupal sites that reuse and enrich Linked Data. We finally discuss the adoption of our modules and report on a use case in the biomedical field and the current status of its deployment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Munro, J.F.; Kristal, J.; Thompson, G.

The Office of Environmental Management is bringing Headquarters and the Field together to implement process improvements throughout the Complex through a systematic process of organizational learning called benchmarking. Simply stated, benchmarking is a process of continuously comparing and measuring practices, processes, or methodologies with those of other private and public organizations. The EM benchmarking program, which began as the result of a recommendation from Xerox Corporation, is building trust and removing barriers to performance enhancement across the DOE organization. The EM benchmarking program is designed to be field-centered with Headquarters providing facilitatory and integrative functions on an ``as needed`` basis.more » One of the main goals of the program is to assist Field Offices and their associated M&O/M&I contractors develop the capabilities to do benchmarking for themselves. In this regard, a central precept is that in order to realize tangible performance benefits, program managers and staff -- the ones closest to the work - must take ownership of the studies. This avoids the ``check the box`` mentality associated with some third party studies. This workshop will provide participants with a basic level of understanding why the EM benchmarking team was developed and the nature and scope of its mission. Participants will also begin to understand the types of study levels and the particular methodology the EM benchmarking team is using to conduct studies. The EM benchmarking team will also encourage discussion on ways that DOE (both Headquarters and the Field) can team with its M&O/M&I contractors to conduct additional benchmarking studies. This ``introduction to benchmarking`` is intended to create a desire to know more and a greater appreciation of how benchmarking processes could be creatively employed to enhance performance.« less

Congenital Heart Surgery Case Mix Across North American Centers and Impact on Performance Assessment.

PubMed

Pasquali, Sara K; Wallace, Amelia S; Gaynor, J William; Jacobs, Marshall L; O'Brien, Sean M; Hill, Kevin D; Gaies, Michael G; Romano, Jennifer C; Shahian, David M; Mayer, John E; Jacobs, Jeffrey P

2016-11-01

Performance assessment in congenital heart surgery is challenging due to the wide heterogeneity of disease. We describe current case mix across centers, evaluate methodology inclusive of all cardiac operations versus the more homogeneous subset of Society of Thoracic Surgeons benchmark operations, and describe implications regarding performance assessment. Centers (n = 119) participating in the Society of Thoracic Surgeons Congenital Heart Surgery Database (2010 through 2014) were included. Index operation type and frequency across centers were described. Center performance (risk-adjusted operative mortality) was evaluated and classified when including the benchmark versus all eligible operations. Overall, 207 types of operations were performed during the study period (112,140 total cases). Few operations were performed across all centers; only 25% were performed at least once by 75% or more of centers. There was 7.9-fold variation across centers in the proportion of total cases comprising high-complexity cases (STAT 5). In contrast, the benchmark operations made up 36% of cases, and all but 2 were performed by at least 90% of centers. When evaluating performance based on benchmark versus all operations, 15% of centers changed performance classification; 85% remained unchanged. Benchmark versus all operation methodology was associated with lower power, with 35% versus 78% of centers meeting sample size thresholds. There is wide variation in congenital heart surgery case mix across centers. Metrics based on benchmark versus all operations are associated with strengths (less heterogeneity) and weaknesses (lower power), and lead to differing performance classification for some centers. These findings have implications for ongoing efforts to optimize performance assessment, including choice of target population and appropriate interpretation of reported metrics. Copyright © 2016 The Society of Thoracic Surgeons. Published by Elsevier Inc. All rights reserved.

The MCNP6 Analytic Criticality Benchmark Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, Forrest B.

2016-06-16

Analytical benchmarks provide an invaluable tool for verifying computer codes used to simulate neutron transport. Several collections of analytical benchmark problems [1-4] are used routinely in the verification of production Monte Carlo codes such as MCNP® [5,6]. Verification of a computer code is a necessary prerequisite to the more complex validation process. The verification process confirms that a code performs its intended functions correctly. The validation process involves determining the absolute accuracy of code results vs. nature. In typical validations, results are computed for a set of benchmark experiments using a particular methodology (code, cross-section data with uncertainties, and modeling)more » and compared to the measured results from the set of benchmark experiments. The validation process determines bias, bias uncertainty, and possibly additional margins. Verification is generally performed by the code developers, while validation is generally performed by code users for a particular application space. The VERIFICATION_KEFF suite of criticality problems [1,2] was originally a set of 75 criticality problems found in the literature for which exact analytical solutions are available. Even though the spatial and energy detail is necessarily limited in analytical benchmarks, typically to a few regions or energy groups, the exact solutions obtained can be used to verify that the basic algorithms, mathematics, and methods used in complex production codes perform correctly. The present work has focused on revisiting this benchmark suite. A thorough review of the problems resulted in discarding some of them as not suitable for MCNP benchmarking. For the remaining problems, many of them were reformulated to permit execution in either multigroup mode or in the normal continuous-energy mode for MCNP. Execution of the benchmarks in continuous-energy mode provides a significant advance to MCNP verification methods.« less

Using benchmarks for radiation testing of microprocessors and FPGAs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quinn, Heather; Robinson, William H.; Rech, Paolo

Performance benchmarks have been used over the years to compare different systems. These benchmarks can be useful for researchers trying to determine how changes to the technology, architecture, or compiler affect the system's performance. No such standard exists for systems deployed into high radiation environments, making it difficult to assess whether changes in the fabrication process, circuitry, architecture, or software affect reliability or radiation sensitivity. In this paper, we propose a benchmark suite for high-reliability systems that is designed for field-programmable gate arrays and microprocessors. As a result, we describe the development process and report neutron test data for themore » hardware and software benchmarks.« less

Using benchmarks for radiation testing of microprocessors and FPGAs

DOE PAGES

Quinn, Heather; Robinson, William H.; Rech, Paolo; ...

2015-12-17

Performance benchmarks have been used over the years to compare different systems. These benchmarks can be useful for researchers trying to determine how changes to the technology, architecture, or compiler affect the system's performance. No such standard exists for systems deployed into high radiation environments, making it difficult to assess whether changes in the fabrication process, circuitry, architecture, or software affect reliability or radiation sensitivity. In this paper, we propose a benchmark suite for high-reliability systems that is designed for field-programmable gate arrays and microprocessors. As a result, we describe the development process and report neutron test data for themore » hardware and software benchmarks.« less

Benchmarking biology research organizations using a new, dedicated tool.

PubMed

van Harten, Willem H; van Bokhorst, Leonard; van Luenen, Henri G A M

2010-02-01

International competition forces fundamental research organizations to assess their relative performance. We present a benchmark tool for scientific research organizations where, contrary to existing models, the group leader is placed in a central position within the organization. We used it in a pilot benchmark study involving six research institutions. Our study shows that data collection and data comparison based on this new tool can be achieved. It proved possible to compare relative performance and organizational characteristics and to generate suggestions for improvement for most participants. However, strict definitions of the parameters used for the benchmark and a thorough insight into the organization of each of the benchmark partners is required to produce comparable data and draw firm conclusions.

Algorithm and Architecture Independent Benchmarking with SEAK

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tallent, Nathan R.; Manzano Franco, Joseph B.; Gawande, Nitin A.

2016-05-23

Many applications of high performance embedded computing are limited by performance or power bottlenecks. We have designed the Suite for Embedded Applications & Kernels (SEAK), a new benchmark suite, (a) to capture these bottlenecks in a way that encourages creative solutions; and (b) to facilitate rigorous, objective, end-user evaluation for their solutions. To avoid biasing solutions toward existing algorithms, SEAK benchmarks use a mission-centric (abstracted from a particular algorithm) and goal-oriented (functional) specification. To encourage solutions that are any combination of software or hardware, we use an end-user black-box evaluation that can capture tradeoffs between performance, power, accuracy, size, andmore » weight. The tradeoffs are especially informative for procurement decisions. We call our benchmarks future proof because each mission-centric interface and evaluation remains useful despite shifting algorithmic preferences. It is challenging to create both concise and precise goal-oriented specifications for mission-centric problems. This paper describes the SEAK benchmark suite and presents an evaluation of sample solutions that highlights power and performance tradeoffs.« less

Comprehensive Benchmark Suite for Simulation of Particle Laden Flows Using the Discrete Element Method with Performance Profiles from the Multiphase Flow with Interface eXchanges (MFiX) Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Peiyuan; Brown, Timothy; Fullmer, William D.

Five benchmark problems are developed and simulated with the computational fluid dynamics and discrete element model code MFiX. The benchmark problems span dilute and dense regimes, consider statistically homogeneous and inhomogeneous (both clusters and bubbles) particle concentrations and a range of particle and fluid dynamic computational loads. Several variations of the benchmark problems are also discussed to extend the computational phase space to cover granular (particles only), bidisperse and heat transfer cases. A weak scaling analysis is performed for each benchmark problem and, in most cases, the scalability of the code appears reasonable up to approx. 103 cores. Profiling ofmore » the benchmark problems indicate that the most substantial computational time is being spent on particle-particle force calculations, drag force calculations and interpolating between discrete particle and continuum fields. Hardware performance analysis was also carried out showing significant Level 2 cache miss ratios and a rather low degree of vectorization. These results are intended to serve as a baseline for future developments to the code as well as a preliminary indicator of where to best focus performance optimizations.« less

Benchmarking forensic mental health organizations.

PubMed

Coombs, Tim; Taylor, Monica; Pirkis, Jane

2011-04-01

This paper describes the forensic mental health forums that were conducted as part of the National Mental Health Benchmarking Project (NMHBP). These forums encouraged participating organizations to compare their performance on a range of key performance indicators (KPIs) with that of their peers. Four forensic mental health organizations took part in the NMHBP. Representatives from these organizations attended eight benchmarking forums at which they documented their performance against previously agreed KPIs. They also undertook three special projects which explored some of the factors that might explain inter-organizational variation in performance. The inter-organizational range for many of the indicators was substantial. Observing this led participants to conduct the special projects to explore three factors which might help explain the variability - seclusion practices, delivery of community mental health services, and provision of court liaison services. The process of conducting the special projects gave participants insights into the practices and structures employed by their counterparts, and provided them with some important lessons for quality improvement. The forensic mental health benchmarking forums have demonstrated that benchmarking is feasible and likely to be useful in improving service performance and quality.

Memory-Intensive Benchmarks: IRAM vs. Cache-Based Machines

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Gaeke, Brian R.; Husbands, Parry; Li, Xiaoye S.; Oliker, Leonid; Yelick, Katherine A.; Biegel, Bryan (Technical Monitor)

2002-01-01

The increasing gap between processor and memory performance has lead to new architectural models for memory-intensive applications. In this paper, we explore the performance of a set of memory-intensive benchmarks and use them to compare the performance of conventional cache-based microprocessors to a mixed logic and DRAM processor called VIRAM. The benchmarks are based on problem statements, rather than specific implementations, and in each case we explore the fundamental hardware requirements of the problem, as well as alternative algorithms and data structures that can help expose fine-grained parallelism or simplify memory access patterns. The benchmarks are characterized by their memory access patterns, their basic control structures, and the ratio of computation to memory operation.

Measuring Distribution Performance? Benchmarking Warrants Your Attention

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ericson, Sean J; Alvarez, Paul

Identifying, designing, and measuring performance metrics is critical to securing customer value, but can be a difficult task. This article examines the use of benchmarks based on publicly available performance data to set challenging, yet fair, metrics and targets.

Competency based training in robotic surgery: benchmark scores for virtual reality robotic simulation.

PubMed

Raison, Nicholas; Ahmed, Kamran; Fossati, Nicola; Buffi, Nicolò; Mottrie, Alexandre; Dasgupta, Prokar; Van Der Poel, Henk

2017-05-01

To develop benchmark scores of competency for use within a competency based virtual reality (VR) robotic training curriculum. This longitudinal, observational study analysed results from nine European Association of Urology hands-on-training courses in VR simulation. In all, 223 participants ranging from novice to expert robotic surgeons completed 1565 exercises. Competency was set at 75% of the mean expert score. Benchmark scores for all general performance metrics generated by the simulator were calculated. Assessment exercises were selected by expert consensus and through learning-curve analysis. Three basic skill and two advanced skill exercises were identified. Benchmark scores based on expert performance offered viable targets for novice and intermediate trainees in robotic surgery. Novice participants met the competency standards for most basic skill exercises; however, advanced exercises were significantly more challenging. Intermediate participants performed better across the seven metrics but still did not achieve the benchmark standard in the more difficult exercises. Benchmark scores derived from expert performances offer relevant and challenging scores for trainees to achieve during VR simulation training. Objective feedback allows both participants and trainers to monitor educational progress and ensures that training remains effective. Furthermore, the well-defined goals set through benchmarking offer clear targets for trainees and enable training to move to a more efficient competency based curriculum. © 2016 The Authors BJU International © 2016 BJU International Published by John Wiley & Sons Ltd.

Benchmarking in national health service procurement in Scotland.

PubMed

Walker, Scott; Masson, Ron; Telford, Ronnie; White, David

2007-11-01

The paper reports the results of a study on benchmarking activities undertaken by the procurement organization within the National Health Service (NHS) in Scotland, namely National Procurement (previously Scottish Healthcare Supplies Contracts Branch). NHS performance is of course politically important, and benchmarking is increasingly seen as a means to improve performance, so the study was carried out to determine if the current benchmarking approaches could be enhanced. A review of the benchmarking activities used by the private sector, local government and NHS organizations was carried out to establish a framework of the motivations, benefits, problems and costs associated with benchmarking. This framework was used to carry out the research through case studies and a questionnaire survey of NHS procurement organizations both in Scotland and other parts of the UK. Nine of the 16 Scottish Health Boards surveyed reported carrying out benchmarking during the last three years. The findings of the research were that there were similarities in approaches between local government and NHS Scotland Health, but differences between NHS Scotland and other UK NHS procurement organizations. Benefits were seen as significant and it was recommended that National Procurement should pursue the formation of a benchmarking group with members drawn from NHS Scotland and external benchmarking bodies to establish measures to be used in benchmarking across the whole of NHS Scotland.

Benchmarking high performance computing architectures with CMS’ skeleton framework

NASA Astrophysics Data System (ADS)

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

2017-10-01

In 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta, Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.

Structural Benchmark Creep Testing for Microcast MarM-247 Advanced Stirling Convertor E2 Heater Head Test Article SN18

NASA Technical Reports Server (NTRS)

Krause, David L.; Brewer, Ethan J.; Pawlik, Ralph

2013-01-01

This report provides test methodology details and qualitative results for the first structural benchmark creep test of an Advanced Stirling Convertor (ASC) heater head of ASC-E2 design heritage. The test article was recovered from a flight-like Microcast MarM-247 heater head specimen previously used in helium permeability testing. The test article was utilized for benchmark creep test rig preparation, wall thickness and diametral laser scan hardware metrological developments, and induction heater custom coil experiments. In addition, a benchmark creep test was performed, terminated after one week when through-thickness cracks propagated at thermocouple weld locations. Following this, it was used to develop a unique temperature measurement methodology using contact thermocouples, thereby enabling future benchmark testing to be performed without the use of conventional welded thermocouples, proven problematic for the alloy. This report includes an overview of heater head structural benchmark creep testing, the origin of this particular test article, test configuration developments accomplished using the test article, creep predictions for its benchmark creep test, qualitative structural benchmark creep test results, and a short summary.

Towards linked open gene mutations data

PubMed Central

2012-01-01

Background With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. Methods A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. Results We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. Conclusions This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development. The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine. PMID:22536974

Towards linked open gene mutations data.

PubMed

Zappa, Achille; Splendiani, Andrea; Romano, Paolo

2012-03-28

With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework. In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data. A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest. Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite. We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application. This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.

Simple Benchmark Specifications for Space Radiation Protection

NASA Technical Reports Server (NTRS)

Singleterry, Robert C. Jr.; Aghara, Sukesh K.

2013-01-01

This report defines space radiation benchmark specifications. This specification starts with simple, monoenergetic, mono-directional particles on slabs and progresses to human models in spacecraft. This report specifies the models and sources needed to what the team performing the benchmark needs to produce in a report. Also included are brief descriptions of how OLTARIS, the NASA Langley website for space radiation analysis, performs its analysis.

Performance of Multi-chaotic PSO on a shifted benchmark functions set

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pluhacek, Michal; Senkerik, Roman; Zelinka, Ivan

2015-03-10

In this paper the performance of Multi-chaotic PSO algorithm is investigated using two shifted benchmark functions. The purpose of shifted benchmark functions is to simulate the time-variant real-world problems. The results of chaotic PSO are compared with canonical version of the algorithm. It is concluded that using the multi-chaotic approach can lead to better results in optimization of shifted functions.

Benchmarking routine psychological services: a discussion of challenges and methods.

PubMed

Delgadillo, Jaime; McMillan, Dean; Leach, Chris; Lucock, Mike; Gilbody, Simon; Wood, Nick

2014-01-01

Policy developments in recent years have led to important changes in the level of access to evidence-based psychological treatments. Several methods have been used to investigate the effectiveness of these treatments in routine care, with different approaches to outcome definition and data analysis. To present a review of challenges and methods for the evaluation of evidence-based treatments delivered in routine mental healthcare. This is followed by a case example of a benchmarking method applied in primary care. High, average and poor performance benchmarks were calculated through a meta-analysis of published data from services working under the Improving Access to Psychological Therapies (IAPT) Programme in England. Pre-post treatment effect sizes (ES) and confidence intervals were estimated to illustrate a benchmarking method enabling services to evaluate routine clinical outcomes. High, average and poor performance ES for routine IAPT services were estimated to be 0.91, 0.73 and 0.46 for depression (using PHQ-9) and 1.02, 0.78 and 0.52 for anxiety (using GAD-7). Data from one specific IAPT service exemplify how to evaluate and contextualize routine clinical performance against these benchmarks. The main contribution of this report is to summarize key recommendations for the selection of an adequate set of psychometric measures, the operational definition of outcomes, and the statistical evaluation of clinical performance. A benchmarking method is also presented, which may enable a robust evaluation of clinical performance against national benchmarks. Some limitations concerned significant heterogeneity among data sources, and wide variations in ES and data completeness.

Unstructured Adaptive (UA) NAS Parallel Benchmark. Version 1.0

NASA Technical Reports Server (NTRS)

Feng, Huiyu; VanderWijngaart, Rob; Biswas, Rupak; Mavriplis, Catherine

2004-01-01

We present a complete specification of a new benchmark for measuring the performance of modern computer systems when solving scientific problems featuring irregular, dynamic memory accesses. It complements the existing NAS Parallel Benchmark suite. The benchmark involves the solution of a stylized heat transfer problem in a cubic domain, discretized on an adaptively refined, unstructured mesh.

Facilitating Semantic Interoperability Among Ocean Data Systems: ODIP-R2R Student Outcomes

NASA Astrophysics Data System (ADS)

Stocks, K. I.; Chen, Y.; Shepherd, A.; Chandler, C. L.; Dockery, N.; Elya, J. L.; Smith, S. R.; Ferreira, R.; Fu, L.; Arko, R. A.

2014-12-01

With informatics providing an increasingly important set of tools for geoscientists, it is critical to train the next generation of scientists in information and data techniques. The NSF-supported Rolling Deck to Repository (R2R) Program works with the academic fleet community to routinely document, assess, and preserve the underway sensor data from U.S. research vessels. The Ocean Data Interoperability Platform (ODIP) is an EU-US-Australian collaboration fostering interoperability among regional e-infrastructures through workshops and joint prototype development. The need to align terminology between systems is a common challenge across all of the ODIP prototypes. Five R2R students were supported to address aspects of semantic interoperability within ODIP. Developing a vocabulary matching service that links terms from different vocabularies with similar concept. The service implements Google Refine reconciliation service interface such that users can leverage Google Refine application as a friendly user interface while linking different vocabulary terms. Developing Resource Description Framework (RDF) resources that map Shipboard Automated Meteorological Oceanographic System (SAMOS) vocabularies to internationally served vocabularies. Each SAMOS vocabulary term (data parameter and quality control flag) will be described as an RDF resource page. These RDF resources allow for enhanced discoverability and retrieval of SAMOS data by enabling data searches based on parameter. Improving data retrieval and interoperability by exposing data and mapped vocabularies using Semantic Web technologies. We have collaborated with ODIP participating organizations in order to build a generalized data model that will be used to populate a SPARQL endpoint in order to provide expressive querying over our data files. Mapping local and regional vocabularies used by R2R to those used by ODIP partners. This work is described more fully in a companion poster. Making published Linked Data Web developer-friendly with a RESTful service. This goal was achieved by defining a proxy layer on top of the existing SPARQL endpoint that 1) translates HTTP requests into SPARQL queries, and 2) renders the returned results as required by the request sender using content negotiation, suffixes and parameters.

A self-updating road map of The Cancer Genome Atlas.

PubMed

Robbins, David E; Grüneberg, Alexander; Deus, Helena F; Tanik, Murat M; Almeida, Jonas S

2013-05-15

Since 2011, The Cancer Genome Atlas' (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is instantiated in only partially overlapping sets of analytical platforms, while the number of data files available doubles approximately every 7 months. We developed an engine to index and annotate the TCGA files, relying exclusively on third-generation web technologies (Web 3.0). Specifically, this engine uses JavaScript in conjunction with the World Wide Web Consortium's (W3C) Resource Description Framework (RDF), and SPARQL, the query language for RDF, to capture metadata of files in the TCGA open-access HTTP directory. The resulting index may be queried using SPARQL, and enables file-level provenance annotations as well as discovery of arbitrary subsets of files, based on their metadata, using web standard languages. In turn, these abilities enhance the reproducibility and distribution of novel results delivered as elements of a web-based computational ecosystem. The development of the TCGA Roadmap engine was found to provide specific clues about how biomedical big data initiatives should be exposed as public resources for exploratory analysis, data mining and reproducible research. These specific design elements align with the concept of knowledge reengineering and represent a sharp departure from top-down approaches in grid initiatives such as CaBIG. They also present a much more interoperable and reproducible alternative to the still pervasive use of data portals. A prepared dashboard, including links to source code and a SPARQL endpoint, is available at http://bit.ly/TCGARoadmap. A video tutorial is available at http://bit.ly/TCGARoadmapTutorial. robbinsd@uab.edu.

A self-updating road map of The Cancer Genome Atlas

PubMed Central

Robbins, David E.; Grüneberg, Alexander; Deus, Helena F.; Tanik, Murat M.; Almeida, Jonas S.

2013-01-01

Motivation: Since 2011, The Cancer Genome Atlas’ (TCGA) files have been accessible through HTTP from a public site, creating entirely new possibilities for cancer informatics by enhancing data discovery and retrieval. Significantly, these enhancements enable the reporting of analysis results that can be fully traced to and reproduced using their source data. However, to realize this possibility, a continually updated road map of files in the TCGA is required. Creation of such a road map represents a significant data modeling challenge, due to the size and fluidity of this resource: each of the 33 cancer types is instantiated in only partially overlapping sets of analytical platforms, while the number of data files available doubles approximately every 7 months. Results: We developed an engine to index and annotate the TCGA files, relying exclusively on third-generation web technologies (Web 3.0). Specifically, this engine uses JavaScript in conjunction with the World Wide Web Consortium’s (W3C) Resource Description Framework (RDF), and SPARQL, the query language for RDF, to capture metadata of files in the TCGA open-access HTTP directory. The resulting index may be queried using SPARQL, and enables file-level provenance annotations as well as discovery of arbitrary subsets of files, based on their metadata, using web standard languages. In turn, these abilities enhance the reproducibility and distribution of novel results delivered as elements of a web-based computational ecosystem. The development of the TCGA Roadmap engine was found to provide specific clues about how biomedical big data initiatives should be exposed as public resources for exploratory analysis, data mining and reproducible research. These specific design elements align with the concept of knowledge reengineering and represent a sharp departure from top-down approaches in grid initiatives such as CaBIG. They also present a much more interoperable and reproducible alternative to the still pervasive use of data portals. Availability: A prepared dashboard, including links to source code and a SPARQL endpoint, is available at http://bit.ly/TCGARoadmap. A video tutorial is available at http://bit.ly/TCGARoadmapTutorial. Contact: robbinsd@uab.edu PMID:23595662

Toxicological Benchmarks for Screening Potential Contaminants of Concern for Effects on Soil and Litter Invertebrates and Heterotrophic Process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Will, M.E.

1994-01-01

This report presents a standard method for deriving benchmarks for the purpose of ''contaminant screening,'' performed by comparing measured ambient concentrations of chemicals. The work was performed under Work Breakdown Structure 1.4.12.2.3.04.07.02 (Activity Data Sheet 8304). In addition, this report presents sets of data concerning the effects of chemicals in soil on invertebrates and soil microbial processes, benchmarks for chemicals potentially associated with United States Department of Energy sites, and literature describing the experiments from which data were drawn for benchmark derivation.

75 FR 6368 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-09

... benchmarking U.S. performance in mathematics and science at the fourth- and eighth-grade levels against other... assessment data for internationally benchmarking U.S. performance in fourth-grade reading. NCES has received...

Benchmarking high performance computing architectures with CMS’ skeleton framework

DOE PAGES

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

2017-11-23

Here, in 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta,more » Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.« less

Benchmarking high performance computing architectures with CMS’ skeleton framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

Here, in 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta,more » Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.« less

Implementation of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for High Performance Computing (HPC). In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for CFD applications.

Performance and Scalability of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for scientific applications. In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for scientific applications.

An automated protocol for performance benchmarking a widefield fluorescence microscope.

PubMed

Halter, Michael; Bier, Elianna; DeRose, Paul C; Cooksey, Gregory A; Choquette, Steven J; Plant, Anne L; Elliott, John T

2014-11-01

Widefield fluorescence microscopy is a highly used tool for visually assessing biological samples and for quantifying cell responses. Despite its widespread use in high content analysis and other imaging applications, few published methods exist for evaluating and benchmarking the analytical performance of a microscope. Easy-to-use benchmarking methods would facilitate the use of fluorescence imaging as a quantitative analytical tool in research applications, and would aid the determination of instrumental method validation for commercial product development applications. We describe and evaluate an automated method to characterize a fluorescence imaging system's performance by benchmarking the detection threshold, saturation, and linear dynamic range to a reference material. The benchmarking procedure is demonstrated using two different materials as the reference material, uranyl-ion-doped glass and Schott 475 GG filter glass. Both are suitable candidate reference materials that are homogeneously fluorescent and highly photostable, and the Schott 475 GG filter glass is currently commercially available. In addition to benchmarking the analytical performance, we also demonstrate that the reference materials provide for accurate day to day intensity calibration. Published 2014 Wiley Periodicals Inc. Published 2014 Wiley Periodicals Inc. This article is a US government work and, as such, is in the public domain in the United States of America.

Comparison of Origin 2000 and Origin 3000 Using NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Turney, Raymond D.

2001-01-01

This report describes results of benchmark tests on the Origin 3000 system currently being installed at the NASA Ames National Advanced Supercomputing facility. This machine will ultimately contain 1024 R14K processors. The first part of the system, installed in November, 2000 and named mendel, is an Origin 3000 with 128 R12K processors. For comparison purposes, the tests were also run on lomax, an Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to determine system performance and measure the impact of changes on the machine as it evolves. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versiqns used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN 3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cohen, J; Dossa, D; Gokhale, M

Critical data science applications requiring frequent access to storage perform poorly on today's computing architectures. This project addresses efficient computation of data-intensive problems in national security and basic science by exploring, advancing, and applying a new form of computing called storage-intensive supercomputing (SISC). Our goal is to enable applications that simply cannot run on current systems, and, for a broad range of data-intensive problems, to deliver an order of magnitude improvement in price/performance over today's data-intensive architectures. This technical report documents much of the work done under LDRD 07-ERD-063 Storage Intensive Supercomputing during the period 05/07-09/07. The following chapters describe:more » (1) a new file I/O monitoring tool iotrace developed to capture the dynamic I/O profiles of Linux processes; (2) an out-of-core graph benchmark for level-set expansion of scale-free graphs; (3) an entity extraction benchmark consisting of a pipeline of eight components; and (4) an image resampling benchmark drawn from the SWarp program in the LSST data processing pipeline. The performance of the graph and entity extraction benchmarks was measured in three different scenarios: data sets residing on the NFS file server and accessed over the network; data sets stored on local disk; and data sets stored on the Fusion I/O parallel NAND Flash array. The image resampling benchmark compared performance of software-only to GPU-accelerated. In addition to the work reported here, an additional text processing application was developed that used an FPGA to accelerate n-gram profiling for language classification. The n-gram application will be presented at SC07 at the High Performance Reconfigurable Computing Technologies and Applications Workshop. The graph and entity extraction benchmarks were run on a Supermicro server housing the NAND Flash 40GB parallel disk array, the Fusion-io. The Fusion system specs are as follows: SuperMicro X7DBE Xeon Dual Socket Blackford Server Motherboard; 2 Intel Xeon Dual-Core 2.66 GHz processors; 1 GB DDR2 PC2-5300 RAM (2 x 512); 80GB Hard Drive (Seagate SATA II Barracuda). The Fusion board is presently capable of 4X in a PCIe slot. The image resampling benchmark was run on a dual Xeon workstation with NVIDIA graphics card (see Chapter 5 for full specification). An XtremeData Opteron+FPGA was used for the language classification application. We observed that these benchmarks are not uniformly I/O intensive. The only benchmark that showed greater that 50% of the time in I/O was the graph algorithm when it accessed data files over NFS. When local disk was used, the graph benchmark spent at most 40% of its time in I/O. The other benchmarks were CPU dominated. The image resampling benchmark and language classification showed order of magnitude speedup over software by using co-processor technology to offload the CPU-intensive kernels. Our experiments to date suggest that emerging hardware technologies offer significant benefit to boosting the performance of data-intensive algorithms. Using GPU and FPGA co-processors, we were able to improve performance by more than an order of magnitude on the benchmark algorithms, eliminating the processor bottleneck of CPU-bound tasks. Experiments with a prototype solid state nonvolative memory available today show 10X better throughput on random reads than disk, with a 2X speedup on a graph processing benchmark when compared to the use of local SATA disk.« less

SU-E-T-148: Benchmarks and Pre-Treatment Reviews: A Study of Quality Assurance Effectiveness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lowenstein, J; Nguyen, H; Roll, J

Purpose: To determine the impact benchmarks and pre-treatment reviews have on improving the quality of submitted clinical trial data. Methods: Benchmarks are used to evaluate a site’s ability to develop a treatment that meets a specific protocol’s treatment guidelines prior to placing their first patient on the protocol. A pre-treatment review is an actual patient placed on the protocol in which the dosimetry and contour volumes are evaluated to be per protocol guidelines prior to allowing the beginning of the treatment. A key component of these QA mechanisms is that sites are provided timely feedback to educate them on howmore » to plan per the protocol and prevent protocol deviations on patients accrued to a protocol. For both benchmarks and pre-treatment reviews a dose volume analysis (DVA) was performed using MIM softwareTM. For pre-treatment reviews a volume contour evaluation was also performed. Results: IROC Houston performed a QA effectiveness analysis of a protocol which required both benchmarks and pre-treatment reviews. In 70 percent of the patient cases submitted, the benchmark played an effective role in assuring that the pre-treatment review of the cases met protocol requirements. The 35 percent of sites failing the benchmark subsequently modified there planning technique to pass the benchmark before being allowed to submit a patient for pre-treatment review. However, in 30 percent of the submitted cases the pre-treatment review failed where the majority (71 percent) failed the DVA. 20 percent of sites submitting patients failed to correct their dose volume discrepancies indicated by the benchmark case. Conclusion: Benchmark cases and pre-treatment reviews can be an effective QA tool to educate sites on protocol guidelines and to minimize deviations. Without the benchmark cases it is possible that 65 percent of the cases undergoing a pre-treatment review would have failed to meet the protocols requirements.Support: U24-CA-180803.« less

On performing semantic queries in small devices

NASA Astrophysics Data System (ADS)

Costea, C.; Petrovan, A.; Neamţ, L.; Chiver, O.

2016-08-01

The sensors have a well-defined role in control or monitoring industrial processes; the data given by them can generate valuable information of the trend of the systems to which they belong, but to store a large volume of data and then analysis offline is not always practical. One solution is on-line analysis, preferably as close to the place where data have been generated (edge computing). An increasing amount of data generated by a growing number of devices connected to the Internet resulted in processing data sensors to the edge of the network, in a middle layer where smart entities should interoperate. Diversity of communication technologies outlined the idea of using intermediate devices such as gateways in sensor networks and for this reason the paper examines the functionality of a SPARQL endpoint in the Raspberry Pi device.

Ontology based log content extraction engine for a posteriori security control.

PubMed

Azkia, Hanieh; Cuppens-Boulahia, Nora; Cuppens, Frédéric; Coatrieux, Gouenou

2012-01-01

In a posteriori access control, users are accountable for actions they performed and must provide evidence, when required by some legal authorities for instance, to prove that these actions were legitimate. Generally, log files contain the needed data to achieve this goal. This logged data can be recorded in several formats; we consider here IHE-ATNA (Integrating the healthcare enterprise-Audit Trail and Node Authentication) as log format. The difficulty lies in extracting useful information regardless of the log format. A posteriori access control frameworks often include a log filtering engine that provides this extraction function. In this paper we define and enforce this function by building an IHE-ATNA based ontology model, which we query using SPARQL, and show how the a posteriori security controls are made effective and easier based on this function.

Thought Experiment to Examine Benchmark Performance for Fusion Nuclear Data

NASA Astrophysics Data System (ADS)

Murata, Isao; Ohta, Masayuki; Kusaka, Sachie; Sato, Fuminobu; Miyamaru, Hiroyuki

2017-09-01

There are many benchmark experiments carried out so far with DT neutrons especially aiming at fusion reactor development. These integral experiments seemed vaguely to validate the nuclear data below 14 MeV. However, no precise studies exist now. The author's group thus started to examine how well benchmark experiments with DT neutrons can play a benchmarking role for energies below 14 MeV. Recently, as a next phase, to generalize the above discussion, the energy range was expanded to the entire region. In this study, thought experiments with finer energy bins have thus been conducted to discuss how to generally estimate performance of benchmark experiments. As a result of thought experiments with a point detector, the sensitivity for a discrepancy appearing in the benchmark analysis is "equally" due not only to contribution directly conveyed to the deterctor, but also due to indirect contribution of neutrons (named (A)) making neutrons conveying the contribution, indirect controbution of neutrons (B) making the neutrons (A) and so on. From this concept, it would become clear from a sensitivity analysis in advance how well and which energy nuclear data could be benchmarked with a benchmark experiment.

Benchmarking Strategies for Measuring the Quality of Healthcare: Problems and Prospects

PubMed Central

Lovaglio, Pietro Giorgio

2012-01-01

Over the last few years, increasing attention has been directed toward the problems inherent to measuring the quality of healthcare and implementing benchmarking strategies. Besides offering accreditation and certification processes, recent approaches measure the performance of healthcare institutions in order to evaluate their effectiveness, defined as the capacity to provide treatment that modifies and improves the patient's state of health. This paper, dealing with hospital effectiveness, focuses on research methods for effectiveness analyses within a strategy comparing different healthcare institutions. The paper, after having introduced readers to the principle debates on benchmarking strategies, which depend on the perspective and type of indicators used, focuses on the methodological problems related to performing consistent benchmarking analyses. Particularly, statistical methods suitable for controlling case-mix, analyzing aggregate data, rare events, and continuous outcomes measured with error are examined. Specific challenges of benchmarking strategies, such as the risk of risk adjustment (case-mix fallacy, underreporting, risk of comparing noncomparable hospitals), selection bias, and possible strategies for the development of consistent benchmarking analyses, are discussed. Finally, to demonstrate the feasibility of the illustrated benchmarking strategies, an application focused on determining regional benchmarks for patient satisfaction (using 2009 Lombardy Region Patient Satisfaction Questionnaire) is proposed. PMID:22666140

Benchmarking strategies for measuring the quality of healthcare: problems and prospects.

PubMed

Lovaglio, Pietro Giorgio

2012-01-01

Over the last few years, increasing attention has been directed toward the problems inherent to measuring the quality of healthcare and implementing benchmarking strategies. Besides offering accreditation and certification processes, recent approaches measure the performance of healthcare institutions in order to evaluate their effectiveness, defined as the capacity to provide treatment that modifies and improves the patient's state of health. This paper, dealing with hospital effectiveness, focuses on research methods for effectiveness analyses within a strategy comparing different healthcare institutions. The paper, after having introduced readers to the principle debates on benchmarking strategies, which depend on the perspective and type of indicators used, focuses on the methodological problems related to performing consistent benchmarking analyses. Particularly, statistical methods suitable for controlling case-mix, analyzing aggregate data, rare events, and continuous outcomes measured with error are examined. Specific challenges of benchmarking strategies, such as the risk of risk adjustment (case-mix fallacy, underreporting, risk of comparing noncomparable hospitals), selection bias, and possible strategies for the development of consistent benchmarking analyses, are discussed. Finally, to demonstrate the feasibility of the illustrated benchmarking strategies, an application focused on determining regional benchmarks for patient satisfaction (using 2009 Lombardy Region Patient Satisfaction Questionnaire) is proposed.

Benchmarking in emergency health systems.

PubMed

Kennedy, Marcus P; Allen, Jacqueline; Allen, Greg

2002-12-01

This paper discusses the role of benchmarking as a component of quality management. It describes the historical background of benchmarking, its competitive origin and the requirement in today's health environment for a more collaborative approach. The classical 'functional and generic' types of benchmarking are discussed with a suggestion to adopt a different terminology that describes the purpose and practicalities of benchmarking. Benchmarking is not without risks. The consequence of inappropriate focus and the need for a balanced overview of process is explored. The competition that is intrinsic to benchmarking is questioned and the negative impact it may have on improvement strategies in poorly performing organizations is recognized. The difficulty in achieving cross-organizational validity in benchmarking is emphasized, as is the need to scrutinize benchmarking measures. The cost effectiveness of benchmarking projects is questioned and the concept of 'best value, best practice' in an environment of fixed resources is examined.

Benchmarking Multilayer-HySEA model for landslide generated tsunami. HTHMP validation process.

NASA Astrophysics Data System (ADS)

Macias, J.; Escalante, C.; Castro, M. J.

2017-12-01

Landslide tsunami hazard may be dominant along significant parts of the coastline around the world, in particular in the USA, as compared to hazards from other tsunamigenic sources. This fact motivated NTHMP about the need of benchmarking models for landslide generated tsunamis, following the same methodology already used for standard tsunami models when the source is seismic. To perform the above-mentioned validation process, a set of candidate benchmarks were proposed. These benchmarks are based on a subset of available laboratory data sets for solid slide experiments and deformable slide experiments, and include both submarine and subaerial slides. A benchmark based on a historic field event (Valdez, AK, 1964) close the list of proposed benchmarks. A total of 7 benchmarks. The Multilayer-HySEA model including non-hydrostatic effects has been used to perform all the benchmarking problems dealing with laboratory experiments proposed in the workshop that was organized at Texas A&M University - Galveston, on January 9-11, 2017 by NTHMP. The aim of this presentation is to show some of the latest numerical results obtained with the Multilayer-HySEA (non-hydrostatic) model in the framework of this validation effort.Acknowledgements. This research has been partially supported by the Spanish Government Research project SIMURISK (MTM2015-70490-C02-01-R) and University of Malaga, Campus de Excelencia Internacional Andalucía Tech. The GPU computations were performed at the Unit of Numerical Methods (University of Malaga).

Clomp

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gylenhaal, J.; Bronevetsky, G.

2007-05-25

CLOMP is the C version of the Livermore OpenMP benchmark deeloped to measure OpenMP overheads and other performance impacts due to threading (like NUMA memory layouts, memory contention, cache effects, etc.) in order to influence future system design. Current best-in-class implementations of OpenMP have overheads at least ten times larger than is required by many of our applications for effective use of OpenMP. This benchmark shows the significant negative performance impact of these relatively large overheads and of other thread effects. The CLOMP benchmark highly configurable to allow a variety of problem sizes and threading effects to be studied andmore » it carefully checks its results to catch many common threading errors. This benchmark is expected to be included as part of the Sequoia Benchmark suite for the Sequoia procurement.« less

All inclusive benchmarking.

PubMed

Ellis, Judith

2006-07-01

The aim of this article is to review published descriptions of benchmarking activity and synthesize benchmarking principles to encourage the acceptance and use of Essence of Care as a new benchmarking approach to continuous quality improvement, and to promote its acceptance as an integral and effective part of benchmarking activity in health services. The Essence of Care, was launched by the Department of Health in England in 2001 to provide a benchmarking tool kit to support continuous improvement in the quality of fundamental aspects of health care, for example, privacy and dignity, nutrition and hygiene. The tool kit is now being effectively used by some frontline staff. However, use is inconsistent, with the value of the tool kit, or the support clinical practice benchmarking requires to be effective, not always recognized or provided by National Health Service managers, who are absorbed with the use of quantitative benchmarking approaches and measurability of comparative performance data. This review of published benchmarking literature, was obtained through an ever-narrowing search strategy commencing from benchmarking within quality improvement literature through to benchmarking activity in health services and including access to not only published examples of benchmarking approaches and models used but the actual consideration of web-based benchmarking data. This supported identification of how benchmarking approaches have developed and been used, remaining true to the basic benchmarking principles of continuous improvement through comparison and sharing (Camp 1989). Descriptions of models and exemplars of quantitative and specifically performance benchmarking activity in industry abound (Camp 1998), with far fewer examples of more qualitative and process benchmarking approaches in use in the public services and then applied to the health service (Bullivant 1998). The literature is also in the main descriptive in its support of the effectiveness of benchmarking activity and although this does not seem to have restricted its popularity in quantitative activity, reticence about the value of the more qualitative approaches, for example Essence of Care, needs to be overcome in order to improve the quality of patient care and experiences. The perceived immeasurability and subjectivity of Essence of Care and clinical practice benchmarks means that these benchmarking approaches are not always accepted or supported by health service organizations as valid benchmarking activity. In conclusion, Essence of Care benchmarking is a sophisticated clinical practice benchmarking approach which needs to be accepted as an integral part of health service benchmarking activity to support improvement in the quality of patient care and experiences.

Implementation of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael; Schultz, Matthew; Jin, Hao-Qiang; Yan, Jerry

2000-01-01

A number of features make Java an attractive but a debatable choice for High Performance Computing (HPC). In order to gauge the applicability of Java to the Computational Fluid Dynamics (CFD) we have implemented NAS Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would move Java closer to Fortran in the competition for CFD applications.

Benchmarking, Total Quality Management, and Libraries.

ERIC Educational Resources Information Center

Shaughnessy, Thomas W.

1993-01-01

Discussion of the use of Total Quality Management (TQM) in higher education and academic libraries focuses on the identification, collection, and use of reliable data. Methods for measuring quality, including benchmarking, are described; performance measures are considered; and benchmarking techniques are examined. (11 references) (MES)

Developing and Trialling an independent, scalable and repeatable IT-benchmarking procedure for healthcare organisations.

PubMed

Liebe, J D; Hübner, U

2013-01-01

Continuous improvements of IT-performance in healthcare organisations require actionable performance indicators, regularly conducted, independent measurements and meaningful and scalable reference groups. Existing IT-benchmarking initiatives have focussed on the development of reliable and valid indicators, but less on the questions about how to implement an environment for conducting easily repeatable and scalable IT-benchmarks. This study aims at developing and trialling a procedure that meets the afore-mentioned requirements. We chose a well established, regularly conducted (inter-) national IT-survey of healthcare organisations (IT-Report Healthcare) as the environment and offered the participants of the 2011 survey (CIOs of hospitals) to enter a benchmark. The 61 structural and functional performance indicators covered among others the implementation status and integration of IT-systems and functions, global user satisfaction and the resources of the IT-department. Healthcare organisations were grouped by size and ownership. The benchmark results were made available electronically and feedback on the use of these results was requested after several months. Fifty-ninehospitals participated in the benchmarking. Reference groups consisted of up to 141 members depending on the number of beds (size) and the ownership (public vs. private). A total of 122 charts showing single indicator frequency views were sent to each participant. The evaluation showed that 94.1% of the CIOs who participated in the evaluation considered this benchmarking beneficial and reported that they would enter again. Based on the feedback of the participants we developed two additional views that provide a more consolidated picture. The results demonstrate that establishing an independent, easily repeatable and scalable IT-benchmarking procedure is possible and was deemed desirable. Based on these encouraging results a new benchmarking round which includes process indicators is currently conducted.

