Improved Information Retrieval Performance on SQL Database Using Data Adapter

NASA Astrophysics Data System (ADS)

Husni, M.; Djanali, S.; Ciptaningtyas, H. T.; Wicaksana, I. G. N. A.

2018-02-01

The NoSQL databases, short for Not Only SQL, are increasingly being used as the number of big data applications increases. Most systems still use relational databases (RDBs), but as the number of data increases each year, the system handles big data with NoSQL databases to analyze and access data more quickly. NoSQL emerged as a result of the exponential growth of the internet and the development of web applications. The query syntax in the NoSQL database differs from the SQL database, therefore requiring code changes in the application. Data adapter allow applications to not change their SQL query syntax. Data adapters provide methods that can synchronize SQL databases with NotSQL databases. In addition, the data adapter provides an interface which is application can access to run SQL queries. Hence, this research applied data adapter system to synchronize data between MySQL database and Apache HBase using direct access query approach, where system allows application to accept query while synchronization process in progress. From the test performed using data adapter, the results obtained that the data adapter can synchronize between SQL databases, MySQL, and NoSQL database, Apache HBase. This system spends the percentage of memory resources in the range of 40% to 60%, and the percentage of processor moving from 10% to 90%. In addition, from this system also obtained the performance of database NoSQL better than SQL database.

The HARPS-N archive through a Cassandra, NoSQL database suite?

NASA Astrophysics Data System (ADS)

Molinari, Emilio; Guerra, Jose; Harutyunyan, Avet; Lodi, Marcello; Martin, Adrian

2016-07-01

The TNG-INAF is developing the science archive for the WEAVE instrument. The underlying architecture of the archive is based on a non relational database, more precisely, on Apache Cassandra cluster, which uses a NoSQL technology. In order to test and validate the use of this architecture, we created a local archive which we populated with all the HARPSN spectra collected at the TNG since the instrument's start of operations in mid-2012, as well as developed tools for the analysis of this data set. The HARPS-N data set is two orders of magnitude smaller than WEAVE, but we want to demonstrate the ability to walk through a complete data set and produce scientific output, as valuable as that produced by an ordinary pipeline, though without accessing directly the FITS files. The analytics is done by Apache Solr and Spark and on a relational PostgreSQL database. As an example, we produce observables like metallicity indexes for the targets in the archive and compare the results with the ones coming from the HARPS-N regular data reduction software. The aim of this experiment is to explore the viability of a high availability cluster and distributed NoSQL database as a platform for complex scientific analytics on a large data set, which will then be ported to the WEAVE Archive System (WAS) which we are developing for the WEAVE multi object, fiber spectrograph.

Modeling and Simulation Behavior Validation Methodology and Extension Model Validation for the Individual Soldier

DTIC Science & Technology

2015-03-01

domains. Major model functions include: • Ground combat: Light and heavy forces. • Air mobile forces. • Future forces. • Fixed-wing and rotary-wing...Constraints: • Study must be completed no later than 31 December 2014. • Entity behavior limited to select COMBATXXI Mobility , Unmanned Aerial System...and SQL backend , as well as any open application programming interface API. • Allows data transparency and data driven navigation through the model

High Capacity Single Table Performance Design Using Partitioning in Oracle or PostgreSQL

DTIC Science & Technology

2012-03-01

Indicators ( KPIs ) 13  5.  Conclusion 14  List of Symbols, Abbreviations, and Acronyms 15  Distribution List 16 iv List of Figures Figure 1. Oracle...Figure 7. Time to seek and return one record. 4. Additional Key Performance Indicators ( KPIs ) In addition to pure response time, there are other...Laboratory ASM Automatic Storage Management CPU central processing unit I/O input/output KPIs key performance indicators OS operating system

An integrated data-analysis and database system for AMS 14C

NASA Astrophysics Data System (ADS)

Kjeldsen, Henrik; Olsen, Jesper; Heinemeier, Jan

2010-04-01

AMSdata is the name of a combined database and data-analysis system for AMS 14C and stable-isotope work that has been developed at Aarhus University. The system (1) contains routines for data analysis of AMS and MS data, (2) allows a flexible and accurate description of sample extraction and pretreatment, also when samples are split into several fractions, and (3) keeps track of all measured, calculated and attributed data. The structure of the database is flexible and allows an unlimited number of measurement and pretreatment procedures. The AMS 14C data analysis routine is fairly advanced and flexible, and it can be easily optimized for different kinds of measuring processes. Technically, the system is based on a Microsoft SQL server and includes stored SQL procedures for the data analysis. Microsoft Office Access is used for the (graphical) user interface, and in addition Excel, Word and Origin are exploited for input and output of data, e.g. for plotting data during data analysis.

Research on high availability architecture of SQL and NoSQL

NASA Astrophysics Data System (ADS)

Wang, Zhiguo; Wei, Zhiqiang; Liu, Hao

2017-03-01

With the advent of the era of big data, amount and importance of data have increased dramatically. SQL database develops in performance and scalability, but more and more companies tend to use NoSQL database as their databases, because NoSQL database has simpler data model and stronger extension capacity than SQL database. Almost all database designers including SQL database and NoSQL database aim to improve performance and ensure availability by reasonable architecture which can reduce the effects of software failures and hardware failures, so that they can provide better experiences for their customers. In this paper, I mainly discuss the architectures of MySQL, MongoDB, and Redis, which are high available and have been deployed in practical application environment, and design a hybrid architecture.

Chandra monitoring, trends, and response

NASA Astrophysics Data System (ADS)

Spitzbart, Brad D.; Wolk, Scott J.; Isobe, Takashi

2002-12-01

The Chandra X-ray Observatory was launched in July, 1999 and has yielded extraordinary scientific results. Behind the scenes, our Monitoring and Trends Analysis (MTA) system has proven to be a valuable resource. With three years worth of on-orbit data, we have available a vast array of both telescope diagnostic information and analysis of scientific data to access Observatory performance. As part of Chandra's Science Operations Team (SOT), the primary goal of MTA is to provide tools for effective decision making leading to the most efficient production of quality science output from the Observatory. We occupy a middle ground between flight operations, chiefly concerned with the health and safety of the spacecraft, and validation and verification, concerned with the scientific validity of the data taken and whether or not they fulfill the observer's requirements. In that role we provide and receive support from systems engineers, instrument experts, operations managers, and scientific users. MTA tools, products, and services include real-time monitoring and alert generation for the most mission critical components, long term trending of all spacecraft systems, detailed analysis of various subsystems for life expectancy or anomaly resolution, and creating and maintaining a large SQL database of relevant information. This is accomplished through the use of a wide variety of input data sources and flexible, accessible programming and analysis techniques. This paper will discuss the overall design of the system, its evolution and the resources available.

Geena 2, improved automated analysis of MALDI/TOF mass spectra.

PubMed

Romano, Paolo; Profumo, Aldo; Rocco, Mattia; Mangerini, Rosa; Ferri, Fabio; Facchiano, Angelo

2016-03-02

Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps. For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples. In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra. Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper. Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters. Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method. Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra.

Research on the technology of detecting the SQL injection attack and non-intrusive prevention in WEB system

NASA Astrophysics Data System (ADS)

Hu, Haibin

2017-05-01

Among numerous WEB security issues, SQL injection is the most notable and dangerous. In this study, characteristics and procedures of SQL injection are analyzed, and the method for detecting the SQL injection attack is illustrated. The defense resistance and remedy model of SQL injection attack is established from the perspective of non-intrusive SQL injection attack and defense. Moreover, the ability of resisting the SQL injection attack of the server has been comprehensively improved through the security strategies on operation system, IIS and database, etc.. Corresponding codes are realized. The method is well applied in the actual projects.

Maintaining Multimedia Data in a Geospatial Database

DTIC Science & Technology

2012-09-01

at PostgreSQL and MySQL as spatial databases was offered. Given their results, as each database produced result sets from zero to 100,000, it was...excelled given multiple conditions. A different look at PostgreSQL and MySQL as spatial databases was offered. Given their results, as each database... MySQL ................................................................................................14  B.  BENCHMARKING DATA RETRIEVED FROM TABLE

PhyloExplorer: a web server to validate, explore and query phylogenetic trees

PubMed Central

Ranwez, Vincent; Clairon, Nicolas; Delsuc, Frédéric; Pourali, Saeed; Auberval, Nicolas; Diser, Sorel; Berry, Vincent

2009-01-01

Background Many important problems in evolutionary biology require molecular phylogenies to be reconstructed. Phylogenetic trees must then be manipulated for subsequent inclusion in publications or analyses such as supertree inference and tree comparisons. However, no tool is currently available to facilitate the management of tree collections providing, for instance: standardisation of taxon names among trees with respect to a reference taxonomy; selection of relevant subsets of trees or sub-trees according to a taxonomic query; or simply computation of descriptive statistics on the collection. Moreover, although several databases of phylogenetic trees exist, there is currently no easy way to find trees that are both relevant and complementary to a given collection of trees. Results We propose a tool to facilitate assessment and management of phylogenetic tree collections. Given an input collection of rooted trees, PhyloExplorer provides facilities for obtaining statistics describing the collection, correcting invalid taxon names, extracting taxonomically relevant parts of the collection using a dedicated query language, and identifying related trees in the TreeBASE database. Conclusion PhyloExplorer is a simple and interactive website implemented through underlying Python libraries and MySQL databases. It is available at: and the source code can be downloaded from: . PMID:19450253

Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases

PubMed Central

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2018-01-01

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form. PMID:29608174

Executing Complexity-Increasing Queries in Relational (MySQL) and NoSQL (MongoDB and EXist) Size-Growing ISO/EN 13606 Standardized EHR Databases.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2018-03-19

This research shows a protocol to assess the computational complexity of querying relational and non-relational (NoSQL (not only Structured Query Language)) standardized electronic health record (EHR) medical information database systems (DBMS). It uses a set of three doubling-sized databases, i.e. databases storing 5000, 10,000 and 20,000 realistic standardized EHR extracts, in three different database management systems (DBMS): relational MySQL object-relational mapping (ORM), document-based NoSQL MongoDB, and native extensible markup language (XML) NoSQL eXist. The average response times to six complexity-increasing queries were computed, and the results showed a linear behavior in the NoSQL cases. In the NoSQL field, MongoDB presents a much flatter linear slope than eXist. NoSQL systems may also be more appropriate to maintain standardized medical information systems due to the special nature of the updating policies of medical information, which should not affect the consistency and efficiency of the data stored in NoSQL databases. One limitation of this protocol is the lack of direct results of improved relational systems such as archetype relational mapping (ARM) with the same data. However, the interpolation of doubling-size database results to those presented in the literature and other published results suggests that NoSQL systems might be more appropriate in many specific scenarios and problems to be solved. For example, NoSQL may be appropriate for document-based tasks such as EHR extracts used in clinical practice, or edition and visualization, or situations where the aim is not only to query medical information, but also to restore the EHR in exactly its original form.

Survey Software Evaluation

DTIC Science & Technology

2009-01-01

Oracle 9i, 10g  MySQL  MS SQL Server MS SQL Server Operating System Supported Windows 2003 Server  Windows 2000 Server (32 bit...WebStar (Mac OS X)  SunOne Internet Information Services (IIS) Database Server Supported MS SQL Server  MS SQL Server  Oracle 9i, 10g...challenges of Web-based surveys are: 1) identifying the best Commercial Off the Shelf (COTS) Web-based survey packages to serve the particular

An Optimization of the Basic School Military Occupational Skill Assignment Process

DTIC Science & Technology

2003-06-01

Corps Intranet (NMCI)23 supports it. We evaluated the use of Microsoft’s SQL Server, but dismissed this after learning that TBS did not possess a SQL ...Server license or a qualified SQL Server administrator.24 SQL Server would have provided for additional security measures not available in MS...administrator. Although not has powerful as SQL Server, MS Access can handle the multi-user environment necessary for this system.25 The training

Quantifying Uncertainty in Expert Judgment: Initial Results

DTIC Science & Technology

2013-03-01

lines of source code were added in . ---------- C++ = 32%; JavaScript = 29%; XML = 15%; C = 7%; CSS = 7%; Java = 5%; Oth- er = 5% LOC = 927,266...much total effort in person years has been spent on this project? CMU/SEI-2013-TR-001 | 33 5 MySQL , the most popular Open Source SQL...as MySQL , Oracle, PostgreSQL, MS SQL Server, ODBC, or Interbase. Features include email reminders, iCal/vCal import/export, re- mote subscriptions

Examining database persistence of ISO/EN 13606 standardized electronic health record extracts: relational vs. NoSQL approaches.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Lozano-Rubí, Raimundo; Serrano-Balazote, Pablo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2017-08-18

The objective of this research is to compare the relational and non-relational (NoSQL) database systems approaches in order to store, recover, query and persist standardized medical information in the form of ISO/EN 13606 normalized Electronic Health Record XML extracts, both in isolation and concurrently. NoSQL database systems have recently attracted much attention, but few studies in the literature address their direct comparison with relational databases when applied to build the persistence layer of a standardized medical information system. One relational and two NoSQL databases (one document-based and one native XML database) of three different sizes have been created in order to evaluate and compare the response times (algorithmic complexity) of six different complexity growing queries, which have been performed on them. Similar appropriate results available in the literature have also been considered. Relational and non-relational NoSQL database systems show almost linear algorithmic complexity query execution. However, they show very different linear slopes, the former being much steeper than the two latter. Document-based NoSQL databases perform better in concurrency than in isolation, and also better than relational databases in concurrency. Non-relational NoSQL databases seem to be more appropriate than standard relational SQL databases when database size is extremely high (secondary use, research applications). Document-based NoSQL databases perform in general better than native XML NoSQL databases. EHR extracts visualization and edition are also document-based tasks more appropriate to NoSQL database systems. However, the appropriate database solution much depends on each particular situation and specific problem.

Comprehensive Routing Security Development and Deployment for the Internet

DTIC Science & Technology

2015-02-01

feature enhancement and bug fixes. • MySQL : MySQL is a widely used and popular open source database package. It was chosen for database support in the...RPSTIR depends on several other open source packages. • MySQL : MySQL is used for the the local RPKI database cache. • OpenSSL: OpenSSL is used for...cryptographic libraries for X.509 certificates. • ODBC mySql Connector: ODBC (Open Database Connectivity) is a standard programming interface (API) for

Social media based NPL system to find and retrieve ARM data: Concept paper

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

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

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

Devarakonda, Ranjeet; Giansiracusa, Michael T.; Kumar, Jitendra

Information connectivity and retrieval has a role in our daily lives. The most pervasive source of online information is databases. The amount of data is growing at rapid rate and database technology is improving and having a profound effect. Almost all online applications are storing and retrieving information from databases. One challenge in supplying the public with wider access to informational databases is the need for knowledge of database languages like Structured Query Language (SQL). Although the SQL language has been published in many forms, not everybody is able to write SQL queries. Another challenge is that it may notmore » be practical to make the public aware of the structure of the database. There is a need for novice users to query relational databases using their natural language. To solve this problem, many natural language interfaces to structured databases have been developed. The goal is to provide more intuitive method for generating database queries and delivering responses. Social media makes it possible to interact with a wide section of the population. Through this medium, and with the help of Natural Language Processing (NLP) we can make the data of the Atmospheric Radiation Measurement Data Center (ADC) more accessible to the public. We propose an architecture for using Apache Lucene/Solr [1], OpenML [2,3], and Kafka [4] to generate an automated query/response system with inputs from Twitter5, our Cassandra DB, and our log database. Using the Twitter API and NLP we can give the public the ability to ask questions of our database and get automated responses.« less

TabSQL: a MySQL tool to facilitate mapping user data to public databases.

PubMed

Xia, Xiao-Qin; McClelland, Michael; Wang, Yipeng

2010-06-23

With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data.

TabSQL: a MySQL tool to facilitate mapping user data to public databases

PubMed Central

2010-01-01

Background With advances in high-throughput genomics and proteomics, it is challenging for biologists to deal with large data files and to map their data to annotations in public databases. Results We developed TabSQL, a MySQL-based application tool, for viewing, filtering and querying data files with large numbers of rows. TabSQL provides functions for downloading and installing table files from public databases including the Gene Ontology database (GO), the Ensembl databases, and genome databases from the UCSC genome bioinformatics site. Any other database that provides tab-delimited flat files can also be imported. The downloaded gene annotation tables can be queried together with users' data in TabSQL using either a graphic interface or command line. Conclusions TabSQL allows queries across the user's data and public databases without programming. It is a convenient tool for biologists to annotate and enrich their data. PMID:20573251

Migration from relational to NoSQL database

NASA Astrophysics Data System (ADS)

Ghotiya, Sunita; Mandal, Juhi; Kandasamy, Saravanakumar

2017-11-01

Data generated by various real time applications, social networking sites and sensor devices is of very huge amount and unstructured, which makes it difficult for Relational database management systems to handle the data. Data is very precious component of any application and needs to be analysed after arranging it in some structure. Relational databases are only able to deal with structured data, so there is need of NoSQL Database management System which can deal with semi -structured data also. Relational database provides the easiest way to manage the data but as the use of NoSQL is increasing it is becoming necessary to migrate the data from Relational to NoSQL databases. Various frameworks has been proposed previously which provides mechanisms for migration of data stored at warehouses in SQL, middle layer solutions which can provide facility of data to be stored in NoSQL databases to handle data which is not structured. This paper provides a literature review of some of the recent approaches proposed by various researchers to migrate data from relational to NoSQL databases. Some researchers proposed mechanisms for the co-existence of NoSQL and Relational databases together. This paper provides a summary of mechanisms which can be used for mapping data stored in Relational databases to NoSQL databases. Various techniques for data transformation and middle layer solutions are summarised in the paper.

NoSQL Data Store Technologies

DTIC Science & Technology

2014-09-01

NoSQL Data Store Technologies John Klein, Software Engineering Institute Patrick Donohoe, Software Engineering Institute Neil Ernst...REPORT TYPE N/A 3. DATES COVERED 4. TITLE AND SUBTITLE NoSQL Data Store Technologies 5a. CONTRACT NUMBER 5b. GRANT NUMBER 5c. PROGRAM ELEMENT...distribute data 4. Data Replication – determines how a NoSQL database facilitates reliable, high performance data replication to build

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL

PubMed Central

2010-01-01

Background Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. Results A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. Conclusions CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL. PMID:20594316

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

PubMed

Laukens, Kris; Hollunder, Jens; Dang, Thanh Hai; De Jaeger, Geert; Kuiper, Martin; Witters, Erwin; Verschoren, Alain; Van Leemput, Koenraad

2010-07-01

Molecular interaction networks can be efficiently studied using network visualization software such as Cytoscape. The relevant nodes, edges and their attributes can be imported in Cytoscape in various file formats, or directly from external databases through specialized third party plugins. However, molecular data are often stored in relational databases with their own specific structure, for which dedicated plugins do not exist. Therefore, a more generic solution is presented. A new Cytoscape plugin 'CytoSQL' is developed to connect Cytoscape to any relational database. It allows to launch SQL ('Structured Query Language') queries from within Cytoscape, with the option to inject node or edge features of an existing network as SQL arguments, and to convert the retrieved data to Cytoscape network components. Supported by a set of case studies we demonstrate the flexibility and the power of the CytoSQL plugin in converting specific data subsets into meaningful network representations. CytoSQL offers a unified approach to let Cytoscape interact with relational databases. Thanks to the power of the SQL syntax, this tool can rapidly generate and enrich networks according to very complex criteria. The plugin is available at http://www.ptools.ua.ac.be/CytoSQL.

Method of validating measurement data of a process parameter from a plurality of individual sensor inputs

DOEpatents

Scarola, Kenneth; Jamison, David S.; Manazir, Richard M.; Rescorl, Robert L.; Harmon, Daryl L.

1998-01-01

A method for generating a validated measurement of a process parameter at a point in time by using a plurality of individual sensor inputs from a scan of said sensors at said point in time. The sensor inputs from said scan are stored and a first validation pass is initiated by computing an initial average of all stored sensor inputs. Each sensor input is deviation checked by comparing each input including a preset tolerance against the initial average input. If the first deviation check is unsatisfactory, the sensor which produced the unsatisfactory input is flagged as suspect. It is then determined whether at least two of the inputs have not been flagged as suspect and are therefore considered good inputs. If two or more inputs are good, a second validation pass is initiated by computing a second average of all the good sensor inputs, and deviation checking the good inputs by comparing each good input including a present tolerance against the second average. If the second deviation check is satisfactory, the second average is displayed as the validated measurement and the suspect sensor as flagged as bad. A validation fault occurs if at least two inputs are not considered good, or if the second deviation check is not satisfactory. In the latter situation the inputs from each of all the sensors are compared against the last validated measurement and the value from the sensor input that deviates the least from the last valid measurement is displayed.

SQL-RAMS

NASA Technical Reports Server (NTRS)

Alfaro, Victor O.; Casey, Nancy J.

2005-01-01

SQL-RAMS (where "SQL" signifies Structured Query Language and "RAMS" signifies Rocketdyne Automated Management System) is a successor to the legacy version of RAMS -- a computer program used to manage all work, nonconformance, corrective action, and configuration management on rocket engines and ground support equipment at Stennis Space Center. The legacy version resided in the File-Maker Pro software system and was constructed in modules that could act as standalone programs. There was little or no integration among modules. Because of limitations on file-management capabilities in FileMaker Pro, and because of difficulty of integration of FileMaker Pro with other software systems for exchange of data using such industry standards as SQL, the legacy version of RAMS proved to be limited, and working to circumvent its limitations too time-consuming. In contrast, SQL-RAMS is an integrated SQL-server-based program that supports all data-exchange software industry standards. Whereas in the legacy version, it was necessary to access individual modules to gain insight into a particular workstatus document, SQL-RAMS provides access through a single-screen presentation of core modules. In addition, SQL-RAMS enables rapid and efficient filtering of displayed statuses by predefined categories and test numbers. SQL-RAMS is rich in functionality and encompasses significant improvements over the legacy system. It provides users the ability to perform many tasks, which in the past required administrator intervention. Additionally, many of the design limitations have been corrected, allowing for a robust application that is user centric.

SQL-RAMS

NASA Technical Reports Server (NTRS)

Alfaro, Victor O.; Casey, Nancy J.

2005-01-01

SQL-RAMS (where "SQL" signifies Structured Query Language and "RAMS" signifies Rocketdyne Automated Management System) is a successor to the legacy version of RAMS a computer program used to manage all work, nonconformance, corrective action, and configuration management on rocket engines and ground support equipment at Stennis Space Center. The legacy version resided in the FileMaker Pro software system and was constructed in modules that could act as stand-alone programs. There was little or no integration among modules. Because of limitations on file-management capabilities in FileMaker Pro, and because of difficulty of integration of FileMaker Pro with other software systems for exchange of data using such industry standards as SQL, the legacy version of RAMS proved to be limited, and working to circumvent its limitations too time-consuming. In contrast, SQL-RAMS is an integrated SQL-server-based program that supports all data-exchange software industry standards. Whereas in the legacy version, it was necessary to access individual modules to gain insight to a particular work-status documents, SQL-RAMS provides access through a single-screen presentation of core modules. In addition, SQL-RAMS enable rapid and efficient filtering of displayed statuses by predefined categories and test numbers. SQL-RAMS is rich in functionality and encompasses significant improvements over the legacy system. It provides users the ability to perform many tasks which in the past required administrator intervention. Additionally many of the design limitations have been corrected allowing for a robust application that is user centric.