An Ebola virus-centered knowledge base

PubMed Central

Kamdar, Maulik R.; Dumontier, Michel

2015-01-01

Ebola virus (EBOV), of the family Filoviridae viruses, is a NIAID category A, lethal human pathogen. It is responsible for causing Ebola virus disease (EVD) that is a severe hemorrhagic fever and has a cumulative death rate of 41% in the ongoing epidemic in West Africa. There is an ever-increasing need to consolidate and make available all the knowledge that we possess on EBOV, even if it is conflicting or incomplete. This would enable biomedical researchers to understand the molecular mechanisms underlying this disease and help develop tools for efficient diagnosis and effective treatment. In this article, we present our approach for the development of an Ebola virus-centered Knowledge Base (Ebola-KB) using Linked Data and Semantic Web Technologies. We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies. This knowledge is transformed to RDF, linked to the Bio2RDF datasets and made available through a SPARQL 1.1 Endpoint. Ebola-KB can also be explored using an interactive Dashboard visualizing the different perspectives of this integrated knowledge. We showcase how different competency questions, asked by domain users researching the druggability of EBOV, can be formulated as SPARQL Queries or answered using the Ebola-KB Dashboard. Database URL: http://ebola.semanticscience.org. PMID:26055098

An Ebola virus-centered knowledge base.

PubMed

Kamdar, Maulik R; Dumontier, Michel

2015-01-01

Ebola virus (EBOV), of the family Filoviridae viruses, is a NIAID category A, lethal human pathogen. It is responsible for causing Ebola virus disease (EVD) that is a severe hemorrhagic fever and has a cumulative death rate of 41% in the ongoing epidemic in West Africa. There is an ever-increasing need to consolidate and make available all the knowledge that we possess on EBOV, even if it is conflicting or incomplete. This would enable biomedical researchers to understand the molecular mechanisms underlying this disease and help develop tools for efficient diagnosis and effective treatment. In this article, we present our approach for the development of an Ebola virus-centered Knowledge Base (Ebola-KB) using Linked Data and Semantic Web Technologies. We retrieve and aggregate knowledge from several open data sources, web services and biomedical ontologies. This knowledge is transformed to RDF, linked to the Bio2RDF datasets and made available through a SPARQL 1.1 Endpoint. Ebola-KB can also be explored using an interactive Dashboard visualizing the different perspectives of this integrated knowledge. We showcase how different competency questions, asked by domain users researching the druggability of EBOV, can be formulated as SPARQL Queries or answered using the Ebola-KB Dashboard. © The Author(s) 2015. Published by Oxford University Press.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

PubMed Central

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-01

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

A Modular Framework for Transforming Structured Data into HTML with Machine-Readable Annotations

NASA Astrophysics Data System (ADS)

Patton, E. W.; West, P.; Rozell, E.; Zheng, J.

2010-12-01

There is a plethora of web-based Content Management Systems (CMS) available for maintaining projects and data, i.a. However, each system varies in its capabilities and often content is stored separately and accessed via non-uniform web interfaces. Moving from one CMS to another (e.g., MediaWiki to Drupal) can be cumbersome, especially if a large quantity of data must be adapted to the new system. To standardize the creation, display, management, and sharing of project information, we have assembled a framework that uses existing web technologies to transform data provided by any service that supports the SPARQL Protocol and RDF Query Language (SPARQL) queries into HTML fragments, allowing it to be embedded in any existing website. The framework utilizes a two-tier XML Stylesheet Transformation (XSLT) that uses existing ontologies (e.g., Friend-of-a-Friend, Dublin Core) to interpret query results and render them as HTML documents. These ontologies can be used in conjunction with custom ontologies suited to individual needs (e.g., domain-specific ontologies for describing data records). Furthermore, this transformation process encodes machine-readable annotations, namely, the Resource Description Framework in attributes (RDFa), into the resulting HTML, so that capable parsers and search engines can extract the relationships between entities (e.g, people, organizations, datasets). To facilitate editing of content, the framework provides a web-based form system, mapping each query to a dynamically generated form that can be used to modify and create entities, while keeping the native data store up-to-date. This open framework makes it easy to duplicate data across many different sites, allowing researchers to distribute their data in many different online forums. In this presentation we will outline the structure of queries and the stylesheets used to transform them, followed by a brief walkthrough that follows the data from storage to human- and machine-accessible web page. We conclude with a discussion on content caching and steps toward performing queries across multiple domains.

Using benchmarking techniques and the 2011 maternity practices infant nutrition and care (mPINC) survey to improve performance among peer groups across the United States.

PubMed

Edwards, Roger A; Dee, Deborah; Umer, Amna; Perrine, Cria G; Shealy, Katherine R; Grummer-Strawn, Laurence M

2014-02-01

A substantial proportion of US maternity care facilities engage in practices that are not evidence-based and that interfere with breastfeeding. The CDC Survey of Maternity Practices in Infant Nutrition and Care (mPINC) showed significant variation in maternity practices among US states. The purpose of this article is to use benchmarking techniques to identify states within relevant peer groups that were top performers on mPINC survey indicators related to breastfeeding support. We used 11 indicators of breastfeeding-related maternity care from the 2011 mPINC survey and benchmarking techniques to organize and compare hospital-based maternity practices across the 50 states and Washington, DC. We created peer categories for benchmarking first by region (grouping states by West, Midwest, South, and Northeast) and then by size (grouping states by the number of maternity facilities and dividing each region into approximately equal halves based on the number of facilities). Thirty-four states had scores high enough to serve as benchmarks, and 32 states had scores low enough to reflect the lowest score gap from the benchmark on at least 1 indicator. No state served as the benchmark on more than 5 indicators and no state was furthest from the benchmark on more than 7 indicators. The small peer group benchmarks in the South, West, and Midwest were better than the large peer group benchmarks on 91%, 82%, and 36% of the indicators, respectively. In the West large, the Midwest large, the Midwest small, and the South large peer groups, 4-6 benchmarks showed that less than 50% of hospitals have ideal practice in all states. The evaluation presents benchmarks for peer group state comparisons that provide potential and feasible targets for improvement.

Hospital benchmarking: are U.S. eye hospitals ready?

PubMed

de Korne, Dirk F; van Wijngaarden, Jeroen D H; Sol, Kees J C A; Betz, Robert; Thomas, Richard C; Schein, Oliver D; Klazinga, Niek S

2012-01-01

Benchmarking is increasingly considered a useful management instrument to improve quality in health care, but little is known about its applicability in hospital settings. The aims of this study were to assess the applicability of a benchmarking project in U.S. eye hospitals and compare the results with an international initiative. We evaluated multiple cases by applying an evaluation frame abstracted from the literature to five U.S. eye hospitals that used a set of 10 indicators for efficiency benchmarking. Qualitative analysis entailed 46 semistructured face-to-face interviews with stakeholders, document analyses, and questionnaires. The case studies only partially met the conditions of the evaluation frame. Although learning and quality improvement were stated as overall purposes, the benchmarking initiative was at first focused on efficiency only. No ophthalmic outcomes were included, and clinicians were skeptical about their reporting relevance and disclosure. However, in contrast with earlier findings in international eye hospitals, all U.S. hospitals worked with internal indicators that were integrated in their performance management systems and supported benchmarking. Benchmarking can support performance management in individual hospitals. Having a certain number of comparable institutes provide similar services in a noncompetitive milieu seems to lay fertile ground for benchmarking. International benchmarking is useful only when these conditions are not met nationally. Although the literature focuses on static conditions for effective benchmarking, our case studies show that it is a highly iterative and learning process. The journey of benchmarking seems to be more important than the destination. Improving patient value (health outcomes per unit of cost) requires, however, an integrative perspective where clinicians and administrators closely cooperate on both quality and efficiency issues. If these worlds do not share such a relationship, the added "public" value of benchmarking in health care is questionable.

A benchmarking program to reduce red blood cell outdating: implementation, evaluation, and a conceptual framework.

PubMed

Barty, Rebecca L; Gagliardi, Kathleen; Owens, Wendy; Lauzon, Deborah; Scheuermann, Sheena; Liu, Yang; Wang, Grace; Pai, Menaka; Heddle, Nancy M

2015-07-01

Benchmarking is a quality improvement tool that compares an organization's performance to that of its peers for selected indicators, to improve practice. Processes to develop evidence-based benchmarks for red blood cell (RBC) outdating in Ontario hospitals, based on RBC hospital disposition data from Canadian Blood Services, have been previously reported. These benchmarks were implemented in 160 hospitals provincewide with a multifaceted approach, which included hospital education, inventory management tools and resources, summaries of best practice recommendations, recognition of high-performing sites, and audit tools on the Transfusion Ontario website (http://transfusionontario.org). In this study we describe the implementation process and the impact of the benchmarking program on RBC outdating. A conceptual framework for continuous quality improvement of a benchmarking program was also developed. The RBC outdating rate for all hospitals trended downward continuously from April 2006 to February 2012, irrespective of hospitals' transfusion rates or their distance from the blood supplier. The highest annual outdating rate was 2.82%, at the beginning of the observation period. Each year brought further reductions, with a nadir outdating rate of 1.02% achieved in 2011. The key elements of the successful benchmarking strategy included dynamic targets, a comprehensive and evidence-based implementation strategy, ongoing information sharing, and a robust data system to track information. The Ontario benchmarking program for RBC outdating resulted in continuous and sustained quality improvement. Our conceptual iterative framework for benchmarking provides a guide for institutions implementing a benchmarking program. © 2015 AABB.

Benchmarking Helps Measure Union Programs, Operations.

ERIC Educational Resources Information Center

Mann, Jerry

2001-01-01

Explores three examples of benchmarking by college student unions. Focuses on how a union can collect information from other unions for use as benchmarking standards for the purposes of selling a concept or justifying program increases, or for comparing a union's financial performance to other unions. (EV)

Performance Characteristics of the Multi-Zone NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Haoqiang; VanderWijngaart, Rob F.

2003-01-01

We describe a new suite of computational benchmarks that models applications featuring multiple levels of parallelism. Such parallelism is often available in realistic flow computations on systems of grids, but had not previously been captured in bench-marks. The new suite, named NPB Multi-Zone, is extended from the NAS Parallel Benchmarks suite, and involves solving the application benchmarks LU, BT and SP on collections of loosely coupled discretization meshes. The solutions on the meshes are updated independently, but after each time step they exchange boundary value information. This strategy provides relatively easily exploitable coarse-grain parallelism between meshes. Three reference implementations are available: one serial, one hybrid using the Message Passing Interface (MPI) and OpenMP, and another hybrid using a shared memory multi-level programming model (SMP+OpenMP). We examine the effectiveness of hybrid parallelization paradigms in these implementations on three different parallel computers. We also use an empirical formula to investigate the performance characteristics of the multi-zone benchmarks.

Analysis of 2D Torus and Hub Topologies of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Pedretti, Kevin T.; Fineberg, Samuel A.; Kutler, Paul (Technical Monitor)

1997-01-01

A variety of different network technologies and topologies are currently being evaluated as part of the Whitney Project. This paper reports on the implementation and performance of a Fast Ethernet network configured in a 4x4 2D torus topology in a testbed cluster of 'commodity' Pentium Pro PCs. Several benchmarks were used for performance evaluation: an MPI point to point message passing benchmark, an MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2). Our results show that for point to point communication on an unloaded network, the hub and 1 hop routes on the torus have about the same bandwidth and latency. However, the bandwidth decreases and the latency increases on the torus for each additional route hop. Collective communication benchmarks show that the torus provides roughly four times more aggregate bandwidth and eight times faster MPI barrier synchronizations than a hub based network for 16 processor systems. Finally, the SOAPBOX benchmarks, which simulate real-world CFD applications, generally demonstrated substantially better performance on the torus than on the hub. In the few cases the hub was faster, the difference was negligible. In total, our experimental results lead to the conclusion that for Fast Ethernet networks, the torus topology has better performance and scales better than a hub based network.

Issues in benchmarking human reliability analysis methods : a literature review.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lois, Erasmia; Forester, John Alan; Tran, Tuan Q.

There is a diversity of human reliability analysis (HRA) methods available for use in assessing human performance within probabilistic risk assessment (PRA). Due to the significant differences in the methods, including the scope, approach, and underlying models, there is a need for an empirical comparison investigating the validity and reliability of the methods. To accomplish this empirical comparison, a benchmarking study is currently underway that compares HRA methods with each other and against operator performance in simulator studies. In order to account for as many effects as possible in the construction of this benchmarking study, a literature review was conducted,more » reviewing past benchmarking studies in the areas of psychology and risk assessment. A number of lessons learned through these studies are presented in order to aid in the design of future HRA benchmarking endeavors.« less

Issues in Benchmarking Human Reliability Analysis Methods: A Literature Review

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronald L. Boring; Stacey M. L. Hendrickson; John A. Forester

There is a diversity of human reliability analysis (HRA) methods available for use in assessing human performance within probabilistic risk assessments (PRA). Due to the significant differences in the methods, including the scope, approach, and underlying models, there is a need for an empirical comparison investigating the validity and reliability of the methods. To accomplish this empirical comparison, a benchmarking study comparing and evaluating HRA methods in assessing operator performance in simulator experiments is currently underway. In order to account for as many effects as possible in the construction of this benchmarking study, a literature review was conducted, reviewing pastmore » benchmarking studies in the areas of psychology and risk assessment. A number of lessons learned through these studies are presented in order to aid in the design of future HRA benchmarking endeavors.« less

XWeB: The XML Warehouse Benchmark

NASA Astrophysics Data System (ADS)

Mahboubi, Hadj; Darmont, Jérôme

With the emergence of XML as a standard for representing business data, new decision support applications are being developed. These XML data warehouses aim at supporting On-Line Analytical Processing (OLAP) operations that manipulate irregular XML data. To ensure feasibility of these new tools, important performance issues must be addressed. Performance is customarily assessed with the help of benchmarks. However, decision support benchmarks do not currently support XML features. In this paper, we introduce the XML Warehouse Benchmark (XWeB), which aims at filling this gap. XWeB derives from the relational decision support benchmark TPC-H. It is mainly composed of a test data warehouse that is based on a unified reference model for XML warehouses and that features XML-specific structures, and its associate XQuery decision support workload. XWeB's usage is illustrated by experiments on several XML database management systems.

Energy saving in WWTP: Daily benchmarking under uncertainty and data availability limitations.

PubMed

Torregrossa, D; Schutz, G; Cornelissen, A; Hernández-Sancho, F; Hansen, J

2016-07-01

Efficient management of Waste Water Treatment Plants (WWTPs) can produce significant environmental and economic benefits. Energy benchmarking can be used to compare WWTPs, identify targets and use these to improve their performance. Different authors have performed benchmark analysis on monthly or yearly basis but their approaches suffer from a time lag between an event, its detection, interpretation and potential actions. The availability of on-line measurement data on many WWTPs should theoretically enable the decrease of the management response time by daily benchmarking. Unfortunately this approach is often impossible because of limited data availability. This paper proposes a methodology to perform a daily benchmark analysis under database limitations. The methodology has been applied to the Energy Online System (EOS) developed in the framework of the project "INNERS" (INNovative Energy Recovery Strategies in the urban water cycle). EOS calculates a set of Key Performance Indicators (KPIs) for the evaluation of energy and process performances. In EOS, the energy KPIs take in consideration the pollutant load in order to enable the comparison between different plants. For example, EOS does not analyse the energy consumption but the energy consumption on pollutant load. This approach enables the comparison of performances for plants with different loads or for a single plant under different load conditions. The energy consumption is measured by on-line sensors, while the pollutant load is measured in the laboratory approximately every 14 days. Consequently, the unavailability of the water quality parameters is the limiting factor in calculating energy KPIs. In this paper, in order to overcome this limitation, the authors have developed a methodology to estimate the required parameters and manage the uncertainty in the estimation. By coupling the parameter estimation with an interval based benchmark approach, the authors propose an effective, fast and reproducible way to manage infrequent inlet measurements. Its use enables benchmarking on a daily basis and prepares the ground for further investigation. Copyright © 2016 Elsevier Inc. All rights reserved.

Benchmarking and the laboratory

PubMed Central

Galloway, M; Nadin, L

2001-01-01

This article describes how benchmarking can be used to assess laboratory performance. Two benchmarking schemes are reviewed, the Clinical Benchmarking Company's Pathology Report and the College of American Pathologists' Q-Probes scheme. The Clinical Benchmarking Company's Pathology Report is undertaken by staff based in the clinical management unit, Keele University with appropriate input from the professional organisations within pathology. Five annual reports have now been completed. Each report is a detailed analysis of 10 areas of laboratory performance. In this review, particular attention is focused on the areas of quality, productivity, variation in clinical practice, skill mix, and working hours. The Q-Probes scheme is part of the College of American Pathologists programme in studies of quality assurance. The Q-Probes scheme and its applicability to pathology in the UK is illustrated by reviewing two recent Q-Probe studies: routine outpatient test turnaround time and outpatient test order accuracy. The Q-Probes scheme is somewhat limited by the small number of UK laboratories that have participated. In conclusion, as a result of the government's policy in the UK, benchmarking is here to stay. Benchmarking schemes described in this article are one way in which pathologists can demonstrate that they are providing a cost effective and high quality service. Key Words: benchmarking • pathology PMID:11477112

Mathematics Content Standards Benchmarks and Performance Standards

ERIC Educational Resources Information Center

New Mexico Public Education Department, 2008

2008-01-01

New Mexico Mathematics Content Standards, Benchmarks, and Performance Standards identify what students should know and be able to do across all grade levels, forming a spiraling framework in the sense that many skills, once introduced, develop over time. While the Performance Standards are set forth at grade-specific levels, they do not exist as…

A comparison of five benchmarks

NASA Technical Reports Server (NTRS)

Huss, Janice E.; Pennline, James A.

1987-01-01

Five benchmark programs were obtained and run on the NASA Lewis CRAY X-MP/24. A comparison was made between the programs codes and between the methods for calculating performance figures. Several multitasking jobs were run to gain experience in how parallel performance is measured.

Benchmarking in the Two-Year Public Postsecondary Sector: A Learning Process

ERIC Educational Resources Information Center

Mitchell, Jennevieve

2015-01-01

The recession prompted reflection on how resource allocation decisions contribute to the performance of community colleges in the United States. Private benchmarking initiatives, most notably those established by the National Higher Education Benchmarking Institute, can only partially begin to address this question. Empirical and financial…

Machine characterization and benchmark performance prediction

NASA Technical Reports Server (NTRS)

Saavedra-Barrera, Rafael H.

1988-01-01

From runs of standard benchmarks or benchmark suites, it is not possible to characterize the machine nor to predict the run time of other benchmarks which have not been run. A new approach to benchmarking and machine characterization is reported. The creation and use of a machine analyzer is described, which measures the performance of a given machine on FORTRAN source language constructs. The machine analyzer yields a set of parameters which characterize the machine and spotlight its strong and weak points. Also described is a program analyzer, which analyzes FORTRAN programs and determines the frequency of execution of each of the same set of source language operations. It is then shown that by combining a machine characterization and a program characterization, we are able to predict with good accuracy the run time of a given benchmark on a given machine. Characterizations are provided for the Cray-X-MP/48, Cyber 205, IBM 3090/200, Amdahl 5840, Convex C-1, VAX 8600, VAX 11/785, VAX 11/780, SUN 3/50, and IBM RT-PC/125, and for the following benchmark programs or suites: Los Alamos (BMK8A1), Baskett, Linpack, Livermore Loops, Madelbrot Set, NAS Kernels, Shell Sort, Smith, Whetstone and Sieve of Erathostenes.

Closed-Loop Neuromorphic Benchmarks

PubMed Central

Stewart, Terrence C.; DeWolf, Travis; Kleinhans, Ashley; Eliasmith, Chris

2015-01-01

Evaluating the effectiveness and performance of neuromorphic hardware is difficult. It is even more difficult when the task of interest is a closed-loop task; that is, a task where the output from the neuromorphic hardware affects some environment, which then in turn affects the hardware's future input. However, closed-loop situations are one of the primary potential uses of neuromorphic hardware. To address this, we present a methodology for generating closed-loop benchmarks that makes use of a hybrid of real physical embodiment and a type of “minimal” simulation. Minimal simulation has been shown to lead to robust real-world performance, while still maintaining the practical advantages of simulation, such as making it easy for the same benchmark to be used by many researchers. This method is flexible enough to allow researchers to explicitly modify the benchmarks to identify specific task domains where particular hardware excels. To demonstrate the method, we present a set of novel benchmarks that focus on motor control for an arbitrary system with unknown external forces. Using these benchmarks, we show that an error-driven learning rule can consistently improve motor control performance across a randomly generated family of closed-loop simulations, even when there are up to 15 interacting joints to be controlled. PMID:26696820

Benchmarking image fusion system design parameters

NASA Astrophysics Data System (ADS)

Howell, Christopher L.

2013-06-01

A clear and absolute method for discriminating between image fusion algorithm performances is presented. This method can effectively be used to assist in the design and modeling of image fusion systems. Specifically, it is postulated that quantifying human task performance using image fusion should be benchmarked to whether the fusion algorithm, at a minimum, retained the performance benefit achievable by each independent spectral band being fused. The established benchmark would then clearly represent the threshold that a fusion system should surpass to be considered beneficial to a particular task. A genetic algorithm is employed to characterize the fused system parameters using a Matlab® implementation of NVThermIP as the objective function. By setting the problem up as a mixed-integer constraint optimization problem, one can effectively look backwards through the image acquisition process: optimizing fused system parameters by minimizing the difference between modeled task difficulty measure and the benchmark task difficulty measure. The results of an identification perception experiment are presented, where human observers were asked to identify a standard set of military targets, and used to demonstrate the effectiveness of the benchmarking process.

A New Performance Improvement Model: Adding Benchmarking to the Analysis of Performance Indicator Data.

PubMed

Al-Kuwaiti, Ahmed; Homa, Karen; Maruthamuthu, Thennarasu

2016-01-01

A performance improvement model was developed that focuses on the analysis and interpretation of performance indicator (PI) data using statistical process control and benchmarking. PIs are suitable for comparison with benchmarks only if the data fall within the statistically accepted limit-that is, show only random variation. Specifically, if there is no significant special-cause variation over a period of time, then the data are ready to be benchmarked. The proposed Define, Measure, Control, Internal Threshold, and Benchmark model is adapted from the Define, Measure, Analyze, Improve, Control (DMAIC) model. The model consists of the following five steps: Step 1. Define the process; Step 2. Monitor and measure the variation over the period of time; Step 3. Check the variation of the process; if stable (no significant variation), go to Step 4; otherwise, control variation with the help of an action plan; Step 4. Develop an internal threshold and compare the process with it; Step 5.1. Compare the process with an internal benchmark; and Step 5.2. Compare the process with an external benchmark. The steps are illustrated through the use of health care-associated infection (HAI) data collected for 2013 and 2014 from the Infection Control Unit, King Fahd Hospital, University of Dammam, Saudi Arabia. Monitoring variation is an important strategy in understanding and learning about a process. In the example, HAI was monitored for variation in 2013, and the need to have a more predictable process prompted the need to control variation by an action plan. The action plan was successful, as noted by the shift in the 2014 data, compared to the historical average, and, in addition, the variation was reduced. The model is subject to limitations: For example, it cannot be used without benchmarks, which need to be calculated the same way with similar patient populations, and it focuses only on the "Analyze" part of the DMAIC model.

Evaluation of CHO Benchmarks on the Arria 10 FPGA using Intel FPGA SDK for OpenCL

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Zheming; Yoshii, Kazutomo; Finkel, Hal

The OpenCL standard is an open programming model for accelerating algorithms on heterogeneous computing system. OpenCL extends the C-based programming language for developing portable codes on different platforms such as CPU, Graphics processing units (GPUs), Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs). The Intel FPGA SDK for OpenCL is a suite of tools that allows developers to abstract away the complex FPGA-based development flow for a high-level software development flow. Users can focus on the design of hardware-accelerated kernel functions in OpenCL and then direct the tools to generate the low-level FPGA implementations. The approach makes themore » FPGA-based development more accessible to software users as the needs for hybrid computing using CPUs and FPGAs are increasing. It can also significantly reduce the hardware development time as users can evaluate different ideas with high-level language without deep FPGA domain knowledge. Benchmarking of OpenCL-based framework is an effective way for analyzing the performance of system by studying the execution of the benchmark applications. CHO is a suite of benchmark applications that provides support for OpenCL [1]. The authors presented CHO as an OpenCL port of the CHStone benchmark. Using Altera OpenCL (AOCL) compiler to synthesize the benchmark applications, they listed the resource usage and performance of each kernel that can be successfully synthesized by the compiler. In this report, we evaluate the resource usage and performance of the CHO benchmark applications using the Intel FPGA SDK for OpenCL and Nallatech 385A FPGA board that features an Arria 10 FPGA device. The focus of the report is to have a better understanding of the resource usage and performance of the kernel implementations using Arria-10 FPGA devices compared to Stratix-5 FPGA devices. In addition, we also gain knowledge about the limitations of the current compiler when it fails to synthesize a benchmark application.« less

Performance of Landslide-HySEA tsunami model for NTHMP benchmarking validation process

NASA Astrophysics Data System (ADS)

Macias, Jorge

2017-04-01

In its FY2009 Strategic Plan, the NTHMP required that all numerical tsunami inundation models be verified as accurate and consistent through a model benchmarking process. This was completed in 2011, but only for seismic tsunami sources and in a limited manner for idealized solid underwater landslides. Recent work by various NTHMP states, however, has shown that landslide tsunami hazard may be dominant along significant parts of the US coastline, as compared to hazards from other tsunamigenic sources. To perform the above-mentioned validation process, a set of candidate benchmarks were proposed. These benchmarks are based on a subset of available laboratory date sets for solid slide experiments and deformable slide experiments, and include both submarine and subaerial slides. A benchmark based on a historic field event (Valdez, AK, 1964) close the list of proposed benchmarks. The Landslide-HySEA model has participated in the workshop that was organized at Texas A&M University - Galveston, on January 9-11, 2017. The aim of this presentation is to show some of the numerical results obtained for Landslide-HySEA in the framework of this benchmarking validation/verification effort. Acknowledgements. This research has been partially supported by the Junta de Andalucía research project TESELA (P11-RNM7069), the Spanish Government Research project SIMURISK (MTM2015-70490-C02-01-R) and Universidad de Málaga, Campus de Excelencia Internacional Andalucía Tech. The GPU computations were performed at the Unit of Numerical Methods (University of Malaga).

7 CFR 245.12 - State agencies and direct certification requirements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... NUTRITION SERVICE, DEPARTMENT OF AGRICULTURE CHILD NUTRITION PROGRAMS DETERMINING ELIGIBILITY FOR FREE AND... performance benchmarks set forth in paragraph (b) of this section for directly certifying children who are.... State agencies must meet performance benchmarks for directly certifying for free school meals children...

Performance Analysis of the ARL Linux Networx Cluster

DTIC Science & Technology

2004-06-01

OVERFLOW, used processors selected by SGE. All benchmarks on the GAMESS, COBALT, LSDYNA and FLUENT. Each code Origin 3800 were executed using IRIX cpusets...scheduler. for these benchmarks defines a missile with grid fins consisting of seventeen million cells [31. 4. Application Performance Results and

The Suite for Embedded Applications and Kernels

DOE Office of Scientific and Technical Information (OSTI.GOV)

2016-05-10

Many applications of high performance embedded computing are limited by performance or power bottlenecks. We havedesigned SEAK, a new benchmark suite, (a) to capture these bottlenecks in a way that encourages creative solutions to these bottlenecks? and (b) to facilitate rigorous, objective, end-user evaluation for their solutions. To avoid biasing solutions toward existing algorithms, SEAK benchmarks use a mission-centric (abstracted from a particular algorithm) andgoal-oriented (functional) specification. To encourage solutions that are any combination of software or hardware, we use an end-user blackbox evaluation that can capture tradeoffs between performance, power, accuracy, size, and weight. The tradeoffs are especially informativemore » for procurement decisions. We call our benchmarks future proof because each mission-centric interface and evaluation remains useful despite shifting algorithmic preferences. It is challenging to create both concise and precise goal-oriented specifications for mission-centric problems. This paper describes the SEAK benchmark suite and presents an evaluation of sample solutions that highlights power and performance tradeoffs.« less

An Exploration of the Gap between Highest and Lowest Ability Readers across 20 Countries

ERIC Educational Resources Information Center

Alivernini, Fabio

2013-01-01

The aim of the present study, based on data from 20 countries, is to identify the pattern of variables (at country, school and student levels), which are typical of students performing below the low international benchmark compared to students performing at the advanced performance benchmark, in the Progress in International Reading Literacy Study…

Benchmark problems for numerical implementations of phase field models

DOE PAGES

Jokisaari, A. M.; Voorhees, P. W.; Guyer, J. E.; ...

2016-10-01

Here, we present the first set of benchmark problems for phase field models that are being developed by the Center for Hierarchical Materials Design (CHiMaD) and the National Institute of Standards and Technology (NIST). While many scientific research areas use a limited set of well-established software, the growing phase field community continues to develop a wide variety of codes and lacks benchmark problems to consistently evaluate the numerical performance of new implementations. Phase field modeling has become significantly more popular as computational power has increased and is now becoming mainstream, driving the need for benchmark problems to validate and verifymore » new implementations. We follow the example set by the micromagnetics community to develop an evolving set of benchmark problems that test the usability, computational resources, numerical capabilities and physical scope of phase field simulation codes. In this paper, we propose two benchmark problems that cover the physics of solute diffusion and growth and coarsening of a second phase via a simple spinodal decomposition model and a more complex Ostwald ripening model. We demonstrate the utility of benchmark problems by comparing the results of simulations performed with two different adaptive time stepping techniques, and we discuss the needs of future benchmark problems. The development of benchmark problems will enable the results of quantitative phase field models to be confidently incorporated into integrated computational materials science and engineering (ICME), an important goal of the Materials Genome Initiative.« less

Neutron Deep Penetration Calculations in Light Water with Monte Carlo TRIPOLI-4® Variance Reduction Techniques

NASA Astrophysics Data System (ADS)

Lee, Yi-Kang

2017-09-01

Nuclear decommissioning takes place in several stages due to the radioactivity in the reactor structure materials. A good estimation of the neutron activation products distributed in the reactor structure materials impacts obviously on the decommissioning planning and the low-level radioactive waste management. Continuous energy Monte-Carlo radiation transport code TRIPOLI-4 has been applied on radiation protection and shielding analyses. To enhance the TRIPOLI-4 application in nuclear decommissioning activities, both experimental and computational benchmarks are being performed. To calculate the neutron activation of the shielding and structure materials of nuclear facilities, the knowledge of 3D neutron flux map and energy spectra must be first investigated. To perform this type of neutron deep penetration calculations with the Monte Carlo transport code, variance reduction techniques are necessary in order to reduce the uncertainty of the neutron activation estimation. In this study, variance reduction options of the TRIPOLI-4 code were used on the NAIADE 1 light water shielding benchmark. This benchmark document is available from the OECD/NEA SINBAD shielding benchmark database. From this benchmark database, a simplified NAIADE 1 water shielding model was first proposed in this work in order to make the code validation easier. Determination of the fission neutron transport was performed in light water for penetration up to 50 cm for fast neutrons and up to about 180 cm for thermal neutrons. Measurement and calculation results were benchmarked. Variance reduction options and their performance were discussed and compared.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

PubMed Central

Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter; Koslicki, David; Janssen, Stefan; Dröge, Johannes; Gregor, Ivan; Majda, Stephan; Fiedler, Jessika; Dahms, Eik; Bremges, Andreas; Fritz, Adrian; Garrido-Oter, Ruben; Jørgensen, Tue Sparholt; Shapiro, Nicole; Blood, Philip D.; Gurevich, Alexey; Bai, Yang; Turaev, Dmitrij; DeMaere, Matthew Z.; Chikhi, Rayan; Nagarajan, Niranjan; Quince, Christopher; Meyer, Fernando; Balvočiūtė, Monika; Hansen, Lars Hestbjerg; Sørensen, Søren J.; Chia, Burton K. H.; Denis, Bertrand; Froula, Jeff L.; Wang, Zhong; Egan, Robert; Kang, Dongwan Don; Cook, Jeffrey J.; Deltel, Charles; Beckstette, Michael; Lemaitre, Claire; Peterlongo, Pierre; Rizk, Guillaume; Lavenier, Dominique; Wu, Yu-Wei; Singer, Steven W.; Jain, Chirag; Strous, Marc; Klingenberg, Heiner; Meinicke, Peter; Barton, Michael; Lingner, Thomas; Lin, Hsin-Hung; Liao, Yu-Chieh; Silva, Genivaldo Gueiros Z.; Cuevas, Daniel A.; Edwards, Robert A.; Saha, Surya; Piro, Vitor C.; Renard, Bernhard Y.; Pop, Mihai; Klenk, Hans-Peter; Göker, Markus; Kyrpides, Nikos C.; Woyke, Tanja; Vorholt, Julia A.; Schulze-Lefert, Paul; Rubin, Edward M.; Darling, Aaron E.; Rattei, Thomas; McHardy, Alice C.

2018-01-01

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions. PMID:28967888

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Der Marck, S. C.

Three nuclear data libraries have been tested extensively using criticality safety benchmark calculations. The three libraries are the new release of the US library ENDF/B-VII.1 (2011), the new release of the Japanese library JENDL-4.0 (2011), and the OECD/NEA library JEFF-3.1 (2006). All calculations were performed with the continuous-energy Monte Carlo code MCNP (version 4C3, as well as version 6-beta1). Around 2000 benchmark cases from the International Handbook of Criticality Safety Benchmark Experiments (ICSBEP) were used. The results were analyzed per ICSBEP category, and per element. Overall, the three libraries show similar performance on most criticality safety benchmarks. The largest differencesmore » are probably caused by elements such as Be, C, Fe, Zr, W. (authors)« less

High-performance conjugate-gradient benchmark: A new metric for ranking high-performance computing systems

DOE PAGES

Dongarra, Jack; Heroux, Michael A.; Luszczek, Piotr

2015-08-17

Here, we describe a new high-performance conjugate-gradient (HPCG) benchmark. HPCG is composed of computations and data-access patterns commonly found in scientific applications. HPCG strives for a better correlation to existing codes from the computational science domain and to be representative of their performance. Furthermore, HPCG is meant to help drive the computer system design and implementation in directions that will better impact future performance improvement.

Using Benchmarking Techniques and the 2011 Maternity Practices Infant Nutrition and Care (mPINC) Survey to Improve Performance among Peer Groups across the United States

PubMed Central

Edwards, Roger A.; Dee, Deborah; Umer, Amna; Perrine, Cria G.; Shealy, Katherine R.; Grummer-Strawn, Laurence M.

2015-01-01

Background A substantial proportion of US maternity care facilities engage in practices that are not evidence-based and that interfere with breastfeeding. The CDC Survey of Maternity Practices in Infant Nutrition and Care (mPINC) showed significant variation in maternity practices among US states. Objective The purpose of this article is to use benchmarking techniques to identify states within relevant peer groups that were top performers on mPINC survey indicators related to breastfeeding support. Methods We used 11 indicators of breastfeeding-related maternity care from the 2011 mPINC survey and benchmarking techniques to organize and compare hospital-based maternity practices across the 50 states and Washington, DC. We created peer categories for benchmarking first by region (grouping states by West, Midwest, South, and Northeast) and then by size (grouping states by the number of maternity facilities and dividing each region into approximately equal halves based on the number of facilities). Results Thirty-four states had scores high enough to serve as benchmarks, and 32 states had scores low enough to reflect the lowest score gap from the benchmark on at least 1 indicator. No state served as the benchmark on more than 5 indicators and no state was furthest from the benchmark on more than 7 indicators. The small peer group benchmarks in the South, West, and Midwest were better than the large peer group benchmarks on 91%, 82%, and 36% of the indicators, respectively. In the West large, the Midwest large, the Midwest small, and the South large peer groups, 4–6 benchmarks showed that less than 50% of hospitals have ideal practice in all states. Conclusion The evaluation presents benchmarks for peer group state comparisons that provide potential and feasible targets for improvement. PMID:24394963

NAS Parallel Benchmark Results 11-96. 1.0

NASA Technical Reports Server (NTRS)

Bailey, David H.; Bailey, David; Chancellor, Marisa K. (Technical Monitor)

1997-01-01

The NAS Parallel Benchmarks have been developed at NASA Ames Research Center to study the performance of parallel supercomputers. The eight benchmark problems are specified in a "pencil and paper" fashion. In other words, the complete details of the problem to be solved are given in a technical document, and except for a few restrictions, benchmarkers are free to select the language constructs and implementation techniques best suited for a particular system. These results represent the best results that have been reported to us by the vendors for the specific 3 systems listed. In this report, we present new NPB (Version 1.0) performance results for the following systems: DEC Alpha Server 8400 5/440, Fujitsu VPP Series (VX, VPP300, and VPP700), HP/Convex Exemplar SPP2000, IBM RS/6000 SP P2SC node (120 MHz), NEC SX-4/32, SGI/CRAY T3E, SGI Origin200, and SGI Origin2000. We also report High Performance Fortran (HPF) based NPB results for IBM SP2 Wide Nodes, HP/Convex Exemplar SPP2000, and SGI/CRAY T3D. These results have been submitted by Applied Parallel Research (APR) and Portland Group Inc. (PGI). We also present sustained performance per dollar for Class B LU, SP and BT benchmarks.

Benchmarking Big Data Systems and the BigData Top100 List.

PubMed

Baru, Chaitanya; Bhandarkar, Milind; Nambiar, Raghunath; Poess, Meikel; Rabl, Tilmann

2013-03-01

"Big data" has become a major force of innovation across enterprises of all sizes. New platforms with increasingly more features for managing big datasets are being announced almost on a weekly basis. Yet, there is currently a lack of any means of comparability among such platforms. While the performance of traditional database systems is well understood and measured by long-established institutions such as the Transaction Processing Performance Council (TCP), there is neither a clear definition of the performance of big data systems nor a generally agreed upon metric for comparing these systems. In this article, we describe a community-based effort for defining a big data benchmark. Over the past year, a Big Data Benchmarking Community has become established in order to fill this void. The effort focuses on defining an end-to-end application-layer benchmark for measuring the performance of big data applications, with the ability to easily adapt the benchmark specification to evolving challenges in the big data space. This article describes the efforts that have been undertaken thus far toward the definition of a BigData Top100 List. While highlighting the major technical as well as organizational challenges, through this article, we also solicit community input into this process.

New NAS Parallel Benchmarks Results

NASA Technical Reports Server (NTRS)

Yarrow, Maurice; Saphir, William; VanderWijngaart, Rob; Woo, Alex; Kutler, Paul (Technical Monitor)

1997-01-01

NPB2 (NAS (NASA Advanced Supercomputing) Parallel Benchmarks 2) is an implementation, based on Fortran and the MPI (message passing interface) message passing standard, of the original NAS Parallel Benchmark specifications. NPB2 programs are run with little or no tuning, in contrast to NPB vendor implementations, which are highly optimized for specific architectures. NPB2 results complement, rather than replace, NPB results. Because they have not been optimized by vendors, NPB2 implementations approximate the performance a typical user can expect for a portable parallel program on distributed memory parallel computers. Together these results provide an insightful comparison of the real-world performance of high-performance computers. New NPB2 features: New implementation (CG), new workstation class problem sizes, new serial sample versions, more performance statistics.

Simulation-based comprehensive benchmarking of RNA-seq aligners

PubMed Central

Baruzzo, Giacomo; Hayer, Katharina E; Kim, Eun Ji; Di Camillo, Barbara; FitzGerald, Garret A; Grant, Gregory R

2018-01-01

Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. We performed a comprehensive benchmarking of 14 common splice-aware aligners for base, read, and exon junction-level accuracy and compared default with optimized parameters. We found that performance varied by genome complexity, and accuracy and popularity were poorly correlated. The most widely cited tool underperforms for most metrics, particularly when using default settings. PMID:27941783

Iowa's Community College Adult Literacy Annual Report. Program Year 2007, July 1, 2006-June 30, 2007

ERIC Educational Resources Information Center

Division of Community Colleges and Workforce Preparation, Iowa Department of Education, 2007

2007-01-01

This comprehensive document replaces the previously published Benchmark Report, Benchmark Report Executive Summary, Iowa's Community College Basic Literacy Skills Credential Report, Iowa GED Statistical Report, GED Annual Performance Report and Iowa's Adult Literacy Program National Reporting System Annual Performance Report (Graphic…

Benchmarking Universities' Efficiency Indicators in the Presence of Internal Heterogeneity

ERIC Educational Resources Information Center

Agasisti, Tommaso; Bonomi, Francesca

2014-01-01

When benchmarking its performance, a university is usually considered as a single strategic unit. According to the evidence, however, lower levels within an organisation (such as faculties, departments and schools) play a significant role in institutional governance, affecting the overall performance. In this article, an empirical analysis was…

Shift Verification and Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pandya, Tara M.; Evans, Thomas M.; Davidson, Gregory G

2016-09-07

This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over amore » burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.« less

FY 2004 Top 200 Users Survey Report

DTIC Science & Technology

2004-10-01

Rating 82% 79% 80% ACSI Federal Government Benchmark* 71.1% 70.2% 70.9% DTIC Excels by +10.9 +8.8 +9.1 *ACSI is the official service quality benchmark...ACSI Federal Government Benchmark* 71.1% 70.2% 70.9% DTIC Excels by +10.9 +8.8 +9.1 *ACSI is the official service quality benchmark for the Federal...Users Survey % DTIC’s Other Overall Product/ Service Quality and Performance: Not only were we able to ascertain product and service usage data from

Benchmarking for Excellence and the Nursing Process

NASA Technical Reports Server (NTRS)

Sleboda, Claire

1999-01-01

Nursing is a service profession. The services provided are essential to life and welfare. Therefore, setting the benchmark for high quality care is fundamental. Exploring the definition of a benchmark value will help to determine a best practice approach. A benchmark is the descriptive statement of a desired level of performance against which quality can be judged. It must be sufficiently well understood by managers and personnel in order that it may serve as a standard against which to measure value.

Accelerating semantic graph databases on commodity clusters

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morari, Alessandro; Castellana, Vito G.; Haglin, David J.

We are developing a full software system for accelerating semantic graph databases on commodity cluster that scales to hundreds of nodes while maintaining constant query throughput. Our framework comprises a SPARQL to C++ compiler, a library of parallel graph methods and a custom multithreaded runtime layer, which provides a Partitioned Global Address Space (PGAS) programming model with fork/join parallelism and automatic load balancing over a commodity clusters. We present preliminary results for the compiler and for the runtime.

Group Centric Information Sharing Using Hierarchical Models

DTIC Science & Technology

2011-01-01

enable people to create data using RDF, build vocabularies using web ontology language (OWL), write rules and query data stores using SPARQL [8...a strict joined and the document was added with a strict add. In order to represent the fact that an action is allowed (or not), we have created a...greatly improve the system’s readiness to handle any number of access decision queries . a. The pair is tested against the gSIS Join and Add semantics

PAUSE: Predictive Analytics Using SPARQL-Endpoints

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sukumar, Sreenivas R; Ainsworth, Keela; Bond, Nathaniel

2014-07-11

This invention relates to the medical industry and more specifically to methods of predicting risks. With the impetus towards personalized and evidence-based medicine, the need for a framework to analyze/interpret quantitative measurements (blood work, toxicology, etc.) with qualitative descriptions (specialist reports after reading images, bio-medical knowledgebase, etc.) to predict diagnostic risks is fast emerging. We describe a software solution that leverages hardware for scalable in-memory analytics and applies next-generation semantic query tools on medical data.

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

PubMed

Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

2017-01-04

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

COEUS: “semantic web in a box” for biomedical applications

PubMed Central

2012-01-01

Background As the “omics” revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter’s complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. Results COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a “semantic web in a box” approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. Conclusions The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/. PMID:23244467

COEUS: "semantic web in a box" for biomedical applications.

PubMed

Lopes, Pedro; Oliveira, José Luís

2012-12-17

As the "omics" revolution unfolds, the growth in data quantity and diversity is bringing about the need for pioneering bioinformatics software, capable of significantly improving the research workflow. To cope with these computer science demands, biomedical software engineers are adopting emerging semantic web technologies that better suit the life sciences domain. The latter's complex relationships are easily mapped into semantic web graphs, enabling a superior understanding of collected knowledge. Despite increased awareness of semantic web technologies in bioinformatics, their use is still limited. COEUS is a new semantic web framework, aiming at a streamlined application development cycle and following a "semantic web in a box" approach. The framework provides a single package including advanced data integration and triplification tools, base ontologies, a web-oriented engine and a flexible exploration API. Resources can be integrated from heterogeneous sources, including CSV and XML files or SQL and SPARQL query results, and mapped directly to one or more ontologies. Advanced interoperability features include REST services, a SPARQL endpoint and LinkedData publication. These enable the creation of multiple applications for web, desktop or mobile environments, and empower a new knowledge federation layer. The platform, targeted at biomedical application developers, provides a complete skeleton ready for rapid application deployment, enhancing the creation of new semantic information systems. COEUS is available as open source at http://bioinformatics.ua.pt/coeus/.

Results Oriented Benchmarking: The Evolution of Benchmarking at NASA from Competitive Comparisons to World Class Space Partnerships

NASA Technical Reports Server (NTRS)

Bell, Michael A.

1999-01-01

Informal benchmarking using personal or professional networks has taken place for many years at the Kennedy Space Center (KSC). The National Aeronautics and Space Administration (NASA) recognized early on, the need to formalize the benchmarking process for better utilization of resources and improved benchmarking performance. The need to compete in a faster, better, cheaper environment has been the catalyst for formalizing these efforts. A pioneering benchmarking consortium was chartered at KSC in January 1994. The consortium known as the Kennedy Benchmarking Clearinghouse (KBC), is a collaborative effort of NASA and all major KSC contractors. The charter of this consortium is to facilitate effective benchmarking, and leverage the resulting quality improvements across KSC. The KBC acts as a resource with experienced facilitators and a proven process. One of the initial actions of the KBC was to develop a holistic methodology for Center-wide benchmarking. This approach to Benchmarking integrates the best features of proven benchmarking models (i.e., Camp, Spendolini, Watson, and Balm). This cost-effective alternative to conventional Benchmarking approaches has provided a foundation for consistent benchmarking at KSC through the development of common terminology, tools, and techniques. Through these efforts a foundation and infrastructure has been built which allows short duration benchmarking studies yielding results gleaned from world class partners that can be readily implemented. The KBC has been recognized with the Silver Medal Award (in the applied research category) from the International Benchmarking Clearinghouse.

Benchmarking the American Society of Breast Surgeon Member Performance for More Than a Million Quality Measure-Patient Encounters.

PubMed

Landercasper, Jeffrey; Fayanju, Oluwadamilola M; Bailey, Lisa; Berry, Tiffany S; Borgert, Andrew J; Buras, Robert; Chen, Steven L; Degnim, Amy C; Froman, Joshua; Gass, Jennifer; Greenberg, Caprice; Mautner, Starr Koslow; Krontiras, Helen; Ramirez, Luis D; Sowden, Michelle; Wexelman, Barbara; Wilke, Lee; Rao, Roshni

2018-02-01

Nine breast cancer quality measures (QM) were selected by the American Society of Breast Surgeons (ASBrS) for the Centers for Medicare and Medicaid Services (CMS) Quality Payment Programs (QPP) and other performance improvement programs. We report member performance. Surgeons entered QM data into an electronic registry. For each QM, aggregate "performance met" (PM) was reported (median, range and percentiles) and benchmarks (target goals) were calculated by CMS methodology, specifically, the Achievable Benchmark of Care™ (ABC) method. A total of 1,286,011 QM encounters were captured from 2011-2015. For 7 QM, first and last PM rates were as follows: (1) needle biopsy (95.8, 98.5%), (2) specimen imaging (97.9, 98.8%), (3) specimen orientation (98.5, 98.3%), (4) sentinel node use (95.1, 93.4%), (5) antibiotic selection (98.0, 99.4%), (6) antibiotic duration (99.0, 99.8%), and (7) no surgical site infection (98.8, 98.9%); all p values < 0.001 for trends. Variability and reasons for noncompliance by surgeon for each QM were identified. The CMS-calculated target goals (ABC™ benchmarks) for PM for 6 QM were 100%, suggesting that not meeting performance is a "never should occur" event. Surgeons self-reported a large number of specialty-specific patient-measure encounters into a registry for self-assessment and participation in QPP. Despite high levels of performance demonstrated initially in 2011 with minimal subsequent change, the ASBrS concluded "perfect" performance was not a realistic goal for QPP. Thus, after review of our normative performance data, the ASBrS recommended different benchmarks than CMS for each QM.

Visual Arts Performance Standards at Grades 4, 8 and 12 for North Dakota Visual Art Standards and Benchmarks.

ERIC Educational Resources Information Center

Shaw-Elgin, Linda; Jackson, Jane; Kurkowski, Bob; Riehl, Lori; Syvertson, Karen; Whitney, Linda

This document outlines the performance standards for visual arts in North Dakota public schools, grades K-12. Four levels of performance are provided for each benchmark by North Dakota educators for K-4, 5-8, and 9-12 grade levels. Level 4 describes advanced proficiency; Level 3, proficiency; Level 2, partial proficiency; and Level 1, novice. Each…

Standardised Benchmarking in the Quest for Orthologs

PubMed Central

Altenhoff, Adrian M.; Boeckmann, Brigitte; Capella-Gutierrez, Salvador; Dalquen, Daniel A.; DeLuca, Todd; Forslund, Kristoffer; Huerta-Cepas, Jaime; Linard, Benjamin; Pereira, Cécile; Pryszcz, Leszek P.; Schreiber, Fabian; Sousa da Silva, Alan; Szklarczyk, Damian; Train, Clément-Marie; Bork, Peer; Lecompte, Odile; von Mering, Christian; Xenarios, Ioannis; Sjölander, Kimmen; Juhl Jensen, Lars; Martin, Maria J.; Muffato, Matthieu; Gabaldón, Toni; Lewis, Suzanna E.; Thomas, Paul D.; Sonnhammer, Erik; Dessimoz, Christophe

2016-01-01

The identification of evolutionarily related genes across different species—orthologs in particular—forms the backbone of many comparative, evolutionary, and functional genomic analyses. Achieving high accuracy in orthology inference is thus essential. Yet the true evolutionary history of genes, required to ascertain orthology, is generally unknown. Furthermore, orthologs are used for very different applications across different phyla, with different requirements in terms of the precision-recall trade-off. As a result, assessing the performance of orthology inference methods remains difficult for both users and method developers. Here, we present a community effort to establish standards in orthology benchmarking and facilitate orthology benchmarking through an automated web-based service (http://orthology.benchmarkservice.org). Using this new service, we characterise the performance of 15 well-established orthology inference methods and resources on a battery of 20 different benchmarks. Standardised benchmarking provides a way for users to identify the most effective methods for the problem at hand, sets a minimal requirement for new tools and resources, and guides the development of more accurate orthology inference methods. PMID:27043882

Benchmarking CRISPR on-target sgRNA design.

PubMed

Yan, Jifang; Chuai, Guohui; Zhou, Chi; Zhu, Chenyu; Yang, Jing; Zhang, Chao; Gu, Feng; Xu, Han; Wei, Jia; Liu, Qi

2017-02-15

CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-based gene editing has been widely implemented in various cell types and organisms. A major challenge in the effective application of the CRISPR system is the need to design highly efficient single-guide RNA (sgRNA) with minimal off-target cleavage. Several tools are available for sgRNA design, while limited tools were compared. In our opinion, benchmarking the performance of the available tools and indicating their applicable scenarios are important issues. Moreover, whether the reported sgRNA design rules are reproducible across different sgRNA libraries, cell types and organisms remains unclear. In our study, a systematic and unbiased benchmark of the sgRNA predicting efficacy was performed on nine representative on-target design tools, based on six benchmark data sets covering five different cell types. The benchmark study presented here provides novel quantitative insights into the available CRISPR tools. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Improving Federal Education Programs through an Integrated Performance and Benchmarking System.

ERIC Educational Resources Information Center

Department of Education, Washington, DC. Office of the Under Secretary.

This document highlights the problems with current federal education program data collection activities and lists several factors that make movement toward a possible solution, then discusses the vision for the Integrated Performance and Benchmarking System (IPBS), a vision of an Internet-based system for harvesting information from states about…

Benchmarking in Academic Pharmacy Departments

PubMed Central

Chisholm-Burns, Marie; Nappi, Jean; Gubbins, Paul O.; Ross, Leigh Ann

2010-01-01

Benchmarking in academic pharmacy, and recommendations for the potential uses of benchmarking in academic pharmacy departments are discussed in this paper. Benchmarking is the process by which practices, procedures, and performance metrics are compared to an established standard or best practice. Many businesses and industries use benchmarking to compare processes and outcomes, and ultimately plan for improvement. Institutions of higher learning have embraced benchmarking practices to facilitate measuring the quality of their educational and research programs. Benchmarking is used internally as well to justify the allocation of institutional resources or to mediate among competing demands for additional program staff or space. Surveying all chairs of academic pharmacy departments to explore benchmarking issues such as department size and composition, as well as faculty teaching, scholarly, and service productivity, could provide valuable information. To date, attempts to gather this data have had limited success. We believe this information is potentially important, urge that efforts to gather it should be continued, and offer suggestions to achieve full participation. PMID:21179251

Benchmarking in academic pharmacy departments.

PubMed

Bosso, John A; Chisholm-Burns, Marie; Nappi, Jean; Gubbins, Paul O; Ross, Leigh Ann

2010-10-11

Benchmarking in academic pharmacy, and recommendations for the potential uses of benchmarking in academic pharmacy departments are discussed in this paper. Benchmarking is the process by which practices, procedures, and performance metrics are compared to an established standard or best practice. Many businesses and industries use benchmarking to compare processes and outcomes, and ultimately plan for improvement. Institutions of higher learning have embraced benchmarking practices to facilitate measuring the quality of their educational and research programs. Benchmarking is used internally as well to justify the allocation of institutional resources or to mediate among competing demands for additional program staff or space. Surveying all chairs of academic pharmacy departments to explore benchmarking issues such as department size and composition, as well as faculty teaching, scholarly, and service productivity, could provide valuable information. To date, attempts to gather this data have had limited success. We believe this information is potentially important, urge that efforts to gather it should be continued, and offer suggestions to achieve full participation.

Predicting Cost/Performance Trade-Offs for Whitney: A Commodity Computing Cluster

NASA Technical Reports Server (NTRS)

Becker, Jeffrey C.; Nitzberg, Bill; VanderWijngaart, Rob F.; Kutler, Paul (Technical Monitor)

1997-01-01

Recent advances in low-end processor and network technology have made it possible to build a "supercomputer" out of commodity components. We develop simple models of the NAS Parallel Benchmarks version 2 (NPB 2) to explore the cost/performance trade-offs involved in building a balanced parallel computer supporting a scientific workload. We develop closed form expressions detailing the number and size of messages sent by each benchmark. Coupling these with measured single processor performance, network latency, and network bandwidth, our models predict benchmark performance to within 30%. A comparison based on total system cost reveals that current commodity technology (200 MHz Pentium Pros with 100baseT Ethernet) is well balanced for the NPBs up to a total system cost of around $1,000,000.

Performance benchmark of LHCb code on state-of-the-art x86 architectures

NASA Astrophysics Data System (ADS)

Campora Perez, D. H.; Neufeld, N.; Schwemmer, R.

2015-12-01

For Run 2 of the LHC, LHCb is replacing a significant part of its event filter farm with new compute nodes. For the evaluation of the best performing solution, we have developed a method to convert our high level trigger application into a stand-alone, bootable benchmark image. With additional instrumentation we turned it into a self-optimising benchmark which explores techniques such as late forking, NUMA balancing and optimal number of threads, i.e. it automatically optimises box-level performance. We have run this procedure on a wide range of Haswell-E CPUs and numerous other architectures from both Intel and AMD, including also the latest Intel micro-blade servers. We present results in terms of performance, power consumption, overheads and relative cost.

RISC Processors and High Performance Computing

NASA Technical Reports Server (NTRS)

Bailey, David H.; Saini, Subhash; Craw, James M. (Technical Monitor)

1995-01-01

This tutorial will discuss the top five RISC microprocessors and the parallel systems in which they are used. It will provide a unique cross-machine comparison not available elsewhere. The effective performance of these processors will be compared by citing standard benchmarks in the context of real applications. The latest NAS Parallel Benchmarks, both absolute performance and performance per dollar, will be listed. The next generation of the NPB will be described. The tutorial will conclude with a discussion of future directions in the field. Technology Transfer Considerations: All of these computer systems are commercially available internationally. Information about these processors is available in the public domain, mostly from the vendors themselves. The NAS Parallel Benchmarks and their results have been previously approved numerous times for public release, beginning back in 1991.

Benchmarks for target tracking

NASA Astrophysics Data System (ADS)

Dunham, Darin T.; West, Philip D.

2011-09-01

The term benchmark originates from the chiseled horizontal marks that surveyors made, into which an angle-iron could be placed to bracket ("bench") a leveling rod, thus ensuring that the leveling rod can be repositioned in exactly the same place in the future. A benchmark in computer terms is the result of running a computer program, or a set of programs, in order to assess the relative performance of an object by running a number of standard tests and trials against it. This paper will discuss the history of simulation benchmarks that are being used by multiple branches of the military and agencies of the US government. These benchmarks range from missile defense applications to chemical biological situations. Typically, a benchmark is used with Monte Carlo runs in order to tease out how algorithms deal with variability and the range of possible inputs. We will also describe problems that can be solved by a benchmark.

Vocabulary services to support scientific data interoperability

NASA Astrophysics Data System (ADS)

Cox, Simon; Mills, Katie; Tan, Florence

2013-04-01

Shared vocabularies are a core element in interoperable systems. Vocabularies need to be available at run-time, and where the vocabularies are shared by a distributed community this implies the use of web technology to provide vocabulary services. Given the ubiquity of vocabularies or classifiers in systems, vocabulary services are effectively the base of the interoperability stack. In contemporary knowledge organization systems, a vocabulary item is considered a concept, with the "terms" denoting it appearing as labels. The Simple Knowledge Organization System (SKOS) formalizes this as an RDF Schema (RDFS) application, with a bridge to formal logic in Web Ontology Language (OWL). For maximum utility, a vocabulary should be made available through the following interfaces: * the vocabulary as a whole - at an ontology URI corresponding to a vocabulary document * each item in the vocabulary - at the item URI * summaries, subsets, and resources derived by transformation * through the standard RDF web API - i.e. a SPARQL endpoint * through a query form for human users. However, the vocabulary data model may be leveraged directly in a standard vocabulary API that uses the semantics provided by SKOS. SISSvoc3 [1] accomplishes this as a standard set of URI templates for a vocabulary. Any URI comforming to the template selects a vocabulary subset based on the SKOS properties, including labels (skos:prefLabel, skos:altLabel, rdfs:label) and a subset of the semantic relations (skos:broader, skos:narrower, etc). SISSvoc3 thus provides a RESTFul SKOS API to query a vocabulary, but hiding the complexity of SPARQL. It has been implemented using the Linked Data API (LDA) [2], which connects to a SPARQL endpoint. By using LDA, we also get content-negotiation, alternative views, paging, metadata and other functionality provided in a standard way. A number of vocabularies have been formalized in SKOS and deployed by CSIRO, the Australian Bureau of Meteorology (BOM) and their collaborators using SISSvoc3, including: * geologic timescale (multiple versions) * soils classification * definitions from OGC standards * geosciml vocabularies * mining commodities * hyperspectral scalars Several other agencies in Australia have adopted SISSvoc3 for their vocabularies. SISSvoc3 differs from other SKOS-based vocabulary-access APIs such as GEMET [3] and NVS [4] in that (a) the service is decoupled from the content store, (b) the service URI is independent of the content URIs This means that a SISSvoc3 interface can be deployed over any SKOS vocabulary which is available at a SPARQL endpoint. As an example, a SISSvoc3 query and presentation interface has been deployed over the NERC vocabulary service hosted by the BODC, providing a search interface which is not available natively. We use vocabulary services to populate menus in user interfaces, to support data validation, and to configure data conversion routines. Related services built on LDA have also been used as a generic registry interface, and extended for serving gazetteer information. ACKNOWLEDGEMENTS The CSIRO SISSvoc3 implementation is built using the Epimorphics ELDA platform http://code.google.com/p/elda/. We thank Jacqui Githaiga and Terry Rankine for their contributions to SISSvoc design and implementation. REFERENCES 1. SISSvoc3 Specification https://www.seegrid.csiro.au/wiki/Siss/SISSvoc30Specification 2. Linked Data API http://code.google.com/p/linked-data-api/wiki/Specification 3. GEMET https://svn.eionet.europa.eu/projects/Zope/wiki/GEMETWebServiceAPI 4. NVS 2.0 http://vocab.nerc.ac.uk/

Benchmarking. Issues in the Design and Implementation of a Benchmarking System for Employment and Training Programs for Young People.

ERIC Educational Resources Information Center

Coughlin, David C.; Bielen, Rhonda P.

This paper has been prepared to assist the United States Department of Labor to explore new approaches to evaluating and measuring the performance of employment and training activities for youth. As one of several tools for evaluating success of local youth training programs, "benchmarking" provides a system for measuring the development…

Developing a benchmark for emotional analysis of music

PubMed Central

Yang, Yi-Hsuan; Soleymani, Mohammad

2017-01-01

Music emotion recognition (MER) field rapidly expanded in the last decade. Many new methods and new audio features are developed to improve the performance of MER algorithms. However, it is very difficult to compare the performance of the new methods because of the data representation diversity and scarcity of publicly available data. In this paper, we address these problems by creating a data set and a benchmark for MER. The data set that we release, a MediaEval Database for Emotional Analysis in Music (DEAM), is the largest available data set of dynamic annotations (valence and arousal annotations for 1,802 songs and song excerpts licensed under Creative Commons with 2Hz time resolution). Using DEAM, we organized the ‘Emotion in Music’ task at MediaEval Multimedia Evaluation Campaign from 2013 to 2015. The benchmark attracted, in total, 21 active teams to participate in the challenge. We analyze the results of the benchmark: the winning algorithms and feature-sets. We also describe the design of the benchmark, the evaluation procedures and the data cleaning and transformations that we suggest. The results from the benchmark suggest that the recurrent neural network based approaches combined with large feature-sets work best for dynamic MER. PMID:28282400

Developing a benchmark for emotional analysis of music.

PubMed

Aljanaki, Anna; Yang, Yi-Hsuan; Soleymani, Mohammad

2017-01-01

Music emotion recognition (MER) field rapidly expanded in the last decade. Many new methods and new audio features are developed to improve the performance of MER algorithms. However, it is very difficult to compare the performance of the new methods because of the data representation diversity and scarcity of publicly available data. In this paper, we address these problems by creating a data set and a benchmark for MER. The data set that we release, a MediaEval Database for Emotional Analysis in Music (DEAM), is the largest available data set of dynamic annotations (valence and arousal annotations for 1,802 songs and song excerpts licensed under Creative Commons with 2Hz time resolution). Using DEAM, we organized the 'Emotion in Music' task at MediaEval Multimedia Evaluation Campaign from 2013 to 2015. The benchmark attracted, in total, 21 active teams to participate in the challenge. We analyze the results of the benchmark: the winning algorithms and feature-sets. We also describe the design of the benchmark, the evaluation procedures and the data cleaning and transformations that we suggest. The results from the benchmark suggest that the recurrent neural network based approaches combined with large feature-sets work best for dynamic MER.

A large-scale benchmark of gene prioritization methods.

PubMed

Guala, Dimitri; Sonnhammer, Erik L L

2017-04-21

In order to maximize the use of results from high-throughput experimental studies, e.g. GWAS, for identification and diagnostics of new disease-associated genes, it is important to have properly analyzed and benchmarked gene prioritization tools. While prospective benchmarks are underpowered to provide statistically significant results in their attempt to differentiate the performance of gene prioritization tools, a strategy for retrospective benchmarking has been missing, and new tools usually only provide internal validations. The Gene Ontology(GO) contains genes clustered around annotation terms. This intrinsic property of GO can be utilized in construction of robust benchmarks, objective to the problem domain. We demonstrate how this can be achieved for network-based gene prioritization tools, utilizing the FunCoup network. We use cross-validation and a set of appropriate performance measures to compare state-of-the-art gene prioritization algorithms: three based on network diffusion, NetRank and two implementations of Random Walk with Restart, and MaxLink that utilizes network neighborhood. Our benchmark suite provides a systematic and objective way to compare the multitude of available and future gene prioritization tools, enabling researchers to select the best gene prioritization tool for the task at hand, and helping to guide the development of more accurate methods.

Paediatric International Nursing Study: using person-centred key performance indicators to benchmark children's services.

PubMed

McCance, Tanya; Wilson, Val; Kornman, Kelly

2016-07-01

The aim of the Paediatric International Nursing Study was to explore the utility of key performance indicators in developing person-centred practice across a range of services provided to sick children. The objective addressed in this paper was evaluating the use of these indicators to benchmark services internationally. This study builds on primary research, which produced indicators that were considered novel both in terms of their positive orientation and use in generating data that privileges the patient voice. This study extends this research through wider testing on an international platform within paediatrics. The overall methodological approach was a realistic evaluation used to evaluate the implementation of the key performance indicators, which combined an integrated development and evaluation methodology. The study involved children's wards/hospitals in Australia (six sites across three states) and Europe (seven sites across four countries). Qualitative and quantitative methods were used during the implementation process, however, this paper reports the quantitative data only, which used survey, observations and documentary review. The findings demonstrate the quality of care being delivered to children and their families across different international sites. The benchmarking does, however, highlight some differences between paediatric and general hospitals, and between the different key performance indicators across all the sites. The findings support the use of the key performance indicators as a novel method to benchmark services internationally. Whilst the data collected across 20 paediatric sites suggest services are more similar than different, benchmarking illuminates variations that encourage a critical dialogue about what works and why. The transferability of the key performance indicators and measurement framework across different settings has significant implications for practice. The findings offer an approach to benchmarking and celebrating the successes within practice, while learning from partners across the globe in further developing person-centred cultures. © 2016 John Wiley & Sons Ltd.

Benchmark experiments at ASTRA facility on definition of space distribution of {sup 235}U fission reaction rate

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bobrov, A. A.; Boyarinov, V. F.; Glushkov, A. E.

2012-07-01

Results of critical experiments performed at five ASTRA facility configurations modeling the high-temperature helium-cooled graphite-moderated reactors are presented. Results of experiments on definition of space distribution of {sup 235}U fission reaction rate performed at four from these five configurations are presented more detail. Analysis of available information showed that all experiments on criticality at these five configurations are acceptable for use them as critical benchmark experiments. All experiments on definition of space distribution of {sup 235}U fission reaction rate are acceptable for use them as physical benchmark experiments. (authors)

Sensitivity Analysis of OECD Benchmark Tests in BISON

DOE Office of Scientific and Technical Information (OSTI.GOV)

Swiler, Laura Painton; Gamble, Kyle; Schmidt, Rodney C.

2015-09-01

This report summarizes a NEAMS (Nuclear Energy Advanced Modeling and Simulation) project focused on sensitivity analysis of a fuels performance benchmark problem. The benchmark problem was defined by the Uncertainty Analysis in Modeling working group of the Nuclear Science Committee, part of the Nuclear Energy Agency of the Organization for Economic Cooperation and Development (OECD ). The benchmark problem involv ed steady - state behavior of a fuel pin in a Pressurized Water Reactor (PWR). The problem was created in the BISON Fuels Performance code. Dakota was used to generate and analyze 300 samples of 17 input parameters defining coremore » boundary conditions, manuf acturing tolerances , and fuel properties. There were 24 responses of interest, including fuel centerline temperatures at a variety of locations and burnup levels, fission gas released, axial elongation of the fuel pin, etc. Pearson and Spearman correlatio n coefficients and Sobol' variance - based indices were used to perform the sensitivity analysis. This report summarizes the process and presents results from this study.« less

Parallelization of NAS Benchmarks for Shared Memory Multiprocessors

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry C.; Saini, Subhash (Technical Monitor)

1998-01-01

This paper presents our experiences of parallelizing the sequential implementation of NAS benchmarks using compiler directives on SGI Origin2000 distributed shared memory (DSM) system. Porting existing applications to new high performance parallel and distributed computing platforms is a challenging task. Ideally, a user develops a sequential version of the application, leaving the task of porting to new generations of high performance computing systems to parallelization tools and compilers. Due to the simplicity of programming shared-memory multiprocessors, compiler developers have provided various facilities to allow the users to exploit parallelism. Native compilers on SGI Origin2000 support multiprocessing directives to allow users to exploit loop-level parallelism in their programs. Additionally, supporting tools can accomplish this process automatically and present the results of parallelization to the users. We experimented with these compiler directives and supporting tools by parallelizing sequential implementation of NAS benchmarks. Results reported in this paper indicate that with minimal effort, the performance gain is comparable with the hand-parallelized, carefully optimized, message-passing implementations of the same benchmarks.

PMLB: a large benchmark suite for machine learning evaluation and comparison.

PubMed

Olson, Randal S; La Cava, William; Orzechowski, Patryk; Urbanowicz, Ryan J; Moore, Jason H

2017-01-01

The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark datasets have emerged from different sources, but their organization and adoption as standards have been inconsistent. As such, selecting and curating specific benchmarks remains an unnecessary burden on machine learning practitioners and data scientists. The present study introduces an accessible, curated, and developing public benchmark resource to facilitate identification of the strengths and weaknesses of different machine learning methodologies. We compare meta-features among the current set of benchmark datasets in this resource to characterize the diversity of available data. Finally, we apply a number of established machine learning methods to the entire benchmark suite and analyze how datasets and algorithms cluster in terms of performance. From this study, we find that existing benchmarks lack the diversity to properly benchmark machine learning algorithms, and there are several gaps in benchmarking problems that still need to be considered. This work represents another important step towards understanding the limitations of popular benchmarking suites and developing a resource that connects existing benchmarking standards to more diverse and efficient standards in the future.

75 FR 68606 - Notice of Submission for OMB Review

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-08

... provides data for internationally benchmarking U.S. performance in mathematics and science at the fourth... years in more than 50 countries and provides assessment data for internationally benchmarking U.S...

Utilizing a Trauma Systems Approach to Benchmark and Improve Combat Casualty Care

DTIC Science & Technology

2010-07-01

modern battlefield utilizing evidence - based medicine . The development of injury care benchmarks enhanced the evolution of the combat casualty care performance improvement process within the trauma system.

Small drinking water systems under spatiotemporal water quality variability: a risk-based performance benchmarking framework.

PubMed

Bereskie, Ty; Haider, Husnain; Rodriguez, Manuel J; Sadiq, Rehan

2017-08-23

Traditional approaches for benchmarking drinking water systems are binary, based solely on the compliance and/or non-compliance of one or more water quality performance indicators against defined regulatory guidelines/standards. The consequence of water quality failure is dependent on location within a water supply system as well as time of the year (i.e., season) with varying levels of water consumption. Conventional approaches used for water quality comparison purposes fail to incorporate spatiotemporal variability and degrees of compliance and/or non-compliance. This can lead to misleading or inaccurate performance assessment data used in the performance benchmarking process. In this research, a hierarchical risk-based water quality performance benchmarking framework is proposed to evaluate small drinking water systems (SDWSs) through cross-comparison amongst similar systems. The proposed framework (R WQI framework) is designed to quantify consequence associated with seasonal and location-specific water quality issues in a given drinking water supply system to facilitate more efficient decision-making for SDWSs striving for continuous performance improvement. Fuzzy rule-based modelling is used to address imprecision associated with measuring performance based on singular water quality guidelines/standards and the uncertainties present in SDWS operations and monitoring. This proposed R WQI framework has been demonstrated using data collected from 16 SDWSs in Newfoundland and Labrador and Quebec, Canada, and compared to the Canadian Council of Ministers of the Environment WQI, a traditional, guidelines/standard-based approach. The study found that the R WQI framework provides an in-depth state of water quality and benchmarks SDWSs more rationally based on the frequency of occurrence and consequence of failure events.

Benchmarking gate-based quantum computers

NASA Astrophysics Data System (ADS)

Michielsen, Kristel; Nocon, Madita; Willsch, Dennis; Jin, Fengping; Lippert, Thomas; De Raedt, Hans

2017-11-01

With the advent of public access to small gate-based quantum processors, it becomes necessary to develop a benchmarking methodology such that independent researchers can validate the operation of these processors. We explore the usefulness of a number of simple quantum circuits as benchmarks for gate-based quantum computing devices and show that circuits performing identity operations are very simple, scalable and sensitive to gate errors and are therefore very well suited for this task. We illustrate the procedure by presenting benchmark results for the IBM Quantum Experience, a cloud-based platform for gate-based quantum computing.

Managing for Results in America's Great City Schools 2014: Results from Fiscal Year 2012-13. A Report of the Performance Measurement and Benchmarking Project

ERIC Educational Resources Information Center

Council of the Great City Schools, 2014

2014-01-01

In 2002 the "Council of the Great City Schools" and its members set out to develop performance measures that could be used to improve business operations in urban public school districts. The Council launched the "Performance Measurement and Benchmarking Project" to achieve these objectives. The purposes of the project was to:…

Developing a Benchmarking Process in Perfusion: A Report of the Perfusion Downunder Collaboration

PubMed Central

Baker, Robert A.; Newland, Richard F.; Fenton, Carmel; McDonald, Michael; Willcox, Timothy W.; Merry, Alan F.

2012-01-01

Abstract: Improving and understanding clinical practice is an appropriate goal for the perfusion community. The Perfusion Downunder Collaboration has established a multi-center perfusion focused database aimed at achieving these goals through the development of quantitative quality indicators for clinical improvement through benchmarking. Data were collected using the Perfusion Downunder Collaboration database from procedures performed in eight Australian and New Zealand cardiac centers between March 2007 and February 2011. At the Perfusion Downunder Meeting in 2010, it was agreed by consensus, to report quality indicators (QI) for glucose level, arterial outlet temperature, and pCO2 management during cardiopulmonary bypass. The values chosen for each QI were: blood glucose ≥4 mmol/L and ≤10 mmol/L; arterial outlet temperature ≤37°C; and arterial blood gas pCO2 ≥ 35 and ≤45 mmHg. The QI data were used to derive benchmarks using the Achievable Benchmark of Care (ABC™) methodology to identify the incidence of QIs at the best performing centers. Five thousand four hundred and sixty-five procedures were evaluated to derive QI and benchmark data. The incidence of the blood glucose QI ranged from 37–96% of procedures, with a benchmark value of 90%. The arterial outlet temperature QI occurred in 16–98% of procedures with the benchmark of 94%; while the arterial pCO2 QI occurred in 21–91%, with the benchmark value of 80%. We have derived QIs and benchmark calculations for the management of several key aspects of cardiopulmonary bypass to provide a platform for improving the quality of perfusion practice. PMID:22730861

[Benchmarking and other functions of ROM: back to basics].

PubMed

Barendregt, M

2015-01-01

Since 2011 outcome data in the Dutch mental health care have been collected on a national scale. This has led to confusion about the position of benchmarking in the system known as routine outcome monitoring (rom). To provide insight into the various objectives and uses of aggregated outcome data. A qualitative review was performed and the findings were analysed. Benchmarking is a strategy for finding best practices and for improving efficacy and it belongs to the domain of quality management. Benchmarking involves comparing outcome data by means of instrumentation and is relatively tolerant with regard to the validity of the data. Although benchmarking is a function of rom, it must be differentiated form other functions from rom. Clinical management, public accountability, research, payment for performance and information for patients are all functions of rom which require different ways of data feedback and which make different demands on the validity of the underlying data. Benchmarking is often wrongly regarded as being simply a synonym for 'comparing institutions'. It is, however, a method which includes many more factors; it can be used to improve quality and has a more flexible approach to the validity of outcome data and is less concerned than other rom functions about funding and the amount of information given to patients. Benchmarking can make good use of currently available outcome data.

Benchmarking of venous thromboembolism prophylaxis practice with ENT.UK guidelines.

PubMed

Al-Qahtani, Ali S

2017-05-01

The aim of this study was to benchmark our guidelines of prevention of venous thromboembolism (VTE) in ENT surgical population against ENT.UK guidelines, and also to encourage healthcare providers to utilize benchmarking as an effective method of improving performance. The study design is prospective descriptive analysis. The setting of this study is tertiary referral centre (Assir Central Hospital, Abha, Saudi Arabia). In this study, we are benchmarking our practice guidelines of the prevention of VTE in the ENT surgical population against that of ENT.UK guidelines to mitigate any gaps. ENT guidelines 2010 were downloaded from the ENT.UK Website. Our guidelines were compared with the possibilities that either our performance meets or fall short of ENT.UK guidelines. Immediate corrective actions will take place if there is quality chasm between the two guidelines. ENT.UK guidelines are evidence-based and updated which may serve as role-model for adoption and benchmarking. Our guidelines were accordingly amended to contain all factors required in providing a quality service to ENT surgical patients. While not given appropriate attention, benchmarking is a useful tool in improving quality of health care. It allows learning from others' practices and experiences, and works towards closing any quality gaps. In addition, benchmarking clinical outcomes is critical for quality improvement and informing decisions concerning service provision. It is recommended to be included on the list of quality improvement methods of healthcare services.

Geoscientific Vocabularies and Linked Data at The British Geological Survey - progress and pragmatism

NASA Astrophysics Data System (ADS)

McCormick, T.; Heaven, R.

2013-12-01

The British Geological Survey makes extensive use of controlled vocabularies to promote standardisation and interoperability between its databases and other digital information systems. Many of our vocabularies are published and searchable at http://www.bgs.ac.uk/data/vocabularies/home.html/. There is a movement to ';open up' government data in both the US and UK. In the UK this is promoted by data.gov.uk. Some view linked data as the best way to share and connect disparate data, information and knowledge, in order to develop a ';Web of Data'. Linked data facilitate connections between data sets, and lower the barriers to accessing data that must otherwise be discovered and exploited using other methods. Recently there has been a rapid increase in the rate of publication of linked data, this increase currently being estimated at 300% per year. In the past 2 years we have undertaken a pilot study to publish some of our authoritative vocabularies as linked data. This study has focussed primarily on publishing BGS' 1:625 000 scale geologic map data for the UK, supported by development of linked data sets for: Earth materials - based on the BGS Rock Classification Scheme; lithostratigraphy - based on the BGS Lexicon of Named Rock Units; and geochronology - based on the International Commission on Stratigraphy. The BGS linked data sets are published at data.bgs.ac.uk. We have learned a number of lessons about the potential and limitations of linked data and associated technologies. We do not envisage SPARQL endpoints being the primary route for public access to linked data because the user would require technical knowledge of the data structure, and because it can be a security threat. Rather, SPARQL may lie behind a user-friendly API. Federated SPARQL queries that can interrogate distributed data sources are in reality too slow, and in practise the data sets would likely be combined in a single store. The data sets in our pilot study are all reasonably static and we solve performance and security issues by serving the linked data as pre-generated static files in a range of formats rather than using a triple-store. This also allows the data to be indexed by search engines. Wherever possible it is good practice to use predicates from well-known published sources, for example RDFS, SKOS, or Dublin Core, in preference to inventing new ones. This promotes re-use of the linked data by as many potential users as possible. Linked data do not directly address logical inference, which is supposed to be one of the aims of the ';Semantic Web'. This sort of ';calculating with knowledge' must be implemented using additional, possibly human-based rather than mechanical, reasoning. Linked data come with all the same issues surrounding provenance and authority of the data that any web resource is subject to. There are issues surrounding versioning and permanence of URIs. Our work on publishing BGS' vocabularies as linked data is proceeding in parallel with our work with the Commission of Geoscience Information (CGI) Geoscience Terminology Working Group which is jointly developing multilingual vocabularies in range of knowledge domains.

RelFinder: Revealing Relationships in RDF Knowledge Bases

NASA Astrophysics Data System (ADS)

Heim, Philipp; Hellmann, Sebastian; Lehmann, Jens; Lohmann, Steffen; Stegemann, Timo

The Semantic Web has recently seen a rise of large knowledge bases (such as DBpedia) that are freely accessible via SPARQL endpoints. The structured representation of the contained information opens up new possibilities in the way it can be accessed and queried. In this paper, we present an approach that extracts a graph covering relationships between two objects of interest. We show an interactive visualization of this graph that supports the systematic analysis of the found relationships by providing highlighting, previewing, and filtering features.

Semantic Web Services with Web Ontology Language (OWL-S) - Specification of Agent-Services for DARPA Agent Markup Language (DAML)

DTIC Science & Technology

2006-08-01

effective for describing taxonomic categories and properties of things, the structures found in SWRL and SPARQL are better suited to describing conditions...up the query processing time, which may occur many times and furthermore it is time critical. In order to maintain information about the...that time spent during this phase does not depend linearly on the number of concepts present in the data structure , but in the order of log of concepts

How Are You Doing? Key Performance Indicators and Benchmarking

ERIC Educational Resources Information Center

Fahey, John P.

2011-01-01

School business officials need to "know and show" that their operations are well managed. To do so, they ask themselves questions, such as "How are they doing? How do they compare with others? Are they making progress fast enough? Are they using the best practices?" Using key performance indicators (KPIs) and benchmarking as regular parts of their…

Is Higher Better? Determinants and Comparisons of Performance on the Major Field Test in Business

ERIC Educational Resources Information Center

Bielinska-Kwapisz, Agnieszka; Brown, F. William; Semenik, Richard

2012-01-01

Student performance on the Major Field Achievement Test in Business is an important benchmark for college of business programs. The authors' results indicate that such benchmarking can only be meaningful if certain student characteristics are taken into account. The differences in achievement between cohorts are explored in detail by separating…

Access to a simulator is not enough: the benefits of virtual reality training based on peer-group-derived benchmarks--a randomized controlled trial.

PubMed

von Websky, Martin W; Raptis, Dimitri A; Vitz, Martina; Rosenthal, Rachel; Clavien, P A; Hahnloser, Dieter

2013-11-01

Virtual reality (VR) simulators are widely used to familiarize surgical novices with laparoscopy, but VR training methods differ in efficacy. In the present trial, self-controlled basic VR training (SC-training) was tested against training based on peer-group-derived benchmarks (PGD-training). First, novice laparoscopic residents were randomized into a SC group (n = 34), and a group using PGD-benchmarks (n = 34) for basic laparoscopic training. After completing basic training, both groups performed 60 VR laparoscopic cholecystectomies for performance analysis. Primary endpoints were simulator metrics; secondary endpoints were program adherence, trainee motivation, and training efficacy. Altogether, 66 residents completed basic training, and 3,837 of 3,960 (96.8 %) cholecystectomies were available for analysis. Course adherence was good, with only two dropouts, both in the SC-group. The PGD-group spent more time and repetitions in basic training until the benchmarks were reached and subsequently showed better performance in the readout cholecystectomies: Median time (gallbladder extraction) showed significant differences of 520 s (IQR 354-738 s) in SC-training versus 390 s (IQR 278-536 s) in the PGD-group (p < 0.001) and 215 s (IQR 175-276 s) in experts, respectively. Path length of the right instrument also showed significant differences, again with the PGD-training group being more efficient. Basic VR laparoscopic training based on PGD benchmarks with external assessment is superior to SC training, resulting in higher trainee motivation and better performance in simulated laparoscopic cholecystectomies. We recommend such a basic course based on PGD benchmarks before advancing to more elaborate VR training.

Validation of tsunami inundation model TUNA-RP using OAR-PMEL-135 benchmark problem set

NASA Astrophysics Data System (ADS)

Koh, H. L.; Teh, S. Y.; Tan, W. K.; Kh'ng, X. Y.

2017-05-01

A standard set of benchmark problems, known as OAR-PMEL-135, is developed by the US National Tsunami Hazard Mitigation Program for tsunami inundation model validation. Any tsunami inundation model must be tested for its accuracy and capability using this standard set of benchmark problems before it can be gainfully used for inundation simulation. The authors have previously developed an in-house tsunami inundation model known as TUNA-RP. This inundation model solves the two-dimensional nonlinear shallow water equations coupled with a wet-dry moving boundary algorithm. This paper presents the validation of TUNA-RP against the solutions provided in the OAR-PMEL-135 benchmark problem set. This benchmark validation testing shows that TUNA-RP can indeed perform inundation simulation with accuracy consistent with that in the tested benchmark problem set.

Preliminary Results for the OECD/NEA Time Dependent Benchmark using Rattlesnake, Rattlesnake-IQS and TDKENO

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeHart, Mark D.; Mausolff, Zander; Weems, Zach

2016-08-01

One goal of the MAMMOTH M&S project is to validate the analysis capabilities within MAMMOTH. Historical data has shown limited value for validation of full three-dimensional (3D) multi-physics methods. Initial analysis considered the TREAT startup minimum critical core and one of the startup transient tests. At present, validation is focusing on measurements taken during the M8CAL test calibration series. These exercises will valuable in preliminary assessment of the ability of MAMMOTH to perform coupled multi-physics calculations; calculations performed to date are being used to validate the neutron transport solver Rattlesnake\\cite{Rattlesnake} and the fuels performance code BISON. Other validation projects outsidemore » of TREAT are available for single-physics benchmarking. Because the transient solution capability of Rattlesnake is one of the key attributes that makes it unique for TREAT transient simulations, validation of the transient solution of Rattlesnake using other time dependent kinetics benchmarks has considerable value. The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has recently developed a computational benchmark for transient simulations. This benchmark considered both two-dimensional (2D) and 3D configurations for a total number of 26 different transients. All are negative reactivity insertions, typically returning to the critical state after some time.« less

Python/Lua Benchmarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Busby, L.

This is an adaptation of the pre-existing Scimark benchmark code to a variety of Python and Lua implementations. It also measures performance of the Fparser expression parser and C and C++ code on a variety of simple scientific expressions.

Kaiser Permanente's performance improvement system, Part 1: From benchmarking to executing on strategic priorities.

PubMed

Schilling, Lisa; Chase, Alide; Kehrli, Sommer; Liu, Amy Y; Stiefel, Matt; Brentari, Ruth

2010-11-01

By 2004, senior leaders at Kaiser Permanente, the largest not-for-profit health plan in the United States, recognizing variations across service areas in quality, safety, service, and efficiency, began developing a performance improvement (PI) system to realizing best-in-class quality performance across all 35 medical centers. MEASURING SYSTEMWIDE PERFORMANCE: In 2005, a Web-based data dashboard, "Big Q," which tracks the performance of each medical center and service area against external benchmarks and internal goals, was created. PLANNING FOR PI AND BENCHMARKING PERFORMANCE: In 2006, Kaiser Permanente national and regional continued planning the PI system, and in 2007, quality, medical group, operations, and information technology leaders benchmarked five high-performing organizations to identify capabilities required to achieve consistent best-in-class organizational performance. THE PI SYSTEM: The PI system addresses the six capabilities: leadership priority setting, a systems approach to improvement, measurement capability, a learning organization, improvement capacity, and a culture of improvement. PI "deep experts" (mentors) consult with national, regional, and local leaders, and more than 500 improvement advisors are trained to manage portfolios of 90-120 day improvement initiatives at medical centers. Between the second quarter of 2008 and the first quarter of 2009, performance across all Kaiser Permanente medical centers improved on the Big Q metrics. The lessons learned in implementing and sustaining PI as it becomes fully integrated into all levels of Kaiser Permanente can be generalized to other health care systems, hospitals, and other health care organizations.

Medical school benchmarking - from tools to programmes.

PubMed

Wilkinson, Tim J; Hudson, Judith N; Mccoll, Geoffrey J; Hu, Wendy C Y; Jolly, Brian C; Schuwirth, Lambert W T

2015-02-01

Benchmarking among medical schools is essential, but may result in unwanted effects. To apply a conceptual framework to selected benchmarking activities of medical schools. We present an analogy between the effects of assessment on student learning and the effects of benchmarking on medical school educational activities. A framework by which benchmarking can be evaluated was developed and applied to key current benchmarking activities in Australia and New Zealand. The analogy generated a conceptual framework that tested five questions to be considered in relation to benchmarking: what is the purpose? what are the attributes of value? what are the best tools to assess the attributes of value? what happens to the results? and, what is the likely "institutional impact" of the results? If the activities were compared against a blueprint of desirable medical graduate outcomes, notable omissions would emerge. Medical schools should benchmark their performance on a range of educational activities to ensure quality improvement and to assure stakeholders that standards are being met. Although benchmarking potentially has positive benefits, it could also result in perverse incentives with unforeseen and detrimental effects on learning if it is undertaken using only a few selected assessment tools.

Toxicological benchmarks for screening potential contaminants of concern for effects on terrestrial plants: 1994 revision

DOE Office of Scientific and Technical Information (OSTI.GOV)

Will, M.E.; Suter, G.W. II

1994-09-01

One of the initial stages in ecological risk assessment for hazardous waste sites is screening contaminants to determine which of them are worthy of further consideration as contaminants of potential concern. This process is termed contaminant screening. It is performed by comparing measured ambient concentrations of chemicals to benchmark concentrations. Currently, no standard benchmark concentrations exist for assessing contaminants in soil with respect to their toxicity to plants. This report presents a standard method for deriving benchmarks for this purpose (phytotoxicity benchmarks), a set of data concerning effects of chemicals in soil or soil solution on plants, and a setmore » of phytotoxicity benchmarks for 38 chemicals potentially associated with United States Department of Energy (DOE) sites. In addition, background information on the phytotoxicity and occurrence of the chemicals in soils is presented, and literature describing the experiments from which data were drawn for benchmark derivation is reviewed. Chemicals that are found in soil at concentrations exceeding both the phytotoxicity benchmark and the background concentration for the soil type should be considered contaminants of potential concern.« less

Toxicological Benchmarks for Screening Potential Contaminants of Concern for Effects on Terrestrial Plants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suter, G.W. II

1993-01-01

One of the initial stages in ecological risk assessment for hazardous waste sites is screening contaminants to determine which of them are worthy of further consideration as contaminants of potential concern. This process is termed contaminant screening. It is performed by comparing measured ambient concentrations of chemicals to benchmark concentrations. Currently, no standard benchmark concentrations exist for assessing contaminants in soil with respect to their toxicity to plants. This report presents a standard method for deriving benchmarks for this purpose (phytotoxicity benchmarks), a set of data concerning effects of chemicals in soil or soil solution on plants, and a setmore » of phytotoxicity benchmarks for 38 chemicals potentially associated with United States Department of Energy (DOE) sites. In addition, background information on the phytotoxicity and occurrence of the chemicals in soils is presented, and literature describing the experiments from which data were drawn for benchmark derivation is reviewed. Chemicals that are found in soil at concentrations exceeding both the phytotoxicity benchmark and the background concentration for the soil type should be considered contaminants of potential concern.« less

A benchmarking method to measure dietary absorption efficiency of chemicals by fish.