Design and Analysis of a Model Reconfigurable Cyber-Exercise Laboratory (RCEL) for Information Assurance Education

DTIC Science & Technology

2004-03-01

with MySQL . This choice was made because MySQL is open source. Any significant database engine such as Oracle or MS- SQL or even MS Access can be used...10 Figure 6. The DoD vs . Commercial Life Cycle...necessarily be interested in SCADA network security 13. MySQL (Database server) – This station represents a typical data server for a web page

Analysis and Development of a Web-Enabled Planning and Scheduling Database Application

DTIC Science & Technology

2013-09-01

establishes an entity—relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web- enabled interface for...development, develop, design, process, re- engineering, reengineering, MySQL , structured query language, SQL, myPHPadmin. 15. NUMBER OF PAGES 107 16...relationship diagram for the desired process, constructs an operable database using MySQL , and provides a web-enabled interface for the population of

Petaminer: Using ROOT for efficient data storage in MySQL database

NASA Astrophysics Data System (ADS)

Cranshaw, J.; Malon, D.; Vaniachine, A.; Fine, V.; Lauret, J.; Hamill, P.

2010-04-01

High Energy and Nuclear Physics (HENP) experiments store Petabytes of event data and Terabytes of calibration data in ROOT files. The Petaminer project is developing a custom MySQL storage engine to enable the MySQL query processor to directly access experimental data stored in ROOT files. Our project is addressing the problem of efficient navigation to PetaBytes of HENP experimental data described with event-level TAG metadata, which is required by data intensive physics communities such as the LHC and RHIC experiments. Physicists need to be able to compose a metadata query and rapidly retrieve the set of matching events, where improved efficiency will facilitate the discovery process by permitting rapid iterations of data evaluation and retrieval. Our custom MySQL storage engine enables the MySQL query processor to directly access TAG data stored in ROOT TTrees. As ROOT TTrees are column-oriented, reading them directly provides improved performance over traditional row-oriented TAG databases. Leveraging the flexible and powerful SQL query language to access data stored in ROOT TTrees, the Petaminer approach enables rich MySQL index-building capabilities for further performance optimization.

Evaluation of relational and NoSQL database architectures to manage genomic annotations.

PubMed

Schulz, Wade L; Nelson, Brent G; Felker, Donn K; Durant, Thomas J S; Torres, Richard

2016-12-01

While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized. To this end, we compared the storage, indexing, and query efficiency of a common relational database (MySQL), a document-oriented NoSQL database (MongoDB), and a relational database with NoSQL support (PostgreSQL). When used to store genomic annotations from the dbSNP database, we found the NoSQL architectures to outperform traditional, relational models for speed of data storage, indexing, and query retrieval in nearly every operation. These findings strongly support the use of novel database technologies to improve the efficiency of data management within the biological sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

New Software for Ensemble Creation in the Spitzer-Space-Telescope Operations Database

NASA Technical Reports Server (NTRS)

Laher, Russ; Rector, John

2004-01-01

Some of the computer pipelines used to process digital astronomical images from NASA's Spitzer Space Telescope require multiple input images, in order to generate high-level science and calibration products. The images are grouped into ensembles according to well documented ensemble-creation rules by making explicit associations in the operations Informix database at the Spitzer Science Center (SSC). The advantage of this approach is that a simple database query can retrieve the required ensemble of pipeline input images. New and improved software for ensemble creation has been developed. The new software is much faster than the existing software because it uses pre-compiled database stored-procedures written in Informix SPL (SQL programming language). The new software is also more flexible because the ensemble creation rules are now stored in and read from newly defined database tables. This table-driven approach was implemented so that ensemble rules can be inserted, updated, or deleted without modifying software.

Knowledge Data Base for Amorphous Metals

DTIC Science & Technology

2007-07-26

not programmatic, updates. Over 100 custom SQL statements that maintain the domain specific data are attached to the workflow entries in a generic...for the form by populating the SQL and run generation tables. Application data may be prepared in different ways for two steps that invoke the same form...run generation mode). There is a single table of SQL commands. Each record has a user-definable ID, the SQL code, and a comment. The run generation

Analysis and comparison of NoSQL databases with an introduction to consistent references in big data storage systems

NASA Astrophysics Data System (ADS)

Dziedzic, Adam; Mulawka, Jan

2014-11-01

NoSQL is a new approach to data storage and manipulation. The aim of this paper is to gain more insight into NoSQL databases, as we are still in the early stages of understanding when to use them and how to use them in an appropriate way. In this submission descriptions of selected NoSQL databases are presented. Each of the databases is analysed with primary focus on its data model, data access, architecture and practical usage in real applications. Furthemore, the NoSQL databases are compared in fields of data references. The relational databases offer foreign keys, whereas NoSQL databases provide us with limited references. An intermediate model between graph theory and relational algebra which can address the problem should be created. Finally, the proposal of a new approach to the problem of inconsistent references in Big Data storage systems is introduced.

Validation of the United States Marine Corps Qualified Candidate Population Model

DTIC Science & Technology

2003-03-01

time. Fields are created in the database to support this forecasting. User forms and a macro are programmed in Microsoft VBA to develop the...at 0.001. To accomplish 50,000 iterations of a minimization problem, this study wrote a macro in the VBA programming language that guides the solver...success in the commissioning process. **To improve the diagnostics of this propensity model, other factors were considered as well. Applying SQL

siRNAmod: A database of experimentally validated chemically modified siRNAs.

PubMed

Dar, Showkat Ahmad; Thakur, Anamika; Qureshi, Abid; Kumar, Manoj

2016-01-28

Small interfering RNA (siRNA) technology has vast potential for functional genomics and development of therapeutics. However, it faces many obstacles predominantly instability of siRNAs due to nuclease digestion and subsequently biologically short half-life. Chemical modifications in siRNAs provide means to overcome these shortcomings and improve their stability and potency. Despite enormous utility bioinformatics resource of these chemically modified siRNAs (cm-siRNAs) is lacking. Therefore, we have developed siRNAmod, a specialized databank for chemically modified siRNAs. Currently, our repository contains a total of 4894 chemically modified-siRNA sequences, comprising 128 unique chemical modifications on different positions with various permutations and combinations. It incorporates important information on siRNA sequence, chemical modification, their number and respective position, structure, simplified molecular input line entry system canonical (SMILES), efficacy of modified siRNA, target gene, cell line, experimental methods, reference etc. It is developed and hosted using Linux Apache MySQL PHP (LAMP) software bundle. Standard user-friendly browse, search facility and analysis tools are also integrated. It would assist in understanding the effect of chemical modifications and further development of stable and efficacious siRNAs for research as well as therapeutics. siRNAmod is freely available at: http://crdd.osdd.net/servers/sirnamod.

Risk Assessment of the Naval Postgraduate School Gigabit Network

DTIC Science & Technology

2004-09-01

Management Server (1) • Ras Server (1) • Remedy Server (1) • Samba Server(2) • SQL Servers (3) • Web Servers (3) • WINS Server (1) • Library...Server Bob Sharp INCA Windows 2000 Advanced Server NPGS Landesk SQL 2000 Alan Pires eagle Microsoft Windows 2000 Advanced Server EWS NPGS Landesk...Advanced Server Special Projects NPGS SQL Alan Pires MC01BDB Microsoft Windows 2000 Advanced Server Special Projects NPGS SQL 2000 Alan Pires

Blind Seer: A Scalable Private DBMS

DTIC Science & Technology

2014-05-01

searchable index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower...than MySQL , although some queries are costlier). We support a rich query set, including searching on arbitrary boolean formulas on keywords and ranges...index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower than MySQL

Performance Evaluation of NoSQL Databases: A Case Study

DTIC Science & Technology

2015-02-01

a centralized relational database. The customer decided to consider NoSQL technologies for two specific uses, namely:  the primary data store for...17 custom specific 6. FU NoSQL availab data mo arking of data g a specific wo sin benchmark f hmark for tran le workload de o publish meas their...The choice of a particular NoSQL database imposes a specific distributed software architecture and data model, and is a major determinant of the

DOMe: A deduplication optimization method for the NewSQL database backups

PubMed Central

Wang, Longxiang; Zhu, Zhengdong; Zhang, Xingjun; Wang, Yinfeng

2017-01-01

Reducing duplicated data of database backups is an important application scenario for data deduplication technology. NewSQL is an emerging database system and is now being used more and more widely. NewSQL systems need to improve data reliability by periodically backing up in-memory data, resulting in a lot of duplicated data. The traditional deduplication method is not optimized for the NewSQL server system and cannot take full advantage of hardware resources to optimize deduplication performance. A recent research pointed out that the future NewSQL server will have thousands of CPU cores, large DRAM and huge NVRAM. Therefore, how to utilize these hardware resources to optimize the performance of data deduplication is an important issue. To solve this problem, we propose a deduplication optimization method (DOMe) for NewSQL system backup. To take advantage of the large number of CPU cores in the NewSQL server to optimize deduplication performance, DOMe parallelizes the deduplication method based on the fork-join framework. The fingerprint index, which is the key data structure in the deduplication process, is implemented as pure in-memory hash table, which makes full use of the large DRAM in NewSQL system, eliminating the performance bottleneck problem of fingerprint index existing in traditional deduplication method. The H-store is used as a typical NewSQL database system to implement DOMe method. DOMe is experimentally analyzed by two representative backup data. The experimental results show that: 1) DOMe can reduce the duplicated NewSQL backup data. 2) DOMe significantly improves deduplication performance by parallelizing CDC algorithms. In the case of the theoretical speedup ratio of the server is 20.8, the speedup ratio of DOMe can achieve up to 18; 3) DOMe improved the deduplication throughput by 1.5 times through the pure in-memory index optimization method. PMID:29049307

Automatically Preparing Safe SQL Queries

NASA Astrophysics Data System (ADS)

Bisht, Prithvi; Sistla, A. Prasad; Venkatakrishnan, V. N.

We present the first sound program source transformation approach for automatically transforming the code of a legacy web application to employ PREPARE statements in place of unsafe SQL queries. Our approach therefore opens the way for eradicating the SQL injection threat vector from legacy web applications.

Using Distinct Sectors in Media Sampling and Full Media Analysis to Detect Presence of Documents from a Corpus

DTIC Science & Technology

2012-09-01

relative performance of several conventional SQL and NoSQL databases with a set of one billion file block hashes. Digital Forensics, Sector Hashing, Full... NoSQL databases with a set of one billion file block hashes. v THIS PAGE INTENTIONALLY LEFT BLANK vi Table of Contents List of Acronyms and...Operating System NOOP No Operation assembly instruction NoSQL “Not only SQL” model for non-relational database management NSRL National Software

Global ISR: Toward a Comprehensive Defense Against Unauthorized Code Execution

DTIC Science & Technology

2010-10-01

implementation using two of the most popular open- source servers: the Apache web server, and the MySQL database server. For Apache, we measure the effect that...utility ab. T o ta l T im e ( s e c ) 0 500 1000 1500 2000 2500 3000 Native Null ISR ISR−MP Fig. 3. The MySQL test-insert bench- mark measures...various SQL operations. The figure draws total execution time as reported by the benchmark utility. Finally, we benchmarked a MySQL database server using

SQL/NF Translator for the Triton Nested Relational Database System

DTIC Science & Technology

1990-12-01

18as., Ohio .. 9~~ ~~ 1 4- AFIT/GCE/ENG/90D-05 SQL/Nk1 TRANSLATOR FOR THE TRITON NESTED RELATIONAL DATABASE SYSTEM THESIS Craig William Schnepf Captain...FOR THE TRITON NESTED RELATIONAL DATABASE SYSTEM THESIS Presented to the Faculty of the School of Engineering of the Air Force Institute of Technnlogy... systems . The SQL/NF query language used for the nested relationil model is an extension of the popular relational model query language SQL. The query

Flexible Decision Support in Device-Saturated Environments

DTIC Science & Technology

2003-10-01

also output tuples to a remote MySQL or Postgres database. 3.3 GUI The GUI allows the user to pose queries using SQL and to display query...DatabaseConnection.java – handles connections to an external database (such as MySQL or Postgres ). • Debug.java – contains the code for printing out Debug messages...also provided. It is possible to output the results of queries to a MySQL or Postgres database for archival and the GUI can query those results

Evaluating a NoSQL Alternative for Chilean Virtual Observatory Services

NASA Astrophysics Data System (ADS)

Antognini, J.; Araya, M.; Solar, M.; Valenzuela, C.; Lira, F.

2015-09-01

Currently, the standards and protocols for data access in the Virtual Observatory architecture (DAL) are generally implemented with relational databases based on SQL. In particular, the Astronomical Data Query Language (ADQL), language used by IVOA to represent queries to VO services, was created to satisfy the different data access protocols, such as Simple Cone Search. ADQL is based in SQL92, and has extra functionality implemented using PgSphere. An emergent alternative to SQL are the so called NoSQL databases, which can be classified in several categories such as Column, Document, Key-Value, Graph, Object, etc.; each one recommended for different scenarios. Within their notable characteristics we can find: schema-free, easy replication support, simple API, Big Data, etc. The Chilean Virtual Observatory (ChiVO) is developing a functional prototype based on the IVOA architecture, with the following relevant factors: Performance, Scalability, Flexibility, Complexity, and Functionality. Currently, it's very difficult to compare these factors, due to a lack of alternatives. The objective of this paper is to compare NoSQL alternatives with SQL through the implementation of a Web API REST that satisfies ChiVO's needs: a SESAME-style name resolver for the data from ALMA. Therefore, we propose a test scenario by configuring a NoSQL database with data from different sources and evaluating the feasibility of creating a Simple Cone Search service and its performance. This comparison will allow to pave the way for the application of Big Data databases in the Virtual Observatory.

Urgent Virtual Machine Eviction with Enlightened Post-Copy

DTIC Science & Technology

2015-12-01

memory is in use, almost all of which is by Memcached. MySQL : The VMs run MySQL 5.6, and the clients execute OLTPBenchmark [3] using the Twitter...workload with scale factor of 960. The VMs are each allocated 16 cores and 30 GB of memory, and MySQL is configured with a 16 GB buffer pool in memory. The...operation mix for 5 minutes as a warm-up. At the time of migration, MySQL uses approximately 17 GB of memory, and almost all of the 30 GB memory is

Overview of Heat Addition and Efficiency Predictions for an Advanced Stirling Convertor

NASA Technical Reports Server (NTRS)

Wilson, Scott D.; Reid, Terry; Schifer, Nicholas; Briggs, Maxwell

2011-01-01

Past methods of predicting net heat input needed to be validated. Validation effort pursued with several paths including improving model inputs, using test hardware to provide validation data, and validating high fidelity models. Validation test hardware provided direct measurement of net heat input for comparison to predicted values. Predicted value of net heat input was 1.7 percent less than measured value and initial calculations of measurement uncertainty were 2.1 percent (under review). Lessons learned during validation effort were incorporated into convertor modeling approach which improved predictions of convertor efficiency.

NoSQL: collection document and cloud by using a dynamic web query form

NASA Astrophysics Data System (ADS)

Abdalla, Hemn B.; Lin, Jinzhao; Li, Guoquan

2015-07-01

Mongo-DB (from "humongous") is an open-source document database and the leading NoSQL database. A NoSQL (Not Only SQL, next generation databases, being non-relational, deal, open-source and horizontally scalable) presenting a mechanism for storage and retrieval of documents. Previously, we stored and retrieved the data using the SQL queries. Here, we use the MonogoDB that means we are not utilizing the MySQL and SQL queries. Directly importing the documents into our Drives, retrieving the documents on that drive by not applying the SQL queries, using the IO BufferReader and Writer, BufferReader for importing our type of document files to my folder (Drive). For retrieving the document files, the usage is BufferWriter from the particular folder (or) Drive. In this sense, providing the security for those storing files for what purpose means if we store the documents in our local folder means all or views that file and modified that file. So preventing that file, we are furnishing the security. The original document files will be changed to another format like in this paper; Binary format is used. Our documents will be converting to the binary format after that direct storing in one of our folder, that time the storage space will provide the private key for accessing that file. Wherever any user tries to discover the Document files means that file data are in the binary format, the document's file owner simply views that original format using that personal key from receive the secret key from the cloud.

Recommender System for Learning SQL Using Hints

ERIC Educational Resources Information Center

Lavbic, Dejan; Matek, Tadej; Zrnec, Aljaž

2017-01-01

Today's software industry requires individuals who are proficient in as many programming languages as possible. Structured query language (SQL), as an adopted standard, is no exception, as it is the most widely used query language to retrieve and manipulate data. However, the process of learning SQL turns out to be challenging. The need for a…

Life in extra dimensions of database world or penetration of NoSQL in HEP community

NASA Astrophysics Data System (ADS)

Kuznetsov, V.; Evans, D.; Metson, S.

2012-12-01

The recent buzzword in IT world is NoSQL. Major players, such as Facebook, Yahoo, Google, etc. are widely adopted different “NoSQL” solutions for their needs. Horizontal scalability, flexible data model and management of big data volumes are only a few advantages of NoSQL. In CMS experiment we use several of them in production environment. Here, we present CMS projects based on NoSQL solutions, their strengths and weaknesses as well as our experience with those tools and their coexistence with standard RDBMS solutions in our applications.

A Database Design for the Brazilian Air Force Military Personnel Control System.

DTIC Science & Technology

1987-06-01

GIVEN A RECNum GET MOVING HISTORICAL". 77 SEL4 PlC X(70) VALUE ". 4. GIVEN A RECNUM GET NOMINATION HISTORICAL". 77 SEL5 PIC X(70) VALUE it 5. GIVEN A...WHERE - "°RECNUM = :RECNUM". 77 SQL-SEL3-LENGTH PIC S9999 VALUE 150 COMP. 77 SQL- SEL4 PIC X(150) VALUE "SELECT ABBREV,DTNOM,DTEXO,SITN FROM...NOMINATION WHERE RECNUM 77 SQL- SEL4 -LENGTH PIC S9999 VALUE 150 COMP. 77 SQL-SEL5 PIC X(150) VALUE "SELECT ABBREVDTDES,DTWAIVER,SITD FROM DESIG WHERE RECNUM It

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters.

PubMed

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software - 'RED' (RNA Editing sites Detector) - for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector.

RED: A Java-MySQL Software for Identifying and Visualizing RNA Editing Sites Using Rule-Based and Statistical Filters

PubMed Central

Sun, Yongmei; Li, Xing; Wu, Di; Pan, Qi; Ji, Yuefeng; Ren, Hong; Ding, Keyue

2016-01-01

RNA editing is one of the post- or co-transcriptional processes that can lead to amino acid substitutions in protein sequences, alternative pre-mRNA splicing, and changes in gene expression levels. Although several methods have been suggested to identify RNA editing sites, there remains challenges to be addressed in distinguishing true RNA editing sites from its counterparts on genome and technical artifacts. In addition, there lacks a software framework to identify and visualize potential RNA editing sites. Here, we presented a software − ‘RED’ (RNA Editing sites Detector) − for the identification of RNA editing sites by integrating multiple rule-based and statistical filters. The potential RNA editing sites can be visualized at the genome and the site levels by graphical user interface (GUI). To improve performance, we used MySQL database management system (DBMS) for high-throughput data storage and query. We demonstrated the validity and utility of RED by identifying the presence and absence of C→U RNA-editing sites experimentally validated, in comparison with REDItools, a command line tool to perform high-throughput investigation of RNA editing. In an analysis of a sample data-set with 28 experimentally validated C→U RNA editing sites, RED had sensitivity and specificity of 0.64 and 0.5. In comparison, REDItools had a better sensitivity (0.75) but similar specificity (0.5). RED is an easy-to-use, platform-independent Java-based software, and can be applied to RNA-seq data without or with DNA sequencing data. The package is freely available under the GPLv3 license at http://github.com/REDetector/RED or https://sourceforge.net/projects/redetector. PMID:26930599

Database Migration for Command and Control

DTIC Science & Technology

2002-11-01

Sql - proprietary JDP Private Area Air defense data Defended asset list Oracle 7.3.2 - Automated process (OLTP...TADIL warnings Oracle 7.3.2 Flat File - Discrete transaction with data upds - NRT response required Pull mission data Std SQL ...level execution data Oracle 7.3 User update External interfaces Auto/manual backup Messaging Proprietary replication (internally) SQL Web server

Oracle Applications Patch Administration Tool (PAT) Beta Version

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

2002-01-04

PAT is a Patch Administration Tool that provides analysis, tracking, and management of Oracle Application patches. This includes capabilities as outlined below: Patch Analysis & Management Tool Outline of capabilities: Administration Patch Data Maintenance -- track Oracle Application patches applied to what database instance & machine Patch Analysis capture text files (readme.txt and driver files) form comparison detail report comparison detail PL/SQL package comparison detail SQL scripts detail JSP module comparison detail Parse and load the current applptch.txt (10.7) or load patch data from Oracle Application database patch tables (11i) Display Analysis -- Compare patch to be applied with currentmore » Oracle Application installed Appl_top code versions Patch Detail Module comparison detail Analyze and display one Oracle Application module patch. Patch Management -- automatic queue and execution of patches Administration Parameter maintenance -- setting for directory structure of Oracle Application appl_top Validation data maintenance -- machine names and instances to patch Operation Patch Data Maintenance Schedule a patch (queue for later execution) Run a patch (queue for immediate execution) Review the patch logs Patch Management Reports« less

Network Configuration of Oracle and Database Programming Using SQL

NASA Technical Reports Server (NTRS)

Davis, Melton; Abdurrashid, Jibril; Diaz, Philip; Harris, W. C.

2000-01-01

A database can be defined as a collection of information organized in such a way that it can be retrieved and used. A database management system (DBMS) can further be defined as the tool that enables us to manage and interact with the database. The Oracle 8 Server is a state-of-the-art information management environment. It is a repository for very large amounts of data, and gives users rapid access to that data. The Oracle 8 Server allows for sharing of data between applications; the information is stored in one place and used by many systems. My research will focus primarily on SQL (Structured Query Language) programming. SQL is the way you define and manipulate data in Oracle's relational database. SQL is the industry standard adopted by all database vendors. When programming with SQL, you work on sets of data (i.e., information is not processed one record at a time).

Teaching Case: Introduction to NoSQL in a Traditional Database Course

ERIC Educational Resources Information Center

Fowler, Brad; Godin, Joy; Geddy, Margaret

2016-01-01

Many organizations are dealing with the increasing demands of big data, so they are turning to NoSQL databases as their preferred system for handling the unique problems of capturing and storing massive amounts of data. Therefore, it is likely that employees in all sizes of organizations will encounter NoSQL databases. Thus, to be more job-ready,…

Zero tolerance for incorrect data: Best practices in SQL transaction programming

NASA Astrophysics Data System (ADS)

Laiho, M.; Skourlas, C.; Dervos, D. A.

2015-02-01

DBMS products differ in the way they support even the basic SQL transaction services. In this paper, a framework of best practices in SQL transaction programming is given and discussed. The SQL developers are advised to experiment with and verify the services supported by the DBMS product used. The framework has been developed by DBTechNet, a European network of teachers, trainers and ICT professionals. A course module on SQL transactions, offered by the LLP "DBTech VET Teachers" programme, is also presented and discussed. Aims and objectives of the programme include the introduction of the topics and content of SQL transactions and concurrency control to HE/VET curricula and addressing the need for initial and continuous training on these topics to in-company trainers, VET teachers, and Higher Education students. An overview of the course module, its learning outcomes, the education and training (E&T) content, virtual database labs with hands-on self-practicing exercises, plus instructions for the teacher/trainer on the pedagogy and the usage of the course modules' content are briefly described. The main principle adopted is to "Learn by verifying in practice" and the transactions course motto is: "Zero Tolerance for Incorrect Data".

CMS users data management service integration and first experiences with its NoSQL data storage

NASA Astrophysics Data System (ADS)

Riahi, H.; Spiga, D.; Boccali, T.; Ciangottini, D.; Cinquilli, M.; Hernàndez, J. M.; Konstantinov, P.; Mascheroni, M.; Santocchia, A.