PubMed

Xiao, Ruiyang; Adolfsson-Erici, Margaretha; Åkerman, Gun; McLachlan, Michael S; MacLeod, Matthew

2013-12-01

Understanding the dietary absorption efficiency of chemicals in the gastrointestinal tract of fish is important from both a scientific and a regulatory point of view. However, reported fish absorption efficiencies for well-studied chemicals are highly variable. In the present study, the authors developed and exploited an internal chemical benchmarking method that has the potential to reduce uncertainty and variability and, thus, to improve the precision of measurements of fish absorption efficiency. The authors applied the benchmarking method to measure the gross absorption efficiency for 15 chemicals with a wide range of physicochemical properties and structures. They selected 2,2',5,6'-tetrachlorobiphenyl (PCB53) and decabromodiphenyl ethane as absorbable and nonabsorbable benchmarks, respectively. Quantities of chemicals determined in fish were benchmarked to the fraction of PCB53 recovered in fish, and quantities of chemicals determined in feces were benchmarked to the fraction of decabromodiphenyl ethane recovered in feces. The performance of the benchmarking procedure was evaluated based on the recovery of the test chemicals and precision of absorption efficiency from repeated tests. Benchmarking did not improve the precision of the measurements; after benchmarking, however, the median recovery for 15 chemicals was 106%, and variability of recoveries was reduced compared with before benchmarking, suggesting that benchmarking could account for incomplete extraction of chemical in fish and incomplete collection of feces from different tests. © 2013 SETAC.

A Privacy-Preserving Platform for User-Centric Quantitative Benchmarking

NASA Astrophysics Data System (ADS)

Herrmann, Dominik; Scheuer, Florian; Feustel, Philipp; Nowey, Thomas; Federrath, Hannes

We propose a centralised platform for quantitative benchmarking of key performance indicators (KPI) among mutually distrustful organisations. Our platform offers users the opportunity to request an ad-hoc benchmarking for a specific KPI within a peer group of their choice. Architecture and protocol are designed to provide anonymity to its users and to hide the sensitive KPI values from other clients and the central server. To this end, we integrate user-centric peer group formation, exchangeable secure multi-party computation protocols, short-lived ephemeral key pairs as pseudonyms, and attribute certificates. We show by empirical evaluation of a prototype that the performance is acceptable for reasonably sized peer groups.

Benchmark Testing of a New 56Fe Evaluation for Criticality Safety Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leal, Luiz C; Ivanov, E.

2015-01-01

The SAMMY code was used to evaluate resonance parameters of the 56Fe cross section in the resolved resonance energy range of 0–2 MeV using transmission data, capture, elastic, inelastic, and double differential elastic cross sections. The resonance analysis was performed with the code SAMMY that fits R-matrix resonance parameters using the generalized least-squares technique (Bayes’ theory). The evaluation yielded a set of resonance parameters that reproduced the experimental data very well, along with a resonance parameter covariance matrix for data uncertainty calculations. Benchmark tests were conducted to assess the evaluation performance in benchmark calculations.

Benchmarking Diagnostic Algorithms on an Electrical Power System Testbed

NASA Technical Reports Server (NTRS)

Kurtoglu, Tolga; Narasimhan, Sriram; Poll, Scott; Garcia, David; Wright, Stephanie

2009-01-01

Diagnostic algorithms (DAs) are key to enabling automated health management. These algorithms are designed to detect and isolate anomalies of either a component or the whole system based on observations received from sensors. In recent years a wide range of algorithms, both model-based and data-driven, have been developed to increase autonomy and improve system reliability and affordability. However, the lack of support to perform systematic benchmarking of these algorithms continues to create barriers for effective development and deployment of diagnostic technologies. In this paper, we present our efforts to benchmark a set of DAs on a common platform using a framework that was developed to evaluate and compare various performance metrics for diagnostic technologies. The diagnosed system is an electrical power system, namely the Advanced Diagnostics and Prognostics Testbed (ADAPT) developed and located at the NASA Ames Research Center. The paper presents the fundamentals of the benchmarking framework, the ADAPT system, description of faults and data sets, the metrics used for evaluation, and an in-depth analysis of benchmarking results obtained from testing ten diagnostic algorithms on the ADAPT electrical power system testbed.

Generating Shifting Workloads to Benchmark Adaptability in Relational Database Systems

NASA Astrophysics Data System (ADS)

Rabl, Tilmann; Lang, Andreas; Hackl, Thomas; Sick, Bernhard; Kosch, Harald

A large body of research concerns the adaptability of database systems. Many commercial systems already contain autonomic processes that adapt configurations as well as data structures and data organization. Yet there is virtually no possibility for a just measurement of the quality of such optimizations. While standard benchmarks have been developed that simulate real-world database applications very precisely, none of them considers variations in workloads produced by human factors. Today’s benchmarks test the performance of database systems by measuring peak performance on homogeneous request streams. Nevertheless, in systems with user interaction access patterns are constantly shifting. We present a benchmark that simulates a web information system with interaction of large user groups. It is based on the analysis of a real online eLearning management system with 15,000 users. The benchmark considers the temporal dependency of user interaction. Main focus is to measure the adaptability of a database management system according to shifting workloads. We will give details on our design approach that uses sophisticated pattern analysis and data mining techniques.

Evaluation and optimization of virtual screening workflows with DEKOIS 2.0--a public library of challenging docking benchmark sets.

PubMed

Bauer, Matthias R; Ibrahim, Tamer M; Vogel, Simon M; Boeckler, Frank M

2013-06-24

The application of molecular benchmarking sets helps to assess the actual performance of virtual screening (VS) workflows. To improve the efficiency of structure-based VS approaches, the selection and optimization of various parameters can be guided by benchmarking. With the DEKOIS 2.0 library, we aim to further extend and complement the collection of publicly available decoy sets. Based on BindingDB bioactivity data, we provide 81 new and structurally diverse benchmark sets for a wide variety of different target classes. To ensure a meaningful selection of ligands, we address several issues that can be found in bioactivity data. We have improved our previously introduced DEKOIS methodology with enhanced physicochemical matching, now including the consideration of molecular charges, as well as a more sophisticated elimination of latent actives in the decoy set (LADS). We evaluate the docking performance of Glide, GOLD, and AutoDock Vina with our data sets and highlight existing challenges for VS tools. All DEKOIS 2.0 benchmark sets will be made accessible at http://www.dekois.com.

SAFE: SPARQL Federation over RDF Data Cubes with Access Control.

PubMed

Khan, Yasar; Saleem, Muhammad; Mehdi, Muntazir; Hogan, Aidan; Mehmood, Qaiser; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2017-02-01

Several query federation engines have been proposed for accessing public Linked Open Data sources. However, in many domains, resources are sensitive and access to these resources is tightly controlled by stakeholders; consequently, privacy is a major concern when federating queries over such datasets. In the Healthcare and Life Sciences (HCLS) domain real-world datasets contain sensitive statistical information: strict ownership is granted to individuals working in hospitals, research labs, clinical trial organisers, etc. Therefore, the legal and ethical concerns on (i) preserving the anonymity of patients (or clinical subjects); and (ii) respecting data ownership through access control; are key challenges faced by the data analytics community working within the HCLS domain. Likewise statistical data play a key role in the domain, where the RDF Data Cube Vocabulary has been proposed as a standard format to enable the exchange of such data. However, to the best of our knowledge, no existing approach has looked to optimise federated queries over such statistical data. We present SAFE: a query federation engine that enables policy-aware access to sensitive statistical datasets represented as RDF data cubes. SAFE is designed specifically to query statistical RDF data cubes in a distributed setting, where access control is coupled with source selection, user profiles and their access rights. SAFE proposes a join-aware source selection method that avoids wasteful requests to irrelevant and unauthorised data sources. In order to preserve anonymity and enforce stricter access control, SAFE's indexing system does not hold any data instances-it stores only predicates and endpoints. The resulting data summary has a significantly lower index generation time and size compared to existing engines, which allows for faster updates when sources change. We validate the performance of the system with experiments over real-world datasets provided by three clinical organisations as well as legacy linked datasets. We show that SAFE enables granular graph-level access control over distributed clinical RDF data cubes and efficiently reduces the source selection and overall query execution time when compared with general-purpose SPARQL query federation engines in the targeted setting.

Surgeon-Specific Reports in General Surgery: Establishing Benchmarks for Peer Comparison Within a Single Hospital.

PubMed

Hatfield, Mark D; Ashton, Carol M; Bass, Barbara L; Shirkey, Beverly A

2016-02-01

Methods to assess a surgeon's individual performance based on clinically meaningful outcomes have not been fully developed, due to small numbers of adverse outcomes and wide variation in case volumes. The Achievable Benchmark of Care (ABC) method addresses these issues by identifying benchmark-setting surgeons with high levels of performance and greater case volumes. This method was used to help surgeons compare their surgical practice to that of their peers by using merged National Surgical Quality Improvement Program (NSQIP) and Metabolic and Bariatric Surgery Accreditation and Quality Improvement Program (MBSAQIP) data to generate surgeon-specific reports. A retrospective cohort study at a single institution's department of surgery was conducted involving 107 surgeons (8,660 cases) over 5.5 years. Stratification of more than 32,000 CPT codes into 16 CPT clusters served as the risk adjustment. Thirty-day outcomes of interest included surgical site infection (SSI), acute kidney injury (AKI), and mortality. Performance characteristics of the ABC method were explored by examining how many surgeons were identified as benchmark-setters in view of volume and outcome rates within CPT clusters. For the data captured, most surgeons performed cases spanning a median of 5 CPT clusters (range 1 to 15 clusters), with a median of 26 cases (range 1 to 776 cases) and a median of 2.8 years (range 0 to 5.5 years). The highest volume surgeon for that CPT cluster set the benchmark for 6 of 16 CPT clusters for SSIs, 8 of 16 CPT clusters for AKIs, and 9 of 16 CPT clusters for mortality. The ABC method appears to be a sound and useful approach to identifying benchmark-setting surgeons within a single institution. Such surgeons may be able to help their peers improve their performance. Copyright © 2016 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

Assessment of Static Delamination Propagation Capabilities in Commercial Finite Element Codes Using Benchmark Analysis

NASA Technical Reports Server (NTRS)

Orifici, Adrian C.; Krueger, Ronald

2010-01-01

With capabilities for simulating delamination growth in composite materials becoming available, the need for benchmarking and assessing these capabilities is critical. In this study, benchmark analyses were performed to assess the delamination propagation simulation capabilities of the VCCT implementations in Marc TM and MD NastranTM. Benchmark delamination growth results for Double Cantilever Beam, Single Leg Bending and End Notched Flexure specimens were generated using a numerical approach. This numerical approach was developed previously, and involves comparing results from a series of analyses at different delamination lengths to a single analysis with automatic crack propagation. Specimens were analyzed with three-dimensional and two-dimensional models, and compared with previous analyses using Abaqus . The results demonstrated that the VCCT implementation in Marc TM and MD Nastran(TradeMark) was capable of accurately replicating the benchmark delamination growth results and that the use of the numerical benchmarks offers advantages over benchmarking using experimental and analytical results.

Can data-driven benchmarks be used to set the goals of healthy people 2010?

PubMed Central

Allison, J; Kiefe, C I; Weissman, N W

1999-01-01

OBJECTIVES: Expert panels determined the public health goals of Healthy People 2000 subjectively. The present study examined whether data-driven benchmarks provide a better alternative. METHODS: We developed the "pared-mean" method to define from data the best achievable health care practices. We calculated the pared-mean benchmark for screening mammography from the 1994 National Health Interview Survey, using the metropolitan statistical area as the "provider" unit. Beginning with the best-performing provider and adding providers in descending sequence, we established the minimum provider subset that included at least 10% of all women surveyed on this question. The pared-mean benchmark is then the proportion of women in this subset who received mammography. RESULTS: The pared-mean benchmark for screening mammography was 71%, compared with the Healthy People 2000 goal of 60%. CONCLUSIONS: For Healthy People 2010, benchmarks derived from data reflecting the best available care provide viable alternatives to consensus-derived targets. We are currently pursuing additional refinements to the data-driven pared-mean benchmark approach. PMID:9987466

Excited, Proud, and Accomplished: Exploring the Effects of Feedback Supplemented with Web-Based Peer Benchmarking on Self-Regulated Learning in Marketing Classrooms

ERIC Educational Resources Information Center

Raska, David

2014-01-01

This research explores and tests the effect of an innovative performance feedback practice--feedback supplemented with web-based peer benchmarking--through a lens of social cognitive framework for self-regulated learning. The results suggest that providing performance feedback with references to exemplary peer output is positively associated with…

Maximizing Use of Extension Beef Cattle Benchmarks Data Derived from Cow Herd Appraisal Performance Software

ERIC Educational Resources Information Center

Ramsay, Jennifer M.; Hanna, Lauren L. Hulsman; Ringwall, Kris A.

2016-01-01

One goal of Extension is to provide practical information that makes a difference to producers. Cow Herd Appraisal Performance Software (CHAPS) has provided beef producers with production benchmarks for 30 years, creating a large historical data set. Many such large data sets contain useful information but are underutilized. Our goal was to create…

Performance Evaluation and Benchmarking of Next Intelligent Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

del Pobil, Angel; Madhavan, Raj; Bonsignorio, Fabio

Performance Evaluation and Benchmarking of Intelligent Systems presents research dedicated to the subject of performance evaluation and benchmarking of intelligent systems by drawing from the experiences and insights of leading experts gained both through theoretical development and practical implementation of intelligent systems in a variety of diverse application domains. This contributed volume offers a detailed and coherent picture of state-of-the-art, recent developments, and further research areas in intelligent systems. The chapters cover a broad range of applications, such as assistive robotics, planetary surveying, urban search and rescue, and line tracking for automotive assembly. Subsystems or components described in this bookmore » include human-robot interaction, multi-robot coordination, communications, perception, and mapping. Chapters are also devoted to simulation support and open source software for cognitive platforms, providing examples of the type of enabling underlying technologies that can help intelligent systems to propagate and increase in capabilities. Performance Evaluation and Benchmarking of Intelligent Systems serves as a professional reference for researchers and practitioners in the field. This book is also applicable to advanced courses for graduate level students and robotics professionals in a wide range of engineering and related disciplines including computer science, automotive, healthcare, manufacturing, and service robotics.« less

The Army Pollution Prevention Program: Improving Performance Through Benchmarking.

DTIC Science & Technology

1995-06-01

Washington, DC 20503. 1. AGENCY USE ONLY (Leave Blank) 2. REPORT DATE June 1995 3. REPORT TYPE AND DATES COVERED Final 4. TITLE AND SUBTITLE...unlimited 12b. DISTRIBUTION CODE 13. ABSTRACT (Maximum 200 words) This report investigates the feasibility of using benchmarking as a method for...could use to determine to what degree it should integrate benchmarking with other quality management tools to support the pollution prevention program

Benchmarking hypercube hardware and software

NASA Technical Reports Server (NTRS)

Grunwald, Dirk C.; Reed, Daniel A.

1986-01-01

It was long a truism in computer systems design that balanced systems achieve the best performance. Message passing parallel processors are no different. To quantify the balance of a hypercube design, an experimental methodology was developed and the associated suite of benchmarks was applied to several existing hypercubes. The benchmark suite includes tests of both processor speed in the absence of internode communication and message transmission speed as a function of communication patterns.

Funnel plot control limits to identify poorly performing healthcare providers when there is uncertainty in the value of the benchmark.

PubMed

Manktelow, Bradley N; Seaton, Sarah E; Evans, T Alun

2016-12-01

There is an increasing use of statistical methods, such as funnel plots, to identify poorly performing healthcare providers. Funnel plots comprise the construction of control limits around a benchmark and providers with outcomes falling outside the limits are investigated as potential outliers. The benchmark is usually estimated from observed data but uncertainty in this estimate is usually ignored when constructing control limits. In this paper, the use of funnel plots in the presence of uncertainty in the value of the benchmark is reviewed for outcomes from a Binomial distribution. Two methods to derive the control limits are shown: (i) prediction intervals; (ii) tolerance intervals Tolerance intervals formally include the uncertainty in the value of the benchmark while prediction intervals do not. The probability properties of 95% control limits derived using each method were investigated through hypothesised scenarios. Neither prediction intervals nor tolerance intervals produce funnel plot control limits that satisfy the nominal probability characteristics when there is uncertainty in the value of the benchmark. This is not necessarily to say that funnel plots have no role to play in healthcare, but that without the development of intervals satisfying the nominal probability characteristics they must be interpreted with care. © The Author(s) 2014.

CompaRNA: a server for continuous benchmarking of automated methods for RNA secondary structure prediction

PubMed Central

Puton, Tomasz; Kozlowski, Lukasz P.; Rother, Kristian M.; Bujnicki, Janusz M.

2013-01-01

We present a continuous benchmarking approach for the assessment of RNA secondary structure prediction methods implemented in the CompaRNA web server. As of 3 October 2012, the performance of 28 single-sequence and 13 comparative methods has been evaluated on RNA sequences/structures released weekly by the Protein Data Bank. We also provide a static benchmark generated on RNA 2D structures derived from the RNAstrand database. Benchmarks on both data sets offer insight into the relative performance of RNA secondary structure prediction methods on RNAs of different size and with respect to different types of structure. According to our tests, on the average, the most accurate predictions obtained by a comparative approach are generated by CentroidAlifold, MXScarna, RNAalifold and TurboFold. On the average, the most accurate predictions obtained by single-sequence analyses are generated by CentroidFold, ContextFold and IPknot. The best comparative methods typically outperform the best single-sequence methods if an alignment of homologous RNA sequences is available. This article presents the results of our benchmarks as of 3 October 2012, whereas the rankings presented online are continuously updated. We will gladly include new prediction methods and new measures of accuracy in the new editions of CompaRNA benchmarks. PMID:23435231

International land Model Benchmarking (ILAMB) Package v002.00

DOE Data Explorer

Collier, Nathaniel [Oak Ridge National Laboratory; Hoffman, Forrest M. [Oak Ridge National Laboratory; Mu, Mingquan [University of California, Irvine; Randerson, James T. [University of California, Irvine; Riley, William J. [Lawrence Berkeley National Laboratory

2016-05-09

As a contribution to International Land Model Benchmarking (ILAMB) Project, we are providing new analysis approaches, benchmarking tools, and science leadership. The goal of ILAMB is to assess and improve the performance of land models through international cooperation and to inform the design of new measurement campaigns and field studies to reduce uncertainties associated with key biogeochemical processes and feedbacks. ILAMB is expected to be a primary analysis tool for CMIP6 and future model-data intercomparison experiments. This team has developed initial prototype benchmarking systems for ILAMB, which will be improved and extended to include ocean model metrics and diagnostics.

International land Model Benchmarking (ILAMB) Package v001.00

DOE Data Explorer

Mu, Mingquan [University of California, Irvine; Randerson, James T. [University of California, Irvine; Riley, William J. [Lawrence Berkeley National Laboratory; Hoffman, Forrest M. [Oak Ridge National Laboratory

2016-05-02

As a contribution to International Land Model Benchmarking (ILAMB) Project, we are providing new analysis approaches, benchmarking tools, and science leadership. The goal of ILAMB is to assess and improve the performance of land models through international cooperation and to inform the design of new measurement campaigns and field studies to reduce uncertainties associated with key biogeochemical processes and feedbacks. ILAMB is expected to be a primary analysis tool for CMIP6 and future model-data intercomparison experiments. This team has developed initial prototype benchmarking systems for ILAMB, which will be improved and extended to include ocean model metrics and diagnostics.

Engine Benchmarking - Final CRADA Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wallner, Thomas

Detailed benchmarking of the powertrains of three light-duty vehicles was performed. Results were presented and provided to CRADA partners. The vehicles included a MY2011 Audi A4, a MY2012 Mini Cooper and a MY2014 Nissan Versa.

Rural and urban transit district benchmarking : effectiveness and efficiency guidance document.

DOT National Transportation Integrated Search

2011-05-01

Rural and urban transit systems have sought ways to compare performance across agencies, : identifying successful service delivery strategies and applying these concepts to achieve : successful results within their agency. Benchmarking is a method us...

Present Status and Extensions of the Monte Carlo Performance Benchmark

NASA Astrophysics Data System (ADS)

Hoogenboom, J. Eduard; Petrovic, Bojan; Martin, William R.

2014-06-01

The NEA Monte Carlo Performance benchmark started in 2011 aiming to monitor over the years the abilities to perform a full-size Monte Carlo reactor core calculation with a detailed power production for each fuel pin with axial distribution. This paper gives an overview of the contributed results thus far. It shows that reaching a statistical accuracy of 1 % for most of the small fuel zones requires about 100 billion neutron histories. The efficiency of parallel execution of Monte Carlo codes on a large number of processor cores shows clear limitations for computer clusters with common type computer nodes. However, using true supercomputers the speedup of parallel calculations is increasing up to large numbers of processor cores. More experience is needed from calculations on true supercomputers using large numbers of processors in order to predict if the requested calculations can be done in a short time. As the specifications of the reactor geometry for this benchmark test are well suited for further investigations of full-core Monte Carlo calculations and a need is felt for testing other issues than its computational performance, proposals are presented for extending the benchmark to a suite of benchmark problems for evaluating fission source convergence for a system with a high dominance ratio, for coupling with thermal-hydraulics calculations to evaluate the use of different temperatures and coolant densities and to study the correctness and effectiveness of burnup calculations. Moreover, other contemporary proposals for a full-core calculation with realistic geometry and material composition will be discussed.

Benchmarking in pathology: development of a benchmarking complexity unit and associated key performance indicators.

PubMed

Neil, Amanda; Pfeffer, Sally; Burnett, Leslie

2013-01-01

This paper details the development of a new type of pathology laboratory productivity unit, the benchmarking complexity unit (BCU). The BCU provides a comparative index of laboratory efficiency, regardless of test mix. It also enables estimation of a measure of how much complex pathology a laboratory performs, and the identification of peer organisations for the purposes of comparison and benchmarking. The BCU is based on the theory that wage rates reflect productivity at the margin. A weighting factor for the ratio of medical to technical staff time was dynamically calculated based on actual participant site data. Given this weighting, a complexity value for each test, at each site, was calculated. The median complexity value (number of BCUs) for that test across all participating sites was taken as its complexity value for the Benchmarking in Pathology Program. The BCU allowed implementation of an unbiased comparison unit and test listing that was found to be a robust indicator of the relative complexity for each test. Employing the BCU data, a number of Key Performance Indicators (KPIs) were developed, including three that address comparative organisational complexity, analytical depth and performance efficiency, respectively. Peer groups were also established using the BCU combined with simple organisational and environmental metrics. The BCU has enabled productivity statistics to be compared between organisations. The BCU corrects for differences in test mix and workload complexity of different organisations and also allows for objective stratification into peer groups.

Using a visual plate waste study to monitor menu performance.

PubMed

Connors, Priscilla L; Rozell, Sarah B

2004-01-01

Two visual plate waste studies were conducted in 1-week phases over a 1-year period in an acute care hospital. A total of 383 trays were evaluated in the first phase and 467 in the second. Food items were ranked for consumption from a low (1) to high (6) score, with a score of 4.0 set as the benchmark denoting a minimum level of acceptable consumption. In the first phase two entrees, four starches, all of the vegetables, sliced white bread, and skim milk scored below the benchmark. As a result six menu items were replaced and one was modified. In the second phase all entrees scored at or above 4.0, as did seven vegetables, and a dinner roll that replaced sliced white bread. Skim milk continued to score below the benchmark. A visual plate waste study assists in benchmarking performance, planning menu changes, and assessing effectiveness.

Analysis of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Fineberg, Samuel A.; Pedretti, Kevin T.; Kutler, Paul (Technical Monitor)

1997-01-01

We evaluate the performance of a Fast Ethernet network configured with a single large switch, a single hub, and a 4x4 2D torus topology in a testbed cluster of "commodity" Pentium Pro PCs. We also evaluated a mixed network composed of ethernet hubs and switches. An MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2) show that the torus network performs best for all sizes that we were able to test (up to 16 nodes). For larger networks the ethernet switch outperforms the hub, though its performance is far less than peak. The hub/switch combination tests indicate that the NAS parallel benchmarks are relatively insensitive to hub densities of less than 7 nodes per hub.

Introducing glycomics data into the Semantic Web

PubMed Central

2013-01-01

Background Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as “switches” that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. Results In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as “proofs-of-concept” to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. Conclusions We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains. PMID:24280648

Improving integrative searching of systems chemical biology data using semantic annotation.

PubMed

Chen, Bin; Ding, Ying; Wild, David J

2012-03-08

Systems chemical biology and chemogenomics are considered critical, integrative disciplines in modern biomedical research, but require data mining of large, integrated, heterogeneous datasets from chemistry and biology. We previously developed an RDF-based resource called Chem2Bio2RDF that enabled querying of such data using the SPARQL query language. Whilst this work has proved useful in its own right as one of the first major resources in these disciplines, its utility could be greatly improved by the application of an ontology for annotation of the nodes and edges in the RDF graph, enabling a much richer range of semantic queries to be issued. We developed a generalized chemogenomics and systems chemical biology OWL ontology called Chem2Bio2OWL that describes the semantics of chemical compounds, drugs, protein targets, pathways, genes, diseases and side-effects, and the relationships between them. The ontology also includes data provenance. We used it to annotate our Chem2Bio2RDF dataset, making it a rich semantic resource. Through a series of scientific case studies we demonstrate how this (i) simplifies the process of building SPARQL queries, (ii) enables useful new kinds of queries on the data and (iii) makes possible intelligent reasoning and semantic graph mining in chemogenomics and systems chemical biology. Chem2Bio2OWL is available at http://chem2bio2rdf.org/owl. The document is available at http://chem2bio2owl.wikispaces.com.

Introducing glycomics data into the Semantic Web.

PubMed

Aoki-Kinoshita, Kiyoko F; Bolleman, Jerven; Campbell, Matthew P; Kawano, Shin; Kim, Jin-Dong; Lütteke, Thomas; Matsubara, Masaaki; Okuda, Shujiro; Ranzinger, Rene; Sawaki, Hiromichi; Shikanai, Toshihide; Shinmachi, Daisuke; Suzuki, Yoshinori; Toukach, Philip; Yamada, Issaku; Packer, Nicolle H; Narimatsu, Hisashi

2013-11-26

Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans)a, which can, for example, serve as "switches" that toggle between different functions of a glycoprotein or glycolipid. Due to the advancement of glycomics technologies that are used to characterize glycan structures, many glycomics databases are now publicly available and provide useful information for glycoscience research. However, these databases have almost no link to other life science databases. In order to implement support for the Semantic Web most efficiently for glycomics research, the developers of major glycomics databases agreed on a minimal standard for representing glycan structure and annotation information using RDF (Resource Description Framework). Moreover, all of the participants implemented this standard prototype and generated preliminary RDF versions of their data. To test the utility of the converted data, all of the data sets were uploaded into a Virtuoso triple store, and several SPARQL queries were tested as "proofs-of-concept" to illustrate the utility of the Semantic Web in querying across databases which were originally difficult to implement. We were able to successfully retrieve information by linking UniCarbKB, GlycomeDB and JCGGDB in a single SPARQL query to obtain our target information. We also tested queries linking UniProt with GlycoEpitope as well as lectin data with GlycomeDB through PDB. As a result, we have been able to link proteomics data with glycomics data through the implementation of Semantic Web technologies, allowing for more flexible queries across these domains.

YummyData: providing high-quality open life science data

PubMed Central

Yamaguchi, Atsuko; Splendiani, Andrea

2018-01-01

Abstract Many life science datasets are now available via Linked Data technologies, meaning that they are represented in a common format (the Resource Description Framework), and are accessible via standard APIs (SPARQL endpoints). While this is an important step toward developing an interoperable bioinformatics data landscape, it also creates a new set of obstacles, as it is often difficult for researchers to find the datasets they need. Different providers frequently offer the same datasets, with different levels of support: as well as having more or less up-to-date data, some providers add metadata to describe the content, structures, and ontologies of the stored datasets while others do not. We currently lack a place where researchers can go to easily assess datasets from different providers in terms of metrics such as service stability or metadata richness. We also lack a space for collecting feedback and improving data providers’ awareness of user needs. To address this issue, we have developed YummyData, which consists of two components. One periodically polls a curated list of SPARQL endpoints, monitoring the states of their Linked Data implementations and content. The other presents the information measured for the endpoints and provides a forum for discussion and feedback. YummyData is designed to improve the findability and reusability of life science datasets provided as Linked Data and to foster its adoption. It is freely accessible at http://yummydata.org/. Database URL: http://yummydata.org/ PMID:29688370

Rapid Deployment of a RESTful Service for Oceanographic Research Cruises

NASA Astrophysics Data System (ADS)

Fu, Linyun; Arko, Robert; Leadbetter, Adam

2014-05-01

The Ocean Data Interoperability Platform (ODIP) seeks to increase data sharing across scientific domains and international boundaries, by providing a forum to harmonize diverse regional data systems. ODIP participants from the US include the Rolling Deck to Repository (R2R) program, whose mission is to capture, catalog, and describe the underway/environmental sensor data from US oceanographic research vessels and submit the data to public long-term archives. R2R publishes information online as Linked Open Data, making it widely available using Semantic Web standards. Each vessel, sensor, cruise, dataset, person, organization, funding award, log, report, etc, has a Uniform Resource Identifier (URI). Complex queries that federate results from other data providers are supported, using the SPARQL query language. To facilitate interoperability, R2R uses controlled vocabularies developed collaboratively by the science community (eg. SeaDataNet device categories) and published online by the NERC Vocabulary Server (NVS). In response to user feedback, we are developing a standard programming interface (API) and Web portal for R2R's Linked Open Data. The API provides a set of simple REST-type URLs that are translated on-the-fly into SPARQL queries, and supports common output formats (eg. JSON). We will demonstrate an implementation based on the Epimorphics Linked Data API (ELDA) open-source Java package. Our experience shows that constructing a simple portal with limited schema elements in this way can significantly reduce development time and maintenance complexity.

FireHose Streaming Benchmarks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karl Anderson, Steve Plimpton

2015-01-27

The FireHose Streaming Benchmarks are a suite of stream-processing benchmarks defined to enable comparison of streaming software and hardware, both quantitatively vis-a-vis the rate at which they can process data, and qualitatively by judging the effort involved to implement and run the benchmarks. Each benchmark has two parts. The first is a generator which produces and outputs datums at a high rate in a specific format. The second is an analytic which reads the stream of datums and is required to perform a well-defined calculation on the collection of datums, typically to find anomalous datums that have been created inmore » the stream by the generator. The FireHose suite provides code for the generators, sample code for the analytics (which users are free to re-implement in their own custom frameworks), and a precise definition of each benchmark calculation.« less

Benchmarking of HEU Mental Annuli Critical Assemblies with Internally Reflected Graphite Cylinder

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiaobo, Liu; Bess, John D.; Marshall, Margaret A.

Three experimental configurations of critical assemblies, performed in 1963 at the Oak Ridge Critical Experiment Facility, which are assembled using three different diameter HEU annuli (15-9 inches, 15-7 inches and 13-7 inches) metal annuli with internally reflected graphite cylinder are evaluated and benchmarked. The experimental uncertainties which are 0.00055, 0.00055 and 0.00055 respectively, and biases to the detailed benchmark models which are -0.00179, -0.00189 and -0.00114 respectively, were determined, and the experimental benchmark keff results were obtained for both detailed and simplified model. The calculation results for both detailed and simplified models using MCNP6-1.0 and ENDF VII.1 agree well tomore » the benchmark experimental results with a difference of less than 0.2%. These are acceptable benchmark experiments for inclusion in the ICSBEP Handbook.« less

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-02-15

We present a new lock-free parallel algorithm for computing betweenness centralityof massive small-world networks. With minor changes to the data structures, ouralgorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in HPCS SSCA#2, a benchmark extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the Threadstorm processor, and a single-socket Sun multicore server with the UltraSPARC T2 processor. For a small-world network of 134 millionmore » vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-05-29

We present a new lock-free parallel algorithm for computing betweenness centrality of massive small-world networks. With minor changes to the data structures, our algorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in the HPCS SSCA#2 Graph Analysis benchmark, which has been extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the ThreadStorm processor, and a single-socket Sun multicore server with the UltraSparc T2 processor.more » For a small-world network of 134 million vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

Optimization of Deep Drilling Performance - Development and Benchmark Testing of Advanced Diamond Product Drill Bits & HP/HT Fluids to Significantly Improve Rates of Penetration

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alan Black; Arnis Judzis

2005-09-30

This document details the progress to date on the OPTIMIZATION OF DEEP DRILLING PERFORMANCE--DEVELOPMENT AND BENCHMARK TESTING OF ADVANCED DIAMOND PRODUCT DRILL BITS AND HP/HT FLUIDS TO SIGNIFICANTLY IMPROVE RATES OF PENETRATION contract for the year starting October 2004 through September 2005. The industry cost shared program aims to benchmark drilling rates of penetration in selected simulated deep formations and to significantly improve ROP through a team development of aggressive diamond product drill bit--fluid system technologies. Overall the objectives are as follows: Phase 1--Benchmark ''best in class'' diamond and other product drilling bits and fluids and develop concepts for amore » next level of deep drilling performance; Phase 2--Develop advanced smart bit-fluid prototypes and test at large scale; and Phase 3--Field trial smart bit--fluid concepts, modify as necessary and commercialize products. As of report date, TerraTek has concluded all Phase 1 testing and is planning Phase 2 development.« less

Reliable B Cell Epitope Predictions: Impacts of Method Development and Improved Benchmarking

PubMed Central

Kringelum, Jens Vindahl; Lundegaard, Claus; Lund, Ole; Nielsen, Morten

2012-01-01

The interaction between antibodies and antigens is one of the most important immune system mechanisms for clearing infectious organisms from the host. Antibodies bind to antigens at sites referred to as B-cell epitopes. Identification of the exact location of B-cell epitopes is essential in several biomedical applications such as; rational vaccine design, development of disease diagnostics and immunotherapeutics. However, experimental mapping of epitopes is resource intensive making in silico methods an appealing complementary approach. To date, the reported performance of methods for in silico mapping of B-cell epitopes has been moderate. Several issues regarding the evaluation data sets may however have led to the performance values being underestimated: Rarely, all potential epitopes have been mapped on an antigen, and antibodies are generally raised against the antigen in a given biological context not against the antigen monomer. Improper dealing with these aspects leads to many artificial false positive predictions and hence to incorrect low performance values. To demonstrate the impact of proper benchmark definitions, we here present an updated version of the DiscoTope method incorporating a novel spatial neighborhood definition and half-sphere exposure as surface measure. Compared to other state-of-the-art prediction methods, Discotope-2.0 displayed improved performance both in cross-validation and in independent evaluations. Using DiscoTope-2.0, we assessed the impact on performance when using proper benchmark definitions. For 13 proteins in the training data set where sufficient biological information was available to make a proper benchmark redefinition, the average AUC performance was improved from 0.791 to 0.824. Similarly, the average AUC performance on an independent evaluation data set improved from 0.712 to 0.727. Our results thus demonstrate that given proper benchmark definitions, B-cell epitope prediction methods achieve highly significant predictive performances suggesting these tools to be a powerful asset in rational epitope discovery. The updated version of DiscoTope is available at www.cbs.dtu.dk/services/DiscoTope-2.0. PMID:23300419

A KPI framework for process-based benchmarking of hospital information systems.

PubMed

Jahn, Franziska; Winter, Alfred

2011-01-01

Benchmarking is a major topic for monitoring, directing and elucidating the performance of hospital information systems (HIS). Current approaches neglect the outcome of the processes that are supported by the HIS and their contribution to the hospital's strategic goals. We suggest to benchmark HIS based on clinical documentation processes and their outcome. A framework consisting of a general process model and outcome criteria for clinical documentation processes is introduced.

Data Don't Drive: Building a Practitioner-Driven Culture of Inquiry to Assess Community College Performance. Lumina Foundation for Education Research Report

ERIC Educational Resources Information Center

Dowd, Alicia C.

2005-01-01

This report reviews the benchmarking practices that are presently being used at community colleges. It introduces the concept of a "culture of inquiry" as a means for judging their potential value. It classifies benchmarking efforts among three types--performance, diagnostic, and process--and characterizes each by its typical use. The…

Restaurant Energy Use Benchmarking Guideline

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hedrick, R.; Smith, V.; Field, K.

2011-07-01

A significant operational challenge for food service operators is defining energy use benchmark metrics to compare against the performance of individual stores. Without metrics, multiunit operators and managers have difficulty identifying which stores in their portfolios require extra attention to bring their energy performance in line with expectations. This report presents a method whereby multiunit operators may use their own utility data to create suitable metrics for evaluating their operations.

Benchmarking: applications to transfusion medicine.

PubMed

Apelseth, Torunn Oveland; Molnar, Laura; Arnold, Emmy; Heddle, Nancy M

2012-10-01

Benchmarking is as a structured continuous collaborative process in which comparisons for selected indicators are used to identify factors that, when implemented, will improve transfusion practices. This study aimed to identify transfusion medicine studies reporting on benchmarking, summarize the benchmarking approaches used, and identify important considerations to move the concept of benchmarking forward in the field of transfusion medicine. A systematic review of published literature was performed to identify transfusion medicine-related studies that compared at least 2 separate institutions or regions with the intention of benchmarking focusing on 4 areas: blood utilization, safety, operational aspects, and blood donation. Forty-five studies were included: blood utilization (n = 35), safety (n = 5), operational aspects of transfusion medicine (n = 5), and blood donation (n = 0). Based on predefined criteria, 7 publications were classified as benchmarking, 2 as trending, and 36 as single-event studies. Three models of benchmarking are described: (1) a regional benchmarking program that collects and links relevant data from existing electronic sources, (2) a sentinel site model where data from a limited number of sites are collected, and (3) an institutional-initiated model where a site identifies indicators of interest and approaches other institutions. Benchmarking approaches are needed in the field of transfusion medicine. Major challenges include defining best practices and developing cost-effective methods of data collection. For those interested in initiating a benchmarking program, the sentinel site model may be most effective and sustainable as a starting point, although the regional model would be the ideal goal. Copyright © 2012 Elsevier Inc. All rights reserved.

Benchmarking, benchmarks, or best practices? Applying quality improvement principles to decrease surgical turnaround time.

PubMed

Mitchell, L

1996-01-01

The processes of benchmarking, benchmark data comparative analysis, and study of best practices are distinctly different. The study of best practices is explained with an example based on the Arthur Andersen & Co. 1992 "Study of Best Practices in Ambulatory Surgery". The results of a national best practices study in ambulatory surgery were used to provide our quality improvement team with the goal of improving the turnaround time between surgical cases. The team used a seven-step quality improvement problem-solving process to improve the surgical turnaround time. The national benchmark for turnaround times between surgical cases in 1992 was 13.5 minutes. The initial turnaround time at St. Joseph's Medical Center was 19.9 minutes. After the team implemented solutions, the time was reduced to an average of 16.3 minutes, an 18% improvement. Cost-benefit analysis showed a potential enhanced revenue of approximately $300,000, or a potential savings of $10,119. Applying quality improvement principles to benchmarking, benchmarks, or best practices can improve process performance. Understanding which form of benchmarking the institution wishes to embark on will help focus a team and use appropriate resources. Communicating with professional organizations that have experience in benchmarking will save time and money and help achieve the desired results.

Performance Modeling and Measurement of Parallelized Code for Distributed Shared Memory Multiprocessors

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry

1998-01-01

This paper presents a model to evaluate the performance and overhead of parallelizing sequential code using compiler directives for multiprocessing on distributed shared memory (DSM) systems. With increasing popularity of shared address space architectures, it is essential to understand their performance impact on programs that benefit from shared memory multiprocessing. We present a simple model to characterize the performance of programs that are parallelized using compiler directives for shared memory multiprocessing. We parallelized the sequential implementation of NAS benchmarks using native Fortran77 compiler directives for an Origin2000, which is a DSM system based on a cache-coherent Non Uniform Memory Access (ccNUMA) architecture. We report measurement based performance of these parallelized benchmarks from four perspectives: efficacy of parallelization process; scalability; parallelization overhead; and comparison with hand-parallelized and -optimized version of the same benchmarks. Our results indicate that sequential programs can conveniently be parallelized for DSM systems using compiler directives but realizing performance gains as predicted by the performance model depends primarily on minimizing architecture-specific data locality overhead.

GeneNetWeaver: in silico benchmark generation and performance profiling of network inference methods.

PubMed

Schaffter, Thomas; Marbach, Daniel; Floreano, Dario

2011-08-15

Over the last decade, numerous methods have been developed for inference of regulatory networks from gene expression data. However, accurate and systematic evaluation of these methods is hampered by the difficulty of constructing adequate benchmarks and the lack of tools for a differentiated analysis of network predictions on such benchmarks. Here, we describe a novel and comprehensive method for in silico benchmark generation and performance profiling of network inference methods available to the community as an open-source software called GeneNetWeaver (GNW). In addition to the generation of detailed dynamical models of gene regulatory networks to be used as benchmarks, GNW provides a network motif analysis that reveals systematic prediction errors, thereby indicating potential ways of improving inference methods. The accuracy of network inference methods is evaluated using standard metrics such as precision-recall and receiver operating characteristic curves. We show how GNW can be used to assess the performance and identify the strengths and weaknesses of six inference methods. Furthermore, we used GNW to provide the international Dialogue for Reverse Engineering Assessments and Methods (DREAM) competition with three network inference challenges (DREAM3, DREAM4 and DREAM5). GNW is available at http://gnw.sourceforge.net along with its Java source code, user manual and supporting data. Supplementary data are available at Bioinformatics online. dario.floreano@epfl.ch.

Benchmarking and Evaluating Unified Memory for OpenMP GPU Offloading

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mishra, Alok; Li, Lingda; Kong, Martin

Here, the latest OpenMP standard offers automatic device offloading capabilities which facilitate GPU programming. Despite this, there remain many challenges. One of these is the unified memory feature introduced in recent GPUs. GPUs in current and future HPC systems have enhanced support for unified memory space. In such systems, CPU and GPU can access each other's memory transparently, that is, the data movement is managed automatically by the underlying system software and hardware. Memory over subscription is also possible in these systems. However, there is a significant lack of knowledge about how this mechanism will perform, and how programmers shouldmore » use it. We have modified several benchmarks codes, in the Rodinia benchmark suite, to study the behavior of OpenMP accelerator extensions and have used them to explore the impact of unified memory in an OpenMP context. We moreover modified the open source LLVM compiler to allow OpenMP programs to exploit unified memory. The results of our evaluation reveal that, while the performance of unified memory is comparable with that of normal GPU offloading for benchmarks with little data reuse, it suffers from significant overhead when GPU memory is over subcribed for benchmarks with large amount of data reuse. Based on these results, we provide several guidelines for programmers to achieve better performance with unified memory.« less

Benchmark calculation for radioactivity inventory using MAXS library based on JENDL-4.0 and JEFF-3.0/A for decommissioning BWR plants

NASA Astrophysics Data System (ADS)

Tanaka, Ken-ichi

2016-06-01

We performed benchmark calculation for radioactivity activated in a Primary Containment Vessel (PCV) of a Boiling Water Reactor (BWR) by using MAXS library, which was developed by collapsing with neutron energy spectra in the PCV of the BWR. Radioactivities due to neutron irradiation were measured by using activation foil detector of Gold (Au) and Nickel (Ni) at thirty locations in the PCV. We performed activation calculations of the foils with SCALE5.1/ORIGEN-S code with irradiation conditions of each foil location as the benchmark calculation. We compared calculations and measurements to estimate an effectiveness of MAXS library.

GEN-IV Benchmarking of Triso Fuel Performance Models under accident conditions modeling input data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collin, Blaise Paul

This document presents the benchmark plan for the calculation of particle fuel performance on safety testing experiments that are representative of operational accidental transients. The benchmark is dedicated to the modeling of fission product release under accident conditions by fuel performance codes from around the world, and the subsequent comparison to post-irradiation experiment (PIE) data from the modeled heating tests. The accident condition benchmark is divided into three parts: • The modeling of a simplified benchmark problem to assess potential numerical calculation issues at low fission product release. • The modeling of the AGR-1 and HFR-EU1bis safety testing experiments. •more » The comparison of the AGR-1 and HFR-EU1bis modeling results with PIE data. The simplified benchmark case, thereafter named NCC (Numerical Calculation Case), is derived from “Case 5” of the International Atomic Energy Agency (IAEA) Coordinated Research Program (CRP) on coated particle fuel technology [IAEA 2012]. It is included so participants can evaluate their codes at low fission product release. “Case 5” of the IAEA CRP-6 showed large code-to-code discrepancies in the release of fission products, which were attributed to “effects of the numerical calculation method rather than the physical model” [IAEA 2012]. The NCC is therefore intended to check if these numerical effects subsist. The first two steps imply the involvement of the benchmark participants with a modeling effort following the guidelines and recommendations provided by this document. The third step involves the collection of the modeling results by Idaho National Laboratory (INL) and the comparison of these results with the available PIE data. The objective of this document is to provide all necessary input data to model the benchmark cases, and to give some methodology guidelines and recommendations in order to make all results suitable for comparison with each other. The participants should read this document thoroughly to make sure all the data needed for their calculations is provided in the document. Missing data will be added to a revision of the document if necessary. 09/2016: Tables 6 and 8 updated. AGR-2 input data added« less

Generation IV benchmarking of TRISO fuel performance models under accident conditions: Modeling input data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Collin, Blaise P.

2014-09-01

This document presents the benchmark plan for the calculation of particle fuel performance on safety testing experiments that are representative of operational accidental transients. The benchmark is dedicated to the modeling of fission product release under accident conditions by fuel performance codes from around the world, and the subsequent comparison to post-irradiation experiment (PIE) data from the modeled heating tests. The accident condition benchmark is divided into three parts: the modeling of a simplified benchmark problem to assess potential numerical calculation issues at low fission product release; the modeling of the AGR-1 and HFR-EU1bis safety testing experiments; and, the comparisonmore » of the AGR-1 and HFR-EU1bis modeling results with PIE data. The simplified benchmark case, thereafter named NCC (Numerical Calculation Case), is derived from ''Case 5'' of the International Atomic Energy Agency (IAEA) Coordinated Research Program (CRP) on coated particle fuel technology [IAEA 2012]. It is included so participants can evaluate their codes at low fission product release. ''Case 5'' of the IAEA CRP-6 showed large code-to-code discrepancies in the release of fission products, which were attributed to ''effects of the numerical calculation method rather than the physical model''[IAEA 2012]. The NCC is therefore intended to check if these numerical effects subsist. The first two steps imply the involvement of the benchmark participants with a modeling effort following the guidelines and recommendations provided by this document. The third step involves the collection of the modeling results by Idaho National Laboratory (INL) and the comparison of these results with the available PIE data. The objective of this document is to provide all necessary input data to model the benchmark cases, and to give some methodology guidelines and recommendations in order to make all results suitable for comparison with each other. The participants should read this document thoroughly to make sure all the data needed for their calculations is provided in the document. Missing data will be added to a revision of the document if necessary.« less

HPGMG 1.0: A Benchmark for Ranking High Performance Computing Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adams, Mark; Brown, Jed; Shalf, John

2014-05-05

This document provides an overview of the benchmark ? HPGMG ? for ranking large scale general purpose computers for use on the Top500 list [8]. We provide a rationale for the need for a replacement for the current metric HPL, some background of the Top500 list and the challenges of developing such a metric; we discuss our design philosophy and methodology, and an overview of the specification of the benchmark. The primary documentation with maintained details on the specification can be found at hpgmg.org and the Wiki and benchmark code itself can be found in the repository https://bitbucket.org/hpgmg/hpgmg.

Ab initio calculations, structure, NBO and NCI analyses of Xsbnd H⋯π interactions

NASA Astrophysics Data System (ADS)

Wu, Qiyang; Su, He; Wang, Hongyan; Wang, Hui

2018-02-01

The performance of ab initio methods (MP2, DFT/B3LYP, random-phase approximation (RPA), CCSD(T) and QCISD(T)) in predicting interaction energy of Xsbnd H⋯π (Xsbnd H = HCCH, HCl, HF; π = C2H2, C2H4, C6H6) hydrogen complexes are assessed systematically. The CCSD(T)/CBS benchmarks of interaction energy are reported. It is found that RPA agrees well with CCSD(T)/CBS benchmarks and experimental results. CCSD(T) and QCISD(T) perform the best only when compared with CCSD(T)/CBS benchmarks, MP2 performs well only for experimental data. B3LYP provides the worst accuracy. Additionally, the equilibrium structure, interaction type of Xsbnd H⋯π hydrogen complexes are investigated by the natural bond orbital (NBO) and the non-covalent interaction index (NCI).

The Alpha consensus meeting on cryopreservation key performance indicators and benchmarks: proceedings of an expert meeting.

PubMed

2012-08-01

This proceedings report presents the outcomes from an international workshop designed to establish consensus on: definitions for key performance indicators (KPIs) for oocyte and embryo cryopreservation, using either slow freezing or vitrification; minimum performance level values for each KPI, representing basic competency; and aspirational benchmark values for each KPI, representing best practice goals. This report includes general presentations about current practice and factors for consideration in the development of KPIs. A total of 14 KPIs were recommended and benchmarks for each are presented. No recommendations were made regarding specific cryopreservation techniques or devices, or whether vitrification is 'better' than slow freezing, or vice versa, for any particular stage or application, as this was considered to be outside the scope of this workshop. Copyright © 2012 Reproductive Healthcare Ltd. Published by Elsevier Ltd. All rights reserved.

Interlaboratory Study Characterizing a Yeast Performance Standard for Benchmarking LC-MS Platform Performance*

PubMed Central

Paulovich, Amanda G.; Billheimer, Dean; Ham, Amy-Joan L.; Vega-Montoto, Lorenzo; Rudnick, Paul A.; Tabb, David L.; Wang, Pei; Blackman, Ronald K.; Bunk, David M.; Cardasis, Helene L.; Clauser, Karl R.; Kinsinger, Christopher R.; Schilling, Birgit; Tegeler, Tony J.; Variyath, Asokan Mulayath; Wang, Mu; Whiteaker, Jeffrey R.; Zimmerman, Lisa J.; Fenyo, David; Carr, Steven A.; Fisher, Susan J.; Gibson, Bradford W.; Mesri, Mehdi; Neubert, Thomas A.; Regnier, Fred E.; Rodriguez, Henry; Spiegelman, Cliff; Stein, Stephen E.; Tempst, Paul; Liebler, Daniel C.

2010-01-01

Optimal performance of LC-MS/MS platforms is critical to generating high quality proteomics data. Although individual laboratories have developed quality control samples, there is no widely available performance standard of biological complexity (and associated reference data sets) for benchmarking of platform performance for analysis of complex biological proteomes across different laboratories in the community. Individual preparations of the yeast Saccharomyces cerevisiae proteome have been used extensively by laboratories in the proteomics community to characterize LC-MS platform performance. The yeast proteome is uniquely attractive as a performance standard because it is the most extensively characterized complex biological proteome and the only one associated with several large scale studies estimating the abundance of all detectable proteins. In this study, we describe a standard operating protocol for large scale production of the yeast performance standard and offer aliquots to the community through the National Institute of Standards and Technology where the yeast proteome is under development as a certified reference material to meet the long term needs of the community. Using a series of metrics that characterize LC-MS performance, we provide a reference data set demonstrating typical performance of commonly used ion trap instrument platforms in expert laboratories; the results provide a basis for laboratories to benchmark their own performance, to improve upon current methods, and to evaluate new technologies. Additionally, we demonstrate how the yeast reference, spiked with human proteins, can be used to benchmark the power of proteomics platforms for detection of differentially expressed proteins at different levels of concentration in a complex matrix, thereby providing a metric to evaluate and minimize preanalytical and analytical variation in comparative proteomics experiments. PMID:19858499

Benchmarking Ada tasking on tightly coupled multiprocessor architectures

NASA Technical Reports Server (NTRS)

Collard, Philippe; Goforth, Andre; Marquardt, Matthew

1989-01-01

The development of benchmarks and performance measures for parallel Ada tasking is reported with emphasis on the macroscopic behavior of the benchmark across a set of load parameters. The application chosen for the study was the NASREM model for telerobot control, relevant to many NASA missions. The results of the study demonstrate the potential of parallel Ada in accomplishing the task of developing a control system for a system such as the Flight Telerobotic Servicer using the NASREM framework.

Toxicological benchmarks for screening potential contaminants of concern for effects on soil and litter invertebrates and heterotrophic process

DOE Office of Scientific and Technical Information (OSTI.GOV)

Will, M.E.; Suter, G.W. II

1994-09-01

One of the initial stages in ecological risk assessments for hazardous waste sites is the screening of contaminants to determine which of them are worthy of further consideration as {open_quotes}contaminants of potential concern.{close_quotes} This process is termed {open_quotes}contaminant screening.{close_quotes} It is performed by comparing measured ambient concentrations of chemicals to benchmark concentrations. Currently, no standard benchmark concentrations exist for assessing contaminants in soil with respect to their toxicity to soil- and litter-dwelling invertebrates, including earthworms, other micro- and macroinvertebrates, or heterotrophic bacteria and fungi. This report presents a standard method for deriving benchmarks for this purpose, sets of data concerningmore » effects of chemicals in soil on invertebrates and soil microbial processes, and benchmarks for chemicals potentially associated with United States Department of Energy sites. In addition, literature describing the experiments from which data were drawn for benchmark derivation. Chemicals that are found in soil at concentrations exceeding both the benchmarks and the background concentration for the soil type should be considered contaminants of potential concern.« less

Ontology for Transforming Geo-Spatial Data for Discovery and Integration of Scientific Data

NASA Astrophysics Data System (ADS)

Nguyen, L.; Chee, T.; Minnis, P.

2013-12-01

Discovery and access to geo-spatial scientific data across heterogeneous repositories and multi-discipline datasets can present challenges for scientist. We propose to build a workflow for transforming geo-spatial datasets into semantic environment by using relationships to describe the resource using OWL Web Ontology, RDF, and a proposed geo-spatial vocabulary. We will present methods for transforming traditional scientific dataset, use of a semantic repository, and querying using SPARQL to integrate and access datasets. This unique repository will enable discovery of scientific data by geospatial bound or other criteria.

Benchmarking Brain-Computer Interfaces Outside the Laboratory: The Cybathlon 2016

PubMed Central

Novak, Domen; Sigrist, Roland; Gerig, Nicolas J.; Wyss, Dario; Bauer, René; Götz, Ulrich; Riener, Robert

2018-01-01

This paper presents a new approach to benchmarking brain-computer interfaces (BCIs) outside the lab. A computer game was created that mimics a real-world application of assistive BCIs, with the main outcome metric being the time needed to complete the game. This approach was used at the Cybathlon 2016, a competition for people with disabilities who use assistive technology to achieve tasks. The paper summarizes the technical challenges of BCIs, describes the design of the benchmarking game, then describes the rules for acceptable hardware, software and inclusion of human pilots in the BCI competition at the Cybathlon. The 11 participating teams, their approaches, and their results at the Cybathlon are presented. Though the benchmarking procedure has some limitations (for instance, we were unable to identify any factors that clearly contribute to BCI performance), it can be successfully used to analyze BCI performance in realistic, less structured conditions. In the future, the parameters of the benchmarking game could be modified to better mimic different applications (e.g., the need to use some commands more frequently than others). Furthermore, the Cybathlon has the potential to showcase such devices to the general public. PMID:29375294

Encoding color information for visual tracking: Algorithms and benchmark.

PubMed

Liang, Pengpeng; Blasch, Erik; Ling, Haibin

2015-12-01

While color information is known to provide rich discriminative clues for visual inference, most modern visual trackers limit themselves to the grayscale realm. Despite recent efforts to integrate color in tracking, there is a lack of comprehensive understanding of the role color information can play. In this paper, we attack this problem by conducting a systematic study from both the algorithm and benchmark perspectives. On the algorithm side, we comprehensively encode 10 chromatic models into 16 carefully selected state-of-the-art visual trackers. On the benchmark side, we compile a large set of 128 color sequences with ground truth and challenge factor annotations (e.g., occlusion). A thorough evaluation is conducted by running all the color-encoded trackers, together with two recently proposed color trackers. A further validation is conducted on an RGBD tracking benchmark. The results clearly show the benefit of encoding color information for tracking. We also perform detailed analysis on several issues, including the behavior of various combinations between color model and visual tracker, the degree of difficulty of each sequence for tracking, and how different challenge factors affect the tracking performance. We expect the study to provide the guidance, motivation, and benchmark for future work on encoding color in visual tracking.

Performance Monitoring of Distributed Data Processing Systems

NASA Technical Reports Server (NTRS)

Ojha, Anand K.

2000-01-01

Test and checkout systems are essential components in ensuring safety and reliability of aircraft and related systems for space missions. A variety of systems, developed over several years, are in use at the NASA/KSC. Many of these systems are configured as distributed data processing systems with the functionality spread over several multiprocessor nodes interconnected through networks. To be cost-effective, a system should take the least amount of resource and perform a given testing task in the least amount of time. There are two aspects of performance evaluation: monitoring and benchmarking. While monitoring is valuable to system administrators in operating and maintaining, benchmarking is important in designing and upgrading computer-based systems. These two aspects of performance evaluation are the foci of this project. This paper first discusses various issues related to software, hardware, and hybrid performance monitoring as applicable to distributed systems, and specifically to the TCMS (Test Control and Monitoring System). Next, a comparison of several probing instructions are made to show that the hybrid monitoring technique developed by the NIST (National Institutes for Standards and Technology) is the least intrusive and takes only one-fourth of the time taken by software monitoring probes. In the rest of the paper, issues related to benchmarking a distributed system have been discussed and finally a prescription for developing a micro-benchmark for the TCMS has been provided.

User and Performance Impacts from Franklin Upgrades

DOE Office of Scientific and Technical Information (OSTI.GOV)

He, Yun

2009-05-10

The NERSC flagship computer Cray XT4 system"Franklin" has gone through three major upgrades: quad core upgrade, CLE 2.1 upgrade, and IO upgrade, during the past year. In this paper, we will discuss the various aspects of the user impacts such as user access, user environment, and user issues etc from these upgrades. The performance impacts on the kernel benchmarks and selected application benchmarks will also be presented.

Implementation of BT, SP, LU, and FT of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Schultz, Matthew; Frumkin, Michael; Jin, Hao-Qiang; Yan, Jerry

2000-01-01

A number of Java features make it an attractive but a debatable choice for High Performance Computing. We have implemented benchmarks working on single structured grid BT,SP,LU and FT in Java. The performance and scalability of the Java code shows that a significant improvement in Java compiler technology and in Java thread implementation are necessary for Java to compete with Fortran in HPC applications.

Automated benchmarking of peptide-MHC class I binding predictions.

PubMed

Trolle, Thomas; Metushi, Imir G; Greenbaum, Jason A; Kim, Yohan; Sidney, John; Lund, Ole; Sette, Alessandro; Peters, Bjoern; Nielsen, Morten

2015-07-01

Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study. The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB. Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto_bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto_bench/mhci/join. mniel@cbs.dtu.dk or bpeters@liai.org Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Validating Cellular Automata Lava Flow Emplacement Algorithms with Standard Benchmarks

NASA Astrophysics Data System (ADS)

Richardson, J. A.; Connor, L.; Charbonnier, S. J.; Connor, C.; Gallant, E.

2015-12-01

A major existing need in assessing lava flow simulators is a common set of validation benchmark tests. We propose three levels of benchmarks which test model output against increasingly complex standards. First, imulated lava flows should be morphologically identical, given changes in parameter space that should be inconsequential, such as slope direction. Second, lava flows simulated in simple parameter spaces can be tested against analytical solutions or empirical relationships seen in Bingham fluids. For instance, a lava flow simulated on a flat surface should produce a circular outline. Third, lava flows simulated over real world topography can be compared to recent real world lava flows, such as those at Tolbachik, Russia, and Fogo, Cape Verde. Success or failure of emplacement algorithms in these validation benchmarks can be determined using a Bayesian approach, which directly tests the ability of an emplacement algorithm to correctly forecast lava inundation. Here we focus on two posterior metrics, P(A|B) and P(¬A|¬B), which describe the positive and negative predictive value of flow algorithms. This is an improvement on less direct statistics such as model sensitivity and the Jaccard fitness coefficient. We have performed these validation benchmarks on a new, modular lava flow emplacement simulator that we have developed. This simulator, which we call MOLASSES, follows a Cellular Automata (CA) method. The code is developed in several interchangeable modules, which enables quick modification of the distribution algorithm from cell locations to their neighbors. By assessing several different distribution schemes with the benchmark tests, we have improved the performance of MOLASSES to correctly match early stages of the 2012-3 Tolbachik Flow, Kamchakta Russia, to 80%. We also can evaluate model performance given uncertain input parameters using a Monte Carlo setup. This illuminates sensitivity to model uncertainty.

Automated benchmarking of peptide-MHC class I binding predictions

PubMed Central

Trolle, Thomas; Metushi, Imir G.; Greenbaum, Jason A.; Kim, Yohan; Sidney, John; Lund, Ole; Sette, Alessandro; Peters, Bjoern; Nielsen, Morten

2015-01-01

Motivation: Numerous in silico methods predicting peptide binding to major histocompatibility complex (MHC) class I molecules have been developed over the last decades. However, the multitude of available prediction tools makes it non-trivial for the end-user to select which tool to use for a given task. To provide a solid basis on which to compare different prediction tools, we here describe a framework for the automated benchmarking of peptide-MHC class I binding prediction tools. The framework runs weekly benchmarks on data that are newly entered into the Immune Epitope Database (IEDB), giving the public access to frequent, up-to-date performance evaluations of all participating tools. To overcome potential selection bias in the data included in the IEDB, a strategy was implemented that suggests a set of peptides for which different prediction methods give divergent predictions as to their binding capability. Upon experimental binding validation, these peptides entered the benchmark study. Results: The benchmark has run for 15 weeks and includes evaluation of 44 datasets covering 17 MHC alleles and more than 4000 peptide-MHC binding measurements. Inspection of the results allows the end-user to make educated selections between participating tools. Of the four participating servers, NetMHCpan performed the best, followed by ANN, SMM and finally ARB. Availability and implementation: Up-to-date performance evaluations of each server can be found online at http://tools.iedb.org/auto_bench/mhci/weekly. All prediction tool developers are invited to participate in the benchmark. Sign-up instructions are available at http://tools.iedb.org/auto_bench/mhci/join. Contact: mniel@cbs.dtu.dk or bpeters@liai.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25717196

A frontier analysis approach for benchmarking hospital performance in the treatment of acute myocardial infarction.

PubMed

Stanford, Robert E

2004-05-01

This paper uses a non-parametric frontier model and adaptations of the concepts of cross-efficiency and peer-appraisal to develop a formal methodology for benchmarking provider performance in the treatment of Acute Myocardial Infarction (AMI). Parameters used in the benchmarking process are the rates of proper recognition of indications of six standard treatment processes for AMI; the decision making units (DMUs) to be compared are the Medicare eligible hospitals of a particular state; the analysis produces an ordinal ranking of individual hospital performance scores. The cross-efficiency/peer-appraisal calculation process is constructed to accommodate DMUs that experience no patients in some of the treatment categories. While continuing to rate highly the performances of DMUs which are efficient in the Pareto-optimal sense, our model produces individual DMU performance scores that correlate significantly with good overall performance, as determined by a comparison of the sums of the individual DMU recognition rates for the six standard treatment processes. The methodology is applied to data collected from 107 state Medicare hospitals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marck, Steven C. van der, E-mail: vandermarck@nrg.eu

Recent releases of three major world nuclear reaction data libraries, ENDF/B-VII.1, JENDL-4.0, and JEFF-3.1.1, have been tested extensively using benchmark calculations. The calculations were performed with the latest release of the continuous energy Monte Carlo neutronics code MCNP, i.e. MCNP6. Three types of benchmarks were used, viz. criticality safety benchmarks, (fusion) shielding benchmarks, and reference systems for which the effective delayed neutron fraction is reported. For criticality safety, more than 2000 benchmarks from the International Handbook of Criticality Safety Benchmark Experiments were used. Benchmarks from all categories were used, ranging from low-enriched uranium, compound fuel, thermal spectrum ones (LEU-COMP-THERM), tomore » mixed uranium-plutonium, metallic fuel, fast spectrum ones (MIX-MET-FAST). For fusion shielding many benchmarks were based on IAEA specifications for the Oktavian experiments (for Al, Co, Cr, Cu, LiF, Mn, Mo, Si, Ti, W, Zr), Fusion Neutronics Source in Japan (for Be, C, N, O, Fe, Pb), and Pulsed Sphere experiments at Lawrence Livermore National Laboratory (for {sup 6}Li, {sup 7}Li, Be, C, N, O, Mg, Al, Ti, Fe, Pb, D2O, H2O, concrete, polyethylene and teflon). The new functionality in MCNP6 to calculate the effective delayed neutron fraction was tested by comparison with more than thirty measurements in widely varying systems. Among these were measurements in the Tank Critical Assembly (TCA in Japan) and IPEN/MB-01 (Brazil), both with a thermal spectrum, two cores in Masurca (France) and three cores in the Fast Critical Assembly (FCA, Japan), all with fast spectra. The performance of the three libraries, in combination with MCNP6, is shown to be good. The results for the LEU-COMP-THERM category are on average very close to the benchmark value. Also for most other categories the results are satisfactory. Deviations from the benchmark values do occur in certain benchmark series, or in isolated cases within benchmark series. Such instances can often be related to nuclear data for specific non-fissile elements, such as C, Fe, or Gd. Indications are that the intermediate and mixed spectrum cases are less well described. The results for the shielding benchmarks are generally good, with very similar results for the three libraries in the majority of cases. Nevertheless there are, in certain cases, strong deviations between calculated and benchmark values, such as for Co and Mg. Also, the results show discrepancies at certain energies or angles for e.g. C, N, O, Mo, and W. The functionality of MCNP6 to calculate the effective delayed neutron fraction yields very good results for all three libraries.« less

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

PubMed

Ó Conchúir, Shane; Barlow, Kyle A; Pache, Roland A; Ollikainen, Noah; Kundert, Kale; O'Meara, Matthew J; Smith, Colin A; Kortemme, Tanja

2015-01-01

The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

Spherical harmonic results for the 3D Kobayashi Benchmark suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brown, P N; Chang, B; Hanebutte, U R

1999-03-02

Spherical harmonic solutions are presented for the Kobayashi benchmark suite. The results were obtained with Ardra, a scalable, parallel neutron transport code developed at Lawrence Livermore National Laboratory (LLNL). The calculations were performed on the IBM ASCI Blue-Pacific computer at LLNL.

The philosophy of benchmark testing a standards-based picture archiving and communications system.

PubMed

Richardson, N E; Thomas, J A; Lyche, D K; Romlein, J; Norton, G S; Dolecek, Q E

1999-05-01

The Department of Defense issued its requirements for a Digital Imaging Network-Picture Archiving and Communications System (DIN-PACS) in a Request for Proposals (RFP) to industry in January 1997, with subsequent contracts being awarded in November 1997 to the Agfa Division of Bayer and IBM Global Government Industry. The Government's technical evaluation process consisted of evaluating a written technical proposal as well as conducting a benchmark test of each proposed system at the vendor's test facility. The purpose of benchmark testing was to evaluate the performance of the fully integrated system in a simulated operational environment. The benchmark test procedures and test equipment were developed through a joint effort between the Government, academic institutions, and private consultants. Herein the authors discuss the resources required and the methods used to benchmark test a standards-based PACS.

An integrated data envelopment analysis-artificial neural network approach for benchmarking of bank branches

NASA Astrophysics Data System (ADS)

Shokrollahpour, Elsa; Hosseinzadeh Lotfi, Farhad; Zandieh, Mostafa

2016-06-01

Efficiency and quality of services are crucial to today's banking industries. The competition in this section has become increasingly intense, as a result of fast improvements in Technology. Therefore, performance analysis of the banking sectors attracts more attention these days. Even though data envelopment analysis (DEA) is a pioneer approach in the literature as of an efficiency measurement tool and finding benchmarks, it is on the other hand unable to demonstrate the possible future benchmarks. The drawback to it could be that the benchmarks it provides us with, may still be less efficient compared to the more advanced future benchmarks. To cover for this weakness, artificial neural network is integrated with DEA in this paper to calculate the relative efficiency and more reliable benchmarks of one of the Iranian commercial bank branches. Therefore, each branch could have a strategy to improve the efficiency and eliminate the cause of inefficiencies based on a 5-year time forecast.

Interactive visual optimization and analysis for RFID benchmarking.

PubMed

Wu, Yingcai; Chung, Ka-Kei; Qu, Huamin; Yuan, Xiaoru; Cheung, S C

2009-01-01

Radio frequency identification (RFID) is a powerful automatic remote identification technique that has wide applications. To facilitate RFID deployment, an RFID benchmarking instrument called aGate has been invented to identify the strengths and weaknesses of different RFID technologies in various environments. However, the data acquired by aGate are usually complex time varying multidimensional 3D volumetric data, which are extremely challenging for engineers to analyze. In this paper, we introduce a set of visualization techniques, namely, parallel coordinate plots, orientation plots, a visual history mechanism, and a 3D spatial viewer, to help RFID engineers analyze benchmark data visually and intuitively. With the techniques, we further introduce two workflow procedures (a visual optimization procedure for finding the optimum reader antenna configuration and a visual analysis procedure for comparing the performance and identifying the flaws of RFID devices) for the RFID benchmarking, with focus on the performance analysis of the aGate system. The usefulness and usability of the system are demonstrated in the user evaluation.

Measurement, Standards, and Peer Benchmarking: One Hospital's Journey.

PubMed

Martin, Brian S; Arbore, Mark

2016-04-01

Peer-to-peer benchmarking is an important component of rapid-cycle performance improvement in patient safety and quality-improvement efforts. Institutions should carefully examine critical success factors before engagement in peer-to-peer benchmarking in order to maximize growth and change opportunities. Solutions for Patient Safety has proven to be a high-yield engagement for Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, with measureable improvement in both organizational process and culture. Copyright © 2016 Elsevier Inc. All rights reserved.

Benchmark Evaluation of HTR-PROTEUS Pebble Bed Experimental Program

DOE PAGES

Bess, John D.; Montierth, Leland; Köberl, Oliver; ...

2014-10-09

Benchmark models were developed to evaluate 11 critical core configurations of the HTR-PROTEUS pebble bed experimental program. Various additional reactor physics measurements were performed as part of this program; currently only a total of 37 absorber rod worth measurements have been evaluated as acceptable benchmark experiments for Cores 4, 9, and 10. Dominant uncertainties in the experimental keff for all core configurations come from uncertainties in the ²³⁵U enrichment of the fuel, impurities in the moderator pebbles, and the density and impurity content of the radial reflector. Calculations of k eff with MCNP5 and ENDF/B-VII.0 neutron nuclear data aremore » greater than the benchmark values but within 1% and also within the 3σ uncertainty, except for Core 4, which is the only randomly packed pebble configuration. Repeated calculations of k eff with MCNP6.1 and ENDF/B-VII.1 are lower than the benchmark values and within 1% (~3σ) except for Cores 5 and 9, which calculate lower than the benchmark eigenvalues within 4σ. The primary difference between the two nuclear data libraries is the adjustment of the absorption cross section of graphite. Simulations of the absorber rod worth measurements are within 3σ of the benchmark experiment values. The complete benchmark evaluation details are available in the 2014 edition of the International Handbook of Evaluated Reactor Physics Benchmark Experiments.« less

Systematic Benchmarking of Diagnostic Technologies for an Electrical Power System

NASA Technical Reports Server (NTRS)

Kurtoglu, Tolga; Jensen, David; Poll, Scott

2009-01-01

Automated health management is a critical functionality for complex aerospace systems. A wide variety of diagnostic algorithms have been developed to address this technical challenge. Unfortunately, the lack of support to perform large-scale V&V (verification and validation) of diagnostic technologies continues to create barriers to effective development and deployment of such algorithms for aerospace vehicles. In this paper, we describe a formal framework developed for benchmarking of diagnostic technologies. The diagnosed system is the Advanced Diagnostics and Prognostics Testbed (ADAPT), a real-world electrical power system (EPS), developed and maintained at the NASA Ames Research Center. The benchmarking approach provides a systematic, empirical basis to the testing of diagnostic software and is used to provide performance assessment for different diagnostic algorithms.

NetBenchmark: a bioconductor package for reproducible benchmarks of gene regulatory network inference.

PubMed

Bellot, Pau; Olsen, Catharina; Salembier, Philippe; Oliveras-Vergés, Albert; Meyer, Patrick E

2015-09-29

In the last decade, a great number of methods for reconstructing gene regulatory networks from expression data have been proposed. However, very few tools and datasets allow to evaluate accurately and reproducibly those methods. Hence, we propose here a new tool, able to perform a systematic, yet fully reproducible, evaluation of transcriptional network inference methods. Our open-source and freely available Bioconductor package aggregates a large set of tools to assess the robustness of network inference algorithms against different simulators, topologies, sample sizes and noise intensities. The benchmarking framework that uses various datasets highlights the specialization of some methods toward network types and data. As a result, it is possible to identify the techniques that have broad overall performances.

Open Rotor - Analysis of Diagnostic Data

NASA Technical Reports Server (NTRS)

Envia, Edmane

2011-01-01

NASA is researching open rotor propulsion as part of its technology research and development plan for addressing the subsonic transport aircraft noise, emission and fuel burn goals. The low-speed wind tunnel test for investigating the aerodynamic and acoustic performance of a benchmark blade set at the approach and takeoff conditions has recently concluded. A high-speed wind tunnel diagnostic test campaign has begun to investigate the performance of this benchmark open rotor blade set at the cruise condition. Databases from both speed regimes will comprise a comprehensive collection of benchmark open rotor data for use in assessing/validating aerodynamic and noise prediction tools (component & system level) as well as providing insights into the physics of open rotors to help guide the development of quieter open rotors.

Heterogeneous Distributed Computing for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Sunderam, Vaidy S.

1998-01-01

The research supported under this award focuses on heterogeneous distributed computing for high-performance applications, with particular emphasis on computational aerosciences. The overall goal of this project was to and investigate issues in, and develop solutions to, efficient execution of computational aeroscience codes in heterogeneous concurrent computing environments. In particular, we worked in the context of the PVM[1] system and, subsequent to detailed conversion efforts and performance benchmarking, devising novel techniques to increase the efficacy of heterogeneous networked environments for computational aerosciences. Our work has been based upon the NAS Parallel Benchmark suite, but has also recently expanded in scope to include the NAS I/O benchmarks as specified in the NHT-1 document. In this report we summarize our research accomplishments under the auspices of the grant.

Relationship between the TCAP and the Pearson Benchmark Assessment in Elementary Students' Reading and Math Performance in a Northeastern Tennessee School District

ERIC Educational Resources Information Center

Dugger-Roberts, Cherith A.

2014-01-01

The purpose of this quantitative study was to determine if there was a relationship between the TCAP test and Pearson Benchmark assessment in elementary students' reading and language arts and math performance in a northeastern Tennessee school district. This study involved 3rd, 4th, 5th, and 6th grade students. The study focused on the following…

Report from the First CERT-RMM Users Group Workshop Series

DTIC Science & Technology

2012-04-01

deploy processes to support our programs – Benchmark our programs to determine current gaps – Complements current work in CMMI® and ISO 27001 19...benchmarking program performance through process analytics and Lean/Six Sigma activities to ensure Performance Excellence. • Provides ISO Standards...Office www.cmu.edu/ iso 29 Carnegie Mellon University • Est 1967 in Pittsburgh, PA • Global, private research university • Ranked 22nd • 15,000

Benchmarking database performance for genomic data.

PubMed

Khushi, Matloob

2015-06-01

Genomic regions represent features such as gene annotations, transcription factor binding sites and epigenetic modifications. Performing various genomic operations such as identifying overlapping/non-overlapping regions or nearest gene annotations are common research needs. The data can be saved in a database system for easy management, however, there is no comprehensive database built-in algorithm at present to identify overlapping regions. Therefore I have developed a novel region-mapping (RegMap) SQL-based algorithm to perform genomic operations and have benchmarked the performance of different databases. Benchmarking identified that PostgreSQL extracts overlapping regions much faster than MySQL. Insertion and data uploads in PostgreSQL were also better, although general searching capability of both databases was almost equivalent. In addition, using the algorithm pair-wise, overlaps of >1000 datasets of transcription factor binding sites and histone marks, collected from previous publications, were reported and it was found that HNF4G significantly co-locates with cohesin subunit STAG1 (SA1).Inc. © 2015 Wiley Periodicals, Inc.

Low Molecular Weight Polymethacrylates as Multi-Functional Lubricant Additives

DOE PAGES

Cosimbescu, Lelia; Vellore, Azhar; Shantini Ramasamy, Uma; ...

2018-04-24

In this study, low molecular weight, moderately polar polymethacrylate polymers are explored as potential multi-functional lubricant additives. The performance of these novel additives in base oil is evaluated in terms of their viscosity index, shear stability, and friction-and-wear. The new compounds are compared to two benchmarks, a typical polymeric viscosity modifier and a fully-formulated oil. Results show that the best performing of the new polymers exhibit viscosity index and friction comparable to that of both benchmarks, far superior shear stability to either benchmark (as much as 15x lower shear loss), and wear reduction significantly better than a typical viscosity modifiermore » (lower wear volume by a factor of 2-3). The findings also suggest that the polarity and molecular weight of the polymers affect their performance which suggests future synthetic strategies may enable this new class of additives to replace multiple additives in typical lubricant formulations.« less

Low Molecular Weight Polymethacrylates as Multi-Functional Lubricant Additives

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cosimbescu, Lelia; Vellore, Azhar; Shantini Ramasamy, Uma

In this study, low molecular weight, moderately polar polymethacrylate polymers are explored as potential multi-functional lubricant additives. The performance of these novel additives in base oil is evaluated in terms of their viscosity index, shear stability, and friction-and-wear. The new compounds are compared to two benchmarks, a typical polymeric viscosity modifier and a fully-formulated oil. Results show that the best performing of the new polymers exhibit viscosity index and friction comparable to that of both benchmarks, far superior shear stability to either benchmark (as much as 15x lower shear loss), and wear reduction significantly better than a typical viscosity modifiermore » (lower wear volume by a factor of 2-3). The findings also suggest that the polarity and molecular weight of the polymers affect their performance which suggests future synthetic strategies may enable this new class of additives to replace multiple additives in typical lubricant formulations.« less

Final Report of the NASA Office of Safety and Mission Assurance Agile Benchmarking Team

NASA Technical Reports Server (NTRS)

Wetherholt, Martha

2016-01-01

To ensure that the NASA Safety and Mission Assurance (SMA) community remains in a position to perform reliable Software Assurance (SA) on NASAs critical software (SW) systems with the software industry rapidly transitioning from waterfall to Agile processes, Terry Wilcutt, Chief, Safety and Mission Assurance, Office of Safety and Mission Assurance (OSMA) established the Agile Benchmarking Team (ABT). The Team's tasks were: 1. Research background literature on current Agile processes, 2. Perform benchmark activities with other organizations that are involved in software Agile processes to determine best practices, 3. Collect information on Agile-developed systems to enable improvements to the current NASA standards and processes to enhance their ability to perform reliable software assurance on NASA Agile-developed systems, 4. Suggest additional guidance and recommendations for updates to those standards and processes, as needed. The ABT's findings and recommendations for software management, engineering and software assurance are addressed herein.

Analysing the performance of personal computers based on Intel microprocessors for sequence aligning bioinformatics applications.

PubMed

Nair, Pradeep S; John, Eugene B

2007-01-01

Aligning specific sequences against a very large number of other sequences is a central aspect of bioinformatics. With the widespread availability of personal computers in biology laboratories, sequence alignment is now often performed locally. This makes it necessary to analyse the performance of personal computers for sequence aligning bioinformatics benchmarks. In this paper, we analyse the performance of a personal computer for the popular BLAST and FASTA sequence alignment suites. Results indicate that these benchmarks have a large number of recurring operations and use memory operations extensively. It seems that the performance can be improved with a bigger L1-cache.

Addressing the Challenges of Multi-Domain Data Integration with the SemantEco Framework

NASA Astrophysics Data System (ADS)

Patton, E. W.; Seyed, P.; McGuinness, D. L.

2013-12-01

Data integration across multiple domains will continue to be a challenge with the proliferation of big data in the sciences. Data origination issues and how data are manipulated are critical to enable scientists to understand and consume disparate datasets as research becomes more multidisciplinary. We present the SemantEco framework as an exemplar for designing an integrative portal for data discovery, exploration, and interpretation that uses best practice W3C Recommendations. We use the Resource Description Framework (RDF) with extensible ontologies described in the Web Ontology Language (OWL) to provide graph-based data representation. Furthermore, SemantEco ingests data via the software package csv2rdf4lod, which generates data provenance using the W3C provenance recommendation (PROV). Our presentation will discuss benefits and challenges of semantic integration, their effect on runtime performance, and how the SemantEco framework assisted in identifying performance issues and improved query performance across multiple domains by an order of magnitude. SemantEco benefits from a semantic approach that provides an 'open world', which allows data to incrementally change just as it does in the real world. SemantEco modules may load new ontologies and data using the W3C's SPARQL Protocol and RDF Query Language via HTTP. Modules may also provide user interface elements for applications and query capabilities to support new use cases. Modules can associate with domains, which are first-class objects in SemantEco. This enables SemantEco to perform integration and reasoning both within and across domains on module-provided data. The SemantEco framework has been used to construct a web portal for environmental and ecological data. The portal includes water and air quality data from the U.S. Geological Survey (USGS) and Environmental Protection Agency (EPA) and species observation counts for birds and fish from the Avian Knowledge Network and the Santa Barbara Long Term Ecological Research, respectively. We provide regulation ontologies using OWL2 datatype facets to detect out-of-range measurements for environmental standards set by the EPA, i.a. Users adjust queries using module-defined facets and a map presents the resulting measurement sites. Custom icons identify sites that violate regulations, making them easy to locate. Selecting a site gives the option of charting spatially proximate data from different domains over time. Our portal currently provides 1.6 billion triples of scientific data in RDF. We segment data by ZIP code and reasoning over 2157 measurements with our EPA regulation ontology that contains 131 regulations takes 2.5 seconds on a 2.4 GHz Intel Core 2 Quad with 8 GB of RAM. SemantEco's modular design and reasoning capabilities make it an exemplar for building multidisciplinary data integration tools that provide data access to scientists and the general population alike. Its provenance tracking provides accountability and its reasoning services can assist users in interpreting data. Future work includes support for geographical queries using the Open Geospatial Consortium's GeoSPARQL standard.

Performance Comparison of HPF and MPI Based NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Saini, Subhash

1997-01-01

Compilers supporting High Performance Form (HPF) features first appeared in late 1994 and early 1995 from Applied Parallel Research (APR), Digital Equipment Corporation, and The Portland Group (PGI). IBM introduced an HPF compiler for the IBM RS/6000 SP2 in April of 1996. Over the past two years, these implementations have shown steady improvement in terms of both features and performance. The performance of various hardware/ programming model (HPF and MPI) combinations will be compared, based on latest NAS Parallel Benchmark results, thus providing a cross-machine and cross-model comparison. Specifically, HPF based NPB results will be compared with MPI based NPB results to provide perspective on performance currently obtainable using HPF versus MPI or versus hand-tuned implementations such as those supplied by the hardware vendors. In addition, we would also present NPB, (Version 1.0) performance results for the following systems: DEC Alpha Server 8400 5/440, Fujitsu CAPP Series (VX, VPP300, and VPP700), HP/Convex Exemplar SPP2000, IBM RS/6000 SP P2SC node (120 MHz), NEC SX-4/32, SGI/CRAY T3E, and SGI Origin2000. We would also present sustained performance per dollar for Class B LU, SP and BT benchmarks.

A Programming Model Performance Study Using the NAS Parallel Benchmarks

DOE PAGES

Shan, Hongzhang; Blagojević, Filip; Min, Seung-Jai; ...

2010-01-01

Harnessing the power of multicore platforms is challenging due to the additional levels of parallelism present. In this paper we use the NAS Parallel Benchmarks to study three programming models, MPI, OpenMP and PGAS to understand their performance and memory usage characteristics on current multicore architectures. To understand these characteristics we use the Integrated Performance Monitoring tool and other ways to measure communication versus computation time, as well as the fraction of the run time spent in OpenMP. The benchmarks are run on two different Cray XT5 systems and an Infiniband cluster. Our results show that in general the threemore » programming models exhibit very similar performance characteristics. In a few cases, OpenMP is significantly faster because it explicitly avoids communication. For these particular cases, we were able to re-write the UPC versions and achieve equal performance to OpenMP. Using OpenMP was also the most advantageous in terms of memory usage. Also we compare performance differences between the two Cray systems, which have quad-core and hex-core processors. We show that at scale the performance is almost always slower on the hex-core system because of increased contention for network resources.« less

Benchmarking of trauma care worldwide: the potential value of an International Trauma Data Bank (ITDB).

PubMed

Haider, Adil H; Hashmi, Zain G; Gupta, Sonia; Zafar, Syed Nabeel; David, Jean-Stephane; Efron, David T; Stevens, Kent A; Zafar, Hasnain; Schneider, Eric B; Voiglio, Eric; Coimbra, Raul; Haut, Elliott R

2014-08-01

National trauma registries have helped improve patient outcomes across the world. Recently, the idea of an International Trauma Data Bank (ITDB) has been suggested to establish global comparative assessments of trauma outcomes. The objective of this study was to determine whether global trauma data could be combined to perform international outcomes benchmarking. We used observed/expected (O/E) mortality ratios to compare two trauma centers [European high-income country (HIC) and Asian lower-middle income country (LMIC)] with centers in the North American National Trauma Data Bank (NTDB). Patients (≥16 years) with blunt/penetrating injuries were included. Multivariable logistic regression, adjusting for known predictors of trauma mortality, was performed. Estimates were used to predict the expected deaths at each center and to calculate O/E mortality ratios for benchmarking. A total of 375,433 patients from 301 centers were included from the NTDB (2002-2010). The LMIC trauma center had 806 patients (2002-2010), whereas the HIC reported 1,003 patients (2002-2004). The most important known predictors of trauma mortality were adequately recorded in all datasets. Mortality benchmarking revealed that the HIC center performed similarly to the NTDB centers [O/E = 1.11 (95% confidence interval (CI) 0.92-1.35)], whereas the LMIC center showed significantly worse survival [O/E = 1.52 (1.23-1.88)]. Subset analyses of patients with blunt or penetrating injury showed similar results. Using only a few key covariates, aggregated global trauma data can be used to adequately perform international trauma center benchmarking. The creation of the ITDB is feasible and recommended as it may be a pivotal step towards improving global trauma outcomes.

The Royal Australian and New Zealand College of Radiologists (RANZCR) relative value unit workload model, its limitations and the evolution to a safety, quality and performance framework.

PubMed

Pitman, A; Jones, D N; Stuart, D; Lloydhope, K; Mallitt, K; O'Rourke, P

2009-10-01

The study reports on the evolution of the Australian radiologist relative value unit (RVU) model of measuring radiologist reporting workloads in teaching hospital departments, and aims to outline a way forward for the development of a broad national safety, quality and performance framework that enables value mapping, measurement and benchmarking. The Radiology International Benchmarking Project of Queensland Health provided a suitable high-level national forum where the existing Pitman-Jones RVU model was applied to contemporaneous data, and its shortcomings and potential avenues for future development were analysed. Application of the Pitman-Jones model to Queensland data and also a Victorian benchmark showed that the original recommendation of 40,000 crude RVU per full-time equivalent consultant radiologist (97-98 baseline level) has risen only moderately, to now lie around 45,000 crude RVU/full-time equivalent. Notwithstanding this, the model has a number of weaknesses and is becoming outdated, as it cannot capture newer time-consuming examinations particularly in CT. A significant re-evaluation of the value of medical imaging is required, and is now occurring. We must rethink how we measure, benchmark, display and continually improve medical imaging safety, quality and performance, throughout the imaging care cycle and beyond. It will be necessary to ensure alignment with patient needs, as well as clinical and organisational objectives. Clear recommendations for the development of an updated national reporting workload RVU system are available, and an opportunity now exists for developing a much broader national model. A more sophisticated and balanced multidimensional safety, quality and performance framework that enables measurement and benchmarking of all important elements of health-care service is needed.

Benchmarking the ATLAS software through the Kit Validation engine

NASA Astrophysics Data System (ADS)

De Salvo, Alessandro; Brasolin, Franco

2010-04-01

The measurement of the experiment software performance is a very important metric in order to choose the most effective resources to be used and to discover the bottlenecks of the code implementation. In this work we present the benchmark techniques used to measure the ATLAS software performance through the ATLAS offline testing engine Kit Validation and the online portal Global Kit Validation. The performance measurements, the data collection, the online analysis and display of the results will be presented. The results of the measurement on different platforms and architectures will be shown, giving a full report on the CPU power and memory consumption of the Monte Carlo generation, simulation, digitization and reconstruction of the most CPU-intensive channels. The impact of the multi-core computing on the ATLAS software performance will also be presented, comparing the behavior of different architectures when increasing the number of concurrent processes. The benchmark techniques described in this paper have been used in the HEPiX group since the beginning of 2008 to help defining the performance metrics for the High Energy Physics applications, based on the real experiment software.