2014-06-01

The distributed data analysis workflow in CMS assumes that jobs run in a different location to where their results are finally stored. Typically the user outputs must be transferred from one site to another by a dedicated CMS service, AsyncStageOut. This new service is originally developed to address the inefficiency in using the CMS computing resources when transferring the analysis job outputs, synchronously, once they are produced in the job execution node to the remote site. The AsyncStageOut is designed as a thin application relying only on the NoSQL database (CouchDB) as input and data storage. It has progressed from a limited prototype to a highly adaptable service which manages and monitors the whole user files steps, namely file transfer and publication. The AsyncStageOut is integrated with the Common CMS/Atlas Analysis Framework. It foresees the management of nearly nearly 200k users' files per day of close to 1000 individual users per month with minimal delays, and providing a real time monitoring and reports to users and service operators, while being highly available. The associated data volume represents a new set of challenges in the areas of database scalability and service performance and efficiency. In this paper, we present an overview of the AsyncStageOut model and the integration strategy with the Common Analysis Framework. The motivations for using the NoSQL technology are also presented, as well as data design and the techniques used for efficient indexing and monitoring of the data. We describe deployment model for the high availability and scalability of the service. We also discuss the hardware requirements and the results achieved as they were determined by testing with actual data and realistic loads during the commissioning and the initial production phase with the Common Analysis Framework.

The BiolAD-DB system : an informatics system for clinical and genetic data.

PubMed

Nielsen, David A; Leidner, Marty; Haynes, Chad; Krauthammer, Michael; Kreek, Mary Jeanne

2007-01-01

The Biology of Addictive Diseases-Database (BiolAD-DB) system is a research bioinformatics system for archiving, analyzing, and processing of complex clinical and genetic data. The database schema employs design principles for handling complex clinical information, such as response items in genetic questionnaires. Data access and validation is provided by the BiolAD-DB client application, which features a data validation engine tightly coupled to a graphical user interface. Data integrity is provided by the password-protected BiolAD-DB SQL compliant server and database. BiolAD-DB tools further provide functionalities for generating customized reports and views. The BiolAD-DB system schema, client, and installation instructions are freely available at http://www.rockefeller.edu/biolad-db/.

Methods to Secure Databases Against Vulnerabilities

DTIC Science & Technology

2015-12-01

for several languages such as C, C++, PHP, Java and Python [16]. MySQL will work well with very large databases. The documentation references...using Eclipse and connected to each database management system using Python and Java drivers provided by MySQL , MongoDB, and Datastax (for Cassandra...tiers in Python and Java . Problem MySQL MongoDB Cassandra 1. Injection a. Tautologies Vulnerable Vulnerable Not Vulnerable b. Illegal query

DESPIC: Detecting Early Signatures of Persuasion in Information Cascades

DTIC Science & Technology

2015-08-27

over NoSQL Databases, Proceedings of the 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2014). 26-MAY-14, . : , P...over NoSQL Databases. Proceedings of the 14th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2014). Chicago, IL, USA...distributed NoSQL databases including HBase and Riak, we finalized the requirements of the optimal computational architecture to support our framework

User’s Manual for a Prototype Binding of ANSI-Standard SQL to Ada Supporting the SAME Methodology for the Software Technology for Adaptable, Reliable Systems (STARS) Program

DTIC Science & Technology

1990-06-30

declaring all of the valid enumeration values for a domain of type enumeration. Example-> In type color_vals is (red, blue , green), color_vals is the name...Color Vals is (red, white, blue ); package Fifth is new domainl.generateenum domain (ColorVals, Colors, enumeration, nullandnotnull); Resulting...generated domain definition-> type colorsnotnull is (red, white, blue ); package colors_ops is new sqlenumeration_pkg(colors notnull); type colors_type is

Joint Battlespace Infosphere: Information Management Within a C2 Enterprise

DTIC Science & Technology

2005-06-01

using. In version 1.2, we support both MySQL and Oracle as underlying implementations where the XML metadata schema is mapped into relational tables in...Identity Servers, Role-Based Access Control, and Policy Representation – Databases: Oracle , MySQL , TigerLogic, Berkeley XML DB 15 Instrumentation Services...converted to SQL for execution. Invocations are then forwarded to the appropriate underlying IOR core components that have the responsibility of issuing

Analyzing Enron Data: Bitmap Indexing Outperforms MySQL Queries bySeveral Orders of Magnitude

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

Stockinger, Kurt; Rotem, Doron; Shoshani, Arie

2006-01-28

FastBit is an efficient, compressed bitmap indexing technology that was developed in our group. In this report we evaluate the performance of MySQL and FastBit for analyzing the email traffic of the Enron dataset. The first finding shows that materializing the join results of several tables significantly improves the query performance. The second finding shows that FastBit outperforms MySQL by several orders of magnitude.

Reactive Aggregate Model Protecting Against Real-Time Threats

DTIC Science & Technology

2014-09-01

on the underlying functionality of three core components. • MS SQL server 2008 backend database. • Microsoft IIS running on Windows server 2008...services. The capstone tested a Linux-based Apache web server with the following software implementations: • MySQL as a Linux-based backend server for...malicious compromise. 1. Assumptions • GINA could connect to a backend MS SQL database through proper configuration of DotNetNuke. • GINA had access

Information Security Considerations for Applications Using Apache Accumulo

DTIC Science & Technology

2014-09-01

Distributed File System INSCOM United States Army Intelligence and Security Command JPA Java Persistence API JSON JavaScript Object Notation MAC Mandatory... MySQL [13]. BigTable can process 20 petabytes per day [14]. High degree of scalability on commodity hardware. NoSQL databases do not rely on highly...manipulation in relational databases. NoSQL databases each have a unique programming interface that uses a lower level procedural language (e.g., Java

Database Entity Persistence with Hibernate for the Network Connectivity Analysis Model

DTIC Science & Technology

2014-04-01

time savings in the Java coding development process. Appendices A and B describe address setup procedures for installing the MySQL database...development environment is required: • The open source MySQL Database Management System (DBMS) from Oracle, which is a Java Database Connectivity (JDBC...compliant DBMS • MySQL JDBC Driver library that comes as a plug-in with the Netbeans distribution • The latest Java Development Kit with the latest

Learning Asset Technology Integration Support Tool Design Document

DTIC Science & Technology

2010-05-11

language known as Hypertext Preprocessor ( PHP ) and by MySQL – a relational database management system that can also be used for content management. It...Requirements The LATIST tool will be implemented utilizing a WordPress platform with MySQL as the database. Also the LATIST system must effectively work... MySQL . When designing the LATIST system there are several considerations which must be accounted for in the working prototype. These include: • DAU

Standard Port-Visit Cost Forecasting Model for U.S. Navy Husbanding Contracts

DTIC Science & Technology

2009-12-01

Protocol (HTTP) server.35 2. MySQL . An open-source database.36 3. PHP . A common scripting language used for Web development.37 E. IMPLEMENTATION OF...Inc. (2009). MySQL Community Server (Version 5.1) [Software]. Available from http://dev.mysql.com/downloads/ 37 The PHP Group (2009). PHP (Version...Logistics Services MySQL My Structured Query Language NAVSUP Navy Supply Systems Command NC Non-Contract Items NPS Naval Postgraduate

Cloud-Based Distributed Control of Unmanned Systems

DTIC Science & Technology

2015-04-01

during mission execution. At best, the data is saved onto hard-drives and is accessible only by the local team. Data history in a form available and...following open source technologies: GeoServer, OpenLayers, PostgreSQL , and PostGIS are chosen to implement the back-end database and server. A brief...geospatial map data. 3. PostgreSQL : An SQL-compliant object-relational database that easily scales to accommodate large amounts of data - upwards to

SigmaCLIPSE = presentation management + NASA CLI PS + SQL

NASA Technical Reports Server (NTRS)

Weiss, Bernard P., Jr.

1990-01-01

SigmaCLIPSE provides an expert systems and 'intelligent' data base development program for diverse systems integration environments that require support for automated reasoning and expert systems technology, presentation management, and access to 'intelligent' SQL data bases. The SigmaCLIPSE technology and and its integrated ability to access 4th generation application development and decision support tools through a portable SQL interface, comprises a sophisticated software development environment for solving knowledge engineering and expert systems development problems in information intensive commercial environments -- financial services, health care, and distributed process control -- where the expert system must be extendable -- a major architectural advantage of NASA CLIPS. SigmaCLIPSE is a research effort intended to test the viability of merging SQL data bases with expert systems technology.

Using PHP/MySQL to Manage Potential Mass Impacts

NASA Technical Reports Server (NTRS)

Hager, Benjamin I.

2010-01-01

This paper presents a new application using commercially available software to manage mass properties for spaceflight vehicles. PHP/MySQL(PHP: Hypertext Preprocessor and My Structured Query Language) are a web scripting language and a database language commonly used in concert with each other. They open up new opportunities to develop cutting edge mass properties tools, and in particular, tools for the management of potential mass impacts (threats and opportunities). The paper begins by providing an overview of the functions and capabilities of PHP/MySQL. The focus of this paper is on how PHP/MySQL are being used to develop an advanced "web accessible" database system for identifying and managing mass impacts on NASA's Ares I Upper Stage program, managed by the Marshall Space Flight Center. To fully describe this application, examples of the data, search functions, and views are provided to promote, not only the function, but the security, ease of use, simplicity, and eye-appeal of this new application. This paper concludes with an overview of the other potential mass properties applications and tools that could be developed using PHP/MySQL. The premise behind this paper is that PHP/MySQL are software tools that are easy to use and readily available for the development of cutting edge mass properties applications. These tools are capable of providing "real-time" searching and status of an active database, automated report generation, and other capabilities to streamline and enhance mass properties management application. By using PHP/MySQL, proven existing methods for managing mass properties can be adapted to present-day information technology to accelerate mass properties data gathering, analysis, and reporting, allowing mass property management to keep pace with today's fast-pace design and development processes.

Designing a Relational Database for the Basic School; Schools Command Web Enabled Officer and Enlisted Database (Sword)

DTIC Science & Technology

2002-06-01

Student memo for personnel MCLLS . . . . . . . . . . . . . . 75 i. Migrate data to SQL Server...The Web Server is on the same server as the SWORD database in the current version. 4: results set 5: dynamic HTML page 6: dynamic HTML page 3: SQL ...still be supported by Access. SQL Server would be a more viable tool for a fully developed application based on the number of potential users and

Multi-Resolution Playback of Network Trace Files

DTIC Science & Technology

2015-06-01

a com- plete MySQL database, C++ developer tools and the libraries utilized in the development of the system (Boost and Libcrafter), and Wireshark...XE suite has a limit to the allowed size of each database. In order to be scalable, the project had to switch to the MySQL database suite. The...programs that access the database use the MySQL C++ connector, provided by Oracle, and the supplied methods and libraries. 4.4 Flow Generator Chapter 3

Supporting Social Data Observatory with Customizable Index Structures on HBase - Architecture and Performance

DTIC Science & Technology

2013-01-01

commercial NoSQL database system. The results show that In-dexedHBase provides a data loading speed that is 6 times faster than Riak, and is...compare it with Riak, a widely adopted commercial NoSQL database system. The results show that In- dexedHBase provides a data loading speed that is 6...events. This chapter describes our research towards building an efficient and scalable storage platform for Truthy. Many existing NoSQL databases

Quality Attribute-Guided Evaluation of NoSQL Databases: A Case Study

DTIC Science & Technology

2015-01-16

evaluations of NoSQL databases specifically, and big data systems in general, that have become apparent during our study. Keywords—NoSQL, distributed...technology, namely that of big data , software systems [1]. At the heart of big data systems are a collection of database technologies that are more...born organizations such as Google and Amazon [3][4], along with those of numerous other big data innovators, have created a variety of open source and

Novel Method of Storing and Reconstructing Events at Fermilab E-906/SeaQuest Using a MySQL Database

NASA Astrophysics Data System (ADS)

Hague, Tyler

2010-11-01

Fermilab E-906/SeaQuest is a fixed target experiment at Fermi National Accelerator Laboratory. We are investigating the antiquark asymmetry in the nucleon sea. By examining the ratio of the Drell- Yan cross sections of proton-proton and proton-deuterium collisions we can determine the asymmetry ratio. An essential feature in the development of the analysis software is to update the event reconstruction to modern software tools. We are doing this in a unique way by doing a majority of the calculations within an SQL database. Using a MySQL database allows us to take advantage of off-the-shelf software without sacrificing ROOT compatibility and avoid network bottlenecks with server-side data selection. Using our raw data we create stubs, or partial tracks, at each station which are pieced together to create full tracks. Our reconstruction process uses dynamically created SQL statements to analyze the data. These SQL statements create tables that contain the final reconstructed tracks as well as intermediate values. This poster will explain the reconstruction process and how it is being implemented.

Managing hydrological measurements for small and intermediate projects: RObsDat

NASA Astrophysics Data System (ADS)

Reusser, Dominik E.

2014-05-01

Hydrological measurements need good management for the data not to be lost. Multiple, often overlapping files from various loggers with heterogeneous formats need to be merged. Data needs to be validated and cleaned and subsequently converted to the format for the hydrological target application. Preferably, all these steps should be easily tracable. RObsDat is an R package designed to support such data management. It comes with a command line user interface to support hydrologists to enter and adjust their data in a database following the Observations Data Model (ODM) standard by QUASHI. RObsDat helps in the setup of the database within one of the free database engines MySQL, PostgreSQL or SQLite. It imports the controlled water vocabulary from the QUASHI web service and provides a smart interface between the hydrologist and the database: Already existing data entries are detected and duplicates avoided. The data import function converts different data table designes to make import simple. Cleaning and modifications of data are handled with a simple version control system. Variable and location names are treated in a user friendly way, accepting and processing multiple versions. A new development is the use of spacetime objects for subsequent processing.

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

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

Dykstra, Dave

One of the main attractions of non-relational NoSQL databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It alsomore » compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.« less

eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies.

PubMed

Weissensteiner, Hansi; Schönherr, Sebastian; Specht, Günther; Kronenberg, Florian; Brandstätter, Anita

2010-03-09

Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle), security aspects (by using database technology) and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs). It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt.

eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies

PubMed Central

2010-01-01

Background Mitochondrial DNA (mtDNA) is widely being used for population genetics, forensic DNA fingerprinting and clinical disease association studies. The recent past has uncovered severe problems with mtDNA genotyping, not only due to the genotyping method itself, but mainly to the post-lab transcription, storage and report of mtDNA genotypes. Description eCOMPAGT, a system to store, administer and connect phenotype data to all kinds of genotype data is now enhanced by the possibility of storing mtDNA profiles and allowing their validation, linking to phenotypes and export as numerous formats. mtDNA profiles can be imported from different sequence evaluation programs, compared between evaluations and their haplogroup affiliations stored. Furthermore, eCOMPAGT has been improved in its sophisticated transparency (support of MySQL and Oracle), security aspects (by using database technology) and the option to import, manage and store genotypes derived from various genotyping methods (SNPlex, TaqMan, and STRs). It is a software solution designed for project management, laboratory work and the evaluation process all-in-one. Conclusions The extended mtDNA version of eCOMPAGT was designed to enable error-free post-laboratory data handling of human mtDNA profiles. This software is suited for small to medium-sized human genetic, forensic and clinical genetic laboratories. The direct support of MySQL and the improved database security options render eCOMPAGT a powerful tool to build an automated workflow architecture for several genotyping methods. eCOMPAGT is freely available at http://dbis-informatik.uibk.ac.at/ecompagt. PMID:20214782

Software Re-Engineering of the Human Factors Analysis and Classification System - (Maintenance Extension) Using Object Oriented Methods in a Microsoft Environment

DTIC Science & Technology

2001-09-01

replication) -- all from Visual Basic and VBA . In fact, we found that the SQL Server engine actually had a plethora of options, most formidable of...2002, the new SQL Server 2000 database engine, and Microsoft Visual Basic.NET. This thesis describes our use of the Spiral Development Model to...versions of Microsoft products? Specifically, the pending release of Microsoft Office 2002, the new SQL Server 2000 database engine, and Microsoft

An XML-Based Knowledge Management System of Port Information for U.S. Coast Guard Cutters

DTIC Science & Technology

2003-03-01

using DTDs was not chosen. XML Schema performs many of the same functions as SQL type schemas, but differ by the unique structure of XML documents...to access data from content files within the developed system. XPath is not equivalent to SQL . While XPath is very powerful at reaching into an XML...document and finding nodes or node sets, it is not a complete query language. For operations like joins, unions, intersections, etc., SQL is far

Defense Information Systems Agency Technical Integration Support (DISA- TIS). MUMPS Study.

DTIC Science & Technology

1993-01-01

usable in DoD, MUMPS must continue to improve in its support of DoD and OSE standards such as SQL , X-Windows, POSIX, PHIGS, etc. MUMPS and large AlSs...Language ( SQL ), X-Windows, and Graphical Kernel Services (GKS)) 2.2.2.3 FIPS Adoption by NIST The National Institute of Standards and Technology (NIST...many of the performance tuning mechanisms that must be performed explicitly with other systems. The VA looks forward to the SQL binding (1993 ANS) that

User Manual for Personnel Inventory Aging and Promotion Model

DTIC Science & Technology

2009-06-01

increased by 12. Now, an SQL 9 statement deletes records where [target] = NULL, and the model calculates the number of E8s that need to be promoted to...the run, the [Likelihood] and [Expected] tables are created. The first step in this process is to dy- namically build an SQL statement, based on the...This table has individual-level, longitudinal records. Next, a dy- namically built SQL statement based on the Number of Years, cre- ates a new data

Reliability Information Analysis Center 1st Quarter 2007, Technical Area Task (TAT) Report

DTIC Science & Technology

2007-02-05

34* Created new SQL server database for "PC Configuration" web application. Added roles for security closed 4235 and posted application to production. "e Wrote...and ran SQL Server scripts to migrate production databases to new server . "e Created backup jobs for new SQL Server databases. "* Continued...second phase of the TENA demo. Extensive tasking was established and assigned. A TENA interface to EW Server was reaffirmed after some uncertainty about

Spectrum Savings from High Performance Recording and Playback Onboard the Test Article

DTIC Science & Technology

2013-02-20

execute within a Windows 7 environment, and data is recorded on SSDs. The underlying database is implemented using MySQL . Figure 1 illustrates the... MySQL database. This is effectively the time at which the recorded data are available for retransmission. CPU and Memory utilization were collected...17.7% MySQL avg. 3.9% EQDR Total avg. 21.6% Table 1 CPU Utilization with260 Mbits/sec Load The difference between the total System CPU (27.8

Information Mining Technologies to Enable Discovery of Actionable Intelligence to Facilitate Maritime Situational Awareness: I-MINE

DTIC Science & Technology

2013-01-01

website). Data mining tools are in-house code developed in Python, C++ and Java . • NGA The National Geospatial-Intelligence Agency (NGA) performs data...as PostgreSQL (with PostGIS), MySQL , Microsoft SQL Server, SQLite, etc. using the appropriate JDBC driver. 14 The documentation and ease to learn are...written in Java that is able to perform various types of regressions, classi- fications, and other data mining tasks. There is also a commercial version

A Brief Assessment of LC2IEDM, MIST and Web Services for use in Naval Tactical Data Management

DTIC Science & Technology

2004-07-01

server software, messaging between the client and server, and a database. The MIST database is implemented in an open source DBMS named PostGreSQL ... PostGreSQL had its beginnings at the University of California, Berkley, in 1986 [11]. The development of PostGreSQL has since evolved into a...contact history from the database. DRDC Atlantic TM 2004-148 9 Request Software Request Software Server Side Response from service

Alternatives to relational database: comparison of NoSQL and XML approaches for clinical data storage.

PubMed

Lee, Ken Ka-Yin; Tang, Wai-Choi; Choi, Kup-Sze

2013-04-01

Clinical data are dynamic in nature, often arranged hierarchically and stored as free text and numbers. Effective management of clinical data and the transformation of the data into structured format for data analysis are therefore challenging issues in electronic health records development. Despite the popularity of relational databases, the scalability of the NoSQL database model and the document-centric data structure of XML databases appear to be promising features for effective clinical data management. In this paper, three database approaches--NoSQL, XML-enabled and native XML--are investigated to evaluate their suitability for structured clinical data. The database query performance is reported, together with our experience in the databases development. The results show that NoSQL database is the best choice for query speed, whereas XML databases are advantageous in terms of scalability, flexibility and extensibility, which are essential to cope with the characteristics of clinical data. While NoSQL and XML technologies are relatively new compared to the conventional relational database, both of them demonstrate potential to become a key database technology for clinical data management as the technology further advances. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Assessment & Commitment Tracking System (ACTS)

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

Bryant, Robert A.; Childs, Teresa A.; Miller, Michael A.

2004-12-20

The ACTS computer code provides a centralized tool for planning and scheduling assessments, tracking and managing actions associated with assessments or that result from an event or condition, and "mining" data for reporting and analyzing information for improving performance. The ACTS application is designed to work with the MS SQL database management system. All database interfaces are written in SQL. The following software is used to develop and support the ACTS application: Cold Fusion HTML JavaScript Quest TOAD Microsoft Visual Source Safe (VSS) HTML Mailer for sending email Microsoft SQL Microsoft Internet Information Server

Introduction to SQL. Ch. 1

NASA Technical Reports Server (NTRS)

McGlynn, T.; Santisteban, M.

2007-01-01

This chapter provides a very brief introduction to the Structured Query Language (SQL) for getting information from relational databases. We make no pretense that this is a complete or comprehensive discussion of SQL. There are many aspects of the language the will be completely ignored in the presentation. The goal here is to provide enough background so that users understand the basic concepts involved in building and using relational databases. We also go through the steps involved in building a particular astronomical database used in some of the other presentations in this volume.

Preventing SQL Code Injection by Combining Static and Runtime Analysis

DTIC Science & Technology

2008-05-01

attacker changes the developer’s intended structure of an SQ L com- mand by inserting new SQ L keywords or operators. (Su and Wasser - mann provide a...FROM b o o k s WHERE a u t h o r = ’ ’ GROUP BY r a t i n g We use symbol as a placeholder for the indeterminate part of the command (in this...dialects of SQL.) In our model, we mark transitions that correspond to externally defined strings with the symbol . To illustrate, Figure 2 shows the SQL

Integrated Array/Metadata Analytics

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Baumann, Peter

2015-04-01

Data comes in various forms and types, and integration usually presents a problem that is often simply ignored and solved with ad-hoc solutions. Multidimensional arrays are an ubiquitous data type, that we find at the core of virtually all science and engineering domains, as sensor, model, image, statistics data. Naturally, arrays are richly described by and intertwined with additional metadata (alphanumeric relational data, XML, JSON, etc). Database systems, however, a fundamental building block of what we call "Big Data", lack adequate support for modelling and expressing these array data/metadata relationships. Array analytics is hence quite primitive or non-existent at all in modern relational DBMS. Recognizing this, we extended SQL with a new SQL/MDA part seamlessly integrating multidimensional array analytics into the standard database query language. We demonstrate the benefits of SQL/MDA with real-world examples executed in ASQLDB, an open-source mediator system based on HSQLDB and rasdaman, that already implements SQL/MDA.

Processing of the WLCG monitoring data using NoSQL

NASA Astrophysics Data System (ADS)

Andreeva, J.; Beche, A.; Belov, S.; Dzhunov, I.; Kadochnikov, I.; Karavakis, E.; Saiz, P.; Schovancova, J.; Tuckett, D.

2014-06-01

The Worldwide LHC Computing Grid (WLCG) today includes more than 150 computing centres where more than 2 million jobs are being executed daily and petabytes of data are transferred between sites. Monitoring the computing activities of the LHC experiments, over such a huge heterogeneous infrastructure, is extremely demanding in terms of computation, performance and reliability. Furthermore, the generated monitoring flow is constantly increasing, which represents another challenge for the monitoring systems. While existing solutions are traditionally based on Oracle for data storage and processing, recent developments evaluate NoSQL for processing large-scale monitoring datasets. NoSQL databases are getting increasingly popular for processing datasets at the terabyte and petabyte scale using commodity hardware. In this contribution, the integration of NoSQL data processing in the Experiment Dashboard framework is described along with first experiences of using this technology for monitoring the LHC computing activities.

Integrating Scientific Array Processing into Standard SQL

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Bachhuber, Johannes; Baumann, Peter

2014-05-01

We live in a time that is dominated by data. Data storage is cheap and more applications than ever accrue vast amounts of data. Storing the emerging multidimensional data sets efficiently, however, and allowing them to be queried by their inherent structure, is a challenge many databases have to face today. Despite the fact that multidimensional array data is almost always linked to additional, non-array information, array databases have mostly developed separately from relational systems, resulting in a disparity between the two database categories. The current SQL standard and SQL DBMS supports arrays - and in an extension also multidimensional arrays - but does so in a very rudimentary and inefficient way. This poster demonstrates the practicality of an SQL extension for array processing, implemented in a proof-of-concept multi-faceted system that manages a federation of array and relational database systems, providing transparent, efficient and scalable access to the heterogeneous data in them.

Interactive DataBase of Cosmic Ray Anisotropy (DB A10)

NASA Astrophysics Data System (ADS)

Asipenka, A.S.; Belov, A.V.; Eroshenko, E.F.; Klepach, E.G.; Oleneva, V.A.; Yake, V.G.

Data on the hourly means of cosmic ray density and anisotropy derived by the GSM method over the 1957-2006 are introduced in to MySQL database. This format allowed an access to data both in local and in the Internet. Using the realized combination of script-language Php and My SQL database the Internet project was created on the access for users data on the CR anisotropy in different formats (http://cr20.izmiran.ru/AnisotropyCR/main.htm/). Usage the sheaf Php and MySQL provides fast receiving data even in the Internet since a request and following process of data are accomplished on the project server. Usage of MySQL basis for the storing data on cosmic ray variations give a possibility to construct requests of different structures, extends the variety of data reflection, makes it possible the conformity data to other systems and usage them in other projects.

Development of a platform-independent receiver control system for SISIFOS

NASA Astrophysics Data System (ADS)

Lemke, Roland; Olberg, Michael

1998-05-01

Up to now receiver control software was a time consuming development usually written by receiver engineers who had mainly the hardware in mind. We are presenting a low-cost and very flexible system which uses a minimal interface to the real hardware, and which makes it easy to adapt to new receivers. Our system uses Tcl/Tk as a graphical user interface (GUI), SpecTcl as a GUI builder, Pgplot as plotting software, a simple query language (SQL) database for information storage and retrieval, Ethernet socket to socket communication and SCPI as a command control language. The complete system is in principal platform independent but for cost saving reasons we are using it actually on a PC486 running Linux 2.0.30, which is a copylefted Unix. The only hardware dependent part are the digital input/output boards, analog to digital and digital to analog convertors. In the case of the Linux PC we are using a device driver development kit to integrate the boards fully into the kernel of the operating system, which indeed makes them look like an ordinary device. The advantage of this system is firstly the low price and secondly the clear separation between the different software components which are available for many operating systems. If it is not possible, due to CPU performance limitations, to run all the software in a single machine,the SQL-database or the graphical user interface could be installed on separate computers.

Chapter 51: How to Build a Simple Cone Search Service Using a Local Database

NASA Astrophysics Data System (ADS)

Kent, B. R.; Greene, G. R.

The cone search service protocol will be examined from the server side in this chapter. A simple cone search service will be setup and configured locally using MySQL. Data will be read into a table, and the Java JDBC will be used to connect to the database. Readers will understand the VO cone search specification and how to use it to query a database on their local systems and return an XML/VOTable file based on an input of RA/DEC coordinates and a search radius. The cone search in this example will be deployed as a Java servlet. The resulting cone search can be tested with a verification service. This basic setup can be used with other languages and relational databases.

Flight Test Validation of Optimal Input Design and Comparison to Conventional Inputs

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

1997-01-01

A technique for designing optimal inputs for aerodynamic parameter estimation was flight tested on the F-18 High Angle of Attack Research Vehicle (HARV). Model parameter accuracies calculated from flight test data were compared on an equal basis for optimal input designs and conventional inputs at the same flight condition. In spite of errors in the a priori input design models and distortions of the input form by the feedback control system, the optimal inputs increased estimated parameter accuracies compared to conventional 3-2-1-1 and doublet inputs. In addition, the tests using optimal input designs demonstrated enhanced design flexibility, allowing the optimal input design technique to use a larger input amplitude to achieve further increases in estimated parameter accuracy without departing from the desired flight test condition. This work validated the analysis used to develop the optimal input designs, and demonstrated the feasibility and practical utility of the optimal input design technique.

Directed Design of Experiments for Validating Probability of Detection Capability of a Testing System

NASA Technical Reports Server (NTRS)

Generazio, Edward R. (Inventor)

2012-01-01

A method of validating a probability of detection (POD) testing system using directed design of experiments (DOE) includes recording an input data set of observed hit and miss or analog data for sample components as a function of size of a flaw in the components. The method also includes processing the input data set to generate an output data set having an optimal class width, assigning a case number to the output data set, and generating validation instructions based on the assigned case number. An apparatus includes a host machine for receiving the input data set from the testing system and an algorithm for executing DOE to validate the test system. The algorithm applies DOE to the input data set to determine a data set having an optimal class width, assigns a case number to that data set, and generates validation instructions based on the case number.

SQL Triggers Reacting on Time Events: An Extension Proposal

NASA Astrophysics Data System (ADS)

Behrend, Andreas; Dorau, Christian; Manthey, Rainer

Being able to activate triggers at timepoints reached or after time intervals elapsed has been acknowledged by many authors as a valuable functionality of a DBMS. Recently, the interest in time-based triggers has been renewed in the context of data stream monitoring. However, up till now SQL triggers react to data changes only, even though research proposals and prototypes have been supporting several other event types, in particular time-based ones, since long. We therefore propose a seamless extension of the SQL trigger concept by time-based triggers, focussing on semantic issues arising from such an extension.

Advancing Future Network Science through Content Understanding

DTIC Science & Technology

2014-05-01

BitTorrent, PostgreSQL, MySQL , and GRSecurity) and emerging technologies (HadoopDFS, Tokutera, Sector/Sphere, HBase, and other BigTable-like...result. • Multi-Source Network Pulse Analyzer and Correlator provides course of action planning by enhancing the understanding of the complex dynamics

Streamlining the Process of Acquiring Secure Open Architecture Software Systems

DTIC Science & Technology

2013-10-08

Microsoft.NET, Enterprise Java Beans, GNU Lesser General Public License (LGPL) libraries, and data communication protocols like the Hypertext Transfer...NetBeans development environments),  customer relationship management (SugarCRM),  database management systems (PostgreSQL, MySQL ),  operating

Trends and New Directions in Software Architecture

DTIC Science & Technology

2014-10-10

frameworks  Open source  Cloud strategies  NoSQL  Machine Learning  MDD  Incremental approaches  Dashboards  Distributed development...complexity grows  NoSQL Models are not created equal 2014 Our Current Research  Lightweight Evaluation and Architecture Prototyping for Big Data

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.

Exploring Large Scale Data Analysis and Visualization for ARM Data Discovery Using NoSQL Technologies

NASA Astrophysics Data System (ADS)

Krishna, B.; Gustafson, W. I., Jr.; Vogelmann, A. M.; Toto, T.; Devarakonda, R.; Palanisamy, G.

2016-12-01

This paper presents a new way of providing ARM data discovery through data analysis and visualization services. ARM stands for Atmospheric Radiation Measurement. This Program was created to study cloud formation processes and their influence on radiative transfer and also include additional measurements of aerosol and precipitation at various highly instrumented ground and mobile stations. The total volume of ARM data is roughly 900TB. The current search for ARM data is performed by using its metadata, such as the site name, instrument name, date, etc. NoSQL technologies were explored to improve the capabilities of data searching, not only by their metadata, but also by using the measurement values. Two technologies that are currently being implemented for testing are Apache Cassandra (noSQL database) and Apache Spark (noSQL based analytics framework). Both of these technologies were developed to work in a distributed environment and hence can handle large data for storing and analytics. D3.js is a JavaScript library that can generate interactive data visualizations in web browsers by making use of commonly used SVG, HTML5, and CSS standards. To test the performance of NoSQL for ARM data, we will be using ARM's popular measurements to locate the data based on its value. Recently noSQL technology has been applied to a pilot project called LASSO, which stands for LES ARM Symbiotic Simulation and Observation Workflow. LASSO will be packaging LES output and observations in "data bundles" and analyses will require the ability for users to analyze both observations and LES model output either individually or together across multiple time periods. The LASSO implementation strategy suggests that enormous data storage is required to store the above mentioned quantities. Thus noSQL was used to provide a powerful means to store portions of the data that provided users with search capabilities on each simulation's traits through a web application. Based on the user selection, plots are created dynamically along with ancillary information that enables the user to locate and download data that fulfilled their required traits.

A searching and reporting system for relational databases using a graph-based metadata representation.

PubMed

Hewitt, Robin; Gobbi, Alberto; Lee, Man-Ling

2005-01-01

Relational databases are the current standard for storing and retrieving data in the pharmaceutical and biotech industries. However, retrieving data from a relational database requires specialized knowledge of the database schema and of the SQL query language. At Anadys, we have developed an easy-to-use system for searching and reporting data in a relational database to support our drug discovery project teams. This system is fast and flexible and allows users to access all data without having to write SQL queries. This paper presents the hierarchical, graph-based metadata representation and SQL-construction methods that, together, are the basis of this system's capabilities.

A Web-based Examination System Based on PHP+MySQL.

PubMed

Wen, Ji; Zhang, Yang; Yan, Yong; Xia, Shunren

2005-01-01

The design and implementation of web-based examination system constructed by PHP and MySQL is presented in this paper. Three primary parts, including students',teachers' and administrators', are introduced and analyzed in detail. Initial application has demonstrated the system's feasibility and reasonability.^*

An effective model for store and retrieve big health data in cloud computing.

PubMed

Goli-Malekabadi, Zohreh; Sargolzaei-Javan, Morteza; Akbari, Mohammad Kazem

2016-08-01

The volume of healthcare data including different and variable text types, sounds, and images is increasing day to day. Therefore, the storage and processing of these data is a necessary and challenging issue. Generally, relational databases are used for storing health data which are not able to handle the massive and diverse nature of them. This study aimed at presenting the model based on NoSQL databases for the storage of healthcare data. Despite different types of NoSQL databases, document-based DBs were selected by a survey on the nature of health data. The presented model was implemented in the Cloud environment for accessing to the distribution properties. Then, the data were distributed on the database by applying the Shard property. The efficiency of the model was evaluated in comparison with the previous data model, Relational Database, considering query time, data preparation, flexibility, and extensibility parameters. The results showed that the presented model approximately performed the same as SQL Server for "read" query while it acted more efficiently than SQL Server for "write" query. Also, the performance of the presented model was better than SQL Server in the case of flexibility, data preparation and extensibility. Based on these observations, the proposed model was more effective than Relational Databases for handling health data. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Evaluation of NoSQL databases for DIRAC monitoring and beyond

NASA Astrophysics Data System (ADS)

Mathe, Z.; Casajus Ramo, A.; Stagni, F.; Tomassetti, L.

2015-12-01

Nowadays, many database systems are available but they may not be optimized for storing time series data. Monitoring DIRAC jobs would be better done using a database optimised for storing time series data. So far it was done using a MySQL database, which is not well suited for such an application. Therefore alternatives have been investigated. Choosing an appropriate database for storing huge amounts of time series data is not trivial as one must take into account different aspects such as manageability, scalability and extensibility. We compared the performance of Elasticsearch, OpenTSDB (based on HBase) and InfluxDB NoSQL databases, using the same set of machines and the same data. We also evaluated the effort required for maintaining them. Using the LHCb Workload Management System (WMS), based on DIRAC as a use case we set up a new monitoring system, in parallel with the current MySQL system, and we stored the same data into the databases under test. We evaluated Grafana (for OpenTSDB) and Kibana (for ElasticSearch) metrics and graph editors for creating dashboards, in order to have a clear picture on the usability of each candidate. In this paper we present the results of this study and the performance of the selected technology. We also give an outlook of other potential applications of NoSQL databases within the DIRAC project.

Design and development of an IoT-based web application for an intelligent remote SCADA system

NASA Astrophysics Data System (ADS)

Kao, Kuang-Chi; Chieng, Wei-Hua; Jeng, Shyr-Long

2018-03-01

This paper presents a design of an intelligent remote electrical power supervisory control and data acquisition (SCADA) system based on the Internet of Things (IoT), with Internet Information Services (IIS) for setting up web servers, an ASP.NET model-view- controller (MVC) for establishing a remote electrical power monitoring and control system by using responsive web design (RWD), and a Microsoft SQL Server as the database. With the web browser connected to the Internet, the sensing data is sent to the client by using the TCP/IP protocol, which supports mobile devices with different screen sizes. The users can provide instructions immediately without being present to check the conditions, which considerably reduces labor and time costs. The developed system incorporates a remote measuring function by using a wireless sensor network and utilizes a visual interface to make the human-machine interface (HMI) more instinctive. Moreover, it contains an analog input/output and a basic digital input/output that can be applied to a motor driver and an inverter for integration with a remote SCADA system based on IoT, and thus achieve efficient power management.

Developing Chemistry and Kinetic Modeling Tools for Low-Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Jenkins, Thomas; Beckwith, Kris; Davidson, Bradley; Kruger, Scott; Pankin, Alexei; Roark, Christine; Stoltz, Peter

2015-09-01

We discuss the use of proper orthogonal decomposition (POD) methods in VSim, a FDTD plasma simulation code capable of both PIC/MCC and fluid modeling. POD methods efficiently generate smooth representations of noisy self-consistent or test-particle PIC data, and are thus advantageous in computing macroscopic fluid quantities from large PIC datasets (e.g. for particle-based closure computations) and in constructing optimal visual representations of the underlying physics. They may also confer performance advantages for massively parallel simulations, due to the significant reduction in dataset sizes conferred by truncated singular-value decompositions of the PIC data. We also demonstrate how complex LTP chemistry scenarios can be modeled in VSim via an interface with MUNCHKIN, a developing standalone python/C++/SQL code that identifies reaction paths for given input species, solves 1D rate equations for the time-dependent chemical evolution of the system, and generates corresponding VSim input blocks with appropriate cross-sections/reaction rates. MUNCHKIN also computes reaction rates from user-specified distribution functions, and conducts principal path analyses to reduce the number of simulated chemical reactions. Supported by U.S. Department of Energy SBIR program, Award DE-SC0009501.

Sputtering, Plasma Chemistry, and RF Sheath Effects in Low-Temperature and Fusion Plasma Modeling

NASA Astrophysics Data System (ADS)

Jenkins, Thomas G.; Kruger, Scott E.; McGugan, James M.; Pankin, Alexei Y.; Roark, Christine M.; Smithe, David N.; Stoltz, Peter H.

2016-09-01

A new sheath boundary condition has been implemented in VSim, a plasma modeling code which makes use of both PIC/MCC and fluid FDTD representations. It enables physics effects associated with DC and RF sheath formation - local sheath potential evolution, heat/particle fluxes, and sputtering effects on complex plasma-facing components - to be included in macroscopic-scale plasma simulations that need not resolve sheath scale lengths. We model these effects in typical ICRF antenna operation scenarios on the Alcator C-Mod fusion device, and present comparisons of our simulation results with experimental data together with detailed 3D animations of antenna operation. Complex low-temperature plasma chemistry modeling in VSim is facilitated by MUNCHKIN, a standalone python/C++/SQL code that identifies possible reaction paths for a given set of input species, solves 1D rate equations for the ensuing system's chemical evolution, and generates VSim input blocks with appropriate cross-sections/reaction rates. These features, as well as principal path analysis (to reduce the number of simulated chemical reactions while retaining accuracy) and reaction rate calculations from user-specified distribution functions, will also be demonstrated. Supported by the U.S. Department of Energy's SBIR program, Award DE-SC0009501.

Landslide prediction system in Slovenia (Masprem)

NASA Astrophysics Data System (ADS)

Šinigoj, Jasna; Jemec Auflič, Mateja; Krivic, Matija

2017-04-01

The landslide prediction system MASPREM has been developed in 2013 to (1) predict rainfall induced landslides on national and local level and (2) inform Civil Protection agency and inhabitants of an increased probability of landslide occurrences. A landslide prediction system on national level integrates three major components: (1) a landslide susceptibility map; (2) landslide triggering rainfall threshold values and (3) precipitation forecasting model's (i.e., ALADIN, INCA). Landslide prediction is also calculated on a local level, including exposure maps of inhabitants, buildings and different types of infrastructure to potential landslide occurrence at a scale of 1: 25,000 for 14 selected municipalities. MASPREM system runs in a 12 hour cycling mode, for 24 hours ahead. The results of the probability of landslide models are classified into five classes, with values ranging from one to five; where class one represents areas with a negligible landslide probability and class five areas with a very high landslide probability. It is a fully automated system based on open source software (PostgreSQL) and web applications for displaying results (Java, GDAL). When precipitation forecasting models are transferred to the GeoZS server the conversion process to raster data starts, stores data in a PostgreSQL database and performs the calculation. Based on final results, the WMS service that is responsible for the distribution of data through the service for download and review of results in a web application is created. In the period, from September 2013 to August 2016, MASPREM gave an alert about the probability of landslide occurrences in 84 cases. While the system has potential to become operational in use after the validation phase, there are also limitations related to the input data that should not be neglected: spatial resolution of the ALADIN model, the incomplete landslide inventory that is important for the validation, defining how many days of antecedent rainfall significantly influence the landslide occurrences, characteristic of lithological units according to water contents. Despite the limitations currently affecting the landslide prediction system, results show that the system demonstrates capability in predicting rainfall induced landslides. When the validation phase will be finished and the certainty of system will be high enough, the system will be able to inform infrastructure owners, civil agencies, and operators of potential landslide hazards. Komac, M., Šinigoj, J., Jemec Auflič, M. 2014: A national warning system for rainfall-induced landslides in Slovenia. V: SASSA, Kyoji (ur.), CANUTI, Paolo (ur.), YIN, Yueping (ur.). Landslide science for a safer geoenvironment. Vol. 2, Methods of landslide studies. Cham ... [etc.]: Springer, cop. 2014, str. 577-582, doi: 10.1007/978-3-319-05050-8_89. Jemec Auflič, M, Šinigoj, J, Krivic, M, Podboj, M, Peternel,T, Komac, M. Landslide prediction system for rainfall induced landslides in Slovenia (Masprem) Geologija, 2016, 59/2, 259-271, doi: 10.5474/geologija.2016.016. Šinigoj, J., Jemec Auflič, M., Kumelj, Š., Krivic, M., Požar, M., Podboj, M., Tukić, M., Peternel, T., Ponjavič, G., Zakrajšek, M. & Prkić, N. 2016: Nadgradnja sistema za obveščanje in opozarjanje v primeru proženja zemeljskih plazov - Masprem2: končno poročilo. Geolo\\vski zavod Slovenije, Ljubljana: 114 p

BioImaging Database

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

David Nix, Lisa Simirenko

2006-10-25

The Biolmaging Database (BID) is a relational database developed to store the data and meta-data for the 3D gene expression in early Drosophila embryo development on a cellular level. The schema was written to be used with the MySQL DBMS but with minor modifications can be used on any SQL compliant relational DBMS.

The SQL Server Database for Non Computer Professional Teaching Reform

ERIC Educational Resources Information Center

Liu, Xiangwei

2012-01-01

A summary of the teaching methods of the non-computer professional SQL Server database, analyzes the current situation of the teaching course. According to non computer professional curriculum teaching characteristic, put forward some teaching reform methods, and put it into practice, improve the students' analysis ability, practice ability and…

Implementing CBM: SQL-Tutor after Fifteen Years

ERIC Educational Resources Information Center

Mitrovic, Antonija; Ohlsson, Stellan

2016-01-01

SQL-Tutor is the first constraint-based tutor. The initial conference papers about the system were published in 1998 (Mitrovic 1998a, 1998b, 1998c), with an "IJAIED" paper published in 1999 (Mitrovic and Ohlsson, "International Journal Artificial Intelligence in Education," 10(3-4), 238-256, 1999). We published another…

CheD: chemical database compilation tool, Internet server, and client for SQL servers.

PubMed

Trepalin, S V; Yarkov, A V

2001-01-01

An efficient program, which runs on a personal computer, for the storage, retrieval, and processing of chemical information, is presented, The program can work both as a stand-alone application or in conjunction with a specifically written Web server application or with some standard SQL servers, e.g., Oracle, Interbase, and MS SQL. New types of data fields are introduced, e.g., arrays for spectral information storage, HTML and database links, and user-defined functions. CheD has an open architecture; thus, custom data types, controls, and services may be added. A WWW server application for chemical data retrieval features an easy and user-friendly installation on Windows NT or 95 platforms.

Agentless Cloud-Wide Monitoring of Virtual Disk State

DTIC Science & Technology

2015-10-01

packages include Apache, MySQL , PHP, Ruby on Rails, Java Application Servers, and many others. Figure 2.12 shows the results of a run of the Software...Linux, Apache, MySQL , PHP (LAMP) set of applications. Thus, many file-level update logs will contain the same versions of files repeated across many

Comparing IndexedHBase and Riak for Serving Truthy: Performance of Data Loading and Query Evaluation

DTIC Science & Technology

2013-08-01

Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS performance evaluation, distributed database, noSQL , HBase, indexing Xiaoming Gao, Judy Qiu...common hashtags created during a given time window. With the purpose of finding a solution for these challenges, we evaluate NoSQL databases such as

Open, Cross Platform Chemistry Application Unifying Structure Manipulation, External Tools, Databases and Visualization

DTIC Science & Technology

2012-11-27

with powerful analysis tools and an informatics approach leveraging best-of-breed NoSQL databases, in order to store, search and retrieve relevant...dictionaries, and JavaScript also has good support. The MongoDB project[15] was chosen as a scalable NoSQL data store for the cheminfor- matics components

An Experimental Investigation of Complexity in Database Query Formulation Tasks

ERIC Educational Resources Information Center

Casterella, Gretchen Irwin; Vijayasarathy, Leo

2013-01-01

Information Technology professionals and other knowledge workers rely on their ability to extract data from organizational databases to respond to business questions and support decision making. Structured query language (SQL) is the standard programming language for querying data in relational databases, and SQL skills are in high demand and are…

Knowledge Query Language (KQL)

DTIC Science & Technology

2016-02-12

Lexington Massachusetts This page intentionally left blank. iii EXECUTIVE SUMMARY Currently, queries for data ...retrieval from non-Structured Query Language (NoSQL) data stores are tightly coupled to the specific implementation of the data store implementation...independent of the storage content and format for querying NoSQL or relational data stores. This approach uses address expressions (or A-Expressions

Research of GIS-services applicability for solution of spatial analysis tasks.

NASA Astrophysics Data System (ADS)

Terekhin, D. A.; Botygin, I. A.; Sherstneva, A. I.; Sherstnev, V. S.

2017-01-01

Experiments for working out the areas of applying various gis-services in the tasks of spatial analysis are discussed in this paper. Google Maps, Yandex Maps, Microsoft SQL Server are used as services of spatial analysis. All services have shown a comparable speed of analyzing the spatial data when carrying out elemental spatial requests (building up the buffer zone of a point object) as well as the preferences of Microsoft SQL Server in operating with more complicated spatial requests. When building up elemental spatial requests, internet-services show higher efficiency due to cliental data handling with JavaScript-subprograms. A weak point of public internet-services is an impossibility to handle data on a server side and a barren variety of spatial analysis functions. Microsoft SQL Server offers a large variety of functions needed for spatial analysis on the server side. The authors conclude that when solving practical problems, the capabilities of internet-services used in building up routes and completing other functions with spatial analysis with Microsoft SQL Server should be involved.