On the predictability of land surface fluxes from meteorological variables

NASA Astrophysics Data System (ADS)

Haughton, Ned; Abramowitz, Gab; Pitman, Andy J.

2018-01-01

Previous research has shown that land surface models (LSMs) are performing poorly when compared with relatively simple empirical models over a wide range of metrics and environments. Atmospheric driving data appear to provide information about land surface fluxes that LSMs are not fully utilising. Here, we further quantify the information available in the meteorological forcing data that are used by LSMs for predicting land surface fluxes, by interrogating FLUXNET data, and extending the benchmarking methodology used in previous experiments. We show that substantial performance improvement is possible for empirical models using meteorological data alone, with no explicit vegetation or soil properties, thus setting lower bounds on a priori expectations on LSM performance. The process also identifies key meteorological variables that provide predictive power. We provide an ensemble of empirical benchmarks that are simple to reproduce and provide a range of behaviours and predictive performance, acting as a baseline benchmark set for future studies. We reanalyse previously published LSM simulations and show that there is more diversity between LSMs than previously indicated, although it remains unclear why LSMs are broadly performing so much worse than simple empirical models.

Benchmark of four popular virtual screening programs: construction of the active/decoy dataset remains a major determinant of measured performance.

PubMed

Chaput, Ludovic; Martinez-Sanz, Juan; Saettel, Nicolas; Mouawad, Liliane

2016-01-01

In a structure-based virtual screening, the choice of the docking program is essential for the success of a hit identification. Benchmarks are meant to help in guiding this choice, especially when undertaken on a large variety of protein targets. Here, the performance of four popular virtual screening programs, Gold, Glide, Surflex and FlexX, is compared using the Directory of Useful Decoys-Enhanced database (DUD-E), which includes 102 targets with an average of 224 ligands per target and 50 decoys per ligand, generated to avoid biases in the benchmarking. Then, a relationship between these program performances and the properties of the targets or the small molecules was investigated. The comparison was based on two metrics, with three different parameters each. The BEDROC scores with α = 80.5, indicated that, on the overall database, Glide succeeded (score > 0.5) for 30 targets, Gold for 27, FlexX for 14 and Surflex for 11. The performance did not depend on the hydrophobicity nor the openness of the protein cavities, neither on the families to which the proteins belong. However, despite the care in the construction of the DUD-E database, the small differences that remain between the actives and the decoys likely explain the successes of Gold, Surflex and FlexX. Moreover, the similarity between the actives of a target and its crystal structure ligand seems to be at the basis of the good performance of Glide. When all targets with significant biases are removed from the benchmarking, a subset of 47 targets remains, for which Glide succeeded for only 5 targets, Gold for 4 and FlexX and Surflex for 2. The performance dramatic drop of all four programs when the biases are removed shows that we should beware of virtual screening benchmarks, because good performances may be due to wrong reasons. Therefore, benchmarking would hardly provide guidelines for virtual screening experiments, despite the tendency that is maintained, i.e., Glide and Gold display better performance than FlexX and Surflex. We recommend to always use several programs and combine their results. Graphical AbstractSummary of the results obtained by virtual screening with the four programs, Glide, Gold, Surflex and FlexX, on the 102 targets of the DUD-E database. The percentage of targets with successful results, i.e., with BDEROC(α = 80.5) > 0.5, when the entire database is considered are in Blue, and when targets with biased chemical libraries are removed are in Red.

[Does implementation of benchmarking in quality circles improve the quality of care of patients with asthma and reduce drug interaction?].

PubMed

Kaufmann-Kolle, Petra; Szecsenyi, Joachim; Broge, Björn; Haefeli, Walter Emil; Schneider, Antonius

2011-01-01

The purpose of this cluster-randomised controlled trial was to evaluate the efficacy of quality circles (QCs) working either with general data-based feedback or with an open benchmark within the field of asthma care and drug-drug interactions. Twelve QCs, involving 96 general practitioners from 85 practices, were randomised. Six QCs worked with traditional anonymous feedback and six with an open benchmark. Two QC meetings supported with feedback reports were held covering the topics "drug-drug interactions" and "asthma"; in both cases discussions were guided by a trained moderator. Outcome measures included health-related quality of life and patient satisfaction with treatment, asthma severity and number of potentially inappropriate drug combinations as well as the general practitioners' satisfaction in relation to the performance of the QC. A significant improvement in the treatment of asthma was observed in both trial arms. However, there was only a slight improvement regarding inappropriate drug combinations. There were no relevant differences between the group with open benchmark (B-QC) and traditional quality circles (T-QC). The physicians' satisfaction with the QC performance was significantly higher in the T-QCs. General practitioners seem to take a critical perspective about open benchmarking in quality circles. Caution should be used when implementing benchmarking in a quality circle as it did not improve healthcare when compared to the traditional procedure with anonymised comparisons. Copyright © 2011. Published by Elsevier GmbH.

Energy benchmarking of commercial buildings: a low-cost pathway toward urban sustainability

NASA Astrophysics Data System (ADS)

Cox, Matt; Brown, Marilyn A.; Sun, Xiaojing

2013-09-01

US cities are beginning to experiment with a regulatory approach to address information failures in the real estate market by mandating the energy benchmarking of commercial buildings. Understanding how a commercial building uses energy has many benefits; for example, it helps building owners and tenants identify poor-performing buildings and subsystems and it enables high-performing buildings to achieve greater occupancy rates, rents, and property values. This paper estimates the possible impacts of a national energy benchmarking mandate through analysis chiefly utilizing the Georgia Tech version of the National Energy Modeling System (GT-NEMS). Correcting input discount rates results in a 4.0% reduction in projected energy consumption for seven major classes of equipment relative to the reference case forecast in 2020, rising to 8.7% in 2035. Thus, the official US energy forecasts appear to overestimate future energy consumption by underestimating investments in energy-efficient equipment. Further discount rate reductions spurred by benchmarking policies yield another 1.3-1.4% in energy savings in 2020, increasing to 2.2-2.4% in 2035. Benchmarking would increase the purchase of energy-efficient equipment, reducing energy bills, CO2 emissions, and conventional air pollution. Achieving comparable CO2 savings would require more than tripling existing US solar capacity. Our analysis suggests that nearly 90% of the energy saved by a national benchmarking policy would benefit metropolitan areas, and the policy’s benefits would outweigh its costs, both to the private sector and society broadly.

Comparing Hospital Processes and Outcomes in California Medicare Beneficiaries: Simulation Prompts Reconsideration.

PubMed

Escobar, Gabriel J; Baker, Jennifer M; Turk, Benjamin J; Draper, David; Liu, Vincent; Kipnis, Patricia

2017-01-01

This article is not a traditional research report. It describes how conducting a specific set of benchmarking analyses led us to broader reflections on hospital benchmarking. We reexamined an issue that has received far less attention from researchers than in the past: How variations in the hospital admission threshold might affect hospital rankings. Considering this threshold made us reconsider what benchmarking is and what future benchmarking studies might be like. Although we recognize that some of our assertions are speculative, they are based on our reading of the literature and previous and ongoing data analyses being conducted in our research unit. We describe the benchmarking analyses that led to these reflections. The Centers for Medicare and Medicaid Services' Hospital Compare Web site includes data on fee-for-service Medicare beneficiaries but does not control for severity of illness, which requires physiologic data now available in most electronic medical records.To address this limitation, we compared hospital processes and outcomes among Kaiser Permanente Northern California's (KPNC) Medicare Advantage beneficiaries and non-KPNC California Medicare beneficiaries between 2009 and 2010. We assigned a simulated severity of illness measure to each record and explored the effect of having the additional information on outcomes. We found that if the admission severity of illness in non-KPNC hospitals increased, KPNC hospitals' mortality performance would appear worse; conversely, if admission severity at non-KPNC hospitals' decreased, KPNC hospitals' performance would appear better. Future hospital benchmarking should consider the impact of variation in admission thresholds.

Benchmarking initiatives in the water industry.

PubMed

Parena, R; Smeets, E

2001-01-01

Customer satisfaction and service care are every day pushing professionals in the water industry to seek to improve their performance, lowering costs and increasing the provided service level. Process Benchmarking is generally recognised as a systematic mechanism of comparing one's own utility with other utilities or businesses with the intent of self-improvement by adopting structures or methods used elsewhere. The IWA Task Force on Benchmarking, operating inside the Statistics and Economics Committee, has been committed to developing a general accepted concept of Process Benchmarking to support water decision-makers in addressing issues of efficiency. In a first step the Task Force disseminated among the Committee members a questionnaire focused on providing suggestions about the kind, the evolution degree and the main concepts of Benchmarking adopted in the represented Countries. A comparison among the guidelines adopted in The Netherlands and Scandinavia has recently challenged the Task Force in drafting a methodology for a worldwide process benchmarking in water industry. The paper provides a framework of the most interesting benchmarking experiences in the water sector and describes in detail both the final results of the survey and the methodology focused on identification of possible improvement areas.

Conceptual Models, Choices, and Benchmarks for Building Quality Work Cultures.

ERIC Educational Resources Information Center

Acker-Hocevar, Michele

1996-01-01

The two models in Florida's Educational Quality Benchmark System represent a new way of thinking about developing schools' work culture. The Quality Performance System Model identifies nine dimensions of work within a quality system. The Change Process Model provides a theoretical framework for changing existing beliefs, attitudes, and behaviors…

Children's Services Statistical Neighbour Benchmarking Tool. Practitioner User Guide

ERIC Educational Resources Information Center

National Foundation for Educational Research, 2007

2007-01-01

Statistical neighbour models provide one method for benchmarking progress. For each local authority (LA), these models designate a number of other LAs deemed to have similar characteristics. These designated LAs are known as statistical neighbours. Any LA may compare its performance (as measured by various indicators) against its statistical…

Benchmarks Momentum on Increase

ERIC Educational Resources Information Center

McNeil, Michele

2008-01-01

No longer content with the patchwork quilt of assessments used to measure states' K-12 performance, top policy groups are pushing states toward international benchmarking as a way to better prepare students for a competitive global economy. The National Governors Association, the Council of Chief State School Officers, and the standards-advocacy…

Toward benchmarking in catalysis science: Best practices, challenges, and opportunities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bligaard, Thomas; Bullock, R. Morris; Campbell, Charles T.

Benchmarking is a community-based and (preferably) community-driven activity involving consensus-based decisions on how to make reproducible, fair, and relevant assessments. In catalysis science, important catalyst performance metrics include activity, selectivity, and the deactivation profile, which enable comparisons between new and standard catalysts. Benchmarking also requires careful documentation, archiving, and sharing of methods and measurements, to ensure that the full value of research data can be realized. Beyond these goals, benchmarking presents unique opportunities to advance and accelerate understanding of complex reaction systems by combining and comparing experimental information from multiple, in situ and operando techniques with theoretical insights derived frommore » calculations characterizing model systems. This Perspective describes the origins and uses of benchmarking and its applications in computational catalysis, heterogeneous catalysis, molecular catalysis, and electrocatalysis. As a result, it also discusses opportunities and challenges for future developments in these fields.« less

Toward benchmarking in catalysis science: Best practices, challenges, and opportunities

DOE PAGES

Bligaard, Thomas; Bullock, R. Morris; Campbell, Charles T.; ...

2016-03-07

Benchmarking is a community-based and (preferably) community-driven activity involving consensus-based decisions on how to make reproducible, fair, and relevant assessments. In catalysis science, important catalyst performance metrics include activity, selectivity, and the deactivation profile, which enable comparisons between new and standard catalysts. Benchmarking also requires careful documentation, archiving, and sharing of methods and measurements, to ensure that the full value of research data can be realized. Beyond these goals, benchmarking presents unique opportunities to advance and accelerate understanding of complex reaction systems by combining and comparing experimental information from multiple, in situ and operando techniques with theoretical insights derived frommore » calculations characterizing model systems. This Perspective describes the origins and uses of benchmarking and its applications in computational catalysis, heterogeneous catalysis, molecular catalysis, and electrocatalysis. As a result, it also discusses opportunities and challenges for future developments in these fields.« less

Phase field benchmark problems for dendritic growth and linear elasticity

DOE PAGES

Jokisaari, Andrea M.; Voorhees, P. W.; Guyer, Jonathan E.; ...

2018-03-26

We present the second set of benchmark problems for phase field models that are being jointly developed by the Center for Hierarchical Materials Design (CHiMaD) and the National Institute of Standards and Technology (NIST) along with input from other members in the phase field community. As the integrated computational materials engineering (ICME) approach to materials design has gained traction, there is an increasing need for quantitative phase field results. New algorithms and numerical implementations increase computational capabilities, necessitating standard problems to evaluate their impact on simulated microstructure evolution as well as their computational performance. We propose one benchmark problem formore » solidifiication and dendritic growth in a single-component system, and one problem for linear elasticity via the shape evolution of an elastically constrained precipitate. We demonstrate the utility and sensitivity of the benchmark problems by comparing the results of 1) dendritic growth simulations performed with different time integrators and 2) elastically constrained precipitate simulations with different precipitate sizes, initial conditions, and elastic moduli. As a result, these numerical benchmark problems will provide a consistent basis for evaluating different algorithms, both existing and those to be developed in the future, for accuracy and computational efficiency when applied to simulate physics often incorporated in phase field models.« less

Phase field benchmark problems for dendritic growth and linear elasticity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jokisaari, Andrea M.; Voorhees, P. W.; Guyer, Jonathan E.

We present the second set of benchmark problems for phase field models that are being jointly developed by the Center for Hierarchical Materials Design (CHiMaD) and the National Institute of Standards and Technology (NIST) along with input from other members in the phase field community. As the integrated computational materials engineering (ICME) approach to materials design has gained traction, there is an increasing need for quantitative phase field results. New algorithms and numerical implementations increase computational capabilities, necessitating standard problems to evaluate their impact on simulated microstructure evolution as well as their computational performance. We propose one benchmark problem formore » solidifiication and dendritic growth in a single-component system, and one problem for linear elasticity via the shape evolution of an elastically constrained precipitate. We demonstrate the utility and sensitivity of the benchmark problems by comparing the results of 1) dendritic growth simulations performed with different time integrators and 2) elastically constrained precipitate simulations with different precipitate sizes, initial conditions, and elastic moduli. As a result, these numerical benchmark problems will provide a consistent basis for evaluating different algorithms, both existing and those to be developed in the future, for accuracy and computational efficiency when applied to simulate physics often incorporated in phase field models.« less

A benchmarking tool to evaluate computer tomography perfusion infarct core predictions against a DWI standard.

PubMed

Cereda, Carlo W; Christensen, Søren; Campbell, Bruce Cv; Mishra, Nishant K; Mlynash, Michael; Levi, Christopher; Straka, Matus; Wintermark, Max; Bammer, Roland; Albers, Gregory W; Parsons, Mark W; Lansberg, Maarten G

2016-10-01

Differences in research methodology have hampered the optimization of Computer Tomography Perfusion (CTP) for identification of the ischemic core. We aim to optimize CTP core identification using a novel benchmarking tool. The benchmarking tool consists of an imaging library and a statistical analysis algorithm to evaluate the performance of CTP. The tool was used to optimize and evaluate an in-house developed CTP-software algorithm. Imaging data of 103 acute stroke patients were included in the benchmarking tool. Median time from stroke onset to CT was 185 min (IQR 180-238), and the median time between completion of CT and start of MRI was 36 min (IQR 25-79). Volumetric accuracy of the CTP-ROIs was optimal at an rCBF threshold of <38%; at this threshold, the mean difference was 0.3 ml (SD 19.8 ml), the mean absolute difference was 14.3 (SD 13.7) ml, and CTP was 67% sensitive and 87% specific for identification of DWI positive tissue voxels. The benchmarking tool can play an important role in optimizing CTP software as it provides investigators with a novel method to directly compare the performance of alternative CTP software packages. © The Author(s) 2015.

OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE - A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arnis Judzis

2002-10-01

This document details the progress to date on the OPTIMIZATION OF MUD HAMMER DRILLING PERFORMANCE -- A PROGRAM TO BENCHMARK THE VIABILITY OF ADVANCED MUD HAMMER DRILLING contract for the quarter starting July 2002 through September 2002. Even though we are awaiting the optimization portion of the testing program, accomplishments include the following: (1) Smith International agreed to participate in the DOE Mud Hammer program. (2) Smith International chromed collars for upcoming benchmark tests at TerraTek, now scheduled for 4Q 2002. (3) ConocoPhillips had a field trial of the Smith fluid hammer offshore Vietnam. The hammer functioned properly, though themore » well encountered hole conditions and reaming problems. ConocoPhillips plan another field trial as a result. (4) DOE/NETL extended the contract for the fluid hammer program to allow Novatek to ''optimize'' their much delayed tool to 2003 and to allow Smith International to add ''benchmarking'' tests in light of SDS Digger Tools' current financial inability to participate. (5) ConocoPhillips joined the Industry Advisors for the mud hammer program. (6) TerraTek acknowledges Smith International, BP America, PDVSA, and ConocoPhillips for cost-sharing the Smith benchmarking tests allowing extension of the contract to complete the optimizations.« less

Toxicological Benchmarks for Screening of Potential Contaminants of Concern for Effects on Aquatic Biota on the Oak Ridge Reservation, Oak Ridge, Tennessee

DOE Office of Scientific and Technical Information (OSTI.GOV)

Suter, G.W., II

1993-01-01

One of the initial stages in ecological risk assessment of hazardous waste sites is the screening of contaminants to determine which, if any, of them are worthy of further consideration; this process is termed contaminant screening. Screening is performed by comparing concentrations in ambient media to benchmark concentrations that are either indicative of a high likelihood of significant effects (upper screening benchmarks) or of a very low likelihood of significant effects (lower screening benchmarks). Exceedance of an upper screening benchmark indicates that the chemical in question is clearly of concern and remedial actions are likely to be needed. Exceedance ofmore » a lower screening benchmark indicates that a contaminant is of concern unless other information indicates that the data are unreliable or the comparison is inappropriate. Chemicals with concentrations below the lower benchmark are not of concern if the ambient data are judged to be adequate. This report presents potential screening benchmarks for protection of aquatic life from contaminants in water. Because there is no guidance for screening benchmarks, a set of alternative benchmarks is presented herein. The alternative benchmarks are based on different conceptual approaches to estimating concentrations causing significant effects. For the upper screening benchmark, there are the acute National Ambient Water Quality Criteria (NAWQC) and the Secondary Acute Values (SAV). The SAV concentrations are values estimated with 80% confidence not to exceed the unknown acute NAWQC for those chemicals with no NAWQC. The alternative chronic benchmarks are the chronic NAWQC, the Secondary Chronic Value (SCV), the lowest chronic values for fish and daphnids, the lowest EC20 for fish and daphnids from chronic toxicity tests, the estimated EC20 for a sensitive species, and the concentration estimated to cause a 20% reduction in the recruit abundance of largemouth bass. It is recommended that ambient chemical concentrations be compared to all of these benchmarks. If NAWQC are exceeded, the chemicals must be contaminants of concern because the NAWQC are applicable or relevant and appropriate requirements (ARARs). If NAWQC are not exceeded, but other benchmarks are, contaminants should be selected on the basis of the number of benchmarks exceeded and the conservatism of the particular benchmark values, as discussed in the text. To the extent that toxicity data are available, this report presents the alternative benchmarks for chemicals that have been detected on the Oak Ridge Reservation. It also presents the data used to calculate the benchmarks and the sources of the data. It compares the benchmarks and discusses their relative conservatism and utility. This report supersedes a prior aquatic benchmarks report (Suter and Mabrey 1994). It adds two new types of benchmarks. It also updates the benchmark values where appropriate, adds some new benchmark values, replaces secondary sources with primary sources, and provides more complete documentation of the sources and derivation of all values.« less

Benchmarking road safety performance: Identifying a meaningful reference (best-in-class).

PubMed

Chen, Faan; Wu, Jiaorong; Chen, Xiaohong; Wang, Jianjun; Wang, Di

2016-01-01

For road safety improvement, comparing and benchmarking performance are widely advocated as the emerging and preferred approaches. However, there is currently no universally agreed upon approach for the process of road safety benchmarking, and performing the practice successfully is by no means easy. This is especially true for the two core activities of which: (1) developing a set of road safety performance indicators (SPIs) and combining them into a composite index; and (2) identifying a meaningful reference (best-in-class), one which has already obtained outstanding road safety practices. To this end, a scientific technique that can combine the multi-dimensional safety performance indicators (SPIs) into an overall index, and subsequently can identify the 'best-in-class' is urgently required. In this paper, the Entropy-embedded RSR (Rank-sum ratio), an innovative, scientific and systematic methodology is investigated with the aim of conducting the above two core tasks in an integrative and concise procedure, more specifically in a 'one-stop' way. Using a combination of results from other methods (e.g. the SUNflower approach) and other measures (e.g. Human Development Index) as a relevant reference, a given set of European countries are robustly ranked and grouped into several classes based on the composite Road Safety Index. Within each class the 'best-in-class' is then identified. By benchmarking road safety performance, the results serve to promote best practice, encourage the adoption of successful road safety strategies and measures and, more importantly, inspire the kind of political leadership needed to create a road transport system that maximizes safety. Copyright © 2015 Elsevier Ltd. All rights reserved.

Design and Implementation of a Web-Based Reporting and Benchmarking Center for Inpatient Glucometrics

PubMed Central

Schnipper, Jeffrey Lawrence; Messler, Jordan; Ramos, Pedro; Kulasa, Kristen; Nolan, Ann; Rogers, Kendall

2014-01-01

Background: Insulin is a top source of adverse drug events in the hospital, and glycemic control is a focus of improvement efforts across the country. Yet, the majority of hospitals have no data to gauge their performance on glycemic control, hypoglycemia rates, or hypoglycemic management. Current tools to outsource glucometrics reports are limited in availability or function. Methods: Society of Hospital Medicine (SHM) faculty designed and implemented a web-based data and reporting center that calculates glucometrics on blood glucose data files securely uploaded by users. Unit labels, care type (critical care, non–critical care), and unit type (eg, medical, surgical, mixed, pediatrics) are defined on upload allowing for robust, flexible reporting. Reports for any date range, care type, unit type, or any combination of units are available on demand for review or downloading into a variety of file formats. Four reports with supporting graphics depict glycemic control, hypoglycemia, and hypoglycemia management by patient day or patient stay. Benchmarking and performance ranking reports are generated periodically for all hospitals in the database. Results: In all, 76 hospitals have uploaded at least 12 months of data for non–critical care areas and 67 sites have uploaded critical care data. Critical care benchmarking reveals wide variability in performance. Some hospitals achieve top quartile performance in both glycemic control and hypoglycemia parameters. Conclusions: This new web-based glucometrics data and reporting tool allows hospitals to track their performance with a flexible reporting system, and provides them with external benchmarking. Tools like this help to establish standardized glucometrics and performance standards. PMID:24876426

Design and implementation of a web-based reporting and benchmarking center for inpatient glucometrics.

PubMed

Maynard, Greg; Schnipper, Jeffrey Lawrence; Messler, Jordan; Ramos, Pedro; Kulasa, Kristen; Nolan, Ann; Rogers, Kendall

2014-07-01

Insulin is a top source of adverse drug events in the hospital, and glycemic control is a focus of improvement efforts across the country. Yet, the majority of hospitals have no data to gauge their performance on glycemic control, hypoglycemia rates, or hypoglycemic management. Current tools to outsource glucometrics reports are limited in availability or function. Society of Hospital Medicine (SHM) faculty designed and implemented a web-based data and reporting center that calculates glucometrics on blood glucose data files securely uploaded by users. Unit labels, care type (critical care, non-critical care), and unit type (eg, medical, surgical, mixed, pediatrics) are defined on upload allowing for robust, flexible reporting. Reports for any date range, care type, unit type, or any combination of units are available on demand for review or downloading into a variety of file formats. Four reports with supporting graphics depict glycemic control, hypoglycemia, and hypoglycemia management by patient day or patient stay. Benchmarking and performance ranking reports are generated periodically for all hospitals in the database. In all, 76 hospitals have uploaded at least 12 months of data for non-critical care areas and 67 sites have uploaded critical care data. Critical care benchmarking reveals wide variability in performance. Some hospitals achieve top quartile performance in both glycemic control and hypoglycemia parameters. This new web-based glucometrics data and reporting tool allows hospitals to track their performance with a flexible reporting system, and provides them with external benchmarking. Tools like this help to establish standardized glucometrics and performance standards. © 2014 Diabetes Technology Society.

International benchmarking and best practice management: in search of health care and hospital excellence.

PubMed

von Eiff, Wilfried

2015-01-01

Hospitals worldwide are facing the same opportunities and threats: the demographics of an aging population; steady increases in chronic diseases and severe illnesses; and a steadily increasing demand for medical services with more intensive treatment for multi-morbid patients. Additionally, patients are becoming more demanding. They expect high quality medicine within a dignity-driven and painless healing environment. The severe financial pressures that these developments entail oblige care providers to more and more cost-containment and to apply process reengineering, as well as continuous performance improvement measures, so as to achieve future financial sustainability. At the same time, regulators are calling for improved patient outcomes. Benchmarking and best practice management are successfully proven performance improvement tools for enabling hospitals to achieve a higher level of clinical output quality, enhanced patient satisfaction, and care delivery capability, while simultaneously containing and reducing costs. This chapter aims to clarify what benchmarking is and what it is not. Furthermore, it is stated that benchmarking is a powerful managerial tool for improving decision-making processes that can contribute to the above-mentioned improvement measures in health care delivery. The benchmarking approach described in this chapter is oriented toward the philosophy of an input-output model and is explained based on practical international examples from different industries in various countries. Benchmarking is not a project with a defined start and end point, but a continuous initiative of comparing key performance indicators, process structures, and best practices from best-in-class companies inside and outside industry. Benchmarking is an ongoing process of measuring and searching for best-in-class performance: Measure yourself with yourself over time against key performance indicators. Measure yourself against others. Identify best practices. Equal or exceed this best practice in your institution. Focus on simple and effective ways to implement solutions. Comparing only figures, such as average length of stay, costs of procedures, infection rates, or out-of-stock rates, can lead easily to wrong conclusions and decision making with often-disastrous consequences. Just looking at figures and ratios is not the basis for detecting potential excellence. It is necessary to look beyond the numbers to understand how processes work and contribute to best-in-class results. Best practices from even quite different industries can enable hospitals to leapfrog results in patient orientation, clinical excellence, and cost-effectiveness. Despite common benchmarking approaches, it is pointed out that a comparison without "looking behind the figures" (what it means to be familiar with the process structure, process dynamic and drivers, process institutions/rules and process-related incentive components) will be extremely limited referring to reliability and quality of findings. In order to demonstrate transferability of benchmarking results between different industries practical examples from health care, automotive, and hotel service have been selected. Additionally, it is depicted that international comparisons between hospitals providing medical services in different health care systems do have a great potential for achieving leapfrog results in medical quality, organization of service provision, effective work structures, purchasing and logistics processes, or management, etc.

Object-Oriented Implementation of the NAS Parallel Benchmarks using Charm++

NASA Technical Reports Server (NTRS)

Krishnan, Sanjeev; Bhandarkar, Milind; Kale, Laxmikant V.

1996-01-01

This report describes experiences with implementing the NAS Computational Fluid Dynamics benchmarks using a parallel object-oriented language, Charm++. Our main objective in implementing the NAS CFD kernel benchmarks was to develop a code that could be used to easily experiment with different domain decomposition strategies and dynamic load balancing. We also wished to leverage the object-orientation provided by the Charm++ parallel object-oriented language, to develop reusable abstractions that would simplify the process of developing parallel applications. We first describe the Charm++ parallel programming model and the parallel object array abstraction, then go into detail about each of the Scalar Pentadiagonal (SP) and Lower/Upper Triangular (LU) benchmarks, along with performance results. Finally we conclude with an evaluation of the methodology used.

Technical Report: Benchmarking for Quasispecies Abundance Inference with Confidence Intervals from Metagenomic Sequence Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

McLoughlin, K.

2016-01-22

The software application “MetaQuant” was developed by our group at Lawrence Livermore National Laboratory (LLNL). It is designed to profile microbial populations in a sample using data from whole-genome shotgun (WGS) metagenomic DNA sequencing. Several other metagenomic profiling applications have been described in the literature. We ran a series of benchmark tests to compare the performance of MetaQuant against that of a few existing profiling tools, using real and simulated sequence datasets. This report describes our benchmarking procedure and results.

[Do you mean benchmarking?].

PubMed

Bonnet, F; Solignac, S; Marty, J

2008-03-01

The purpose of benchmarking is to settle improvement processes by comparing the activities to quality standards. The proposed methodology is illustrated by benchmark business cases performed inside medical plants on some items like nosocomial diseases or organization of surgery facilities. Moreover, the authors have built a specific graphic tool, enhanced with balance score numbers and mappings, so that the comparison between different anesthesia-reanimation services, which are willing to start an improvement program, is easy and relevant. This ready-made application is even more accurate as far as detailed tariffs of activities are implemented.

EVA Health and Human Performance Benchmarking Study

NASA Technical Reports Server (NTRS)

Abercromby, A. F.; Norcross, J.; Jarvis, S. L.

2016-01-01

Multiple HRP Risks and Gaps require detailed characterization of human health and performance during exploration extravehicular activity (EVA) tasks; however, a rigorous and comprehensive methodology for characterizing and comparing the health and human performance implications of current and future EVA spacesuit designs does not exist. This study will identify and implement functional tasks and metrics, both objective and subjective, that are relevant to health and human performance, such as metabolic expenditure, suit fit, discomfort, suited postural stability, cognitive performance, and potentially biochemical responses for humans working inside different EVA suits doing functional tasks under the appropriate simulated reduced gravity environments. This study will provide health and human performance benchmark data for humans working in current EVA suits (EMU, Mark III, and Z2) as well as shirtsleeves using a standard set of tasks and metrics with quantified reliability. Results and methodologies developed during this test will provide benchmark data against which future EVA suits, and different suit configurations (eg, varied pressure, mass, CG) may be reliably compared in subsequent tests. Results will also inform fitness for duty standards as well as design requirements and operations concepts for future EVA suits and other exploration systems.

Surflex-Dock: Docking benchmarks and real-world application

NASA Astrophysics Data System (ADS)

Spitzer, Russell; Jain, Ajay N.

2012-06-01

Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is reported on the DUD set of 40 protein targets. In both cases, prepared structures of targets and ligands were provided by symposium organizers. The re-prepared data sets yielded results not significantly different than previous reports of Surflex-Dock on the two benchmarks. Minor changes to protein coordinates resulting from complex pre-optimization had large effects on observed performance, highlighting the limitations of cognate ligand re-docking for pose prediction assessment. Docking protocols developed for cross-docking, which address protein flexibility and produce discrete families of predicted poses, produced substantially better performance for pose prediction. Performance on virtual screening performance was shown to benefit by employing and combining multiple screening methods: docking, 2D molecular similarity, and 3D molecular similarity. In addition, use of multiple protein conformations significantly improved screening enrichment.

How does audit and feedback influence intentions of health professionals to improve practice? A laboratory experiment and field study in cardiac rehabilitation.

PubMed

Gude, Wouter T; van Engen-Verheul, Mariëtte M; van der Veer, Sabine N; de Keizer, Nicolette F; Peek, Niels

2017-04-01

To identify factors that influence the intentions of health professionals to improve their practice when confronted with clinical performance feedback, which is an essential first step in the audit and feedback mechanism. We conducted a theory-driven laboratory experiment with 41 individual professionals, and a field study in 18 centres in the context of a cluster-randomised trial of electronic audit and feedback in cardiac rehabilitation. Feedback reports were provided through a web-based application, and included performance scores and benchmark comparisons (high, intermediate or low performance) for a set of process and outcome indicators. From each report participants selected indicators for improvement into their action plan. Our unit of observation was an indicator presented in a feedback report (selected yes/no); we considered selecting an indicator to reflect an intention to improve. We analysed 767 observations in the laboratory experiment and 614 in the field study, respectively. Each 10% decrease in performance score increased the probability of an indicator being selected by 54% (OR, 1.54; 95% CI 1.29% to 1.83%) in the laboratory experiment, and 25% (OR, 1.25; 95% CI 1.13% to 1.39%) in the field study. Also, performance being benchmarked as low and intermediate increased this probability in laboratory settings. Still, participants ignored the benchmarks in 34% (laboratory experiment) and 48% (field study) of their selections. When confronted with clinical performance feedback, performance scores and benchmark comparisons influenced health professionals' intentions to improve practice. However, there was substantial variation in these intentions, because professionals disagreed with benchmarks, deemed improvement unfeasible or did not consider the indicator an essential aspect of care quality. These phenomena impede intentions to improve practice, and are thus likely to dilute the effects of audit and feedback interventions. NTR3251, pre-results. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Benchmarking of protein descriptor sets in proteochemometric modeling (part 2): modeling performance of 13 amino acid descriptor sets

PubMed Central

2013-01-01

Background While a large body of work exists on comparing and benchmarking descriptors of molecular structures, a similar comparison of protein descriptor sets is lacking. Hence, in the current work a total of 13 amino acid descriptor sets have been benchmarked with respect to their ability of establishing bioactivity models. The descriptor sets included in the study are Z-scales (3 variants), VHSE, T-scales, ST-scales, MS-WHIM, FASGAI, BLOSUM, a novel protein descriptor set (termed ProtFP (4 variants)), and in addition we created and benchmarked three pairs of descriptor combinations. Prediction performance was evaluated in seven structure-activity benchmarks which comprise Angiotensin Converting Enzyme (ACE) dipeptidic inhibitor data, and three proteochemometric data sets, namely (1) GPCR ligands modeled against a GPCR panel, (2) enzyme inhibitors (NNRTIs) with associated bioactivities against a set of HIV enzyme mutants, and (3) enzyme inhibitors (PIs) with associated bioactivities on a large set of HIV enzyme mutants. Results The amino acid descriptor sets compared here show similar performance (<0.1 log units RMSE difference and <0.1 difference in MCC), while errors for individual proteins were in some cases found to be larger than those resulting from descriptor set differences ( > 0.3 log units RMSE difference and >0.7 difference in MCC). Combining different descriptor sets generally leads to better modeling performance than utilizing individual sets. The best performers were Z-scales (3) combined with ProtFP (Feature), or Z-Scales (3) combined with an average Z-Scale value for each target, while ProtFP (PCA8), ST-Scales, and ProtFP (Feature) rank last. Conclusions While amino acid descriptor sets capture different aspects of amino acids their ability to be used for bioactivity modeling is still – on average – surprisingly similar. Still, combining sets describing complementary information consistently leads to small but consistent improvement in modeling performance (average MCC 0.01 better, average RMSE 0.01 log units lower). Finally, performance differences exist between the targets compared thereby underlining that choosing an appropriate descriptor set is of fundamental for bioactivity modeling, both from the ligand- as well as the protein side. PMID:24059743

Inclusion of Highest Glasgow Coma Scale Motor Component Score in Mortality Risk Adjustment for Benchmarking of Trauma Center Performance.

PubMed

Gomez, David; Byrne, James P; Alali, Aziz S; Xiong, Wei; Hoeft, Chris; Neal, Melanie; Subacius, Harris; Nathens, Avery B

2017-12-01

The Glasgow Coma Scale (GCS) is the most widely used measure of traumatic brain injury (TBI) severity. Currently, the arrival GCS motor component (mGCS) score is used in risk-adjustment models for external benchmarking of mortality. However, there is evidence that the highest mGCS score in the first 24 hours after injury might be a better predictor of death. Our objective was to evaluate the impact of including the highest mGCS score on the performance of risk-adjustment models and subsequent external benchmarking results. Data were derived from the Trauma Quality Improvement Program analytic dataset (January 2014 through March 2015) and were limited to the severe TBI cohort (16 years or older, isolated head injury, GCS ≤8). Risk-adjustment models were created that varied in the mGCS covariates only (initial score, highest score, or both initial and highest mGCS scores). Model performance and fit, as well as external benchmarking results, were compared. There were 6,553 patients with severe TBI across 231 trauma centers included. Initial and highest mGCS scores were different in 47% of patients (n = 3,097). Model performance and fit improved when both initial and highest mGCS scores were included, as evidenced by improved C-statistic, Akaike Information Criterion, and adjusted R-squared values. Three-quarters of centers changed their adjusted odds ratio decile, 2.6% of centers changed outlier status, and 45% of centers exhibited a ≥0.5-SD change in the odds ratio of death after including highest mGCS score in the model. This study supports the concept that additional clinical information has the potential to not only improve the performance of current risk-adjustment models, but can also have a meaningful impact on external benchmarking strategies. Highest mGCS score is a good potential candidate for inclusion in additional models. Copyright © 2017 American College of Surgeons. Published by Elsevier Inc. All rights reserved.

A Prototype Tool to Enable Farmers to Measure and Improve the Welfare Performance of the Farm Animal Enterprise: The Unified Field Index

PubMed Central

Colditz, Ian G.; Ferguson, Drewe M.; Collins, Teresa; Matthews, Lindsay; Hemsworth, Paul H.

2014-01-01

Simple Summary Benchmarking is a tool widely used in agricultural industries that harnesses the experience of farmers to generate knowledge of practices that lead to better on-farm productivity and performance. We propose, by analogy with production performance, a method for measuring the animal welfare performance of an enterprise and describe a tool for farmers to monitor and improve the animal welfare performance of their business. A general framework is outlined for assessing and monitoring risks to animal welfare based on measures of animals, the environment they are kept in and how they are managed. The tool would enable farmers to continually improve animal welfare. Abstract Schemes for the assessment of farm animal welfare and assurance of welfare standards have proliferated in recent years. An acknowledged short-coming has been the lack of impact of these schemes on the welfare standards achieved on farm due in part to sociological factors concerning their implementation. Here we propose the concept of welfare performance based on a broad set of performance attributes of an enterprise and describe a tool based on risk assessment and benchmarking methods for measuring and managing welfare performance. The tool termed the Unified Field Index is presented in a general form comprising three modules addressing animal, resource, and management factors. Domains within these modules accommodate the principle conceptual perspectives for welfare assessment: biological functioning; emotional states; and naturalness. Pan-enterprise analysis in any livestock sector could be used to benchmark welfare performance of individual enterprises and also provide statistics of welfare performance for the livestock sector. An advantage of this concept of welfare performance is its use of continuous scales of measurement rather than traditional pass/fail measures. Through the feedback provided via benchmarking, the tool should help farmers better engage in on-going improvement of farm practices that affect animal welfare. PMID:26480317

Performance Comparison of NAMI DANCE and FLOW-3D® Models in Tsunami Propagation, Inundation and Currents using NTHMP Benchmark Problems

NASA Astrophysics Data System (ADS)

Velioglu Sogut, Deniz; Yalciner, Ahmet Cevdet

2018-06-01

Field observations provide valuable data regarding nearshore tsunami impact, yet only in inundation areas where tsunami waves have already flooded. Therefore, tsunami modeling is essential to understand tsunami behavior and prepare for tsunami inundation. It is necessary that all numerical models used in tsunami emergency planning be subject to benchmark tests for validation and verification. This study focuses on two numerical codes, NAMI DANCE and FLOW-3D®, for validation and performance comparison. NAMI DANCE is an in-house tsunami numerical model developed by the Ocean Engineering Research Center of Middle East Technical University, Turkey and Laboratory of Special Research Bureau for Automation of Marine Research, Russia. FLOW-3D® is a general purpose computational fluid dynamics software, which was developed by scientists who pioneered in the design of the Volume-of-Fluid technique. The codes are validated and their performances are compared via analytical, experimental and field benchmark problems, which are documented in the ``Proceedings and Results of the 2011 National Tsunami Hazard Mitigation Program (NTHMP) Model Benchmarking Workshop'' and the ``Proceedings and Results of the NTHMP 2015 Tsunami Current Modeling Workshop". The variations between the numerical solutions of these two models are evaluated through statistical error analysis.

Benchmarking a Soil Moisture Data Assimilation System for Agricultural Drought Monitoring

NASA Technical Reports Server (NTRS)

Hun, Eunjin; Crow, Wade T.; Holmes, Thomas; Bolten, John

2014-01-01

Despite considerable interest in the application of land surface data assimilation systems (LDAS) for agricultural drought applications, relatively little is known about the large-scale performance of such systems and, thus, the optimal methodological approach for implementing them. To address this need, this paper evaluates an LDAS for agricultural drought monitoring by benchmarking individual components of the system (i.e., a satellite soil moisture retrieval algorithm, a soil water balance model and a sequential data assimilation filter) against a series of linear models which perform the same function (i.e., have the same basic inputoutput structure) as the full system component. Benchmarking is based on the calculation of the lagged rank cross-correlation between the normalized difference vegetation index (NDVI) and soil moisture estimates acquired for various components of the system. Lagged soil moistureNDVI correlations obtained using individual LDAS components versus their linear analogs reveal the degree to which non-linearities andor complexities contained within each component actually contribute to the performance of the LDAS system as a whole. Here, a particular system based on surface soil moisture retrievals from the Land Parameter Retrieval Model (LPRM), a two-layer Palmer soil water balance model and an Ensemble Kalman filter (EnKF) is benchmarked. Results suggest significant room for improvement in each component of the system.

Thermal Performance Benchmarking: Annual Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Moreno, Gilbert

2016-04-08

The goal for this project is to thoroughly characterize the performance of state-of-the-art (SOA) automotive power electronics and electric motor thermal management systems. Information obtained from these studies will be used to: Evaluate advantages and disadvantages of different thermal management strategies; establish baseline metrics for the thermal management systems; identify methods of improvement to advance the SOA; increase the publicly available information related to automotive traction-drive thermal management systems; help guide future electric drive technologies (EDT) research and development (R&D) efforts. The performance results combined with component efficiency and heat generation information obtained by Oak Ridge National Laboratory (ORNL) maymore » then be used to determine the operating temperatures for the EDT components under drive-cycle conditions. In FY15, the 2012 Nissan LEAF power electronics and electric motor thermal management systems were benchmarked. Testing of the 2014 Honda Accord Hybrid power electronics thermal management system started in FY15; however, due to time constraints it was not possible to include results for this system in this report. The focus of this project is to benchmark the thermal aspects of the systems. ORNL's benchmarking of electric and hybrid electric vehicle technology reports provide detailed descriptions of the electrical and packaging aspects of these automotive systems.« less

Benchmarking and Self-Assessment in the Wine Industry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galitsky, Christina; Radspieler, Anthony; Worrell, Ernst

2005-12-01

Not all industrial facilities have the staff or theopportunity to perform a detailed audit of their operations. The lack ofknowledge of energy efficiency opportunities provides an importantbarrier to improving efficiency. Benchmarking programs in the U.S. andabroad have shown to improve knowledge of the energy performance ofindustrial facilities and buildings and to fuel energy managementpractices. Benchmarking provides a fair way to compare the energyintensity of plants, while accounting for structural differences (e.g.,the mix of products produced, climate conditions) between differentfacilities. In California, the winemaking industry is not only one of theeconomic pillars of the economy; it is also a large energymore » consumer, witha considerable potential for energy-efficiency improvement. LawrenceBerkeley National Laboratory and Fetzer Vineyards developed the firstbenchmarking tool for the California wine industry called "BEST(Benchmarking and Energy and water Savings Tool) Winery". BEST Wineryenables a winery to compare its energy efficiency to a best practicereference winery. Besides overall performance, the tool enables the userto evaluate the impact of implementing efficiency measures. The toolfacilitates strategic planning of efficiency measures, based on theestimated impact of the measures, their costs and savings. The tool willraise awareness of current energy intensities and offer an efficient wayto evaluate the impact of future efficiency measures.« less

In-context query reformulation for failing SPARQL queries

NASA Astrophysics Data System (ADS)

Viswanathan, Amar; Michaelis, James R.; Cassidy, Taylor; de Mel, Geeth; Hendler, James

2017-05-01

Knowledge bases for decision support systems are growing increasingly complex, through continued advances in data ingest and management approaches. However, humans do not possess the cognitive capabilities to retain a bird's-eyeview of such knowledge bases, and may end up issuing unsatisfiable queries to such systems. This work focuses on the implementation of a query reformulation approach for graph-based knowledge bases, specifically designed to support the Resource Description Framework (RDF). The reformulation approach presented is instance-and schema-aware. Thus, in contrast to relaxation techniques found in the state-of-the-art, the presented approach produces in-context query reformulation.

Processor Emulator with Benchmark Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lloyd, G. Scott; Pearce, Roger; Gokhale, Maya

2015-11-13

A processor emulator and a suite of benchmark applications have been developed to assist in characterizing the performance of data-centric workloads on current and future computer architectures. Some of the applications have been collected from other open source projects. For more details on the emulator and an example of its usage, see reference [1].