2MASS Catalog Server Kit Version 2.1

NASA Astrophysics Data System (ADS)

Yamauchi, C.

2013-10-01

The 2MASS Catalog Server Kit is open source software for use in easily constructing a high performance search server for important astronomical catalogs. This software utilizes the open source RDBMS PostgreSQL, therefore, any users can setup the database on their local computers by following step-by-step installation guide. The kit provides highly optimized stored functions for positional searchs similar to SDSS SkyServer. Together with these, the powerful SQL environment of PostgreSQL will meet various user's demands. We released 2MASS Catalog Server Kit version 2.1 in 2012 May, which supports the latest WISE All-Sky catalog (563,921,584 rows) and 9 major all-sky catalogs. Local databases are often indispensable for observatories with unstable or narrow-band networks or severe use, such as retrieving large numbers of records within a small period of time. This software is the best for such purposes, and increasing supported catalogs and improvements of version 2.1 can cover a wider range of applications including advanced calibration system, scientific studies using complicated SQL queries, etc. Official page: http://www.ir.isas.jaxa.jp/~cyamauch/2masskit/

Use of Graph Database for the Integration of Heterogeneous Biological Data.

PubMed

Yoon, Byoung-Ha; Kim, Seon-Kyu; Kim, Seon-Young

2017-03-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data.

Use of Graph Database for the Integration of Heterogeneous Biological Data

PubMed Central

Yoon, Byoung-Ha; Kim, Seon-Kyu

2017-01-01

Understanding complex relationships among heterogeneous biological data is one of the fundamental goals in biology. In most cases, diverse biological data are stored in relational databases, such as MySQL and Oracle, which store data in multiple tables and then infer relationships by multiple-join statements. Recently, a new type of database, called the graph-based database, was developed to natively represent various kinds of complex relationships, and it is widely used among computer science communities and IT industries. Here, we demonstrate the feasibility of using a graph-based database for complex biological relationships by comparing the performance between MySQL and Neo4j, one of the most widely used graph databases. We collected various biological data (protein-protein interaction, drug-target, gene-disease, etc.) from several existing sources, removed duplicate and redundant data, and finally constructed a graph database containing 114,550 nodes and 82,674,321 relationships. When we tested the query execution performance of MySQL versus Neo4j, we found that Neo4j outperformed MySQL in all cases. While Neo4j exhibited a very fast response for various queries, MySQL exhibited latent or unfinished responses for complex queries with multiple-join statements. These results show that using graph-based databases, such as Neo4j, is an efficient way to store complex biological relationships. Moreover, querying a graph database in diverse ways has the potential to reveal novel relationships among heterogeneous biological data. PMID:28416946

Distributed Episodic Exploratory Planning (DEEP)

DTIC Science & Technology

2008-12-01

API). For DEEP, Hibernate offered the following advantages: • Abstracts SQL by utilizing HQL so any database with a Java Database Connectivity... Hibernate SQL ICCRTS International Command and Control Research and Technology Symposium JDB Java Distributed Blackboard JDBC Java Database Connectivity...selected because of its opportunistic reasoning capabilities and implemented in Java for platform independence. Java was chosen for ease of

Investigating the Limitations of Advanced Design Methods through Real World Application

DTIC Science & Technology

2016-03-31

36 War Room Laptop Display ( MySQL , JMP 9 Pro, 64-bit Windows) Georgia Tech Secure Collaborative Visualization Environment ( MySQL , JMP 9 Pro...investigate expanding the EA for VC3ATS • Would like to consider both an expansion of the use of current Java -based BPM approach and other potential EA

A 5E Learning Cycle Approach-Based, Multimedia-Supplemented Instructional Unit for Structured Query Language

ERIC Educational Resources Information Center

Piyayodilokchai, Hongsiri; Panjaburee, Patcharin; Laosinchai, Parames; Ketpichainarong, Watcharee; Ruenwongsa, Pintip

2013-01-01

With the benefit of multimedia and the learning cycle approach in promoting effective active learning, this paper proposed a learning cycle approach-based, multimedia-supplemented instructional unit for Structured Query Language (SQL) for second-year undergraduate students with the aim of enhancing their basic knowledge of SQL and ability to apply…

Large Declarative Memories in ACT-R

DTIC Science & Technology

2009-12-01

containing the persistent DM of interest PDM-user Username required by the PostgreSQL DBMS for DB access PDM- passwd Password required by the PostgreSQL...34model-v5-DM" :pdm-user "Scott" :pdm- passwd “Open_Seseme" :pdm-resets-clear-db T :pdm-add-dm-serializes T :pdm-active T ... Figure 1: Activating and

Software Application for Supporting the Education of Database Systems

ERIC Educational Resources Information Center

Vágner, Anikó

2015-01-01

The article introduces an application which supports the education of database systems, particularly the teaching of SQL and PL/SQL in Oracle Database Management System environment. The application has two parts, one is the database schema and its content, and the other is a C# application. The schema is to administrate and store the tasks and the…

Developing an Excel Decision Support System Using In-Transit Visibility to Decrease DoD Transportation Delays

DTIC Science & Technology

2008-03-01

Fortunately, built into Excel is the capability to use ActiveX Data Objects (ADO), a software feature which uses VBA to interface with external...part of Excel’s ActiveX Direct Objects (ADO) functionality, Excel can execute SQL queries in Access with VBA. An SQL query statement can be written

Examining Learning Styles and Perceived Benefits of Analogical Problem Construction on SQL Knowledge Acquisition

ERIC Educational Resources Information Center

Mills, Robert J.; Dupin-Bryant, Pamela A.; Johnson, John D.; Beaulieu, Tanya Y.

2015-01-01

The demand for Information Systems (IS) graduates with expertise in Structured Query Language (SQL) and database management is vast and projected to increase as "big data" becomes ubiquitous. To prepare students to solve complex problems in a data-driven world, educators must explore instructional strategies to help link prior knowledge…

Knowledge Query Language (KQL)

DTIC Science & Technology

2016-02-01

unlimited. This page intentionally left blank. iii EXECUTIVE SUMMARY Currently, queries for data ...retrieval from non-Structured Query Language (NoSQL) data stores are tightly coupled to the specific implementation of the data store implementation, making...of the storage content and format for querying NoSQL or relational data stores. This approach uses address expressions (or A-Expressions) embedded in

Evolution of the LBT Telemetry System

NASA Astrophysics Data System (ADS)

Summers, K.; Biddick, C.; De La Peña, M. D.; Summers, D.

2014-05-01

The Large Binocular Telescope (LBT) Telescope Control System (TCS) records about 10GB of telemetry data per night. Additionally, the vibration monitoring system records about 9GB of telemetry data per night. Through 2013, we have amassed over 6TB of Hierarchical Data Format (HDF5) files and almost 9TB in a MySQL database of TCS and vibration data. The LBT telemetry system, in its third major revision since 2004, provides the mechanism to capture and store this data. The telemetry system has evolved from a simple HDF file system with MySQL stream definitions within the TCS, to a separate system using a MySQL database system for the definitions and data, and finally to no database use at all, using HDF5 files.

Wireless data collection of self-administered surveys using tablet computers.

PubMed

Singleton, Kyle W; Lan, Mars; Arnold, Corey; Vahidi, Mani; Arangua, Lisa; Gelberg, Lillian; Bui, Alex A T

2011-01-01

The accurate and expeditious collection of survey data by coordinators in the field is critical in the support of research studies. Early methods that used paper documentation have slowly evolved into electronic capture systems. Indeed, tools such as REDCap and others illustrate this transition. However, many current systems are tailored web-browsers running on desktop/laptop computers, requiring keyboard and mouse input. We present a system that utilizes a touch screen interface running on a tablet PC with consideration for portability, limited screen space, wireless connectivity, and potentially inexperienced and low literacy users. The system was developed using C#, ASP.net, and SQL Server by multiple programmers over the course of a year. The system was developed in coordination with UCLA Family Medicine and is currently deployed for the collection of data in a group of Los Angeles area clinics of community health centers for a study on drug addiction and intervention.

Insect barcode information system.

PubMed

Pratheepa, Maria; Jalali, Sushil Kumar; Arokiaraj, Robinson Silvester; Venkatesan, Thiruvengadam; Nagesh, Mandadi; Panda, Madhusmita; Pattar, Sharath

2014-01-01

Insect Barcode Information System called as Insect Barcode Informática (IBIn) is an online database resource developed by the National Bureau of Agriculturally Important Insects, Bangalore. This database provides acquisition, storage, analysis and publication of DNA barcode records of agriculturally important insects, for researchers specifically in India and other countries. It bridges a gap in bioinformatics by integrating molecular, morphological and distribution details of agriculturally important insects. IBIn was developed using PHP/My SQL by using relational database management concept. This database is based on the client- server architecture, where many clients can access data simultaneously. IBIn is freely available on-line and is user-friendly. IBIn allows the registered users to input new information, search and view information related to DNA barcode of agriculturally important insects.This paper provides a current status of insect barcode in India and brief introduction about the database IBIn. http://www.nabg-nbaii.res.in/barcode.

Wireless Data Collection of Self-administered Surveys using Tablet Computers

PubMed Central

Singleton, Kyle W.; Lan, Mars; Arnold, Corey; Vahidi, Mani; Arangua, Lisa; Gelberg, Lillian; Bui, Alex A.T.

2011-01-01

The accurate and expeditious collection of survey data by coordinators in the field is critical in the support of research studies. Early methods that used paper documentation have slowly evolved into electronic capture systems. Indeed, tools such as REDCap and others illustrate this transition. However, many current systems are tailored web-browsers running on desktop/laptop computers, requiring keyboard and mouse input. We present a system that utilizes a touch screen interface running on a tablet PC with consideration for portability, limited screen space, wireless connectivity, and potentially inexperienced and low literacy users. The system was developed using C#, ASP.net, and SQL Server by multiple programmers over the course of a year. The system was developed in coordination with UCLA Family Medicine and is currently deployed for the collection of data in a group of Los Angeles area clinics of community health centers for a study on drug addiction and intervention. PMID:22195187

Validating Performance Level Descriptors (PLDs) for the AP® Environmental Science Exam

ERIC Educational Resources Information Center

Reshetar, Rosemary; Kaliski, Pamela; Chajewski, Michael; Lionberger, Karen

2012-01-01

This presentation summarizes a pilot study conducted after the May 2011 administration of the AP Environmental Science Exam. The study used analytical methods based on scaled anchoring as input to a Performance Level Descriptor validation process that solicited systematic input from subject matter experts.

Quantum displacement receiver for M-ary phase-shift-keyed coherent states

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

Izumi, Shuro; Takeoka, Masahiro; Fujiwara, Mikio

2014-12-04

We propose quantum receivers for 3- and 4-ary phase-shift-keyed (PSK) coherent state signals to overcome the standard quantum limit (SQL). Our receiver, consisting of a displacement operation and on-off detectors with or without feedforward, provides an error probability performance beyond the SQL. We show feedforward operations can tolerate the requirement for the detector specifications.

Tomcat, Oracle & XML Web Archive

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

Cothren, D. C.

2008-01-01

The TOX (Tomcat Oracle & XML) web archive is a foundation for development of HTTP-based applications using Tomcat (or some other servlet container) and an Oracle RDBMS. Use of TOX requires coding primarily in PL/SQL, JavaScript, and XSLT, but also in HTML, CSS and potentially Java. Coded in Java and PL/SQL itself, TOX provides the foundation for more complex applications to be built.

Architecture Knowledge for Evaluating Scalable Databases

DTIC Science & Technology

2015-01-16

problems, arising from the proliferation of new data models and distributed technologies for building scalable, available data stores . Architects must...longer are relational databases the de facto standard for building data repositories. Highly distributed, scalable “ NoSQL ” databases [11] have emerged...This is especially challenging at the data storage layer. The multitude of competing NoSQL database technologies creates a complex and rapidly

Comparison of the Frontier Distributed Database Caching System to NoSQL Databases

NASA Astrophysics Data System (ADS)

Dykstra, Dave

2012-12-01

One of the main attractions of non-relational “NoSQL” databases is their ability to scale to large numbers of readers, including readers spread over a wide area. The Frontier distributed database caching system, used in production by the Large Hadron Collider CMS and ATLAS detector projects for Conditions data, is based on traditional SQL databases but also adds high scalability and the ability to be distributed over a wide-area for an important subset of applications. This paper compares the major characteristics of the two different approaches and identifies the criteria for choosing which approach to prefer over the other. It also compares in some detail the NoSQL databases used by CMS and ATLAS: MongoDB, CouchDB, HBase, and Cassandra.

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.

F-18 High Alpha Research Vehicle (HARV) parameter identification flight test maneuvers for optimal input design validation and lateral control effectiveness

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

1995-01-01

Flight test maneuvers are specified for the F-18 High Alpha Research Vehicle (HARV). The maneuvers were designed for open loop parameter identification purposes, specifically for optimal input design validation at 5 degrees angle of attack, identification of individual strake effectiveness at 40 and 50 degrees angle of attack, and study of lateral dynamics and lateral control effectiveness at 40 and 50 degrees angle of attack. Each maneuver is to be realized by applying square wave inputs to specific control effectors using the On-Board Excitation System (OBES). Maneuver descriptions and complete specifications of the time/amplitude points define each input are included, along with plots of the input time histories.

A database for coconut crop improvement.

PubMed

Rajagopal, Velamoor; Manimekalai, Ramaswamy; Devakumar, Krishnamurthy; Rajesh; Karun, Anitha; Niral, Vittal; Gopal, Murali; Aziz, Shamina; Gunasekaran, Marimuthu; Kumar, Mundappurathe Ramesh; Chandrasekar, Arumugam

2005-12-08

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. http://www.bioinfcpcri.org.

Rapid Diagnostics of Onboard Sequences

NASA Technical Reports Server (NTRS)

Starbird, Thomas W.; Morris, John R.; Shams, Khawaja S.; Maimone, Mark W.

2012-01-01

Keeping track of sequences onboard a spacecraft is challenging. When reviewing Event Verification Records (EVRs) of sequence executions on the Mars Exploration Rover (MER), operators often found themselves wondering which version of a named sequence the EVR corresponded to. The lack of this information drastically impacts the operators diagnostic capabilities as well as their situational awareness with respect to the commands the spacecraft has executed, since the EVRs do not provide argument values or explanatory comments. Having this information immediately available can be instrumental in diagnosing critical events and can significantly enhance the overall safety of the spacecraft. This software provides auditing capability that can eliminate that uncertainty while diagnosing critical conditions. Furthermore, the Restful interface provides a simple way for sequencing tools to automatically retrieve binary compiled sequence SCMFs (Space Command Message Files) on demand. It also enables developers to change the underlying database, while maintaining the same interface to the existing applications. The logging capabilities are also beneficial to operators when they are trying to recall how they solved a similar problem many days ago: this software enables automatic recovery of SCMF and RML (Robot Markup Language) sequence files directly from the command EVRs, eliminating the need for people to find and validate the corresponding sequences. To address the lack of auditing capability for sequences onboard a spacecraft during earlier missions, extensive logging support was added on the Mars Science Laboratory (MSL) sequencing server. This server is responsible for generating all MSL binary SCMFs from RML input sequences. The sequencing server logs every SCMF it generates into a MySQL database, as well as the high-level RML file and dictionary name inputs used to create the SCMF. The SCMF is then indexed by a hash value that is automatically included in all command EVRs by the onboard flight software. Second, both the binary SCMF result and the RML input file can be retrieved simply by specifying the hash to a Restful web interface. This interface enables command line tools as well as large sophisticated programs to download the SCMF and RMLs on-demand from the database, enabling a vast array of tools to be built on top of it. One such command line tool can retrieve and display RML files, or annotate a list of EVRs by interleaving them with the original sequence commands. This software has been integrated with the MSL sequencing pipeline where it will serve sequences useful in diagnostics, debugging, and situational awareness throughout the mission.

Water vapour correction of the daily 1 km AVHRR global land dataset: Part I validation and use of the Water Vapour input field

USGS Publications Warehouse

DeFelice, Thomas P.; Lloyd, D.; Meyer, D.J.; Baltzer, T. T.; Piraina, P.

2003-01-01

An atmospheric correction algorithm developed for the 1 km Advanced Very High Resolution Radiometer (AVHRR) global land dataset was modified to include a near real-time total column water vapour data input field to account for the natural variability of atmospheric water vapour. The real-time data input field used for this study is the Television and Infrared Observational Satellite (TIROS) Operational Vertical Sounder (TOVS) Pathfinder A global total column water vapour dataset. It was validated prior to its use in the AVHRR atmospheric correction process using two North American AVHRR scenes, namely 13 June and 28 November 1996. The validation results are consistent with those reported by others and entail a comparison between TOVS, radiosonde, experimental sounding, microwave radiometer, and data from a hand-held sunphotometer. The use of this data layer as input to the AVHRR atmospheric correction process is discussed.

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature

PubMed Central

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry BF; Tipton, Keith F

2007-01-01

Background We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. Description The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at . The data are available for download as SQL and XML files via FTP. Conclusion ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List. PMID:17662133

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

PubMed

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

2007-07-27

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency.

PubMed

Aniceto, Rodrigo; Xavier, Rene; Guimarães, Valeria; Hondo, Fernanda; Holanda, Maristela; Walter, Maria Emilia; Lifschitz, Sérgio

2015-01-01

Rapid advances in high-throughput sequencing techniques have created interesting computational challenges in bioinformatics. One of them refers to management of massive amounts of data generated by automatic sequencers. We need to deal with the persistency of genomic data, particularly storing and analyzing these large-scale processed data. To find an alternative to the frequently considered relational database model becomes a compelling task. Other data models may be more effective when dealing with a very large amount of nonconventional data, especially for writing and retrieving operations. In this paper, we discuss the Cassandra NoSQL database approach for storing genomic data. We perform an analysis of persistency and I/O operations with real data, using the Cassandra database system. We also compare the results obtained with a classical relational database system and another NoSQL database approach, MongoDB.

Engineering the ATLAS TAG Browser

NASA Astrophysics Data System (ADS)

Zhang, Qizhi; ATLAS Collaboration

2011-12-01

ELSSI is a web-based event metadata (TAG) browser and event-level selection service for ATLAS. In this paper, we describe some of the challenges encountered in the process of developing ELSSI, and the software engineering strategies adopted to address those challenges. Approaches to management of access to data, browsing, data rendering, query building, query validation, execution, connection management, and communication with auxiliary services are discussed. We also describe strategies for dealing with data that may vary over time, such as run-dependent trigger decision decoding. Along with examples, we illustrate how programming techniques in multiple languages (PHP, JAVASCRIPT, XML, AJAX, and PL/SQL) have been blended to achieve the required results. Finally, we evaluate features of the ELSSI service in terms of functionality, scalability, and performance.

Comparisons of Attacks on Honeypots With Those on Real Networks

DTIC Science & Technology

2006-03-01

Oracle , MySQL , or PostgreSQL. Figure 2 shows an incoming packet and the process involved before and after the Snort engine detects the suspicious...stored on a separate, secured system.”[2]. Honeypots have several other uses besides monitoring attackers. They serve to protect real networks and...interaction vs . high-interaction. Although, both low-interaction and high-interaction honeypots are effective in soliciting attacks, high-interaction

Network Security Visualization

DTIC Science & Technology

1999-09-27

performing SQL generation and result-set binding, inserting acquired security events into the database and gathering the requested data for Console scene...objects is also auto-generated by a VBA script. Built into the auto-generated table access objects are the preferred join paths between tables. This...much of the Server itself) never have to deal with SQL directly. This is one aspect of laying the groundwork for supporting RDBMSs from multiple vendors

A Data Warehouse to Support Condition Based Maintenance (CBM)

DTIC Science & Technology

2005-05-01

Application ( VBA ) code sequence to import the original MAST-generated CSV and then create a single output table in DBASE IV format. The DBASE IV format...database architecture (Oracle, Sybase, MS- SQL , etc). This design includes table definitions, comments, specification of table attributes, primary and foreign...built queries and applications. Needs the application developers to construct data views. No SQL programming experience. b. Power Database User - knows

Development of a Big Data Application Architecture for Navy Manpower, Personnel, Training, and Education

DTIC Science & Technology

2016-03-01

science IT information technology JBOD just a bunch of disks JDBC java database connectivity xviii JPME Joint Professional Military Education JSO...Joint Service Officer JVM java virtual machine MPP massively parallel processing MPTE Manpower, Personnel, Training, and Education NAVMAC Navy...27 external database, whether it is MySQL , Oracle, DB2, or SQL Server (Teller, 2015). Connectors optimize the data transfer by obtaining metadata

A database for coconut crop improvement

PubMed Central

Rajagopal, Velamoor; Manimekalai, Ramaswamy; Devakumar, Krishnamurthy; Rajesh; Karun, Anitha; Niral, Vittal; Gopal, Murali; Aziz, Shamina; Gunasekaran, Marimuthu; Kumar, Mundappurathe Ramesh; Chandrasekar, Arumugam

2005-01-01

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. Availability http://www.bioinfcpcri.org PMID:17597858

Quality Attribute-Guided Evaluation of NoSQL Databases: An Experience Report

DTIC Science & Technology

2014-10-18

detailed technical evaluations of NoSQL databases specifically, and big data systems in general, that have become apparent during our study... big data , software systems [Agarwal 2011]. Internet-born organizations such as Google and Amazon are at the cutting edge of this revolution...Chang 2008], along with those of numerous other big data innovators, have made a variety of open source and commercial data management technologies

Alignment of high-throughput sequencing data inside in-memory databases.

PubMed

Firnkorn, Daniel; Knaup-Gregori, Petra; Lorenzo Bermejo, Justo; Ganzinger, Matthias

2014-01-01

In times of high-throughput DNA sequencing techniques, performance-capable analysis of DNA sequences is of high importance. Computer supported DNA analysis is still an intensive time-consuming task. In this paper we explore the potential of a new In-Memory database technology by using SAP's High Performance Analytic Appliance (HANA). We focus on read alignment as one of the first steps in DNA sequence analysis. In particular, we examined the widely used Burrows-Wheeler Aligner (BWA) and implemented stored procedures in both, HANA and the free database system MySQL, to compare execution time and memory management. To ensure that the results are comparable, MySQL has been running in memory as well, utilizing its integrated memory engine for database table creation. We implemented stored procedures, containing exact and inexact searching of DNA reads within the reference genome GRCh37. Due to technical restrictions in SAP HANA concerning recursion, the inexact matching problem could not be implemented on this platform. Hence, performance analysis between HANA and MySQL was made by comparing the execution time of the exact search procedures. Here, HANA was approximately 27 times faster than MySQL which means, that there is a high potential within the new In-Memory concepts, leading to further developments of DNA analysis procedures in the future.

Development of new on-line statistical program for the Korean Society for Radiation Oncology

PubMed Central

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Choi, Eun Kyung; Cho, Kwan Ho

2015-01-01

Purpose To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. Materials and Methods The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Results Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. Conclusion The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology. PMID:26157684

Development of new on-line statistical program for the Korean Society for Radiation Oncology.

PubMed

Song, Si Yeol; Ahn, Seung Do; Chung, Weon Kuu; Shin, Kyung Hwan; Choi, Eun Kyung; Cho, Kwan Ho

2015-06-01

To develop new on-line statistical program for the Korean Society for Radiation Oncology (KOSRO) to collect and extract medical data in radiation oncology more efficiently. The statistical program is a web-based program. The directory was placed in a sub-folder of the homepage of KOSRO and its web address is http://www.kosro.or.kr/asda. The operating systems server is Linux and the webserver is the Apache HTTP server. For database (DB) server, MySQL is adopted and dedicated scripting language is the PHP. Each ID and password are controlled independently and all screen pages for data input or analysis are made to be friendly to users. Scroll-down menu is actively used for the convenience of user and the consistence of data analysis. Year of data is one of top categories and main topics include human resource, equipment, clinical statistics, specialized treatment and research achievement. Each topic or category has several subcategorized topics. Real-time on-line report of analysis is produced immediately after entering each data and the administrator is able to monitor status of data input of each hospital. Backup of data as spread sheets can be accessed by the administrator and be used for academic works by any members of the KOSRO. The new on-line statistical program was developed to collect data from nationwide departments of radiation oncology. Intuitive screen and consistent input structure are expected to promote entering data of member hospitals and annual statistics should be a cornerstone of advance in radiation oncology.

Input Range Testing for the General Mission Analysis Tool (GMAT)

NASA Technical Reports Server (NTRS)

Hughes, Steven P.

2007-01-01

This document contains a test plan for testing input values to the General Mission Analysis Tool (GMAT). The plan includes four primary types of information, which rigorously define all tests that should be performed to validate that GMAT will accept allowable inputs and deny disallowed inputs. The first is a complete list of all allowed object fields in GMAT. The second type of information, is test input to be attempted for each field. The third type of information is allowable input values for all objects fields in GMAT. The final piece of information is how GMAT should respond to both valid and invalid information. It is VERY important to note that the tests below must be performed for both the Graphical User Interface and the script!! The examples are illustrated using a scripting perspective, because it is simpler to write up. However, the test must be performed for both interfaces to GMAT.

Factors Leading to Effectiveness and Satisfaction in Civil Engineer Information Systems

DTIC Science & Technology

2008-03-01

recently acquired MySQL in 2008 shortly after Oracle failed to acquire MySQL in 2007. For more information on policy implications concerning the use...individual level serves as the pertinent outcome variable and is used to evaluate and compare information systems in this study. Researchers have found...interim work information management system used by the Civil Engineer Operations Flight. The functions served by this system date back to the late

Computing and Communications Infrastructure for Network-Centric Warfare: Exploiting COTS, Assuring Performance

DTIC Science & Technology

2004-06-01

remote databases, has seen little vendor acceptance. Each database ( Oracle , DB2, MySQL , etc.) has its own client- server protocol. Therefore each...existing standards – SQL , X.500/LDAP, FTP, etc. • View information dissemination as selective replication – State-oriented vs . message-oriented...allowing the 8 application to start. The resource management system would serve as a broker to the resources, making sure that resources are not

Using XML/HTTP to Store, Serve and Annotate Tactical Scenarios for X3D Operational Visualization and Anti-Terrorist Training

DTIC Science & Technology

2003-03-01

PXSLServlet Paul A. Open Source Relational x X 23 Tchistopolskii sql2dtd David Mertz Public domain Relational x -- sql2xml Scott Hathaway Public...March 2003. [Hunter 2001] Hunter, David ; Cagle, Kurt; Dix, Chris; Kovack, Roger; Pinnock, Jonathan, Rafter, Jeff; Beginning XML (2nd Edition...Postgraduate School Monterey, California 4. Curt Blais Naval Postgraduate School Monterey, California 5 Erik Chaum NAVSEA Undersea

Large-scale Graph Computation on Just a PC

DTIC Science & Technology

2014-05-01

edges for several vertices simultaneously). We compared the performance of GraphChi-DB to Neo4j using their Java API (we discuss MySQL comparison in the...75 4.7.6 Comparison to RDBMS ( MySQL ) . . . . . . . . . . . . . . . . . . . . . 75 4.7.7 Summary of the...Windows method, GraphChi. The C++ implementation has circa 8,000 lines of code. We have also de- veloped a Java -version of GraphChi, but it does not

Delayed Instantiation Bulk Operations for Management of Distributed, Object-Based Storage Systems

DTIC Science & Technology

2009-08-01

source and destination object sets, while they have attribute pages to indicate that history . Fourth, we allow for operations to occur on any objects...client dialogue to the PostgreSQL database where server-side functions implement the service logic for the requests. The translation is done...to satisfy client requests, and performs delayed instantiation bulk operations. It is built around a PostgreSQL database with tables for storing

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

PubMed

Wong, Wing Chung; Kim, Dewey; Carter, Hannah; Diekhans, Mark; Ryan, Michael C; Karchin, Rachel

2011-08-01

Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM.

Motivational and metacognitive feedback in SQL-Tutor*

NASA Astrophysics Data System (ADS)

Hull, Alison; du Boulay, Benedict

2015-04-01

Motivation and metacognition are strongly intertwined, with learners high in self-efficacy more likely to use a variety of self-regulatory learning strategies, as well as to persist longer on challenging tasks. The aim of the research was to improve the learner's focus on the process and experience of problem-solving while using an Intelligent Tutoring System (ITS) and including motivational and metacognitive feedback based on the learner's past states and experiences. An existing ITS, SQL-Tutor, was used with first-year undergraduates studying a database module. The study used two versions of SQL-Tutor: the Control group used a base version providing domain feedback and the Study group used an extended version that also provided motivational and metacognitive feedback. This paper summarises the pre- and post-process results. Comparisons between groups showed some differing trends both in learning outcomes and behaviour in favour of the Study group.

Evaluating the Cassandra NoSQL Database Approach for Genomic Data Persistency

PubMed Central

Aniceto, Rodrigo; Xavier, Rene; Guimarães, Valeria; Hondo, Fernanda; Holanda, Maristela; Walter, Maria Emilia; Lifschitz, Sérgio

2015-01-01

Rapid advances in high-throughput sequencing techniques have created interesting computational challenges in bioinformatics. One of them refers to management of massive amounts of data generated by automatic sequencers. We need to deal with the persistency of genomic data, particularly storing and analyzing these large-scale processed data. To find an alternative to the frequently considered relational database model becomes a compelling task. Other data models may be more effective when dealing with a very large amount of nonconventional data, especially for writing and retrieving operations. In this paper, we discuss the Cassandra NoSQL database approach for storing genomic data. We perform an analysis of persistency and I/O operations with real data, using the Cassandra database system. We also compare the results obtained with a classical relational database system and another NoSQL database approach, MongoDB. PMID:26558254

Protecting Database Centric Web Services against SQL/XPath Injection Attacks

NASA Astrophysics Data System (ADS)

Laranjeiro, Nuno; Vieira, Marco; Madeira, Henrique

Web services represent a powerful interface for back-end database systems and are increasingly being used in business critical applications. However, field studies show that a large number of web services are deployed with security flaws (e.g., having SQL Injection vulnerabilities). Although several techniques for the identification of security vulnerabilities have been proposed, developing non-vulnerable web services is still a difficult task. In fact, security-related concerns are hard to apply as they involve adding complexity to already complex code. This paper proposes an approach to secure web services against SQL and XPath Injection attacks, by transparently detecting and aborting service invocations that try to take advantage of potential vulnerabilities. Our mechanism was applied to secure several web services specified by the TPC-App benchmark, showing to be 100% effective in stopping attacks, non-intrusive and very easy to use.

Managing Complex Interoperability Solutions using Model-Driven Architecture

DTIC Science & Technology

2011-06-01

such as Oracle or MySQL . Each data model for a specific RDBMS is a distinct PSM. Or the system may want to exchange information with other C2...reduced number of transformations, e.g., from an RDBMS physical schema to the corresponding SQL script needed to instantiate the tables in a relational...tance of models. In engineering, a model serves several purposes: 1. It presents an abstract view of a complex system or of a complex information

Information Collection using Handheld Devices in Unreliable Networking Environments

DTIC Science & Technology

2014-06-01

different types of mobile devices that connect wirelessly to a database 8 server. The actual backend database is not important to the mobile clients...Google’s infrastructure and local servers with MySQL and PostgreSQL on the backend (ODK 2014b). (2) Google Fusion Tables are used to do basic link...how we conduct business. Our requirements to share information do not change simply because there is little or no existing infrastructure in our

Reuse of the Cloud Analytics and Collaboration Environment within Tactical Applications (TacApps): A Feasibility Analysis

DTIC Science & Technology

2016-03-01

Representational state transfer  Java messaging service  Java application programming interface (API)  Internet relay chat (IRC)/extensible messaging and...JBoss application server or an Apache Tomcat servlet container instance. The relational database management system can be either PostgreSQL or MySQL ... Java library called direct web remoting. This library has been part of the core CACE architecture for quite some time; however, there have not been

MicroRNA Gene Regulatory Networks in Peripheral Nerve Sheath Tumors

DTIC Science & Technology

2013-09-01

3.0 hierarchical clustering of both the X and the Y-axis using Centroid linkage. The resulting clustered matrixes were visualized using Java Treeview...To score potential ceRNA interactions, the 54979 human interactions were loaded into a mySQL database and when the user selects a given mRNA all...on the fly using PHP interactions with mySQL in a similar fashion as previously described in our publicly available databases such as sarcoma

Understanding and Capturing People’s Mobile App Privacy Preferences

DTIC Science & Technology

2013-10-28

The entire apps’ metadata takes up about 500MB of storage space when stored in a MySQL database and all the binary files take approximately 300GB of...functionality that can de- compile Dalvik bytecodes to Java source code faster than other de-compilers. Given the scale of the app analysis we planned on... java libraries, such as parser, sql connectors, etc Targeted Ads 137 admob, adwhirl, greystripe… Provided by mobile behavioral ads company to

Shark: SQL and Analytics with Cost-Based Query Optimization on Coarse-Grained Distributed Memory

DTIC Science & Technology

2014-01-13

RDBMS and contains a database (often MySQL or Derby) with a namespace for tables, table metadata and partition information. Table data is stored in an...serialization/deserialization) Java interface implementations with corresponding object inspectors. The Hive driver controls the processing of queries, coordinat...native API, RDD operations are invoked through a functional interface similar to DryadLINQ [32] in Scala, Java or Python. For example, the Scala code for

Implementing an Intrusion Detection System in the Mysea Architecture

DTIC Science & Technology

2008-06-01

password for each user passwd <username> then follow the prompts 2. PostgreSQL 7.4.18 Installation Perform the following steps as root: 1. Copy...password changed Repeat for user snort. exit After making the groups and users the group and passwd file needs to be updated. Set security and...untrusted/bin/xtsmkgroup > /etc/group chmod 644 /etc/group /xts/untrusted/bin/xtsmkpasswd > /etc/ passwd chmod 644 /etc/ passwd 3. PostgreSQL 7.4.18

Astronomical Archive at Tartu Observatory

NASA Astrophysics Data System (ADS)

Annuk, K.

2007-10-01

Archiving astronomical data is important task not only at large observatories but also at small observatories. Here we describe the astronomical archive at Tartu Observatory. The archive consists of old photographic plate images, photographic spectrograms, CCD direct--images and CCD spectroscopic data. The photographic plate digitizing project was started in 2005. An on-line database (based on MySQL) was created. The database includes CCD data as well photographic data. A PHP-MySQL interface was written for access to all data.

Shark: SQL and Rich Analytics at Scale

DTIC Science & Technology

2012-11-26

learning programs up to 100 faster than Hadoop. Unlike previous systems, Shark shows that it is possible to achieve these speedups while retaining a...Shark to run SQL queries up to 100× faster than Apache Hive, and machine learning programs up to 100× faster than Hadoop. Unlike previous systems, Shark...so using a runtime that is optimized for such workloads and a programming model that is designed to express machine learn - ing algorithms. 4.1

Nosql for Storage and Retrieval of Large LIDAR Data Collections

NASA Astrophysics Data System (ADS)

Boehm, J.; Liu, K.

2015-08-01

Developments in LiDAR technology over the past decades have made LiDAR to become a mature and widely accepted source of geospatial information. This in turn has led to an enormous growth in data volume. The central idea for a file-centric storage of LiDAR point clouds is the observation that large collections of LiDAR data are typically delivered as large collections of files, rather than single files of terabyte size. This split of the dataset, commonly referred to as tiling, was usually done to accommodate a specific processing pipeline. It makes therefore sense to preserve this split. A document oriented NoSQL database can easily emulate this data partitioning, by representing each tile (file) in a separate document. The document stores the metadata of the tile. The actual files are stored in a distributed file system emulated by the NoSQL database. We demonstrate the use of MongoDB a highly scalable document oriented NoSQL database for storing large LiDAR files. MongoDB like any NoSQL database allows for queries on the attributes of the document. As a specialty MongoDB also allows spatial queries. Hence we can perform spatial queries on the bounding boxes of the LiDAR tiles. Inserting and retrieving files on a cloud-based database is compared to native file system and cloud storage transfer speed.

Evaluating the Sensitivity of Agricultural Model Performance to Different Climate Inputs: Supplemental Material

NASA Technical Reports Server (NTRS)

Glotter, Michael J.; Ruane, Alex C.; Moyer, Elisabeth J.; Elliott, Joshua W.

2015-01-01

Projections of future food production necessarily rely on models, which must themselves be validated through historical assessments comparing modeled and observed yields. Reliable historical validation requires both accurate agricultural models and accurate climate inputs. Problems with either may compromise the validation exercise. Previous studies have compared the effects of different climate inputs on agricultural projections but either incompletely or without a ground truth of observed yields that would allow distinguishing errors due to climate inputs from those intrinsic to the crop model. This study is a systematic evaluation of the reliability of a widely used crop model for simulating U.S. maize yields when driven by multiple observational data products. The parallelized Decision Support System for Agrotechnology Transfer (pDSSAT) is driven with climate inputs from multiple sources reanalysis, reanalysis that is bias corrected with observed climate, and a control dataset and compared with observed historical yields. The simulations show that model output is more accurate when driven by any observation-based precipitation product than when driven by non-bias-corrected reanalysis. The simulations also suggest, in contrast to previous studies, that biased precipitation distribution is significant for yields only in arid regions. Some issues persist for all choices of climate inputs: crop yields appear to be oversensitive to precipitation fluctuations but under sensitive to floods and heat waves. These results suggest that the most important issue for agricultural projections may be not climate inputs but structural limitations in the crop models themselves.

Evaluating the sensitivity of agricultural model performance to different climate inputs

PubMed Central

Glotter, Michael J.; Moyer, Elisabeth J.; Ruane, Alex C.; Elliott, Joshua W.

2017-01-01

Projections of future food production necessarily rely on models, which must themselves be validated through historical assessments comparing modeled to observed yields. Reliable historical validation requires both accurate agricultural models and accurate climate inputs. Problems with either may compromise the validation exercise. Previous studies have compared the effects of different climate inputs on agricultural projections, but either incompletely or without a ground truth of observed yields that would allow distinguishing errors due to climate inputs from those intrinsic to the crop model. This study is a systematic evaluation of the reliability of a widely-used crop model for simulating U.S. maize yields when driven by multiple observational data products. The parallelized Decision Support System for Agrotechnology Transfer (pDSSAT) is driven with climate inputs from multiple sources – reanalysis, reanalysis bias-corrected with observed climate, and a control dataset – and compared to observed historical yields. The simulations show that model output is more accurate when driven by any observation-based precipitation product than when driven by un-bias-corrected reanalysis. The simulations also suggest, in contrast to previous studies, that biased precipitation distribution is significant for yields only in arid regions. However, some issues persist for all choices of climate inputs: crop yields appear oversensitive to precipitation fluctuations but undersensitive to floods and heat waves. These results suggest that the most important issue for agricultural projections may be not climate inputs but structural limitations in the crop models themselves. PMID:29097985

Web-based application on employee performance assessment using exponential comparison method

NASA Astrophysics Data System (ADS)

Maryana, S.; Kurnia, E.; Ruyani, A.

2017-02-01

Employee performance assessment is also called a performance review, performance evaluation, or assessment of employees, is an effort to assess the achievements of staffing performance with the aim to increase productivity of employees and companies. This application helps in the assessment of employee performance using five criteria: Presence, Quality of Work, Quantity of Work, Discipline, and Teamwork. The system uses the Exponential Comparative Method and Weighting Eckenrode. Calculation results using graphs were provided to see the assessment of each employee. Programming language used in this system is written in Notepad++ and MySQL database. The testing result on the system can be concluded that this application is correspond with the design and running properly. The test conducted is structural test, functional test, and validation, sensitivity analysis, and SUMI testing.

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data

PubMed Central

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest. PMID:26958859

Comparing the Performance of NoSQL Approaches for Managing Archetype-Based Electronic Health Record Data.

PubMed

Freire, Sergio Miranda; Teodoro, Douglas; Wei-Kleiner, Fang; Sundvall, Erik; Karlsson, Daniel; Lambrix, Patrick

2016-01-01

This study provides an experimental performance evaluation on population-based queries of NoSQL databases storing archetype-based Electronic Health Record (EHR) data. There are few published studies regarding the performance of persistence mechanisms for systems that use multilevel modelling approaches, especially when the focus is on population-based queries. A healthcare dataset with 4.2 million records stored in a relational database (MySQL) was used to generate XML and JSON documents based on the openEHR reference model. Six datasets with different sizes were created from these documents and imported into three single machine XML databases (BaseX, eXistdb and Berkeley DB XML) and into a distributed NoSQL database system based on the MapReduce approach, Couchbase, deployed in different cluster configurations of 1, 2, 4, 8 and 12 machines. Population-based queries were submitted to those databases and to the original relational database. Database size and query response times are presented. The XML databases were considerably slower and required much more space than Couchbase. Overall, Couchbase had better response times than MySQL, especially for larger datasets. However, Couchbase requires indexing for each differently formulated query and the indexing time increases with the size of the datasets. The performances of the clusters with 2, 4, 8 and 12 nodes were not better than the single node cluster in relation to the query response time, but the indexing time was reduced proportionally to the number of nodes. The tested XML databases had acceptable performance for openEHR-based data in some querying use cases and small datasets, but were generally much slower than Couchbase. Couchbase also outperformed the response times of the relational database, but required more disk space and had a much longer indexing time. Systems like Couchbase are thus interesting research targets for scalable storage and querying of archetype-based EHR data when population-based use cases are of interest.

CGDM: collaborative genomic data model for molecular profiling data using NoSQL.

PubMed

Wang, Shicai; Mares, Mihaela A; Guo, Yi-Ke

2016-12-01

High-throughput molecular profiling has greatly improved patient stratification and mechanistic understanding of diseases. With the increasing amount of data used in translational medicine studies in recent years, there is a need to improve the performance of data warehouses in terms of data retrieval and statistical processing. Both relational and Key Value models have been used for managing molecular profiling data. Key Value models such as SeqWare have been shown to be particularly advantageous in terms of query processing speed for large datasets. However, more improvement can be achieved, particularly through better indexing techniques of the Key Value models, taking advantage of the types of queries which are specific for the high-throughput molecular profiling data. In this article, we introduce a Collaborative Genomic Data Model (CGDM), aimed at significantly increasing the query processing speed for the main classes of queries on genomic databases. CGDM creates three Collaborative Global Clustering Index Tables (CGCITs) to solve the velocity and variety issues at the cost of limited extra volume. Several benchmarking experiments were carried out, comparing CGDM implemented on HBase to the traditional SQL data model (TDM) implemented on both HBase and MySQL Cluster, using large publicly available molecular profiling datasets taken from NCBI and HapMap. In the microarray case, CGDM on HBase performed up to 246 times faster than TDM on HBase and 7 times faster than TDM on MySQL Cluster. In single nucleotide polymorphism case, CGDM on HBase outperformed TDM on HBase by up to 351 times and TDM on MySQL Cluster by up to 9 times. The CGDM source code is available at https://github.com/evanswang/CGDM. y.guo@imperial.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

High dimensional biological data retrieval optimization with NoSQL technology.

PubMed

Wang, Shicai; Pandis, Ioannis; Wu, Chao; He, Sijin; Johnson, David; Emam, Ibrahim; Guitton, Florian; Guo, Yike

2014-01-01

High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data. In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB. The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data.

High dimensional biological data retrieval optimization with NoSQL technology

PubMed Central

2014-01-01

Background High-throughput transcriptomic data generated by microarray experiments is the most abundant and frequently stored kind of data currently used in translational medicine studies. Although microarray data is supported in data warehouses such as tranSMART, when querying relational databases for hundreds of different patient gene expression records queries are slow due to poor performance. Non-relational data models, such as the key-value model implemented in NoSQL databases, hold promise to be more performant solutions. Our motivation is to improve the performance of the tranSMART data warehouse with a view to supporting Next Generation Sequencing data. Results In this paper we introduce a new data model better suited for high-dimensional data storage and querying, optimized for database scalability and performance. We have designed a key-value pair data model to support faster queries over large-scale microarray data and implemented the model using HBase, an implementation of Google's BigTable storage system. An experimental performance comparison was carried out against the traditional relational data model implemented in both MySQL Cluster and MongoDB, using a large publicly available transcriptomic data set taken from NCBI GEO concerning Multiple Myeloma. Our new key-value data model implemented on HBase exhibits an average 5.24-fold increase in high-dimensional biological data query performance compared to the relational model implemented on MySQL Cluster, and an average 6.47-fold increase on query performance on MongoDB. Conclusions The performance evaluation found that the new key-value data model, in particular its implementation in HBase, outperforms the relational model currently implemented in tranSMART. We propose that NoSQL technology holds great promise for large-scale data management, in particular for high-dimensional biological data such as that demonstrated in the performance evaluation described in this paper. We aim to use this new data model as a basis for migrating tranSMART's implementation to a more scalable solution for Big Data. PMID:25435347

A Look Under the Hood: How the JPL Tropical Cyclone Information System Uses Database Technologies to Present Big Data to Users

NASA Astrophysics Data System (ADS)

Knosp, B.; Gangl, M.; Hristova-Veleva, S. M.; Kim, R. M.; Li, P.; Turk, J.; Vu, Q. A.

2015-12-01

The JPL Tropical Cyclone Information System (TCIS) brings together satellite, aircraft, and model forecast data from several NASA, NOAA, and other data centers to assist researchers in comparing and analyzing data and model forecast related to tropical cyclones. The TCIS has been running a near-real time (NRT) data portal during North Atlantic hurricane season that typically runs from June through October each year, since 2010. Data collected by the TCIS varies by type, format, contents, and frequency and is served to the user in two ways: (1) as image overlays on a virtual globe and (2) as derived output from a suite of analysis tools. In order to support these two functions, the data must be collected and then made searchable by criteria such as date, mission, product, pressure level, and geospatial region. Creating a database architecture that is flexible enough to manage, intelligently interrogate, and ultimately present this disparate data to the user in a meaningful way has been the primary challenge. The database solution for the TCIS has been to use a hybrid MySQL + Solr implementation. After testing other relational database and NoSQL solutions, such as PostgreSQL and MongoDB respectively, this solution has given the TCIS the best offerings in terms of query speed and result reliability. This database solution also supports the challenging (and memory overwhelming) geospatial queries that are necessary to support analysis tools requested by users. Though hardly new technologies on their own, our implementation of MySQL + Solr had to be customized and tuned to be able to accurately store, index, and search the TCIS data holdings. In this presentation, we will discuss how we arrived on our MySQL + Solr database architecture, why it offers us the most consistent fast and reliable results, and how it supports our front end so that we can offer users a look into our "big data" holdings.

Alternatives to relational databases in precision medicine: Comparison of NoSQL approaches for big data storage using supercomputers

NASA Astrophysics Data System (ADS)

Velazquez, Enrique Israel

Improvements in medical and genomic technologies have dramatically increased the production of electronic data over the last decade. As a result, data management is rapidly becoming a major determinant, and urgent challenge, for the development of Precision Medicine. Although successful data management is achievable using Relational Database Management Systems (RDBMS), exponential data growth is a significant contributor to failure scenarios. Growing amounts of data can also be observed in other sectors, such as economics and business, which, together with the previous facts, suggests that alternate database approaches (NoSQL) may soon be required for efficient storage and management of big databases. However, this hypothesis has been difficult to test in the Precision Medicine field since alternate database architectures are complex to assess and means to integrate heterogeneous electronic health records (EHR) with dynamic genomic data are not easily available. In this dissertation, we present a novel set of experiments for identifying NoSQL database approaches that enable effective data storage and management in Precision Medicine using patients' clinical and genomic information from the cancer genome atlas (TCGA). The first experiment draws on performance and scalability from biologically meaningful queries with differing complexity and database sizes. The second experiment measures performance and scalability in database updates without schema changes. The third experiment assesses performance and scalability in database updates with schema modifications due dynamic data. We have identified two NoSQL approach, based on Cassandra and Redis, which seems to be the ideal database management systems for our precision medicine queries in terms of performance and scalability. We present NoSQL approaches and show how they can be used to manage clinical and genomic big data. Our research is relevant to the public health since we are focusing on one of the main challenges to the development of Precision Medicine and, consequently, investigating a potential solution to the progressively increasing demands on health care.

footprintDB: a database of transcription factors with annotated cis elements and binding interfaces.