Using Web-Based Peer Benchmarking to Manage the Client-Based Project

ERIC Educational Resources Information Center

Raska, David; Keller, Eileen Weisenbach; Shaw, Doris

2013-01-01

The complexities of integrating client-based projects into marketing courses provide challenges for the instructor but produce richness of context and active learning for the student. This paper explains the integration of Web-based peer benchmarking as a means of improving student performance on client-based projects within a single semester in…

Taking Aims: New CASE Study Benchmarks Advancement Investments and Returns

ERIC Educational Resources Information Center

Goldsmith, Rae

2012-01-01

Advancement professionals have always been thirsty for information that will help them understand how their programs compare with those of their peers. But in recent years the demand for benchmarking data has exploded as budgets have become leaner, leaders have become more business minded, and terms like "performance metrics and return on…

Can Human Capital Metrics Effectively Benchmark Higher Education with For-Profit Companies?

ERIC Educational Resources Information Center

Hagedorn, Kathy; Forlaw, Blair

2007-01-01

Last fall, Saint Louis University participated in St. Louis, Missouri's, first Human Capital Performance Study alongside several of the region's largest for-profit employers. The university also participated this year in the benchmarking of employee engagement factors conducted by the St. Louis Business Journal in its effort to quantify and select…

The OpenMP Implementation of NAS Parallel Benchmarks and its Performance

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry

1999-01-01

As the new ccNUMA architecture became popular in recent years, parallel programming with compiler directives on these machines has evolved to accommodate new needs. In this study, we examine the effectiveness of OpenMP directives for parallelizing the NAS Parallel Benchmarks. Implementation details will be discussed and performance will be compared with the MPI implementation. We have demonstrated that OpenMP can achieve very good results for parallelization on a shared memory system, but effective use of memory and cache is very important.

Multi-Core Processor Memory Contention Benchmark Analysis Case Study

NASA Technical Reports Server (NTRS)

Simon, Tyler; McGalliard, James

2009-01-01

Multi-core processors dominate current mainframe, server, and high performance computing (HPC) systems. This paper provides synthetic kernel and natural benchmark results from an HPC system at the NASA Goddard Space Flight Center that illustrate the performance impacts of multi-core (dual- and quad-core) vs. single core processor systems. Analysis of processor design, application source code, and synthetic and natural test results all indicate that multi-core processors can suffer from significant memory subsystem contention compared to similar single-core processors.

Accelerating progress in Artificial General Intelligence: Choosing a benchmark for natural world interaction

NASA Astrophysics Data System (ADS)

Rohrer, Brandon

2010-12-01

Measuring progress in the field of Artificial General Intelligence (AGI) can be difficult without commonly accepted methods of evaluation. An AGI benchmark would allow evaluation and comparison of the many computational intelligence algorithms that have been developed. In this paper I propose that a benchmark for natural world interaction would possess seven key characteristics: fitness, breadth, specificity, low cost, simplicity, range, and task focus. I also outline two benchmark examples that meet most of these criteria. In the first, the direction task, a human coach directs a machine to perform a novel task in an unfamiliar environment. The direction task is extremely broad, but may be idealistic. In the second, the AGI battery, AGI candidates are evaluated based on their performance on a collection of more specific tasks. The AGI battery is designed to be appropriate to the capabilities of currently existing systems. Both the direction task and the AGI battery would require further definition before implementing. The paper concludes with a description of a task that might be included in the AGI battery: the search and retrieve task.

Avoiding unintended incentives in ACO payment models.

PubMed

Douven, Rudy; McGuire, Thomas G; McWilliams, J Michael

2015-01-01

One goal of the Medicare Shared Savings Program for accountable care organizations (ACOs) is to reduce Medicare spending for ACOs' patients relative to the organizations' spending history. However, we found that current rules for setting ACO spending targets (or benchmarks) diminish ACOs' incentives to generate savings and may even encourage higher instead of lower Medicare spending. Spending in the three years before ACOs enter or renew a contract is weighted unequally in the benchmark calculation, with a high weight of 0.6 given to the year just before a new contract starts. Thus, ACOs have incentives to increase spending in that year to inflate their benchmark for future years and thereby make it easier to obtain shared savings from Medicare in the new contract period. We suggest strategies to improve incentives for ACOs, including changes to the weights used to determine benchmarks and new payment models that base an ACO's spending target not only on its own past performance but also on the performance of other ACOs or Medicare providers. Project HOPE—The People-to-People Health Foundation, Inc.

Benchmarking NNWSI flow and transport codes: COVE 1 results

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hayden, N.K.

1985-06-01

The code verification (COVE) activity of the Nevada Nuclear Waste Storage Investigations (NNWSI) Project is the first step in certification of flow and transport codes used for NNWSI performance assessments of a geologic repository for disposing of high-level radioactive wastes. The goals of the COVE activity are (1) to demonstrate and compare the numerical accuracy and sensitivity of certain codes, (2) to identify and resolve problems in running typical NNWSI performance assessment calculations, and (3) to evaluate computer requirements for running the codes. This report describes the work done for COVE 1, the first step in benchmarking some of themore » codes. Isothermal calculations for the COVE 1 benchmarking have been completed using the hydrologic flow codes SAGUARO, TRUST, and GWVIP; the radionuclide transport codes FEMTRAN and TRUMP; and the coupled flow and transport code TRACR3D. This report presents the results of three cases of the benchmarking problem solved for COVE 1, a comparison of the results, questions raised regarding sensitivities to modeling techniques, and conclusions drawn regarding the status and numerical sensitivities of the codes. 30 refs.« less

Benchmarking for the competitive marketplace.

PubMed

Clarke, R W; Sucher, T O

1999-07-01

One would get little argument these days regarding the importance of performance measurement in the health care industry. The traditional approach has been the straightforward use of measurable units such as financial comparisons and clinical indicators (e.g., length of stay). Also we in the health care industry have traditionally benchmarked our performance and strategies against those most like ourselves. Today's competitive market demands a more customer-focused set of performance measures that go beyond traditional approaches such as customer service. The most important task in today's environment is to study the customers' emerging priorities and adjust our business to meet those priorities.

Comparing Hospital Processes and Outcomes in California Medicare Beneficiaries: Simulation Prompts Reconsideration

PubMed Central

Escobar, Gabriel J; Baker, Jennifer M; Turk, Benjamin J; Draper, David; Liu, Vincent; Kipnis, Patricia

2017-01-01

Introduction This article is not a traditional research report. It describes how conducting a specific set of benchmarking analyses led us to broader reflections on hospital benchmarking. We reexamined an issue that has received far less attention from researchers than in the past: How variations in the hospital admission threshold might affect hospital rankings. Considering this threshold made us reconsider what benchmarking is and what future benchmarking studies might be like. Although we recognize that some of our assertions are speculative, they are based on our reading of the literature and previous and ongoing data analyses being conducted in our research unit. We describe the benchmarking analyses that led to these reflections. Objectives The Centers for Medicare and Medicaid Services’ Hospital Compare Web site includes data on fee-for-service Medicare beneficiaries but does not control for severity of illness, which requires physiologic data now available in most electronic medical records. To address this limitation, we compared hospital processes and outcomes among Kaiser Permanente Northern California’s (KPNC) Medicare Advantage beneficiaries and non-KPNC California Medicare beneficiaries between 2009 and 2010. Methods We assigned a simulated severity of illness measure to each record and explored the effect of having the additional information on outcomes. Results We found that if the admission severity of illness in non-KPNC hospitals increased, KPNC hospitals’ mortality performance would appear worse; conversely, if admission severity at non-KPNC hospitals’ decreased, KPNC hospitals’ performance would appear better. Conclusion Future hospital benchmarking should consider the impact of variation in admission thresholds. PMID:29035176

Benchmarking Heavy Ion Transport Codes FLUKA, HETC-HEDS MARS15, MCNPX, and PHITS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ronningen, Reginald Martin; Remec, Igor; Heilbronn, Lawrence H.

Powerful accelerators such as spallation neutron sources, muon-collider/neutrino facilities, and rare isotope beam facilities must be designed with the consideration that they handle the beam power reliably and safely, and they must be optimized to yield maximum performance relative to their design requirements. The simulation codes used for design purposes must produce reliable results. If not, component and facility designs can become costly, have limited lifetime and usefulness, and could even be unsafe. The objective of this proposal is to assess the performance of the currently available codes PHITS, FLUKA, MARS15, MCNPX, and HETC-HEDS that could be used for designmore » simulations involving heavy ion transport. We plan to access their performance by performing simulations and comparing results against experimental data of benchmark quality. Quantitative knowledge of the biases and the uncertainties of the simulations is essential as this potentially impacts the safe, reliable and cost effective design of any future radioactive ion beam facility. Further benchmarking of heavy-ion transport codes was one of the actions recommended in the Report of the 2003 RIA R&D Workshop".« less

A fast elitism Gaussian estimation of distribution algorithm and application for PID optimization.

PubMed

Xu, Qingyang; Zhang, Chengjin; Zhang, Li

2014-01-01

Estimation of distribution algorithm (EDA) is an intelligent optimization algorithm based on the probability statistics theory. A fast elitism Gaussian estimation of distribution algorithm (FEGEDA) is proposed in this paper. The Gaussian probability model is used to model the solution distribution. The parameters of Gaussian come from the statistical information of the best individuals by fast learning rule. A fast learning rule is used to enhance the efficiency of the algorithm, and an elitism strategy is used to maintain the convergent performance. The performances of the algorithm are examined based upon several benchmarks. In the simulations, a one-dimensional benchmark is used to visualize the optimization process and probability model learning process during the evolution, and several two-dimensional and higher dimensional benchmarks are used to testify the performance of FEGEDA. The experimental results indicate the capability of FEGEDA, especially in the higher dimensional problems, and the FEGEDA exhibits a better performance than some other algorithms and EDAs. Finally, FEGEDA is used in PID controller optimization of PMSM and compared with the classical-PID and GA.

A Fast Elitism Gaussian Estimation of Distribution Algorithm and Application for PID Optimization

PubMed Central

Xu, Qingyang; Zhang, Chengjin; Zhang, Li

2014-01-01

Estimation of distribution algorithm (EDA) is an intelligent optimization algorithm based on the probability statistics theory. A fast elitism Gaussian estimation of distribution algorithm (FEGEDA) is proposed in this paper. The Gaussian probability model is used to model the solution distribution. The parameters of Gaussian come from the statistical information of the best individuals by fast learning rule. A fast learning rule is used to enhance the efficiency of the algorithm, and an elitism strategy is used to maintain the convergent performance. The performances of the algorithm are examined based upon several benchmarks. In the simulations, a one-dimensional benchmark is used to visualize the optimization process and probability model learning process during the evolution, and several two-dimensional and higher dimensional benchmarks are used to testify the performance of FEGEDA. The experimental results indicate the capability of FEGEDA, especially in the higher dimensional problems, and the FEGEDA exhibits a better performance than some other algorithms and EDAs. Finally, FEGEDA is used in PID controller optimization of PMSM and compared with the classical-PID and GA. PMID:24892059

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Hribar, Michelle; Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but the task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study,potentials of applying some of the techniques to realistic aerospace applications will be presented

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Hribar, M.; Waheed, A.; Yan, J.; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but this task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study, we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study, potentials of applying some of the techniques to realistic aerospace applications will be presented.

A benchmark for statistical microarray data analysis that preserves actual biological and technical variance.

PubMed

De Hertogh, Benoît; De Meulder, Bertrand; Berger, Fabrice; Pierre, Michael; Bareke, Eric; Gaigneaux, Anthoula; Depiereux, Eric

2010-01-11

Recent reanalysis of spike-in datasets underscored the need for new and more accurate benchmark datasets for statistical microarray analysis. We present here a fresh method using biologically-relevant data to evaluate the performance of statistical methods. Our novel method ranks the probesets from a dataset composed of publicly-available biological microarray data and extracts subset matrices with precise information/noise ratios. Our method can be used to determine the capability of different methods to better estimate variance for a given number of replicates. The mean-variance and mean-fold change relationships of the matrices revealed a closer approximation of biological reality. Performance analysis refined the results from benchmarks published previously.We show that the Shrinkage t test (close to Limma) was the best of the methods tested, except when two replicates were examined, where the Regularized t test and the Window t test performed slightly better. The R scripts used for the analysis are available at http://urbm-cluster.urbm.fundp.ac.be/~bdemeulder/.

A Simulation Environment for Benchmarking Sensor Fusion-Based Pose Estimators.

PubMed

Ligorio, Gabriele; Sabatini, Angelo Maria

2015-12-19

In-depth analysis and performance evaluation of sensor fusion-based estimators may be critical when performed using real-world sensor data. For this reason, simulation is widely recognized as one of the most powerful tools for algorithm benchmarking. In this paper, we present a simulation framework suitable for assessing the performance of sensor fusion-based pose estimators. The systems used for implementing the framework were magnetic/inertial measurement units (MIMUs) and a camera, although the addition of further sensing modalities is straightforward. Typical nuisance factors were also included for each sensor. The proposed simulation environment was validated using real-life sensor data employed for motion tracking. The higher mismatch between real and simulated sensors was about 5% of the measured quantity (for the camera simulation), whereas a lower correlation was found for an axis of the gyroscope (0.90). In addition, a real benchmarking example of an extended Kalman filter for pose estimation from MIMU and camera data is presented.

Commercial Building Energy Saver, Web App

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

The CBES App is a web-based toolkit for use by small businesses and building owners and operators of small and medium size commercial buildings to perform energy benchmarking and retrofit analysis for buildings. The CBES App analyzes the energy performance of user's building for pre-and posto-retrofit, in conjunction with user's input data, to identify recommended retrofit measures, energy savings and economic analysis for the selected measures. The CBES App provides energy benchmarking, including getting an EnergyStar score using EnergyStar API and benchmarking against California peer buildings using the EnergyIQ API. The retrofit analysis includes a preliminary analysis by looking upmore » retrofit measures from a pre-simulated database DEEP, and a detailed analysis creating and running EnergyPlus models to calculate energy savings of retrofit measures. The CBES App builds upon the LBNL CBES API.« less

Benchmarking study of the MCNP code against cold critical experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sitaraman, S.

1991-01-01

The purpose of this study was to benchmark the widely used Monte Carlo code MCNP against a set of cold critical experiments with a view to using the code as a means of independently verifying the performance of faster but less accurate Monte Carlo and deterministic codes. The experiments simulated consisted of both fast and thermal criticals as well as fuel in a variety of chemical forms. A standard set of benchmark cold critical experiments was modeled. These included the two fast experiments, GODIVA and JEZEBEL, the TRX metallic uranium thermal experiments, the Babcock and Wilcox oxide and mixed oxidemore » experiments, and the Oak Ridge National Laboratory (ORNL) and Pacific Northwest Laboratory (PNL) nitrate solution experiments. The principal case studied was a small critical experiment that was performed with boiling water reactor bundles.« less

Assessing and benchmarking multiphoton microscopes for biologists

PubMed Central

Corbin, Kaitlin; Pinkard, Henry; Peck, Sebastian; Beemiller, Peter; Krummel, Matthew F.

2017-01-01

Multiphoton microscopy has become staple tool for tracking cells within tissues and organs due to superior depth of penetration, low excitation volumes, and reduced phototoxicity. Many factors, ranging from laser pulse width to relay optics to detectors and electronics, contribute to the overall ability of these microscopes to excite and detect fluorescence deep within tissues. However, we have found that there are few standard ways already described in the literature to distinguish between microscopes or to benchmark existing microscopes to measure the overall quality and efficiency of these instruments. Here, we discuss some simple parameters and methods that can either be used within a multiphoton facility or by a prospective purchaser to benchmark performance. This can both assist in identifying decay in microscope performance and in choosing features of a scope that are suited to experimental needs. PMID:24974026

Revel8or: Model Driven Capacity Planning Tool Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Liming; Liu, Yan; Bui, Ngoc B.

2007-05-31

Designing complex multi-tier applications that must meet strict performance requirements is a challenging software engineering problem. Ideally, the application architect could derive accurate performance predictions early in the project life-cycle, leveraging initial application design-level models and a description of the target software and hardware platforms. To this end, we have developed a capacity planning tool suite for component-based applications, called Revel8tor. The tool adheres to the model driven development paradigm and supports benchmarking and performance prediction for J2EE, .Net and Web services platforms. The suite is composed of three different tools: MDAPerf, MDABench and DSLBench. MDAPerf allows annotation of designmore » diagrams and derives performance analysis models. MDABench allows a customized benchmark application to be modeled in the UML 2.0 Testing Profile and automatically generates a deployable application, with measurement automatically conducted. DSLBench allows the same benchmark modeling and generation to be conducted using a simple performance engineering Domain Specific Language (DSL) in Microsoft Visual Studio. DSLBench integrates with Visual Studio and reuses its load testing infrastructure. Together, the tool suite can assist capacity planning across platforms in an automated fashion.« less

Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks.

PubMed

Jimenez-Del-Toro, Oscar; Muller, Henning; Krenn, Markus; Gruenberg, Katharina; Taha, Abdel Aziz; Winterstein, Marianne; Eggel, Ivan; Foncubierta-Rodriguez, Antonio; Goksel, Orcun; Jakab, Andras; Kontokotsios, Georgios; Langs, Georg; Menze, Bjoern H; Salas Fernandez, Tomas; Schaer, Roger; Walleyo, Anna; Weber, Marc-Andre; Dicente Cid, Yashin; Gass, Tobias; Heinrich, Mattias; Jia, Fucang; Kahl, Fredrik; Kechichian, Razmig; Mai, Dominic; Spanier, Assaf B; Vincent, Graham; Wang, Chunliang; Wyeth, Daniel; Hanbury, Allan

2016-11-01

Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the cloud where participants can only access the training data and can be run privately by the benchmark administrators to objectively compare their performance in an unseen common test set. Overall, 120 computed tomography and magnetic resonance patient volumes were manually annotated to create a standard Gold Corpus containing a total of 1295 structures and 1760 landmarks. Ten participants contributed with automatic algorithms for the organ segmentation task, and three for the landmark localization task. Different algorithms obtained the best scores in the four available imaging modalities and for subsets of anatomical structures. The annotation framework, resulting data set, evaluation setup, results and performance analysis from the three VISCERAL Anatomy benchmarks are presented in this article. Both the VISCERAL data set and Silver Corpus generated with the fusion of the participant algorithms on a larger set of non-manually-annotated medical images are available to the research community.

Deepthi Vaidhynathan | NREL

Science.gov Websites

Complex Systems Simulation and Optimization Group on performance analysis and benchmarking latest . Research Interests High Performance Computing|Embedded System |Microprocessors & Microcontrollers

Performance effects of irregular communications patterns on massively parallel multiprocessors

NASA Technical Reports Server (NTRS)

Saltz, Joel; Petiton, Serge; Berryman, Harry; Rifkin, Adam

1991-01-01

A detailed study of the performance effects of irregular communications patterns on the CM-2 was conducted. The communications capabilities of the CM-2 were characterized under a variety of controlled conditions. In the process of carrying out the performance evaluation, extensive use was made of a parameterized synthetic mesh. In addition, timings with unstructured meshes generated for aerodynamic codes and a set of sparse matrices with banded patterns on non-zeroes were performed. This benchmarking suite stresses the communications capabilities of the CM-2 in a range of different ways. Benchmark results demonstrate that it is possible to make effective use of much of the massive concurrency available in the communications network.

Improving HEI Productivity and Performance through Project Management: Implications from a Benchmarking Case Study

ERIC Educational Resources Information Center

Bryde, David; Leighton, Diana

2009-01-01

As higher education institutions (HEIs) look to be more commercial in their outlook they are likely to become more dependent on the successful implementation of projects. This article reports a benchmarking survey of PM maturity in a HEI, with the purpose of assessing its capability to implement projects. Data were collected via questionnaires…

DOGMA: A Disk-Oriented Graph Matching Algorithm for RDF Databases

NASA Astrophysics Data System (ADS)

Bröcheler, Matthias; Pugliese, Andrea; Subrahmanian, V. S.

RDF is an increasingly important paradigm for the representation of information on the Web. As RDF databases increase in size to approach tens of millions of triples, and as sophisticated graph matching queries expressible in languages like SPARQL become increasingly important, scalability becomes an issue. To date, there is no graph-based indexing method for RDF data where the index was designed in a way that makes it disk-resident. There is therefore a growing need for indexes that can operate efficiently when the index itself resides on disk. In this paper, we first propose the DOGMA index for fast subgraph matching on disk and then develop a basic algorithm to answer queries over this index. This algorithm is then significantly sped up via an optimized algorithm that uses efficient (but correct) pruning strategies when combined with two different extensions of the index. We have implemented a preliminary system and tested it against four existing RDF database systems developed by others. Our experiments show that our algorithm performs very well compared to these systems, with orders of magnitude improvements for complex graph queries.

Standard biological parts knowledgebase.

PubMed

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Legacy2Drupal - Conversion of an existing oceanographic relational database to a semantically enabled Drupal content management system

NASA Astrophysics Data System (ADS)

Maffei, A. R.; Chandler, C. L.; Work, T.; Allen, J.; Groman, R. C.; Fox, P. A.

2009-12-01

Content Management Systems (CMSs) provide powerful features that can be of use to oceanographic (and other geo-science) data managers. However, in many instances, geo-science data management offices have previously designed customized schemas for their metadata. The WHOI Ocean Informatics initiative and the NSF funded Biological Chemical and Biological Data Management Office (BCO-DMO) have jointly sponsored a project to port an existing, relational database containing oceanographic metadata, along with an existing interface coded in Cold Fusion middleware, to a Drupal6 Content Management System. The goal was to translate all the existing database tables, input forms, website reports, and other features present in the existing system to employ Drupal CMS features. The replacement features include Drupal content types, CCK node-reference fields, themes, RDB, SPARQL, workflow, and a number of other supporting modules. Strategic use of some Drupal6 CMS features enables three separate but complementary interfaces that provide access to oceanographic research metadata via the MySQL database: 1) a Drupal6-powered front-end; 2) a standard SQL port (used to provide a Mapserver interface to the metadata and data; and 3) a SPARQL port (feeding a new faceted search capability being developed). Future plans include the creation of science ontologies, by scientist/technologist teams, that will drive semantically-enabled faceted search capabilities planned for the site. Incorporation of semantic technologies included in the future Drupal 7 core release is also anticipated. Using a public domain CMS as opposed to proprietary middleware, and taking advantage of the many features of Drupal 6 that are designed to support semantically-enabled interfaces will help prepare the BCO-DMO database for interoperability with other ecosystem databases.

Semantic e-Science: From Microformats to Models

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Freemantle, J. R.; Aldridge, K. D.

2009-05-01

A platform has been developed to transform semi-structured ASCII data into a representation based on the eXtensible Markup Language (XML). A subsequent transformation allows the XML-based representation to be rendered in the Resource Description Format (RDF). Editorial metadata, expressed as external annotations (via XML Pointer Language), also survives this transformation process (e.g., Lumb et al., http://dx.doi.org/10.1016/j.cageo.2008.03.009). Because the XML-to-RDF transformation uses XSLT (eXtensible Stylesheet Language Transformations), semantic microformats ultimately encode the scientific data (Lumb & Aldridge, http://dx.doi.org/10.1109/HPCS.2006.26). In building the relationship-centric representation in RDF, a Semantic Model of the scientific data is extracted. The systematic enhancement in the expressivity and richness of the scientific data results in representations of knowledge that are readily understood and manipulated by intelligent software agents. Thus scientists are able to draw upon various resources within and beyond their discipline to use in their scientific applications. Since the resulting Semantic Models are independent conceptualizations of the science itself, the representation of scientific knowledge and interaction with the same can stimulate insight from different perspectives. Using the Global Geodynamics Project (GGP) for the purpose of illustration, the introduction of GGP microformats enable a Semantic Model for the GGP that can be semantically queried (e.g., via SPARQL, http://www.w3.org/TR/rdf-sparql-query). Although the present implementation uses the Open Source Redland RDF Libraries (http://librdf.org/), the approach is generalizable to other platforms and to projects other than the GGP (e.g., Baker et al., Informatics and the 2007-2008 Electronic Geophysical Year, Eos Trans. Am. Geophys. Un., 89(48), 485-486, 2008).

Linking descriptive geology and quantitative machine learning through an ontology of lithological concepts

NASA Astrophysics Data System (ADS)

Klump, J. F.; Huber, R.; Robertson, J.; Cox, S. J. D.; Woodcock, R.

2014-12-01

Despite the recent explosion of quantitative geological data, geology remains a fundamentally qualitative science. Numerical data only constitute a certain part of data collection in the geosciences. In many cases, geological observations are compiled as text into reports and annotations on drill cores, thin sections or drawings of outcrops. The observations are classified into concepts such as lithology, stratigraphy, geological structure, etc. These descriptions are semantically rich and are generally supported by more quantitative observations using geochemical analyses, XRD, hyperspectral scanning, etc, but the goal is geological semantics. In practice it has been difficult to bring the different observations together due to differing perception or granularity of classification in human observation, or the partial observation of only some characteristics using quantitative sensors. In the past years many geological classification schemas have been transferred into ontologies and vocabularies, formalized using RDF and OWL, and published through SPARQL endpoints. Several lithological ontologies were compiled by stratigraphy.net and published through a SPARQL endpoint. This work is complemented by the development of a Python API to integrate this vocabulary into Python-based text mining applications. The applications for the lithological vocabulary and Python API are automated semantic tagging of geochemical data and descriptions of drill cores, machine learning of geochemical compositions that are diagnostic for lithological classifications, and text mining for lithological concepts in reports and geological literature. This combination of applications can be used to identify anomalies in databases, where composition and lithological classification do not match. It can also be used to identify lithological concepts in the literature and infer quantitative values. The resulting semantic tagging opens new possibilities for linking these diverse sources of data.

Approaches to Linked Open Data at data.oceandrilling.org

NASA Astrophysics Data System (ADS)

Fils, D.

2012-12-01

The data.oceandrilling.org web application applies Linked Open Data (LOD) patterns to expose Deep Sea Drilling Project (DSDP), Ocean Drilling Program (ODP) and Integrated Ocean Drilling Program (IODP) data. Ocean drilling data is represented in a rich range of data formats: high resolution images, file based data sets and sample based data. This richness of data types has been well met by semantic approaches and will be demonstrated. Data has been extracted from CSV, HTML and RDBMS through custom software and existing packages for loading into a SPARQL 1.1 compliant triple store. Practices have been developed to streamline the maintenance of the RDF graphs and properly expose them using LOD approaches like VoID and HTML embedded structured data. Custom and existing vocabularies are used to allow semantic relations between resources. Use of the W3c draft RDF Data Cube Vocabulary and other approaches for encoding time scales, taxonomic fossil data and other graphs will be shown. A software layer written in Google Go mediates the RDF to web pipeline. The approach used is general and can be applied to other similar environments like node.js or Python Twisted. To facilitate communication user interface software libraries such as D3 and packages such as S2S and LodLive have been used. Additionally OpenSearch API's, structured data in HTML and SPARQL endpoints provide various access methods for applications. The data.oceandrilling.org is not viewed as a web site but as an application that communicate with a range of clients. This approach helps guide the development more along software practices than along web site authoring approaches.

Smart POI: Open and linked spatial data

NASA Astrophysics Data System (ADS)

Cerba, Otakar; Berzins, Raitis; Charvat, Karel; Mildorf, Tomas

2016-04-01

The Smart Point of Interest (SPOI) represents an unique seamless spatial data set based on standards recommended for Linked and open data, which are supported by scientist and researchers as well as by several government authorities and European Union. This data set developed in cooperation of partners of SDI4Apps project contains almost 24 millions points of interest focused mainly on tourism, natural features, transport or citizen services. The SPOI data covers almost all countries and territories over the world. It is created as a harmonized combination of global data resources (selected points from OpenStreetMap, Natural Earth and GeoNames.org) and several local data sets (for example data published by the Citadel on the Move project, data from Posumavi region in the Czech Republic or experimental ontologies developed in the University of West Bohemia including ski regions in Europe or historical sights in Rome). The added value of the SDI4Apps approach in comparison to other similar solutions consists in implementation of linked data approach (several objects are connected to DBpedia or GeoNames.org), using of universal RDF format, using of standardized and respected properties or vocabularies (for example FOAF or GeoSPARQL) and development of the completely harmonized data set with uniform data model and common classification (not only a copy of original resources). The SPOI data is published as SPARQL endpoint as well as in the map client. The SPOI dataset is a specific set of POIs which could be "a data fuel" for applications and services related to tourism, local business, statistics or landscape monitoring. It can be used also as a background data layer for thematic maps.

OntoFox: web-based support for ontology reuse

PubMed Central

2010-01-01

Background Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms. Findings OntoFox http://ontofox.hegroup.org/ is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated. Conclusions OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies. PMID:20569493

Highly Enriched Uranium Metal Cylinders Surrounded by Various Reflector Materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bernard Jones; J. Blair Briggs; Leland Monteirth

A series of experiments was performed at Los Alamos Scientific Laboratory in 1958 to determine critical masses of cylinders of Oralloy (Oy) reflected by a number of materials. The experiments were all performed on the Comet Universal Critical Assembly Machine, and consisted of discs of highly enriched uranium (93.3 wt.% 235U) reflected by half-inch and one-inch-thick cylindrical shells of various reflector materials. The experiments were performed by members of Group N-2, particularly K. W. Gallup, G. E. Hansen, H. C. Paxton, and R. H. White. This experiment was intended to ascertain critical masses for criticality safety purposes, as well asmore » to compare neutron transport cross sections to those obtained from danger coefficient measurements with the Topsy Oralloy-Tuballoy reflected and Godiva unreflected critical assemblies. The reflector materials examined in this series of experiments are as follows: magnesium, titanium, aluminum, graphite, mild steel, nickel, copper, cobalt, molybdenum, natural uranium, tungsten, beryllium, aluminum oxide, molybdenum carbide, and polythene (polyethylene). Also included are two special configurations of composite beryllium and iron reflectors. Analyses were performed in which uncertainty associated with six different parameters was evaluated; namely, extrapolation to the uranium critical mass, uranium density, 235U enrichment, reflector density, reflector thickness, and reflector impurities. In addition to the idealizations made by the experimenters (removal of the platen and diaphragm), two simplifications were also made to the benchmark models that resulted in a small bias and additional uncertainty. First of all, since impurities in core and reflector materials are only estimated, they are not included in the benchmark models. Secondly, the room, support structure, and other possible surrounding equipment were not included in the model. Bias values that result from these two simplifications were determined and associated uncertainty in the bias values were included in the overall uncertainty in benchmark keff values. Bias values were very small, ranging from 0.0004 ?k low to 0.0007 ?k low. Overall uncertainties range from ? 0.0018 to ? 0.0030. Major contributors to the overall uncertainty include uncertainty in the extrapolation to the uranium critical mass and the uranium density. Results are summarized in Figure 1. Figure 1. Experimental, Benchmark-Model, and MCNP/KENO Calculated Results The 32 configurations described and evaluated under ICSBEP Identifier HEU-MET-FAST-084 are judged to be acceptable for use as criticality safety benchmark experiments and should be valuable integral benchmarks for nuclear data testing of the various reflector materials. Details of the benchmark models, uncertainty analyses, and final results are given in this paper.« less

A new deadlock resolution protocol and message matching algorithm for the extreme-scale simulator

DOE PAGES

Engelmann, Christian; Naughton, III, Thomas J.

2016-03-22

Investigating the performance of parallel applications at scale on future high-performance computing (HPC) architectures and the performance impact of different HPC architecture choices is an important component of HPC hardware/software co-design. The Extreme-scale Simulator (xSim) is a simulation toolkit for investigating the performance of parallel applications at scale. xSim scales to millions of simulated Message Passing Interface (MPI) processes. The overhead introduced by a simulation tool is an important performance and productivity aspect. This paper documents two improvements to xSim: (1)~a new deadlock resolution protocol to reduce the parallel discrete event simulation overhead and (2)~a new simulated MPI message matchingmore » algorithm to reduce the oversubscription management overhead. The results clearly show a significant performance improvement. The simulation overhead for running the NAS Parallel Benchmark suite was reduced from 102% to 0% for the embarrassingly parallel (EP) benchmark and from 1,020% to 238% for the conjugate gradient (CG) benchmark. xSim offers a highly accurate simulation mode for better tracking of injected MPI process failures. Furthermore, with highly accurate simulation, the overhead was reduced from 3,332% to 204% for EP and from 37,511% to 13,808% for CG.« less

Regression Tree-Based Methodology for Customizing Building Energy Benchmarks to Individual Commercial Buildings

NASA Astrophysics Data System (ADS)

Kaskhedikar, Apoorva Prakash

According to the U.S. Energy Information Administration, commercial buildings represent about 40% of the United State's energy consumption of which office buildings consume a major portion. Gauging the extent to which an individual building consumes energy in excess of its peers is the first step in initiating energy efficiency improvement. Energy Benchmarking offers initial building energy performance assessment without rigorous evaluation. Energy benchmarking tools based on the Commercial Buildings Energy Consumption Survey (CBECS) database are investigated in this thesis. This study proposes a new benchmarking methodology based on decision trees, where a relationship between the energy use intensities (EUI) and building parameters (continuous and categorical) is developed for different building types. This methodology was applied to medium office and school building types contained in the CBECS database. The Random Forest technique was used to find the most influential parameters that impact building energy use intensities. Subsequently, correlations which were significant were identified between EUIs and CBECS variables. Other than floor area, some of the important variables were number of workers, location, number of PCs and main cooling equipment. The coefficient of variation was used to evaluate the effectiveness of the new model. The customization technique proposed in this thesis was compared with another benchmarking model that is widely used by building owners and designers namely, the ENERGY STAR's Portfolio Manager. This tool relies on the standard Linear Regression methods which is only able to handle continuous variables. The model proposed uses data mining technique and was found to perform slightly better than the Portfolio Manager. The broader impacts of the new benchmarking methodology proposed is that it allows for identifying important categorical variables, and then incorporating them in a local, as against a global, model framework for EUI pertinent to the building type. The ability to identify and rank the important variables is of great importance in practical implementation of the benchmarking tools which rely on query-based building and HVAC variable filters specified by the user.

Methodology and issues of integral experiments selection for nuclear data validation

NASA Astrophysics Data System (ADS)

Tatiana, Ivanova; Ivanov, Evgeny; Hill, Ian

2017-09-01

Nuclear data validation involves a large suite of Integral Experiments (IEs) for criticality, reactor physics and dosimetry applications. [1] Often benchmarks are taken from international Handbooks. [2, 3] Depending on the application, IEs have different degrees of usefulness in validation, and usually the use of a single benchmark is not advised; indeed, it may lead to erroneous interpretation and results. [1] This work aims at quantifying the importance of benchmarks used in application dependent cross section validation. The approach is based on well-known General Linear Least Squared Method (GLLSM) extended to establish biases and uncertainties for given cross sections (within a given energy interval). The statistical treatment results in a vector of weighting factors for the integral benchmarks. These factors characterize the value added by a benchmark for nuclear data validation for the given application. The methodology is illustrated by one example, selecting benchmarks for 239Pu cross section validation. The studies were performed in the framework of Subgroup 39 (Methods and approaches to provide feedback from nuclear and covariance data adjustment for improvement of nuclear data files) established at the Working Party on International Nuclear Data Evaluation Cooperation (WPEC) of the Nuclear Science Committee under the Nuclear Energy Agency (NEA/OECD).

Decoys Selection in Benchmarking Datasets: Overview and Perspectives

PubMed Central

Réau, Manon; Langenfeld, Florent; Zagury, Jean-François; Lagarde, Nathalie; Montes, Matthieu

2018-01-01

Virtual Screening (VS) is designed to prospectively help identifying potential hits, i.e., compounds capable of interacting with a given target and potentially modulate its activity, out of large compound collections. Among the variety of methodologies, it is crucial to select the protocol that is the most adapted to the query/target system under study and that yields the most reliable output. To this aim, the performance of VS methods is commonly evaluated and compared by computing their ability to retrieve active compounds in benchmarking datasets. The benchmarking datasets contain a subset of known active compounds together with a subset of decoys, i.e., assumed non-active molecules. The composition of both the active and the decoy compounds subsets is critical to limit the biases in the evaluation of the VS methods. In this review, we focus on the selection of decoy compounds that has considerably changed over the years, from randomly selected compounds to highly customized or experimentally validated negative compounds. We first outline the evolution of decoys selection in benchmarking databases as well as current benchmarking databases that tend to minimize the introduction of biases, and secondly, we propose recommendations for the selection and the design of benchmarking datasets. PMID:29416509

Electric load shape benchmarking for small- and medium-sized commercial buildings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Luo, Xuan; Hong, Tianzhen; Chen, Yixing

Small- and medium-sized commercial buildings owners and utility managers often look for opportunities for energy cost savings through energy efficiency and energy waste minimization. However, they currently lack easy access to low-cost tools that help interpret the massive amount of data needed to improve understanding of their energy use behaviors. Benchmarking is one of the techniques used in energy audits to identify which buildings are priorities for an energy analysis. Traditional energy performance indicators, such as the energy use intensity (annual energy per unit of floor area), consider only the total annual energy consumption, lacking consideration of the fluctuation ofmore » energy use behavior over time, which reveals the time of use information and represents distinct energy use behaviors during different time spans. To fill the gap, this study developed a general statistical method using 24-hour electric load shape benchmarking to compare a building or business/tenant space against peers. Specifically, the study developed new forms of benchmarking metrics and data analysis methods to infer the energy performance of a building based on its load shape. We first performed a data experiment with collected smart meter data using over 2,000 small- and medium-sized businesses in California. We then conducted a cluster analysis of the source data, and determined and interpreted the load shape features and parameters with peer group analysis. Finally, we implemented the load shape benchmarking feature in an open-access web-based toolkit (the Commercial Building Energy Saver) to provide straightforward and practical recommendations to users. The analysis techniques were generic and flexible for future datasets of other building types and in other utility territories.« less

Electric load shape benchmarking for small- and medium-sized commercial buildings

DOE PAGES

Luo, Xuan; Hong, Tianzhen; Chen, Yixing; ...

2017-07-28

Small- and medium-sized commercial buildings owners and utility managers often look for opportunities for energy cost savings through energy efficiency and energy waste minimization. However, they currently lack easy access to low-cost tools that help interpret the massive amount of data needed to improve understanding of their energy use behaviors. Benchmarking is one of the techniques used in energy audits to identify which buildings are priorities for an energy analysis. Traditional energy performance indicators, such as the energy use intensity (annual energy per unit of floor area), consider only the total annual energy consumption, lacking consideration of the fluctuation ofmore » energy use behavior over time, which reveals the time of use information and represents distinct energy use behaviors during different time spans. To fill the gap, this study developed a general statistical method using 24-hour electric load shape benchmarking to compare a building or business/tenant space against peers. Specifically, the study developed new forms of benchmarking metrics and data analysis methods to infer the energy performance of a building based on its load shape. We first performed a data experiment with collected smart meter data using over 2,000 small- and medium-sized businesses in California. We then conducted a cluster analysis of the source data, and determined and interpreted the load shape features and parameters with peer group analysis. Finally, we implemented the load shape benchmarking feature in an open-access web-based toolkit (the Commercial Building Energy Saver) to provide straightforward and practical recommendations to users. The analysis techniques were generic and flexible for future datasets of other building types and in other utility territories.« less

GROWTH OF THE INTERNATIONAL CRITICALITY SAFETY AND REACTOR PHYSICS EXPERIMENT EVALUATION PROJECTS

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. Blair Briggs; John D. Bess; Jim Gulliford

2011-09-01

Since the International Conference on Nuclear Criticality Safety (ICNC) 2007, the International Criticality Safety Benchmark Evaluation Project (ICSBEP) and the International Reactor Physics Experiment Evaluation Project (IRPhEP) have continued to expand their efforts and broaden their scope. Eighteen countries participated on the ICSBEP in 2007. Now, there are 20, with recent contributions from Sweden and Argentina. The IRPhEP has also expanded from eight contributing countries in 2007 to 16 in 2011. Since ICNC 2007, the contents of the 'International Handbook of Evaluated Criticality Safety Benchmark Experiments1' have increased from 442 evaluations (38000 pages), containing benchmark specifications for 3955 critical ormore » subcritical configurations to 516 evaluations (nearly 55000 pages), containing benchmark specifications for 4405 critical or subcritical configurations in the 2010 Edition of the ICSBEP Handbook. The contents of the Handbook have also increased from 21 to 24 criticality-alarm-placement/shielding configurations with multiple dose points for each, and from 20 to 200 configurations categorized as fundamental physics measurements relevant to criticality safety applications. Approximately 25 new evaluations and 150 additional configurations are expected to be added to the 2011 edition of the Handbook. Since ICNC 2007, the contents of the 'International Handbook of Evaluated Reactor Physics Benchmark Experiments2' have increased from 16 different experimental series that were performed at 12 different reactor facilities to 53 experimental series that were performed at 30 different reactor facilities in the 2011 edition of the Handbook. Considerable effort has also been made to improve the functionality of the searchable database, DICE (Database for the International Criticality Benchmark Evaluation Project) and verify the accuracy of the data contained therein. DICE will be discussed in separate papers at ICNC 2011. The status of the ICSBEP and the IRPhEP will be discussed in the full paper, selected benchmarks that have been added to the ICSBEP Handbook will be highlighted, and a preview of the new benchmarks that will appear in the September 2011 edition of the Handbook will be provided. Accomplishments of the IRPhEP will also be highlighted and the future of both projects will be discussed. REFERENCES (1) International Handbook of Evaluated Criticality Safety Benchmark Experiments, NEA/NSC/DOC(95)03/I-IX, Organisation for Economic Co-operation and Development-Nuclear Energy Agency (OECD-NEA), September 2010 Edition, ISBN 978-92-64-99140-8. (2) International Handbook of Evaluated Reactor Physics Benchmark Experiments, NEA/NSC/DOC(2006)1, Organisation for Economic Co-operation and Development-Nuclear Energy Agency (OECD-NEA), March 2011 Edition, ISBN 978-92-64-99141-5.« less

Benchmark for Peak Detection Algorithms in Fiber Bragg Grating Interrogation and a New Neural Network for its Performance Improvement

PubMed Central

Negri, Lucas; Nied, Ademir; Kalinowski, Hypolito; Paterno, Aleksander

2011-01-01

This paper presents a benchmark for peak detection algorithms employed in fiber Bragg grating spectrometric interrogation systems. The accuracy, precision, and computational performance of currently used algorithms and those of a new proposed artificial neural network algorithm are compared. Centroid and gaussian fitting algorithms are shown to have the highest precision but produce systematic errors that depend on the FBG refractive index modulation profile. The proposed neural network displays relatively good precision with reduced systematic errors and improved computational performance when compared to other networks. Additionally, suitable algorithms may be chosen with the general guidelines presented. PMID:22163806

Polarization Control with Piezoelectric and LiNbO3 Transducers

NASA Astrophysics Data System (ADS)

Bradley, E.; Miles, E.; Loginov, B.; Vu, N.

Several Polarization control transducers have appeared on the market, and now automated, endless polarization control systems using these transducers are becoming available. Unfortunately it is not entirely clear what benchmark performance tests a polarization control system must pass, and the polarization disturbances a system must handle are open to some debate. We present quantitative measurements of realistic polarization disturbances and two benchmark tests we have successfully used to evaluate the performance of an automated, endless polarization control system. We use these tests to compare the performance of a system using piezoelectric transducers to that of a system using LiNbO3 transducers.

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mardirossian, Narbe; Head-Gordon, Martin

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

Better Medicare Cost Report data are needed to help hospitals benchmark costs and performance.

PubMed

Magnus, S A; Smith, D G

2000-01-01

To evaluate costs and achieve cost control in the face of new technology and demands for efficiency from both managed care and governmental payers, hospitals need to benchmark their costs against those of other comparable hospitals. Since they typically use Medicare Cost Report (MCR) data for this purpose, a variety of cost accounting problems with the MCR may hamper hospitals' understanding of their relative costs and performance. Managers and researchers alike need to investigate the validity, accuracy, and timeliness of the MCR's cost accounting data.

Note: The performance of new density functionals for a recent blind test of non-covalent interactions

DOE PAGES

Mardirossian, Narbe; Head-Gordon, Martin

2016-11-09

Benchmark datasets of non-covalent interactions are essential for assessing the performance of density functionals and other quantum chemistry approaches. In a recent blind test, Taylor et al. benchmarked 14 methods on a new dataset consisting of 10 dimer potential energy curves calculated using coupled cluster with singles, doubles, and perturbative triples (CCSD(T)) at the complete basis set (CBS) limit (80 data points in total). Finally, the dataset is particularly interesting because compressed, near-equilibrium, and stretched regions of the potential energy surface are extensively sampled.

Revenue cycle management.