PubMed

Sebastian, Alvaro; Contreras-Moreira, Bruno

2014-01-15

Traditional and high-throughput techniques for determining transcription factor (TF) binding specificities are generating large volumes of data of uneven quality, which are scattered across individual databases. FootprintDB integrates some of the most comprehensive freely available libraries of curated DNA binding sites and systematically annotates the binding interfaces of the corresponding TFs. The first release contains 2422 unique TF sequences, 10 112 DNA binding sites and 3662 DNA motifs. A survey of the included data sources, organisms and TF families was performed together with proprietary database TRANSFAC, finding that footprintDB has a similar coverage of multicellular organisms, while also containing bacterial regulatory data. A search engine has been designed that drives the prediction of DNA motifs for input TFs, or conversely of TF sequences that might recognize input regulatory sequences, by comparison with database entries. Such predictions can also be extended to a single proteome chosen by the user, and results are ranked in terms of interface similarity. Benchmark experiments with bacterial, plant and human data were performed to measure the predictive power of footprintDB searches, which were able to correctly recover 10, 55 and 90% of the tested sequences, respectively. Correctly predicted TFs had a higher interface similarity than the average, confirming its diagnostic value. Web site implemented in PHP,Perl, MySQL and Apache. Freely available from http://floresta.eead.csic.es/footprintdb.

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

Sun, Z. J.; Wells, D.; Green, J.

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switchingmore » the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.« less

Making generic tutorials content specific: recycling evidence-based practice (EBP) tutorials for two disciplines.

PubMed

Jeffery, Keven M; Maggio, Lauren; Blanchard, Mary

2009-01-01

Librarians at the Boston University Medical Center constructed two interactive online tutorials, "Introduction to EBM" and "Formulating a Clinical Question (PICO)," for a Family Medicine Clerkship and then quickly repurposed the existing tutorials to support an Evidence-based Dentistry course. Adobe's ColdFusion software was used to populate the tutorials with course-specific content based on the URL used to enter each tutorial, and a MySQL database was used to collect student input. Student responses were viewable immediately by course faculty on a password-protected Web site. The tutorials ensured that all students received the same baseline training and allowed librarians to tailor a subsequent library skills workshop to student tutorial answers. The tutorials were well-received by the medical and dental schools and have been added to mandatory first-year Evidence-based Medicine (EBM) and Evidence-based Dentistry (EBD) courses, meaning that every medical and dental student at BUMC will be expected to complete these tutorials.

ImmuneDB: a system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data.

PubMed

Rosenfeld, Aaron M; Meng, Wenzhao; Luning Prak, Eline T; Hershberg, Uri

2017-01-15

As high-throughput sequencing of B cells becomes more common, the need for tools to analyze the large quantity of data also increases. This article introduces ImmuneDB, a system for analyzing vast amounts of heavy chain variable region sequences and exploring the resulting data. It can take as input raw FASTA/FASTQ data, identify genes, determine clones, construct lineages, as well as provide information such as selection pressure and mutation analysis. It uses an industry leading database, MySQL, to provide fast analysis and avoid the complexities of using error prone flat-files. ImmuneDB is freely available at http://immunedb.comA demo of the ImmuneDB web interface is available at: http://immunedb.com/demo CONTACT: Uh25@drexel.eduSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

The design of 1-wire net meteorological observatory for 2.4 m telescope

NASA Astrophysics Data System (ADS)

Zhu, Gao-Feng; Wei, Ka-Ning; Fan, Yu-Feng; Xu, Jun; Qin, Wei

2005-03-01

The weather is an important factor to affect astronomical observations. The 2.4 m telescope can not work in Robotic Mode without the weather data input. Therefore it is necessary to build a meteorological observatory near the 2.4 m telescope. In this article, the design of the 1-wire net meteorological observatory, which includes hardware and software systems, is introduced. The hardware system is made up of some kinds of sensors and ADC. A suited power station system is also designed. The software system is based on Windows XP operating system and MySQL data management system, and a prototype system of browse/server model is developed by JAVA and JSP. After being tested, the meteorological observatory can register the immediate data of weather, such as raining, snowing, and wind speed. At last, the data will be stored for feature use. The product and the design can work well for the 2.4 m telescope.

Visualizing Phenology and Climate Data at the National Scale

NASA Astrophysics Data System (ADS)

Rosemartin, A.; Marsh, L.

2013-12-01

Nature's Notebook is the USA National Phenology Network's national-scale plant and animal phenology observation program, designed to address the challenges posed by global change and its impacts on ecosystems and human health. Since its inception in 2009, 2,500 participants in Nature's Notebook have submitted 2.3 million records on the phenology of 17,000 organisms across the United States. An information architecture has been developed to facilitate collaboration and participatory data collection and digitization. Browser-based and mobile applications support data submission, and a MySQL/Drupal multi-site infrastructure enables data storage, access and discovery. Web services are available for both input and export of data resources. In this presentation we will focus on a tool for visualizing phenology data at the national scale. Effective data exploration for this multi-dimensional dataset requires the ability to plot sites, select species and phenophases, graph organismal phenology through time, and view integrated precipitation and temperature data. We will demonstrate the existing tool's capacity, discuss future directions and solicit feedback from the community.

Open-source Framework for Storing and Manipulation of Plasma Chemical Reaction Data

NASA Astrophysics Data System (ADS)

Jenkins, T. G.; Averkin, S. N.; Cary, J. R.; Kruger, S. E.

2017-10-01

We present a new open-source framework for storage and manipulation of plasma chemical reaction data that has emerged from our in-house project MUNCHKIN. This framework consists of python scripts and C + + programs. It stores data in an SQL data base for fast retrieval and manipulation. For example, it is possible to fit cross-section data into most widely used analytical expressions, calculate reaction rates for Maxwellian distribution functions of colliding particles, and fit them into different analytical expressions. Another important feature of this framework is the ability to calculate transport properties based on the cross-section data and supplied distribution functions. In addition, this framework allows the export of chemical reaction descriptions in LaTeX format for ease of inclusion in scientific papers. With the help of this framework it is possible to generate corresponding VSim (Particle-In-Cell simulation code) and USim (unstructured multi-fluid code) input blocks with appropriate cross-sections.

Warehouses information system design and development

NASA Astrophysics Data System (ADS)

Darajatun, R. A.; Sukanta

2017-12-01

Materials/goods handling industry is fundamental for companies to ensure the smooth running of their warehouses. Efficiency and organization within every aspect of the business is essential in order to gain a competitive advantage. The purpose of this research is design and development of Kanban of inventory storage and delivery system. Application aims to facilitate inventory stock checks to be more efficient and effective. Users easily input finished goods from production department, warehouse, customer, and also suppliers. Master data designed as complete as possible to be prepared applications used in a variety of process logistic warehouse variations. The author uses Java programming language to develop the application, which is used for building Java Web applications, while the database used is MySQL. System development methodology that I use is the Waterfall methodology. Waterfall methodology has several stages of the Analysis, System Design, Implementation, Integration, Operation and Maintenance. In the process of collecting data the author uses the method of observation, interviews, and literature.

Workstation Analytics in Distributed Warfighting Experimentation: Results from Coalition Attack Guidance Experiment 3A

DTIC Science & Technology

2014-06-01

central location. Each of the SQLite databases are converted and stored in one MySQL database and the pcap files are parsed to extract call information...from the specific communications applications used during the experiment. This extracted data is then stored in the same MySQL database. With all...rhythm of the event. Figure 3 demonstrates the application usage over the course of the experiment for the EXDIR. As seen, the EXDIR spent the majority

An Analysis Platform for Mobile Ad Hoc Network (MANET) Scenario Execution Log Data

DTIC Science & Technology

2016-01-01

these technologies. 4.1 Backend Technologies • Java 1.8 • my-sql-connector- java -5.0.8.jar • Tomcat • VirtualBox • Kali MANET Virtual Machine 4.2...Frontend Technologies • LAMPP 4.3 Database • MySQL Server 5. Database The SEDAP database settings and structure are described in this section...contains all the backend java functionality including the web services, should be placed in the webapps directory inside the Tomcat installation

Design and Implementation of 3D Model Data Management System Based on SQL

NASA Astrophysics Data System (ADS)

Li, Shitao; Zhang, Shixin; Zhang, Zhanling; Li, Shiming; Jia, Kun; Hu, Zhongxu; Ping, Liang; Hu, Youming; Li, Yanlei

CAD/CAM technology plays an increasingly important role in the machinery manufacturing industry. As an important means of production, the accumulated three-dimensional models in many years of design work are valuable. Thus the management of these three-dimensional models is of great significance. This paper gives detailed explanation for a method to design three-dimensional model databases based on SQL and to implement the functions such as insertion, modification, inquiry, preview and so on.

SLAM, a Mathematica interface for SUSY spectrum generators

NASA Astrophysics Data System (ADS)

Marquard, Peter; Zerf, Nikolai

2014-03-01

We present and publish a Mathematica package, which can be used to automatically obtain any numerical MSSM input parameter from SUSY spectrum generators, which follow the SLHA standard, like SPheno, SOFTSUSY, SuSeFLAV or Suspect. The package enables a very comfortable way of numerical evaluations within the MSSM using Mathematica. It implements easy to use predefined high scale and low scale scenarios like mSUGRA or mhmax and if needed enables the user to directly specify the input required by the spectrum generators. In addition it supports an automatic saving and loading of SUSY spectra to and from a SQL data base, avoiding the rerun of a spectrum generator for a known spectrum. Catalogue identifier: AERX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AERX_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 4387 No. of bytes in distributed program, including test data, etc.: 37748 Distribution format: tar.gz Programming language: Mathematica. Computer: Any computer where Mathematica version 6 or higher is running providing bash and sed. Operating system: Linux. Classification: 11.1. External routines: A SUSY spectrum generator such as SPheno, SOFTSUSY, SuSeFLAV or SUSPECT Nature of problem: Interfacing published spectrum generators for automated creation, saving and loading of SUSY particle spectra. Solution method: SLAM automatically writes/reads SLHA spectrum generator input/output and is able to save/load generated data in/from a data base. Restrictions: No general restrictions, specific restrictions are given in the manuscript. Running time: A single spectrum calculation takes much less than one second on a modern PC.

Bilinearity in Spatiotemporal Integration of Synaptic Inputs

PubMed Central

Li, Songting; Liu, Nan; Zhang, Xiao-hui; Zhou, Douglas; Cai, David

2014-01-01

Neurons process information via integration of synaptic inputs from dendrites. Many experimental results demonstrate dendritic integration could be highly nonlinear, yet few theoretical analyses have been performed to obtain a precise quantitative characterization analytically. Based on asymptotic analysis of a two-compartment passive cable model, given a pair of time-dependent synaptic conductance inputs, we derive a bilinear spatiotemporal dendritic integration rule. The summed somatic potential can be well approximated by the linear summation of the two postsynaptic potentials elicited separately, plus a third additional bilinear term proportional to their product with a proportionality coefficient . The rule is valid for a pair of synaptic inputs of all types, including excitation-inhibition, excitation-excitation, and inhibition-inhibition. In addition, the rule is valid during the whole dendritic integration process for a pair of synaptic inputs with arbitrary input time differences and input locations. The coefficient is demonstrated to be nearly independent of the input strengths but is dependent on input times and input locations. This rule is then verified through simulation of a realistic pyramidal neuron model and in electrophysiological experiments of rat hippocampal CA1 neurons. The rule is further generalized to describe the spatiotemporal dendritic integration of multiple excitatory and inhibitory synaptic inputs. The integration of multiple inputs can be decomposed into the sum of all possible pairwise integration, where each paired integration obeys the bilinear rule. This decomposition leads to a graph representation of dendritic integration, which can be viewed as functionally sparse. PMID:25521832

Detecting Distributed SQL Injection Attacks in a Eucalyptus Cloud Environment

NASA Technical Reports Server (NTRS)

Kebert, Alan; Barnejee, Bikramjit; Solano, Juan; Solano, Wanda

2013-01-01

The cloud computing environment offers malicious users the ability to spawn multiple instances of cloud nodes that are similar to virtual machines, except that they can have separate external IP addresses. In this paper we demonstrate how this ability can be exploited by an attacker to distribute his/her attack, in particular SQL injection attacks, in such a way that an intrusion detection system (IDS) could fail to identify this attack. To demonstrate this, we set up a small private cloud, established a vulnerable website in one instance, and placed an IDS within the cloud to monitor the network traffic. We found that an attacker could quite easily defeat the IDS by periodically altering its IP address. To detect such an attacker, we propose to use multi-agent plan recognition, where the multiple source IPs are considered as different agents who are mounting a collaborative attack. We show that such a formulation of this problem yields a more sophisticated approach to detecting SQL injection attacks within a cloud computing environment.

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer

PubMed Central

Carter, Hannah; Diekhans, Mark; Ryan, Michael C.; Karchin, Rachel

2011-01-01

Summary: Thousands of cancer exomes are currently being sequenced, yielding millions of non-synonymous single nucleotide variants (SNVs) of possible relevance to disease etiology. Here, we provide a software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. It includes a database of precomputed, predictive features covering all positions in the annotated human exome and can be used either stand-alone or as part of a larger variant discovery pipeline. Availability and Implementation: MySQL database, source code and binaries freely available for academic/government use at http://wiki.chasmsoftware.org, Source in Python and C++. Requires 32 or 64-bit Linux system (tested on Fedora Core 8,10,11 and Ubuntu 10), 2.5*≤ Python <3.0*, MySQL server >5.0, 60 GB available hard disk space (50 MB for software and data files, 40 GB for MySQL database dump when uncompressed), 2 GB of RAM. Contact: karchin@jhu.edu Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:21685053

Datacube Services in Action, Using Open Source and Open Standards

NASA Astrophysics Data System (ADS)

Baumann, P.; Misev, D.

2016-12-01

Array Databases comprise novel, promising technology for massive spatio-temporal datacubes, extending the SQL paradigm of "any query, anytime" to n-D arrays. On server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. The rasdaman ("raster data manager") system, which has pioneered Array Databases, is available in open source on www.rasdaman.org. Its declarative query language extends SQL with array operators which are optimized and parallelized on server side. The rasdaman engine, which is part of OSGeo Live, is mature and in operational use databases individually holding dozens of Terabytes. Further, the rasdaman concepts have strongly impacted international Big Data standards in the field, including the forthcoming MDA ("Multi-Dimensional Array") extension to ISO SQL, the OGC Web Coverage Service (WCS) and Web Coverage Processing Service (WCPS) standards, and the forthcoming INSPIRE WCS/WCPS; in both OGC and INSPIRE, OGC is WCS Core Reference Implementation. In our talk we present concepts, architecture, operational services, and standardization impact of open-source rasdaman, as well as experiences made.

Providing R-Tree Support for Mongodb

NASA Astrophysics Data System (ADS)

Xiang, Longgang; Shao, Xiaotian; Wang, Dehao

2016-06-01

Supporting large amounts of spatial data is a significant characteristic of modern databases. However, unlike some mature relational databases, such as Oracle and PostgreSQL, most of current burgeoning NoSQL databases are not well designed for storing geospatial data, which is becoming increasingly important in various fields. In this paper, we propose a novel method to provide R-tree index, as well as corresponding spatial range query and nearest neighbour query functions, for MongoDB, one of the most prevalent NoSQL databases. First, after in-depth analysis of MongoDB's features, we devise an efficient tabular document structure which flattens R-tree index into MongoDB collections. Further, relevant mechanisms of R-tree operations are issued, and then we discuss in detail how to integrate R-tree into MongoDB. Finally, we present the experimental results which show that our proposed method out-performs the built-in spatial index of MongoDB. Our research will greatly facilitate big data management issues with MongoDB in a variety of geospatial information applications.

SiC: An Agent Based Architecture for Preventing and Detecting Attacks to Ubiquitous Databases

NASA Astrophysics Data System (ADS)

Pinzón, Cristian; de Paz, Yanira; Bajo, Javier; Abraham, Ajith; Corchado, Juan M.

One of the main attacks to ubiquitous databases is the structure query language (SQL) injection attack, which causes severe damages both in the commercial aspect and in the user’s confidence. This chapter proposes the SiC architecture as a solution to the SQL injection attack problem. This is a hierarchical distributed multiagent architecture, which involves an entirely new approach with respect to existing architectures for the prevention and detection of SQL injections. SiC incorporates a kind of intelligent agent, which integrates a case-based reasoning system. This agent, which is the core of the architecture, allows the application of detection techniques based on anomalies as well as those based on patterns, providing a great degree of autonomy, flexibility, robustness and dynamic scalability. The characteristics of the multiagent system allow an architecture to detect attacks from different types of devices, regardless of the physical location. The architecture has been tested on a medical database, guaranteeing safe access from various devices such as PDAs and notebook computers.

Evaluation of Advanced Stirling Convertor Net Heat Input Correlation Methods Using a Thermal Standard

NASA Technical Reports Server (NTRS)

Briggs, Maxwell; Schifer, Nicholas

2011-01-01

Test hardware used to validate net heat prediction models. Problem: Net Heat Input cannot be measured directly during operation. Net heat input is a key parameter needed in prediction of efficiency for convertor performance. Efficiency = Electrical Power Output (Measured) divided by Net Heat Input (Calculated). Efficiency is used to compare convertor designs and trade technology advantages for mission planning.

Input variable selection for data-driven models of Coriolis flowmeters for two-phase flow measurement

NASA Astrophysics Data System (ADS)

Wang, Lijuan; Yan, Yong; Wang, Xue; Wang, Tao

2017-03-01

Input variable selection is an essential step in the development of data-driven models for environmental, biological and industrial applications. Through input variable selection to eliminate the irrelevant or redundant variables, a suitable subset of variables is identified as the input of a model. Meanwhile, through input variable selection the complexity of the model structure is simplified and the computational efficiency is improved. This paper describes the procedures of the input variable selection for the data-driven models for the measurement of liquid mass flowrate and gas volume fraction under two-phase flow conditions using Coriolis flowmeters. Three advanced input variable selection methods, including partial mutual information (PMI), genetic algorithm-artificial neural network (GA-ANN) and tree-based iterative input selection (IIS) are applied in this study. Typical data-driven models incorporating support vector machine (SVM) are established individually based on the input candidates resulting from the selection methods. The validity of the selection outcomes is assessed through an output performance comparison of the SVM based data-driven models and sensitivity analysis. The validation and analysis results suggest that the input variables selected from the PMI algorithm provide more effective information for the models to measure liquid mass flowrate while the IIS algorithm provides a fewer but more effective variables for the models to predict gas volume fraction.

NoSQL technologies for the CMS Conditions Database

NASA Astrophysics Data System (ADS)

Sipos, Roland

2015-12-01

With the restart of the LHC in 2015, the growth of the CMS Conditions dataset will continue, therefore the need of consistent and highly available access to the Conditions makes a great cause to revisit different aspects of the current data storage solutions. We present a study of alternative data storage backends for the Conditions Databases, by evaluating some of the most popular NoSQL databases to support a key-value representation of the CMS Conditions. The definition of the database infrastructure is based on the need of storing the conditions as BLOBs. Because of this, each condition can reach the size that may require special treatment (splitting) in these NoSQL databases. As big binary objects may be problematic in several database systems, and also to give an accurate baseline, a testing framework extension was implemented to measure the characteristics of the handling of arbitrary binary data in these databases. Based on the evaluation, prototypes of a document store, using a column-oriented and plain key-value store, are deployed. An adaption layer to access the backends in the CMS Offline software was developed to provide transparent support for these NoSQL databases in the CMS context. Additional data modelling approaches and considerations in the software layer, deployment and automatization of the databases are also covered in the research. In this paper we present the results of the evaluation as well as a performance comparison of the prototypes studied.

A Computational Methodology for Simulating Thermal Loss Testing of the Advanced Stirling Convertor

NASA Technical Reports Server (NTRS)

Reid, Terry V.; Wilson, Scott D.; Schifer, Nicholas A.; Briggs, Maxwell H.

2012-01-01

The U.S. Department of Energy (DOE) and Lockheed Martin Space Systems Company (LMSSC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. This generator would use two highefficiency Advanced Stirling Convertors (ASCs), developed by Sunpower Inc. and NASA Glenn Research Center (GRC). The ASCs convert thermal energy from a radioisotope heat source into electricity. As part of ground testing of these ASCs, different operating conditions are used to simulate expected mission conditions. These conditions require achieving a particular operating frequency, hot end and cold end temperatures, and specified electrical power output for a given net heat input. In an effort to improve net heat input predictions, numerous tasks have been performed which provided a more accurate value for net heat input into the ASCs, including the use of multidimensional numerical models. Validation test hardware has also been used to provide a direct comparison of numerical results and validate the multi-dimensional numerical models used to predict convertor net heat input and efficiency. These validation tests were designed to simulate the temperature profile of an operating Stirling convertor and resulted in a measured net heat input of 244.4 W. The methodology was applied to the multi-dimensional numerical model which resulted in a net heat input of 240.3 W. The computational methodology resulted in a value of net heat input that was 1.7 percent less than that measured during laboratory testing. The resulting computational methodology and results are discussed.

Cascade Back-Propagation Learning in Neural Networks

NASA Technical Reports Server (NTRS)

Duong, Tuan A.

2003-01-01

The cascade back-propagation (CBP) algorithm is the basis of a conceptual design for accelerating learning in artificial neural networks. The neural networks would be implemented as analog very-large-scale integrated (VLSI) circuits, and circuits to implement the CBP algorithm would be fabricated on the same VLSI circuit chips with the neural networks. Heretofore, artificial neural networks have learned slowly because it has been necessary to train them via software, for lack of a good on-chip learning technique. The CBP algorithm is an on-chip technique that provides for continuous learning in real time. Artificial neural networks are trained by example: A network is presented with training inputs for which the correct outputs are known, and the algorithm strives to adjust the weights of synaptic connections in the network to make the actual outputs approach the correct outputs. The input data are generally divided into three parts. Two of the parts, called the "training" and "cross-validation" sets, respectively, must be such that the corresponding input/output pairs are known. During training, the cross-validation set enables verification of the status of the input-to-output transformation learned by the network to avoid over-learning. The third part of the data, termed the "test" set, consists of the inputs that are required to be transformed into outputs; this set may or may not include the training set and/or the cross-validation set. Proposed neural-network circuitry for on-chip learning would be divided into two distinct networks; one for training and one for validation. Both networks would share the same synaptic weights.

Evaluation of Advanced Stirling Convertor Net Heat Input Correlation Methods Using a Thermal Standard

NASA Technical Reports Server (NTRS)

Briggs, Maxwell H.; Schifer, Nicholas A.

2012-01-01

The U.S. Department of Energy (DOE) and Lockheed Martin Space Systems Company (LMSSC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. This generator would use two high-efficiency Advanced Stirling Convertors (ASCs), developed by Sunpower Inc. and NASA Glenn Research Center (GRC). The ASCs convert thermal energy from a radioisotope heat source into electricity. As part of ground testing of these ASCs, different operating conditions are used to simulate expected mission conditions. These conditions require achieving a particular operating frequency, hot end and cold end temperatures, and specified electrical power output for a given net heat input. In an effort to improve net heat input predictions, numerous tasks have been performed which provided a more accurate value for net heat input into the ASCs, including testing validation hardware, known as the Thermal Standard, to provide a direct comparison to numerical and empirical models used to predict convertor net heat input. This validation hardware provided a comparison for scrutinizing and improving empirical correlations and numerical models of ASC-E2 net heat input. This hardware simulated the characteristics of an ASC-E2 convertor in both an operating and non-operating mode. This paper describes the Thermal Standard testing and the conclusions of the validation effort applied to the empirical correlation methods used by the Radioisotope Power System (RPS) team at NASA Glenn.