PubMed

Manley, Ray; Satiani, Bhagwan

2009-11-01

With the widening gap between overhead expenses and reimbursement, management of the revenue cycle is a critical part of a successful vascular surgery practice. It is important to review the data on all the components of the revenue cycle: payer contracting, appointment scheduling, preregistration, registration process, coding and capturing charges, proper billing of patients and insurers, follow-up of accounts receivable, and finally using appropriate benchmarking. The industry benchmarks used should be those of peers in identical groups. Warning signs of poor performance are discussed enabling the practice to formulate a performance improvement plan.

An automated benchmarking platform for MHC class II binding prediction methods.

PubMed

Andreatta, Massimo; Trolle, Thomas; Yan, Zhen; Greenbaum, Jason A; Peters, Bjoern; Nielsen, Morten

2018-05-01

Computational methods for the prediction of peptide-MHC binding have become an integral and essential component for candidate selection in experimental T cell epitope discovery studies. The sheer amount of published prediction methods-and often discordant reports on their performance-poses a considerable quandary to the experimentalist who needs to choose the best tool for their research. With the goal to provide an unbiased, transparent evaluation of the state-of-the-art in the field, we created an automated platform to benchmark peptide-MHC class II binding prediction tools. The platform evaluates the absolute and relative predictive performance of all participating tools on data newly entered into the Immune Epitope Database (IEDB) before they are made public, thereby providing a frequent, unbiased assessment of available prediction tools. The benchmark runs on a weekly basis, is fully automated, and displays up-to-date results on a publicly accessible website. The initial benchmark described here included six commonly used prediction servers, but other tools are encouraged to join with a simple sign-up procedure. Performance evaluation on 59 data sets composed of over 10 000 binding affinity measurements suggested that NetMHCIIpan is currently the most accurate tool, followed by NN-align and the IEDB consensus method. Weekly reports on the participating methods can be found online at: http://tools.iedb.org/auto_bench/mhcii/weekly/. mniel@bioinformatics.dtu.dk. Supplementary data are available at Bioinformatics online.

Benchmark CCSD(T) and DFT study of binding energies in Be7 - 12: in search of reliable DFT functional for beryllium clusters

NASA Astrophysics Data System (ADS)

Labanc, Daniel; Šulka, Martin; Pitoňák, Michal; Černušák, Ivan; Urban, Miroslav; Neogrády, Pavel

2018-05-01

We present a computational study of the stability of small homonuclear beryllium clusters Be7 - 12 in singlet electronic states. Our predictions are based on highly correlated CCSD(T) coupled cluster calculations. Basis set convergence towards the complete basis set limit as well as the role of the 1s core electron correlation are carefully examined. Our CCSD(T) data for binding energies of Be7 - 12 clusters serve as a benchmark for performance assessment of several density functional theory (DFT) methods frequently used in beryllium cluster chemistry. We observe that, from Be10 clusters on, the deviation from CCSD(T) benchmarks is stable with respect to size, and fluctuating within 0.02 eV error bar for most examined functionals. This opens up the possibility of scaling the DFT binding energies for large Be clusters using CCSD(T) benchmark values for smaller clusters. We also tried to find analogies between the performance of DFT functionals for Be clusters and for the valence-isoelectronic Mg clusters investigated recently in Truhlar's group. We conclude that it is difficult to find DFT functionals that perform reasonably well for both beryllium and magnesium clusters. Out of 12 functionals examined, only the M06-2X functional gives reasonably accurate and balanced binding energies for both Be and Mg clusters.

Optimized selection of benchmark test parameters for image watermark algorithms based on Taguchi methods and corresponding influence on design decisions for real-world applications

NASA Astrophysics Data System (ADS)

Rodriguez, Tony F.; Cushman, David A.

2003-06-01

With the growing commercialization of watermarking techniques in various application scenarios it has become increasingly important to quantify the performance of watermarking products. The quantification of relative merits of various products is not only essential in enabling further adoption of the technology by society as a whole, but will also drive the industry to develop testing plans/methodologies to ensure quality and minimize cost (to both vendors & customers.) While the research community understands the theoretical need for a publicly available benchmarking system to quantify performance, there has been less discussion on the practical application of these systems. By providing a standard set of acceptance criteria, benchmarking systems can dramatically increase the quality of a particular watermarking solution, validating the product performances if they are used efficiently and frequently during the design process. In this paper we describe how to leverage specific design of experiments techniques to increase the quality of a watermarking scheme, to be used with the benchmark tools being developed by the Ad-Hoc Watermark Verification Group. A Taguchi Loss Function is proposed for an application and orthogonal arrays used to isolate optimal levels for a multi-factor experimental situation. Finally, the results are generalized to a population of cover works and validated through an exhaustive test.

PFLOTRAN Verification: Development of a Testing Suite to Ensure Software Quality

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Frederick, J. M.

2016-12-01

In scientific computing, code verification ensures the reliability and numerical accuracy of a model simulation by comparing the simulation results to experimental data or known analytical solutions. The model is typically defined by a set of partial differential equations with initial and boundary conditions, and verification ensures whether the mathematical model is solved correctly by the software. Code verification is especially important if the software is used to model high-consequence systems which cannot be physically tested in a fully representative environment [Oberkampf and Trucano (2007)]. Justified confidence in a particular computational tool requires clarity in the exercised physics and transparency in its verification process with proper documentation. We present a quality assurance (QA) testing suite developed by Sandia National Laboratories that performs code verification for PFLOTRAN, an open source, massively-parallel subsurface simulator. PFLOTRAN solves systems of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport processes in porous media. PFLOTRAN's QA test suite compares the numerical solutions of benchmark problems in heat and mass transport against known, closed-form, analytical solutions, including documentation of the exercised physical process models implemented in each PFLOTRAN benchmark simulation. The QA test suite development strives to follow the recommendations given by Oberkampf and Trucano (2007), which describes four essential elements in high-quality verification benchmark construction: (1) conceptual description, (2) mathematical description, (3) accuracy assessment, and (4) additional documentation and user information. Several QA tests within the suite will be presented, including details of the benchmark problems and their closed-form analytical solutions, implementation of benchmark problems in PFLOTRAN simulations, and the criteria used to assess PFLOTRAN's performance in the code verification procedure. References Oberkampf, W. L., and T. G. Trucano (2007), Verification and Validation Benchmarks, SAND2007-0853, 67 pgs., Sandia National Laboratories, Albuquerque, NM.

Optimally stopped variational quantum algorithms

NASA Astrophysics Data System (ADS)

Vinci, Walter; Shabani, Alireza

2018-04-01

Quantum processors promise a paradigm shift in high-performance computing which needs to be assessed by accurate benchmarking measures. In this article, we introduce a benchmark for the variational quantum algorithm (VQA), recently proposed as a heuristic algorithm for small-scale quantum processors. In VQA, a classical optimization algorithm guides the processor's quantum dynamics to yield the best solution for a given problem. A complete assessment of the scalability and competitiveness of VQA should take into account both the quality and the time of dynamics optimization. The method of optimal stopping, employed here, provides such an assessment by explicitly including time as a cost factor. Here, we showcase this measure for benchmarking VQA as a solver for some quadratic unconstrained binary optimization. Moreover, we show that a better choice for the cost function of the classical routine can significantly improve the performance of the VQA algorithm and even improve its scaling properties.

An Integrated Development Environment for Adiabatic Quantum Programming

DOE Office of Scientific and Technical Information (OSTI.GOV)

Humble, Travis S; McCaskey, Alex; Bennink, Ryan S

2014-01-01

Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware raises the question of how well quantum programs perform. Benchmarking behavior is challenging since the multiple steps to synthesize an adiabatic quantum program are highly tunable. We present an adiabatic quantum programming environment called JADE that provides control over all the steps taken during program development. JADE captures the workflow needed to rigorously benchmark performance while also allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation enginemore » that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its use for benchmarking adiabatic quantum programs.« less

Benchmarking Memory Performance with the Data Cube Operator

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Shabanov, Leonid V.

2004-01-01

Data movement across a computer memory hierarchy and across computational grids is known to be a limiting factor for applications processing large data sets. We use the Data Cube Operator on an Arithmetic Data Set, called ADC, to benchmark capabilities of computers and of computational grids to handle large distributed data sets. We present a prototype implementation of a parallel algorithm for computation of the operatol: The algorithm follows a known approach for computing views from the smallest parent. The ADC stresses all levels of grid memory and storage by producing some of 2d views of an Arithmetic Data Set of d-tuples described by a small number of integers. We control data intensity of the ADC by selecting the tuple parameters, the sizes of the views, and the number of realized views. Benchmarking results of memory performance of a number of computer architectures and of a small computational grid are presented.

Space network scheduling benchmark: A proof-of-concept process for technology transfer

NASA Technical Reports Server (NTRS)

Moe, Karen; Happell, Nadine; Hayden, B. J.; Barclay, Cathy

1993-01-01

This paper describes a detailed proof-of-concept activity to evaluate flexible scheduling technology as implemented in the Request Oriented Scheduling Engine (ROSE) and applied to Space Network (SN) scheduling. The criteria developed for an operational evaluation of a reusable scheduling system is addressed including a methodology to prove that the proposed system performs at least as well as the current system in function and performance. The improvement of the new technology must be demonstrated and evaluated against the cost of making changes. Finally, there is a need to show significant improvement in SN operational procedures. Successful completion of a proof-of-concept would eventually lead to an operational concept and implementation transition plan, which is outside the scope of this paper. However, a high-fidelity benchmark using actual SN scheduling requests has been designed to test the ROSE scheduling tool. The benchmark evaluation methodology, scheduling data, and preliminary results are described.

The impact of a scheduling change on ninth grade high school performance on biology benchmark exams and the California Standards Test

NASA Astrophysics Data System (ADS)

Leonardi, Marcelo

The primary purpose of this study was to examine the impact of a scheduling change from a trimester 4x4 block schedule to a modified hybrid schedule on student achievement in ninth grade biology courses. This study examined the impact of the scheduling change on student achievement through teacher created benchmark assessments in Genetics, DNA, and Evolution and on the California Standardized Test in Biology. The secondary purpose of this study examined the ninth grade biology teacher perceptions of ninth grade biology student achievement. Using a mixed methods research approach, data was collected both quantitatively and qualitatively as aligned to research questions. Quantitative methods included gathering data from departmental benchmark exams and California Standardized Test in Biology and conducting multiple analysis of covariance and analysis of covariance to determine significance differences. Qualitative methods include journal entries questions and focus group interviews. The results revealed a statistically significant increase in scores on both the DNA and Evolution benchmark exams. DNA and Evolution benchmark exams showed significant improvements from a change in scheduling format. The scheduling change was responsible for 1.5% of the increase in DNA benchmark scores and 2% of the increase in Evolution benchmark scores. The results revealed a statistically significant decrease in scores on the Genetics Benchmark exam as a result of the scheduling change. The scheduling change was responsible for 1% of the decrease in Genetics benchmark scores. The results also revealed a statistically significant increase in scores on the CST Biology exam. The scheduling change was responsible for .7% of the increase in CST Biology scores. Results of the focus group discussions indicated that all teachers preferred the modified hybrid schedule over the trimester schedule and that it improved student achievement.

Elementary School Students' Science Talk Ability in Inquiry-Oriented Settings in Taiwan: Test Development, Verification, and Performance Benchmarks

ERIC Educational Resources Information Center

Lin, Sheau-Wen; Liu, Yu; Chen, Shin-Feng; Wang, Jing-Ru; Kao, Huey-Lien

2016-01-01

The purpose of this study was to develop a computer-based measure of elementary students' science talk and to report students' benchmarks. The development procedure had three steps: defining the framework of the test, collecting and identifying key reference sets of science talk, and developing and verifying the science talk instrument. The…

75 FR 43554 - Notice of Lodging of Consent Decree Under the Federal Water Pollution Control Act (“Clean Water...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-26

... Benchmark Engineering Corp., Civil Action No. 10-40131 was lodged with the United States District Court for... requires Defendants to pay a civil penalty of $150,000, perform a Supplemental Environmental Project, and.... Fafard Real Estate and Development Corp., FRE Building Co. Inc., and Benchmark Engineering Corp., D.J...

PSO algorithm enhanced with Lozi Chaotic Map - Tuning experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pluhacek, Michal; Senkerik, Roman; Zelinka, Ivan

2015-03-10

In this paper it is investigated the effect of tuning of control parameters of the Lozi Chaotic Map employed as a chaotic pseudo-random number generator for the particle swarm optimization algorithm. Three different benchmark functions are selected from the IEEE CEC 2013 competition benchmark set. The Lozi map is extensively tuned and the performance of PSO is evaluated.

Design and development of a community carbon cycle benchmarking system for CMIP5 models

NASA Astrophysics Data System (ADS)

Mu, M.; Hoffman, F. M.; Lawrence, D. M.; Riley, W. J.; Keppel-Aleks, G.; Randerson, J. T.

2013-12-01

Benchmarking has been widely used to assess the ability of atmosphere, ocean, sea ice, and land surface models to capture the spatial and temporal variability of observations during the historical period. For the carbon cycle and terrestrial ecosystems, the design and development of an open-source community platform has been an important goal as part of the International Land Model Benchmarking (ILAMB) project. Here we designed and developed a software system that enables the user to specify the models, benchmarks, and scoring systems so that results can be tailored to specific model intercomparison projects. We used this system to evaluate the performance of CMIP5 Earth system models (ESMs). Our scoring system used information from four different aspects of climate, including the climatological mean spatial pattern of gridded surface variables, seasonal cycle dynamics, the amplitude of interannual variability, and long-term decadal trends. We used this system to evaluate burned area, global biomass stocks, net ecosystem exchange, gross primary production, and ecosystem respiration from CMIP5 historical simulations. Initial results indicated that the multi-model mean often performed better than many of the individual models for most of the observational constraints.

Toward Automated Benchmarking of Atomistic Force Fields: Neat Liquid Densities and Static Dielectric Constants from the ThermoML Data Archive.

PubMed

Beauchamp, Kyle A; Behr, Julie M; Rustenburg, Ariën S; Bayly, Christopher I; Kroenlein, Kenneth; Chodera, John D

2015-10-08

Atomistic molecular simulations are a powerful way to make quantitative predictions, but the accuracy of these predictions depends entirely on the quality of the force field employed. Although experimental measurements of fundamental physical properties offer a straightforward approach for evaluating force field quality, the bulk of this information has been tied up in formats that are not machine-readable. Compiling benchmark data sets of physical properties from non-machine-readable sources requires substantial human effort and is prone to the accumulation of human errors, hindering the development of reproducible benchmarks of force-field accuracy. Here, we examine the feasibility of benchmarking atomistic force fields against the NIST ThermoML data archive of physicochemical measurements, which aggregates thousands of experimental measurements in a portable, machine-readable, self-annotating IUPAC-standard format. As a proof of concept, we present a detailed benchmark of the generalized Amber small-molecule force field (GAFF) using the AM1-BCC charge model against experimental measurements (specifically, bulk liquid densities and static dielectric constants at ambient pressure) automatically extracted from the archive and discuss the extent of data available for use in larger scale (or continuously performed) benchmarks. The results of even this limited initial benchmark highlight a general problem with fixed-charge force fields in the representation low-dielectric environments, such as those seen in binding cavities or biological membranes.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bailey, David H.

The NAS Parallel Benchmarks (NPB) are a suite of parallel computer performance benchmarks. They were originally developed at the NASA Ames Research Center in 1991 to assess high-end parallel supercomputers. Although they are no longer used as widely as they once were for comparing high-end system performance, they continue to be studied and analyzed a great deal in the high-performance computing community. The acronym 'NAS' originally stood for the Numerical Aeronautical Simulation Program at NASA Ames. The name of this organization was subsequently changed to the Numerical Aerospace Simulation Program, and more recently to the NASA Advanced Supercomputing Center, althoughmore » the acronym remains 'NAS.' The developers of the original NPB suite were David H. Bailey, Eric Barszcz, John Barton, David Browning, Russell Carter, LeoDagum, Rod Fatoohi, Samuel Fineberg, Paul Frederickson, Thomas Lasinski, Rob Schreiber, Horst Simon, V. Venkatakrishnan and Sisira Weeratunga. The original NAS Parallel Benchmarks consisted of eight individual benchmark problems, each of which focused on some aspect of scientific computing. The principal focus was in computational aerophysics, although most of these benchmarks have much broader relevance, since in a much larger sense they are typical of many real-world scientific computing applications. The NPB suite grew out of the need for a more rational procedure to select new supercomputers for acquisition by NASA. The emergence of commercially available highly parallel computer systems in the late 1980s offered an attractive alternative to parallel vector supercomputers that had been the mainstay of high-end scientific computing. However, the introduction of highly parallel systems was accompanied by a regrettable level of hype, not only on the part of the commercial vendors but even, in some cases, by scientists using the systems. As a result, it was difficult to discern whether the new systems offered any fundamental performance advantage over vector supercomputers, and, if so, which of the parallel offerings would be most useful in real-world scientific computation. In part to draw attention to some of the performance reporting abuses prevalent at the time, the present author wrote a humorous essay 'Twelve Ways to Fool the Masses,' which described in a light-hearted way a number of the questionable ways in which both vendor marketing people and scientists were inflating and distorting their performance results. All of this underscored the need for an objective and scientifically defensible measure to compare performance on these systems.« less

Career performance trajectories of Olympic swimmers: benchmarks for talent development.

PubMed

Allen, Sian V; Vandenbogaerde, Tom J; Hopkins, William G

2014-01-01

The age-related progression of elite athletes to their career-best performances can provide benchmarks for talent development. The purpose of this study was to model career performance trajectories of Olympic swimmers to develop these benchmarks. We searched the Web for annual best times of swimmers who were top 16 in pool events at the 2008 or 2012 Olympics, from each swimmer's earliest available competitive performance through to 2012. There were 6959 times in the 13 events for each sex, for 683 swimmers, with 10 ± 3 performances per swimmer (mean ± s). Progression to peak performance was tracked with individual quadratic trajectories derived using a mixed linear model that included adjustments for better performance in Olympic years and for the use of full-body polyurethane swimsuits in 2009. Analysis of residuals revealed appropriate fit of quadratic trends to the data. The trajectories provided estimates of age of peak performance and the duration of the age window of trivial improvement and decline around the peak. Men achieved peak performance later than women (24.2 ± 2.1 vs. 22.5 ± 2.4 years), while peak performance occurred at later ages for the shorter distances for both sexes (∼1.5-2.0 years between sprint and distance-event groups). Men and women had a similar duration in the peak-performance window (2.6 ± 1.5 years) and similar progressions to peak performance over four years (2.4 ± 1.2%) and eight years (9.5 ± 4.8%). These data provide performance targets for swimmers aiming to achieve elite-level performance.

Validating the performance of correlated fission multiplicity implementation in radiation transport codes with subcritical neutron multiplication benchmark experiments

DOE PAGES

Arthur, Jennifer; Bahran, Rian; Hutchinson, Jesson; ...

2018-06-14

Historically, radiation transport codes have uncorrelated fission emissions. In reality, the particles emitted by both spontaneous and induced fissions are correlated in time, energy, angle, and multiplicity. This work validates the performance of various current Monte Carlo codes that take into account the underlying correlated physics of fission neutrons, specifically neutron multiplicity distributions. The performance of 4 Monte Carlo codes - MCNP®6.2, MCNP®6.2/FREYA, MCNP®6.2/CGMF, and PoliMi - was assessed using neutron multiplicity benchmark experiments. In addition, MCNP®6.2 simulations were run using JEFF-3.2 and JENDL-4.0, rather than ENDF/B-VII.1, data for 239Pu and 240Pu. The sensitive benchmark parameters that in this workmore » represent the performance of each correlated fission multiplicity Monte Carlo code include the singles rate, the doubles rate, leakage multiplication, and Feynman histograms. Although it is difficult to determine which radiation transport code shows the best overall performance in simulating subcritical neutron multiplication inference benchmark measurements, it is clear that correlations exist between the underlying nuclear data utilized by (or generated by) the various codes, and the correlated neutron observables of interest. This could prove useful in nuclear data validation and evaluation applications, in which a particular moment of the neutron multiplicity distribution is of more interest than the other moments. It is also quite clear that, because transport is handled by MCNP®6.2 in 3 of the 4 codes, with the 4th code (PoliMi) being based on an older version of MCNP®, the differences in correlated neutron observables of interest are most likely due to the treatment of fission event generation in each of the different codes, as opposed to the radiation transport.« less

Validating the performance of correlated fission multiplicity implementation in radiation transport codes with subcritical neutron multiplication benchmark experiments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arthur, Jennifer; Bahran, Rian; Hutchinson, Jesson

Historically, radiation transport codes have uncorrelated fission emissions. In reality, the particles emitted by both spontaneous and induced fissions are correlated in time, energy, angle, and multiplicity. This work validates the performance of various current Monte Carlo codes that take into account the underlying correlated physics of fission neutrons, specifically neutron multiplicity distributions. The performance of 4 Monte Carlo codes - MCNP®6.2, MCNP®6.2/FREYA, MCNP®6.2/CGMF, and PoliMi - was assessed using neutron multiplicity benchmark experiments. In addition, MCNP®6.2 simulations were run using JEFF-3.2 and JENDL-4.0, rather than ENDF/B-VII.1, data for 239Pu and 240Pu. The sensitive benchmark parameters that in this workmore » represent the performance of each correlated fission multiplicity Monte Carlo code include the singles rate, the doubles rate, leakage multiplication, and Feynman histograms. Although it is difficult to determine which radiation transport code shows the best overall performance in simulating subcritical neutron multiplication inference benchmark measurements, it is clear that correlations exist between the underlying nuclear data utilized by (or generated by) the various codes, and the correlated neutron observables of interest. This could prove useful in nuclear data validation and evaluation applications, in which a particular moment of the neutron multiplicity distribution is of more interest than the other moments. It is also quite clear that, because transport is handled by MCNP®6.2 in 3 of the 4 codes, with the 4th code (PoliMi) being based on an older version of MCNP®, the differences in correlated neutron observables of interest are most likely due to the treatment of fission event generation in each of the different codes, as opposed to the radiation transport.« less

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium.

PubMed

Han, Jeong-Hwan; Oda, Takuji

2018-04-14

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Performance of exchange-correlation functionals in density functional theory calculations for liquid metal: A benchmark test for sodium

NASA Astrophysics Data System (ADS)

Han, Jeong-Hwan; Oda, Takuji

2018-04-01

The performance of exchange-correlation functionals in density-functional theory (DFT) calculations for liquid metal has not been sufficiently examined. In the present study, benchmark tests of Perdew-Burke-Ernzerhof (PBE), Armiento-Mattsson 2005 (AM05), PBE re-parameterized for solids, and local density approximation (LDA) functionals are conducted for liquid sodium. The pair correlation function, equilibrium atomic volume, bulk modulus, and relative enthalpy are evaluated at 600 K and 1000 K. Compared with the available experimental data, the errors range from -11.2% to 0.0% for the atomic volume, from -5.2% to 22.0% for the bulk modulus, and from -3.5% to 2.5% for the relative enthalpy depending on the DFT functional. The generalized gradient approximation functionals are superior to the LDA functional, and the PBE and AM05 functionals exhibit the best performance. In addition, we assess whether the error tendency in liquid simulations is comparable to that in solid simulations, which would suggest that the atomic volume and relative enthalpy performances are comparable between solid and liquid states but that the bulk modulus performance is not. These benchmark test results indicate that the results of liquid simulations are significantly dependent on the exchange-correlation functional and that the DFT functional performance in solid simulations can be used to roughly estimate the performance in liquid simulations.

Information processing using a single dynamical node as complex system

PubMed Central

Appeltant, L.; Soriano, M.C.; Van der Sande, G.; Danckaert, J.; Massar, S.; Dambre, J.; Schrauwen, B.; Mirasso, C.R.; Fischer, I.

2011-01-01

Novel methods for information processing are highly desired in our information-driven society. Inspired by the brain's ability to process information, the recently introduced paradigm known as 'reservoir computing' shows that complex networks can efficiently perform computation. Here we introduce a novel architecture that reduces the usually required large number of elements to a single nonlinear node with delayed feedback. Through an electronic implementation, we experimentally and numerically demonstrate excellent performance in a speech recognition benchmark. Complementary numerical studies also show excellent performance for a time series prediction benchmark. These results prove that delay-dynamical systems, even in their simplest manifestation, can perform efficient information processing. This finding paves the way to feasible and resource-efficient technological implementations of reservoir computing. PMID:21915110

Performance and scalability evaluation of "Big Memory" on Blue Gene Linux.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yoshii, K.; Iskra, K.; Naik, H.

2011-05-01

We address memory performance issues observed in Blue Gene Linux and discuss the design and implementation of 'Big Memory' - an alternative, transparent memory space introduced to eliminate the memory performance issues. We evaluate the performance of Big Memory using custom memory benchmarks, NAS Parallel Benchmarks, and the Parallel Ocean Program, at a scale of up to 4,096 nodes. We find that Big Memory successfully resolves the performance issues normally encountered in Blue Gene Linux. For the ocean simulation program, we even find that Linux with Big Memory provides better scalability than does the lightweight compute node kernel designed solelymore » for high-performance applications. Originally intended exclusively for compute node tasks, our new memory subsystem dramatically improves the performance of certain I/O node applications as well. We demonstrate this performance using the central processor of the LOw Frequency ARray radio telescope as an example.« less

High Performance Computing at NASA

NASA Technical Reports Server (NTRS)

Bailey, David H.; Cooper, D. M. (Technical Monitor)

1994-01-01

The speaker will give an overview of high performance computing in the U.S. in general and within NASA in particular, including a description of the recently signed NASA-IBM cooperative agreement. The latest performance figures of various parallel systems on the NAS Parallel Benchmarks will be presented. The speaker was one of the authors of the NAS (National Aerospace Standards) Parallel Benchmarks, which are now widely cited in the industry as a measure of sustained performance on realistic high-end scientific applications. It will be shown that significant progress has been made by the highly parallel supercomputer industry during the past year or so, with several new systems, based on high-performance RISC processors, that now deliver superior performance per dollar compared to conventional supercomputers. Various pitfalls in reporting performance will be discussed. The speaker will then conclude by assessing the general state of the high performance computing field.

Benchmarking multimedia performance

NASA Astrophysics Data System (ADS)

Zandi, Ahmad; Sudharsanan, Subramania I.

1998-03-01

With the introduction of faster processors and special instruction sets tailored to multimedia, a number of exciting applications are now feasible on the desktops. Among these is the DVD playback consisting, among other things, of MPEG-2 video and Dolby digital audio or MPEG-2 audio. Other multimedia applications such as video conferencing and speech recognition are also becoming popular on computer systems. In view of this tremendous interest in multimedia, a group of major computer companies have formed, Multimedia Benchmarks Committee as part of Standard Performance Evaluation Corp. to address the performance issues of multimedia applications. The approach is multi-tiered with three tiers of fidelity from minimal to full compliant. In each case the fidelity of the bitstream reconstruction as well as quality of the video or audio output are measured and the system is classified accordingly. At the next step the performance of the system is measured. In many multimedia applications such as the DVD playback the application needs to be run at a specific rate. In this case the measurement of the excess processing power, makes all the difference. All these make a system level, application based, multimedia benchmark very challenging. Several ideas and methodologies for each aspect of the problems will be presented and analyzed.

A comparison of common programming languages used in bioinformatics.

PubMed

Fourment, Mathieu; Gillings, Michael R

2008-02-05

The performance of different programming languages has previously been benchmarked using abstract mathematical algorithms, but not using standard bioinformatics algorithms. We compared the memory usage and speed of execution for three standard bioinformatics methods, implemented in programs using one of six different programming languages. Programs for the Sellers algorithm, the Neighbor-Joining tree construction algorithm and an algorithm for parsing BLAST file outputs were implemented in C, C++, C#, Java, Perl and Python. Implementations in C and C++ were fastest and used the least memory. Programs in these languages generally contained more lines of code. Java and C# appeared to be a compromise between the flexibility of Perl and Python and the fast performance of C and C++. The relative performance of the tested languages did not change from Windows to Linux and no clear evidence of a faster operating system was found. Source code and additional information are available from http://www.bioinformatics.org/benchmark/. This benchmark provides a comparison of six commonly used programming languages under two different operating systems. The overall comparison shows that a developer should choose an appropriate language carefully, taking into account the performance expected and the library availability for each language.

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool

PubMed Central

Clark, Neil R.; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D.; Jones, Matthew R.; Ma’ayan, Avi

2016-01-01

Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community. PMID:26848405

Principal Angle Enrichment Analysis (PAEA): Dimensionally Reduced Multivariate Gene Set Enrichment Analysis Tool.

PubMed

Clark, Neil R; Szymkiewicz, Maciej; Wang, Zichen; Monteiro, Caroline D; Jones, Matthew R; Ma'ayan, Avi

2015-11-01

Gene set analysis of differential expression, which identifies collectively differentially expressed gene sets, has become an important tool for biology. The power of this approach lies in its reduction of the dimensionality of the statistical problem and its incorporation of biological interpretation by construction. Many approaches to gene set analysis have been proposed, but benchmarking their performance in the setting of real biological data is difficult due to the lack of a gold standard. In a previously published work we proposed a geometrical approach to differential expression which performed highly in benchmarking tests and compared well to the most popular methods of differential gene expression. As reported, this approach has a natural extension to gene set analysis which we call Principal Angle Enrichment Analysis (PAEA). PAEA employs dimensionality reduction and a multivariate approach for gene set enrichment analysis. However, the performance of this method has not been assessed nor its implementation as a web-based tool. Here we describe new benchmarking protocols for gene set analysis methods and find that PAEA performs highly. The PAEA method is implemented as a user-friendly web-based tool, which contains 70 gene set libraries and is freely available to the community.

Benchmarking government action for obesity prevention--an innovative advocacy strategy.

PubMed

Martin, J; Peeters, A; Honisett, S; Mavoa, H; Swinburn, B; de Silva-Sanigorski, A

2014-01-01

Successful obesity prevention will require a leading role for governments, but internationally they have been slow to act. League tables of benchmark indicators of action can be a valuable advocacy and evaluation tool. To develop a benchmarking tool for government action on obesity prevention, implement it across Australian jurisdictions and to publicly award the best and worst performers. A framework was developed which encompassed nine domains, reflecting best practice government action on obesity prevention: whole-of-government approaches; marketing restrictions; access to affordable, healthy food; school food and physical activity; food in public facilities; urban design and transport; leisure and local environments; health services, and; social marketing. A scoring system was used by non-government key informants to rate the performance of their government. National rankings were generated and the results were communicated to all Premiers/Chief Ministers, the media and the national obesity research and practice community. Evaluation of the initial tool in 2010 showed it to be feasible to implement and able to discriminate the better and worse performing governments. Evaluation of the rubric in 2011 confirmed this to be a robust and useful method. In relation to government action, the best performing governments were those with whole-of-government approaches, had extended common initiatives and demonstrated innovation and strong political will. This new benchmarking tool, the Obesity Action Award, has enabled identification of leading government action on obesity prevention and the key characteristics associated with their success. We recommend this tool for other multi-state/country comparisons. Copyright © 2013 Asian Oceanian Association for the Study of Obesity. Published by Elsevier Ltd. All rights reserved.

BACT Simulation User Guide (Version 7.0)

NASA Technical Reports Server (NTRS)

Waszak, Martin R.

1997-01-01

This report documents the structure and operation of a simulation model of the Benchmark Active Control Technology (BACT) Wind-Tunnel Model. The BACT system was designed, built, and tested at NASA Langley Research Center as part of the Benchmark Models Program and was developed to perform wind-tunnel experiments to obtain benchmark quality data to validate computational fluid dynamics and computational aeroelasticity codes, to verify the accuracy of current aeroservoelasticity design and analysis tools, and to provide an active controls testbed for evaluating new and innovative control algorithms for flutter suppression and gust load alleviation. The BACT system has been especially valuable as a control system testbed.

Hazards of benchmarking complications with the National Trauma Data Bank: numerators in search of denominators.

PubMed

Kardooni, Shahrzad; Haut, Elliott R; Chang, David C; Pierce, Charles A; Efron, David T; Haider, Adil H; Pronovost, Peter J; Cornwell, Edward E

2008-02-01

Complication rates after trauma may serve as important indicators of quality of care. Meaningful performance benchmarks for complication rates require reference standards from valid and reliable data. Selection of appropriate numerators and denominators is a major consideration for data validity in performance improvement and benchmarking. We examined the suitability of the National Trauma Data Bank (NTDB) as a reference for benchmarking trauma center complication rates. We selected the five most commonly reported complications in the NTDB v. 6.1 (pneumonia, urinary tract infection, acute respiratory distress syndrome, deep vein thrombosis, myocardial infarction). We compared rates for each complication using three different denominators defined by different populations at risk. A-all patients from all 700 reporting facilities as the denominator (n = 1,466,887); B-only patients from the 441 hospitals reporting at least one complication (n = 1,307,729); C-patients from hospitals reporting at least one occurrence of each specific complication, giving a unique denominator for each complication (n range = 869,675-1,167,384). We also looked at differences in hospital characteristics between complication reporters and nonreporters. There was a 12.2% increase in the rate of each complication when patients from facilities not reporting any complications were excluded from the denominator. When rates were calculated using a unique denominator for each complication, rates increased 25% to 70%. The change from rate A to rate C produced a new rank order for the top five complications. When compared directly, rates B and C were also significantly different for all complications (all p < 0.01). Hospitals that reported complication information had significantly higher annual admissions and were more likely to be designated level I or II trauma centers and be university teaching hospitals. There is great variability in complication data reported in the NTDB that may introduce bias and significantly influence rates of complications reported. This potential for bias creates a challenge for appropriately interpreting complication rates for hospital performance benchmarking. We recognize the value of large aggregated registries such as the NTDB as a valuable tool for benchmarking and performance improvement purposes. However, we strongly advocate the need for conscientious selection of numerators and denominators that serve as the basic foundation for research.

Improving patient safety culture in Saudi Arabia (2012-2015): trending, improvement and benchmarking.

PubMed

Alswat, Khalid; Abdalla, Rawia Ahmad Mustafa; Titi, Maher Abdelraheim; Bakash, Maram; Mehmood, Faiza; Zubairi, Beena; Jamal, Diana; El-Jardali, Fadi

2017-08-02

Measuring patient safety culture can provide insight into areas for improvement and help monitor changes over time. This study details the findings of a re-assessment of patient safety culture in a multi-site Medical City in Riyadh, Kingdom of Saudi Arabia (KSA). Results were compared to an earlier assessment conducted in 2012 and benchmarked with regional and international studies. Such assessments can provide hospital leadership with insight on how their hospital is performing on patient safety culture composites as a result of quality improvement plans. This paper also explored the association between patient safety culture predictors and patient safety grade, perception of patient safety, frequency of events reported and number of events reported. We utilized a customized version of the patient safety culture survey developed by the Agency for Healthcare Research and Quality. The Medical City is a tertiary care teaching facility composed of two sites (total capacity of 904 beds). Data was analyzed using SPSS 24 at a significance level of 0.05. A t-Test was used to compare results from the 2012 survey to that conducted in 2015. Two adopted Generalized Estimating Equations in addition to two linear models were used to assess the association between composites and patient safety culture outcomes. Results were also benchmarked against similar initiatives in Lebanon, Palestine and USA. Areas of strength in 2015 included Teamwork within units, and Organizational Learning-Continuous Improvement; areas requiring improvement included Non-Punitive Response to Error, and Staffing. Comparing results to the 2012 survey revealed improvement on some areas but non-punitive response to error and Staffing remained the lowest scoring composites in 2015. Regression highlighted significant association between managerial support, organizational learning and feedback and improved survey outcomes. Comparison to international benchmarks revealed that the hospital is performing at or better than benchmark on several composites. The Medical City has made significant progress on several of the patient safety culture composites despite still having areas requiring additional improvement. Patient safety culture outcomes are evidently linked to better performance on specific composites. While results are comparable with regional and international benchmarks, findings confirm that regular assessment can allow hospitals to better understand and visualize changes in their performance and identify additional areas for improvement.

International benchmarking of specialty hospitals. A series of case studies on comprehensive cancer centres.

PubMed

van Lent, Wineke A M; de Beer, Relinde D; van Harten, Wim H

2010-08-31

Benchmarking is one of the methods used in business that is applied to hospitals to improve the management of their operations. International comparison between hospitals can explain performance differences. As there is a trend towards specialization of hospitals, this study examines the benchmarking process and the success factors of benchmarking in international specialized cancer centres. Three independent international benchmarking studies on operations management in cancer centres were conducted. The first study included three comprehensive cancer centres (CCC), three chemotherapy day units (CDU) were involved in the second study and four radiotherapy departments were included in the final study. Per multiple case study a research protocol was used to structure the benchmarking process. After reviewing the multiple case studies, the resulting description was used to study the research objectives. We adapted and evaluated existing benchmarking processes through formalizing stakeholder involvement and verifying the comparability of the partners. We also devised a framework to structure the indicators to produce a coherent indicator set and better improvement suggestions. Evaluating the feasibility of benchmarking as a tool to improve hospital processes led to mixed results. Case study 1 resulted in general recommendations for the organizations involved. In case study 2, the combination of benchmarking and lean management led in one CDU to a 24% increase in bed utilization and a 12% increase in productivity. Three radiotherapy departments of case study 3, were considering implementing the recommendations.Additionally, success factors, such as a well-defined and small project scope, partner selection based on clear criteria, stakeholder involvement, simple and well-structured indicators, analysis of both the process and its results and, adapt the identified better working methods to the own setting, were found. The improved benchmarking process and the success factors can produce relevant input to improve the operations management of specialty hospitals.

International benchmarking of specialty hospitals. A series of case studies on comprehensive cancer centres

PubMed Central

2010-01-01

Background Benchmarking is one of the methods used in business that is applied to hospitals to improve the management of their operations. International comparison between hospitals can explain performance differences. As there is a trend towards specialization of hospitals, this study examines the benchmarking process and the success factors of benchmarking in international specialized cancer centres. Methods Three independent international benchmarking studies on operations management in cancer centres were conducted. The first study included three comprehensive cancer centres (CCC), three chemotherapy day units (CDU) were involved in the second study and four radiotherapy departments were included in the final study. Per multiple case study a research protocol was used to structure the benchmarking process. After reviewing the multiple case studies, the resulting description was used to study the research objectives. Results We adapted and evaluated existing benchmarking processes through formalizing stakeholder involvement and verifying the comparability of the partners. We also devised a framework to structure the indicators to produce a coherent indicator set and better improvement suggestions. Evaluating the feasibility of benchmarking as a tool to improve hospital processes led to mixed results. Case study 1 resulted in general recommendations for the organizations involved. In case study 2, the combination of benchmarking and lean management led in one CDU to a 24% increase in bed utilization and a 12% increase in productivity. Three radiotherapy departments of case study 3, were considering implementing the recommendations. Additionally, success factors, such as a well-defined and small project scope, partner selection based on clear criteria, stakeholder involvement, simple and well-structured indicators, analysis of both the process and its results and, adapt the identified better working methods to the own setting, were found. Conclusions The improved benchmarking process and the success factors can produce relevant input to improve the operations management of specialty hospitals. PMID:20807408

FX-87 performance measurements: data-flow implementation. Technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammel, R.T.; Gifford, D.K.

1988-11-01

This report documents a series of experiments performed to explore the thesis that the FX-87 effect system permits a compiler to schedule imperative programs (i.e., programs that may contain side-effects) for execution on a parallel computer. The authors analyze how much the FX-87 static effect system can improve the execution times of five benchmark programs on a parallel graph interpreter. Three of their benchmark programs do not use side-effects (factorial, fibonacci, and polynomial division) and thus did not have any effect-induced constraints. Their FX-87 performance was comparable to their performance in a purely functional language. Two of the benchmark programsmore » use side effects (DNA sequence matching and Scheme interpretation) and the compiler was able to use effect information to reduce their execution times by factors of 1.7 to 5.4 when compared with sequential execution times. These results support the thesis that a static effect system is a powerful tool for compilation to multiprocessor computers. However, the graph interpreter we used was based on unrealistic assumptions, and thus our results may not accurately reflect the performance of a practical FX-87 implementation. The results also suggest that conventional loop analysis would complement the FX-87 effect system« less

Benchmarking and audit of breast units improves quality of care

PubMed Central

van Dam, P.A.; Verkinderen, L.; Hauspy, J.; Vermeulen, P.; Dirix, L.; Huizing, M.; Altintas, S.; Papadimitriou, K.; Peeters, M.; Tjalma, W.

2013-01-01

Quality Indicators (QIs) are measures of health care quality that make use of readily available hospital inpatient administrative data. Assessment quality of care can be performed on different levels: national, regional, on a hospital basis or on an individual basis. It can be a mandatory or voluntary system. In all cases development of an adequate database for data extraction, and feedback of the findings is of paramount importance. In the present paper we performed a Medline search on “QIs and breast cancer” and “benchmarking and breast cancer care”, and we have added some data from personal experience. The current data clearly show that the use of QIs for breast cancer care, regular internal and external audit of performance of breast units, and benchmarking are effective to improve quality of care. Adherence to guidelines improves markedly (particularly regarding adjuvant treatment) and there are data emerging showing that this results in a better outcome. As quality assurance benefits patients, it will be a challenge for the medical and hospital community to develop affordable quality control systems, which are not leading to excessive workload. PMID:24753926

Intercomparison of Monte Carlo radiation transport codes to model TEPC response in low-energy neutron and gamma-ray fields.

PubMed

Ali, F; Waker, A J; Waller, E J

2014-10-01

Tissue-equivalent proportional counters (TEPC) can potentially be used as a portable and personal dosemeter in mixed neutron and gamma-ray fields, but what hinders this use is their typically large physical size. To formulate compact TEPC designs, the use of a Monte Carlo transport code is necessary to predict the performance of compact designs in these fields. To perform this modelling, three candidate codes were assessed: MCNPX 2.7.E, FLUKA 2011.2 and PHITS 2.24. In each code, benchmark simulations were performed involving the irradiation of a 5-in. TEPC with monoenergetic neutron fields and a 4-in. wall-less TEPC with monoenergetic gamma-ray fields. The frequency and dose mean lineal energies and dose distributions calculated from each code were compared with experimentally determined data. For the neutron benchmark simulations, PHITS produces data closest to the experimental values and for the gamma-ray benchmark simulations, FLUKA yields data closest to the experimentally determined quantities. © The Author 2013. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

A Benchmark for Endoluminal Scene Segmentation of Colonoscopy Images.

PubMed

Vázquez, David; Bernal, Jorge; Sánchez, F Javier; Fernández-Esparrach, Gloria; López, Antonio M; Romero, Adriana; Drozdzal, Michal; Courville, Aaron

2017-01-01

Colorectal cancer (CRC) is the third cause of cancer death worldwide. Currently, the standard approach to reduce CRC-related mortality is to perform regular screening in search for polyps and colonoscopy is the screening tool of choice. The main limitations of this screening procedure are polyp miss rate and the inability to perform visual assessment of polyp malignancy. These drawbacks can be reduced by designing decision support systems (DSS) aiming to help clinicians in the different stages of the procedure by providing endoluminal scene segmentation. Thus, in this paper, we introduce an extended benchmark of colonoscopy image segmentation, with the hope of establishing a new strong benchmark for colonoscopy image analysis research. The proposed dataset consists of 4 relevant classes to inspect the endoluminal scene, targeting different clinical needs. Together with the dataset and taking advantage of advances in semantic segmentation literature, we provide new baselines by training standard fully convolutional networks (FCNs). We perform a comparative study to show that FCNs significantly outperform, without any further postprocessing, prior results in endoluminal scene segmentation, especially with respect to polyp segmentation and localization.

Semi-active control of a cable-stayed bridge under multiple-support excitations.

PubMed

Dai, Ze-Bing; Huang, Jin-Zhi; Wang, Hong-Xia

2004-03-01

This paper presents a semi-active strategy for seismic protection of a benchmark cable-stayed bridge with consideration of multiple-support excitations. In this control strategy, Magnetorheological (MR) dampers are proposed as control devices, a LQG-clipped-optimal control algorithm is employed. An active control strategy, shown in previous researches to perform well at controlling the benchmark bridge when uniform earthquake motion was assumed, is also used in this study to control this benchmark bridge with consideration of multiple-support excitations. The performance of active control system is compared to that of the presented semi-active control strategy. Because the MR fluid damper is a controllable energy- dissipation device that cannot add mechanical energy to the structural system, the proposed control strategy is fail-safe in that bounded-input, bounded-output stability of the controlled structure is guaranteed. The numerical results demonstrated that the performance of the presented control design is nearly the same as that of the active control system; and that the MR dampers can effectively be used to control seismically excited cable-stayed bridges with multiple-support excitations.

RASSP Benchmark 4 Technical Description.

DTIC Science & Technology

1998-01-09

be carried out. Based on results of the study, an implementation of all, or part, of the system described in this benchmark technical description...validate interface and timing constraints. The ISA level of modeling defines the limit of detail expected in the VHDL virtual prototype. It does not...develop a set of candidate architectures and perform an architecture trade-off study. Candidate proces- sor implementations must then be examined for