Re-Engineering the United States Marine Corps’ Enlisted Assignment Model (EAM)

DTIC Science & Technology

1998-06-01

and Execution button opens the switchboard in Figure 12. This form accesses all of the VBA code that is associated with this form and the code that...the prototype to prompt the user and to inform him of what he is about to do. Each of the buttons that are on these forms is connected to an SQL ...into the field for building a rule are the values 2;3;4;5;6;7. The user can enter an SQL statement that would determine the values or the user could

Virtual file system on NoSQL for processing high volumes of HL7 messages.

PubMed

Kimura, Eizen; Ishihara, Ken

2015-01-01

The Standardized Structured Medical Information Exchange (SS-MIX) is intended to be the standard repository for HL7 messages that depend on a local file system. However, its scalability is limited. We implemented a virtual file system using NoSQL to incorporate modern computing technology into SS-MIX and allow the system to integrate local patient IDs from different healthcare systems into a universal system. We discuss its implementation using the database MongoDB and describe its performance in a case study.

Sensitivity Analysis of the Integrated Medical Model for ISS Programs

NASA Technical Reports Server (NTRS)

Goodenow, D. A.; Myers, J. G.; Arellano, J.; Boley, L.; Garcia, Y.; Saile, L.; Walton, M.; Kerstman, E.; Reyes, D.; Young, M.

2016-01-01

Sensitivity analysis estimates the relative contribution of the uncertainty in input values to the uncertainty of model outputs. Partial Rank Correlation Coefficient (PRCC) and Standardized Rank Regression Coefficient (SRRC) are methods of conducting sensitivity analysis on nonlinear simulation models like the Integrated Medical Model (IMM). The PRCC method estimates the sensitivity using partial correlation of the ranks of the generated input values to each generated output value. The partial part is so named because adjustments are made for the linear effects of all the other input values in the calculation of correlation between a particular input and each output. In SRRC, standardized regression-based coefficients measure the sensitivity of each input, adjusted for all the other inputs, on each output. Because the relative ranking of each of the inputs and outputs is used, as opposed to the values themselves, both methods accommodate the nonlinear relationship of the underlying model. As part of the IMM v4.0 validation study, simulations are available that predict 33 person-missions on ISS and 111 person-missions on STS. These simulated data predictions feed the sensitivity analysis procedures. The inputs to the sensitivity procedures include the number occurrences of each of the one hundred IMM medical conditions generated over the simulations and the associated IMM outputs: total quality time lost (QTL), number of evacuations (EVAC), and number of loss of crew lives (LOCL). The IMM team will report the results of using PRCC and SRRC on IMM v4.0 predictions of the ISS and STS missions created as part of the external validation study. Tornado plots will assist in the visualization of the condition-related input sensitivities to each of the main outcomes. The outcomes of this sensitivity analysis will drive review focus by identifying conditions where changes in uncertainty could drive changes in overall model output uncertainty. These efforts are an integral part of the overall verification, validation, and credibility review of IMM v4.0.

miRWalk--database: prediction of possible miRNA binding sites by "walking" the genes of three genomes.

PubMed

Dweep, Harsh; Sticht, Carsten; Pandey, Priyanka; Gretz, Norbert

2011-10-01

MicroRNAs are small, non-coding RNA molecules that can complementarily bind to the mRNA 3'-UTR region to regulate the gene expression by transcriptional repression or induction of mRNA degradation. Increasing evidence suggests a new mechanism by which miRNAs may regulate target gene expression by binding in promoter and amino acid coding regions. Most of the existing databases on miRNAs are restricted to mRNA 3'-UTR region. To address this issue, we present miRWalk, a comprehensive database on miRNAs, which hosts predicted as well as validated miRNA binding sites, information on all known genes of human, mouse and rat. All mRNAs, mitochondrial genes and 10 kb upstream flanking regions of all known genes of human, mouse and rat were analyzed by using a newly developed algorithm named 'miRWalk' as well as with eight already established programs for putative miRNA binding sites. An automated and extensive text-mining search was performed on PubMed database to extract validated information on miRNAs. Combined information was put into a MySQL database. miRWalk presents predicted and validated information on miRNA-target interaction. Such a resource enables researchers to validate new targets of miRNA not only on 3'-UTR, but also on the other regions of all known genes. The 'Validated Target module' is updated every month and the 'Predicted Target module' is updated every 6 months. miRWalk is freely available at http://mirwalk.uni-hd.de/. Copyright © 2011 Elsevier Inc. All rights reserved.

Monitoring of IaaS and scientific applications on the Cloud using the Elasticsearch ecosystem

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Guarise, A.; Lusso, S.; Masera, M.; Vallero, S.

2015-05-01

The private Cloud at the Torino INFN computing centre offers IaaS services to different scientific computing applications. The infrastructure is managed with the OpenNebula cloud controller. The main stakeholders of the facility are a grid Tier-2 site for the ALICE collaboration at LHC, an interactive analysis facility for the same experiment and a grid Tier-2 site for the BES-III collaboration, plus an increasing number of other small tenants. Besides keeping track of the usage, the automation of dynamic allocation of resources to tenants requires detailed monitoring and accounting of the resource usage. As a first investigation towards this, we set up a monitoring system to inspect the site activities both in terms of IaaS and applications running on the hosted virtual instances. For this purpose we used the Elasticsearch, Logstash and Kibana stack. In the current implementation, the heterogeneous accounting information is fed to different MySQL databases and sent to Elasticsearch via a custom Logstash plugin. For the IaaS metering, we developed sensors for the OpenNebula API. The IaaS level information gathered through the API is sent to the MySQL database through an ad-hoc developed RESTful web service, which is also used for other accounting purposes. Concerning the application level, we used the Root plugin TProofMonSenderSQL to collect accounting data from the interactive analysis facility. The BES-III virtual instances used to be monitored with Zabbix, as a proof of concept we also retrieve the information contained in the Zabbix database. Each of these three cases is indexed separately in Elasticsearch. We are now starting to consider dismissing the intermediate level provided by the SQL database and evaluating a NoSQL option as a unique central database for all the monitoring information. We setup a set of Kibana dashboards with pre-defined queries in order to monitor the relevant information in each case. In this way we have achieved a uniform monitoring interface for both the IaaS and the scientific applications, mostly leveraging off-the-shelf tools.

"Science SQL" as a Building Block for Flexible, Standards-based Data Infrastructures

NASA Astrophysics Data System (ADS)

Baumann, Peter

2016-04-01

We have learnt to live with the pain of separating data and metadata into non-interoperable silos. For metadata, we enjoy the flexibility of databases, be they relational, graph, or some other NoSQL. Contrasting this, users still "drown in files" as an unstructured, low-level archiving paradigm. It is time to bridge this chasm which once was technologically induced, but today can be overcome. One building block towards a common re-integrated information space is to support massive multi-dimensional spatio-temporal arrays. These "datacubes" appear as sensor, image, simulation, and statistics data in all science and engineering domains, and beyond. For example, 2-D satellilte imagery, 2-D x/y/t image timeseries and x/y/z geophysical voxel data, and 4-D x/y/z/t climate data contribute to today's data deluge in the Earth sciences. Virtual observatories in the Space sciences routinely generate Petabytes of such data. Life sciences deal with microarray data, confocal microscopy, human brain data, which all fall into the same category. The ISO SQL/MDA (Multi-Dimensional Arrays) candidate standard is extending SQL with modelling and query support for n-D arrays ("datacubes") in a flexible, domain-neutral way. This heralds a new generation of services with new quality parameters, such as flexibility, ease of access, embedding into well-known user tools, and scalability mechanisms that remain completely transparent to users. Technology like the EU rasdaman ("raster data manager") Array Database system can support all of the above examples simultaneously, with one technology. This is practically proven: As of today, rasdaman is in operational use on hundreds of Terabytes of satellite image timeseries datacubes, with transparent query distribution across more than 1,000 nodes. Therefore, Array Databases offering SQL/MDA constitute a natural common building block for next-generation data infrastructures. Being initiator and editor of the standard we present principles, implementation facets, and application examples as a basis for further discussion. Further, we highlight recent implementation progress in parallelization, data distribution, and query optimization showing their effects on real-life use cases.

Agile Datacube Analytics (not just) for the Earth Sciences

NASA Astrophysics Data System (ADS)

Misev, Dimitar; Merticariu, Vlad; Baumann, Peter

2017-04-01

Metadata are considered small, smart, and queryable; data, on the other hand, are known as big, clumsy, hard to analyze. Consequently, gridded data - such as images, image timeseries, and climate datacubes - are managed separately from the metadata, and with different, restricted retrieval capabilities. One reason for this silo approach is that databases, while good at tables, XML hierarchies, RDF graphs, etc., traditionally do not support multi-dimensional arrays well. This gap is being closed by Array Databases which extend the SQL paradigm of "any query, anytime" to NoSQL arrays. They introduce semantically rich modelling combined with declarative, high-level query languages on n-D arrays. On Server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. This way, they offer new vistas in flexibility, scalability, performance, and data integration. In this respect, the forthcoming ISO SQL extension MDA ("Multi-dimensional Arrays") will be a game changer in Big Data Analytics. We introduce concepts and opportunities through the example of rasdaman ("raster data manager") which in fact has pioneered the field of Array Databases and forms the blueprint for ISO SQL/MDA and further Big Data standards, such as OGC WCPS for querying spatio-temporal Earth datacubes. With operational installations exceeding 140 TB queries have been split across more than one thousand cloud nodes, using CPUs as well as GPUs. Installations can easily be mashed up securely, enabling large-scale location-transparent query processing in federations. Federation queries have been demonstrated live at EGU 2016 spanning Europe and Australia in the context of the intercontinental EarthServer initiative, visualized through NASA WorldWind.

Agile Datacube Analytics (not just) for the Earth Sciences

NASA Astrophysics Data System (ADS)

Baumann, P.

2016-12-01

Metadata are considered small, smart, and queryable; data, on the other hand, are known as big, clumsy, hard to analyze. Consequently, gridded data - such as images, image timeseries, and climate datacubes - are managed separately from the metadata, and with different, restricted retrieval capabilities. One reason for this silo approach is that databases, while good at tables, XML hierarchies, RDF graphs, etc., traditionally do not support multi-dimensional arrays well.This gap is being closed by Array Databases which extend the SQL paradigm of "any query, anytime" to NoSQL arrays. They introduce semantically rich modelling combined with declarative, high-level query languages on n-D arrays. On Server side, such queries can be optimized, parallelized, and distributed based on partitioned array storage. This way, they offer new vistas in flexibility, scalability, performance, and data integration. In this respect, the forthcoming ISO SQL extension MDA ("Multi-dimensional Arrays") will be a game changer in Big Data Analytics.We introduce concepts and opportunities through the example of rasdaman ("raster data manager") which in fact has pioneered the field of Array Databases and forms the blueprint for ISO SQL/MDA and further Big Data standards, such as OGC WCPS for querying spatio-temporal Earth datacubes. With operational installations exceeding 140 TB queries have been split across more than one thousand cloud nodes, using CPUs as well as GPUs. Installations can easily be mashed up securely, enabling large-scale location-transparent query processing in federations. Federation queries have been demonstrated live at EGU 2016 spanning Europe and Australia in the context of the intercontinental EarthServer initiative, visualized through NASA WorldWind.

Enhancement of CFD validation exercise along the roof profile of a low-rise building

NASA Astrophysics Data System (ADS)

Deraman, S. N. C.; Majid, T. A.; Zaini, S. S.; Yahya, W. N. W.; Abdullah, J.; Ismail, M. A.

2018-04-01

The aim of this study is to enhance the validation of CFD exercise along the roof profile of a low-rise building. An isolated gabled-roof house having 26.6° roof pitch was simulated to obtain the pressure coefficient around the house. Validation of CFD analysis with experimental data requires many input parameters. This study performed CFD simulation based on the data from a previous study. Where the input parameters were not clearly stated, new input parameters were established from the open literatures. The numerical simulations were performed in FLUENT 14.0 by applying the Computational Fluid Dynamics (CFD) approach based on steady RANS equation together with RNG k-ɛ model. Hence, the result from CFD was analysed by using quantitative test (statistical analysis) and compared with CFD results from the previous study. The statistical analysis results from ANOVA test and error measure showed that the CFD results from the current study produced good agreement and exhibited the closest error compared to the previous study. All the input data used in this study can be extended to other types of CFD simulation involving wind flow over an isolated single storey house.

Improving Broadband Displacement Detection with Quantum Correlations

NASA Astrophysics Data System (ADS)

Kampel, N. S.; Peterson, R. W.; Fischer, R.; Yu, P.-L.; Cicak, K.; Simmonds, R. W.; Lehnert, K. W.; Regal, C. A.

2017-04-01

Interferometers enable ultrasensitive measurement in a wide array of applications from gravitational wave searches to force microscopes. The role of quantum mechanics in the metrological limits of interferometers has a rich history, and a large number of techniques to surpass conventional limits have been proposed. In a typical measurement configuration, the trade-off between the probe's shot noise (imprecision) and its quantum backaction results in what is known as the standard quantum limit (SQL). In this work, we investigate how quantum correlations accessed by modifying the readout of the interferometer can access physics beyond the SQL and improve displacement sensitivity. Specifically, we use an optical cavity to probe the motion of a silicon nitride membrane off mechanical resonance, as one would do in a broadband displacement or force measurement, and observe sensitivity better than the SQL dictates for our quantum efficiency. Our measurement illustrates the core idea behind a technique known as variational readout, in which the optical readout quadrature is changed as a function of frequency to improve broadband displacement detection. And, more generally, our result is a salient example of how correlations can aid sensing in the presence of backaction.

Experience with ATLAS MySQL PanDA database service

NASA Astrophysics Data System (ADS)

Smirnov, Y.; Wlodek, T.; De, K.; Hover, J.; Ozturk, N.; Smith, J.; Wenaus, T.; Yu, D.

2010-04-01

The PanDA distributed production and analysis system has been in production use for ATLAS data processing and analysis since late 2005 in the US, and globally throughout ATLAS since early 2008. Its core architecture is based on a set of stateless web services served by Apache and backed by a suite of MySQL databases that are the repository for all PanDA information: active and archival job queues, dataset and file catalogs, site configuration information, monitoring information, system control parameters, and so on. This database system is one of the most critical components of PanDA, and has successfully delivered the functional and scaling performance required by PanDA, currently operating at a scale of half a million jobs per week, with much growth still to come. In this paper we describe the design and implementation of the PanDA database system, its architecture of MySQL servers deployed at BNL and CERN, backup strategy and monitoring tools. The system has been developed, thoroughly tested, and brought to production to provide highly reliable, scalable, flexible and available database services for ATLAS Monte Carlo production, reconstruction and physics analysis.

Survey data and metadata modelling using document-oriented NoSQL

NASA Astrophysics Data System (ADS)

Rahmatuti Maghfiroh, Lutfi; Gusti Bagus Baskara Nugraha, I.

2018-03-01

Survey data that are collected from year to year have metadata change. However it need to be stored integratedly to get statistical data faster and easier. Data warehouse (DW) can be used to solve this limitation. However there is a change of variables in every period that can not be accommodated by DW. Traditional DW can not handle variable change via Slowly Changing Dimension (SCD). Previous research handle the change of variables in DW to manage metadata by using multiversion DW (MVDW). MVDW is designed using relational model. Some researches also found that developing nonrelational model in NoSQL database has reading time faster than the relational model. Therefore, we propose changes to metadata management by using NoSQL. This study proposes a model DW to manage change and algorithms to retrieve data with metadata changes. Evaluation of the proposed models and algorithms result in that database with the proposed design can retrieve data with metadata changes properly. This paper has contribution in comprehensive data analysis with metadata changes (especially data survey) in integrated storage.

Efficient data management tools for the heterogeneous big data warehouse

NASA Astrophysics Data System (ADS)

Alekseev, A. A.; Osipova, V. V.; Ivanov, M. A.; Klimentov, A.; Grigorieva, N. V.; Nalamwar, H. S.

2016-09-01

The traditional RDBMS has been consistent for the normalized data structures. RDBMS served well for decades, but the technology is not optimal for data processing and analysis in data intensive fields like social networks, oil-gas industry, experiments at the Large Hadron Collider, etc. Several challenges have been raised recently on the scalability of data warehouse like workload against the transactional schema, in particular for the analysis of archived data or the aggregation of data for summary and accounting purposes. The paper evaluates new database technologies like HBase, Cassandra, and MongoDB commonly referred as NoSQL databases for handling messy, varied and large amount of data. The evaluation depends upon the performance, throughput and scalability of the above technologies for several scientific and industrial use-cases. This paper outlines the technologies and architectures needed for processing Big Data, as well as the description of the back-end application that implements data migration from RDBMS to NoSQL data warehouse, NoSQL database organization and how it could be useful for further data analytics.

Approach for Input Uncertainty Propagation and Robust Design in CFD Using Sensitivity Derivatives

NASA Technical Reports Server (NTRS)

Putko, Michele M.; Taylor, Arthur C., III; Newman, Perry A.; Green, Lawrence L.

2002-01-01

An implementation of the approximate statistical moment method for uncertainty propagation and robust optimization for quasi 3-D Euler CFD code is presented. Given uncertainties in statistically independent, random, normally distributed input variables, first- and second-order statistical moment procedures are performed to approximate the uncertainty in the CFD output. Efficient calculation of both first- and second-order sensitivity derivatives is required. In order to assess the validity of the approximations, these moments are compared with statistical moments generated through Monte Carlo simulations. The uncertainties in the CFD input variables are also incorporated into a robust optimization procedure. For this optimization, statistical moments involving first-order sensitivity derivatives appear in the objective function and system constraints. Second-order sensitivity derivatives are used in a gradient-based search to successfully execute a robust optimization. The approximate methods used throughout the analyses are found to be valid when considering robustness about input parameter mean values.

Overview of Heat Addition and Efficiency Predictions for an Advanced Stirling Convertor

NASA Technical Reports Server (NTRS)

Wilson, Scott D.; Reid, Terry V.; Schifer, Nicholas A.; Briggs, Maxwell H.

2012-01-01

The U.S. Department of Energy (DOE) and Lockheed Martin Space Systems Company (LMSSC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. This generator would use two high-efficiency Advanced Stirling Convertors (ASCs), developed by Sunpower Inc. and NASA Glenn Research Center (GRC). The ASCs convert thermal energy from a radioisotope heat source into electricity. As part of ground testing of these ASCs, different operating conditions are used to simulate expected mission conditions. These conditions require achieving a particular operating frequency, hot end and cold end temperatures, and specified electrical power output for a given net heat input. Microporous bulk insulation is used in the ground support test hardware to minimize the loss of thermal energy from the electric heat source to the environment. The insulation package is characterized before operation to predict how much heat will be absorbed by the convertor and how much will be lost to the environment during operation. In an effort to validate these predictions, numerous tasks have been performed, which provided a more accurate value for net heat input into the ASCs. This test and modeling effort included: (a) making thermophysical property measurements of test setup materials to provide inputs to the numerical models, (b) acquiring additional test data that was collected during convertor tests to provide numerical models with temperature profiles of the test setup via thermocouple and infrared measurements, (c) using multidimensional numerical models (computational fluid dynamics code) to predict net heat input of an operating convertor, and (d) using validation test hardware to provide direct comparison of numerical results and validate the multidimensional numerical models used to predict convertor net heat input. This effort produced high fidelity ASC net heat input predictions, which were successfully validated using specially designed test hardware enabling measurement of heat transferred through a simulated Stirling cycle. The overall effort and results are discussed.

Inverse optimal design of input-to-state stabilisation for affine nonlinear systems with input delays

NASA Astrophysics Data System (ADS)

Cai, Xiushan; Meng, Lingxin; Zhang, Wei; Liu, Leipo

2018-03-01

We establish robustness of the predictor feedback control law to perturbations appearing at the system input for affine nonlinear systems with time-varying input delay and additive disturbances. Furthermore, it is shown that it is inverse optimal with respect to a differential game problem. All of the stability and inverse optimality proofs are based on the infinite-dimensional backstepping transformation and an appropriate Lyapunov functional. A single-link manipulator subject to input delays and disturbances is given to illustrate the validity of the proposed method.

A Quality-Control-Oriented Database for a Mesoscale Meteorological Observation Network

NASA Astrophysics Data System (ADS)

Lussana, C.; Ranci, M.; Uboldi, F.

2012-04-01

In the operational context of a local weather service, data accessibility and quality related issues must be managed by taking into account a wide set of user needs. This work describes the structure and the operational choices made for the operational implementation of a database system storing data from highly automated observing stations, metadata and information on data quality. Lombardy's environmental protection agency, ARPA Lombardia, manages a highly automated mesoscale meteorological network. A Quality Assurance System (QAS) ensures that reliable observational information is collected and disseminated to the users. The weather unit in ARPA Lombardia, at the same time an important QAS component and an intensive data user, has developed a database specifically aimed to: 1) providing quick access to data for operational activities and 2) ensuring data quality for real-time applications, by means of an Automatic Data Quality Control (ADQC) procedure. Quantities stored in the archive include hourly aggregated observations of: precipitation amount, temperature, wind, relative humidity, pressure, global and net solar radiation. The ADQC performs several independent tests on raw data and compares their results in a decision-making procedure. An important ADQC component is the Spatial Consistency Test based on Optimal Interpolation. Interpolated and Cross-Validation analysis values are also stored in the database, providing further information to human operators and useful estimates in case of missing data. The technical solution adopted is based on a LAMP (Linux, Apache, MySQL and Php) system, constituting an open source environment suitable for both development and operational practice. The ADQC procedure itself is performed by R scripts directly interacting with the MySQL database. Users and network managers can access the database by using a set of web-based Php applications.

Lowering the Barrier for Standards-Compliant and Discoverable Hydrological Data Publication

NASA Astrophysics Data System (ADS)

Kadlec, J.

2013-12-01

The growing need for sharing and integration of hydrological and climate data across multiple organizations has resulted in the development of distributed, services-based, standards-compliant hydrological data management and data hosting systems. The problem with these systems is complicated set-up and deployment. Many existing systems assume that the data publisher has remote-desktop access to a locally managed server and experience with computer network setup. For corporate websites, shared web hosting services with limited root access provide an inexpensive, dynamic web presence solution using the Linux, Apache, MySQL and PHP (LAMP) software stack. In this paper, we hypothesize that a webhosting service provides an optimal, low-cost solution for hydrological data hosting. We propose a software architecture of a standards-compliant, lightweight and easy-to-deploy hydrological data management system that can be deployed on the majority of existing shared internet webhosting services. The architecture and design is validated by developing Hydroserver Lite: a PHP and MySQL-based hydrological data hosting package that is fully standards-compliant and compatible with the Consortium of Universities for Advancement of Hydrologic Sciences (CUAHSI) hydrologic information system. It is already being used for management of field data collection by students of the McCall Outdoor Science School in Idaho. For testing, the Hydroserver Lite software has been installed on multiple different free and low-cost webhosting sites including Godaddy, Bluehost and 000webhost. The number of steps required to set-up the server is compared with the number of steps required to set-up other standards-compliant hydrologic data hosting systems including THREDDS, IstSOS and MapServer SOS.

A System for Web-based Access to the HSOS Database

NASA Astrophysics Data System (ADS)

Lin, G.

Huairou Solar Observing Station's (HSOS) magnetogram and dopplergram are world-class instruments. Access to their data has opened to the world. Web-based access to the data will provide a powerful, convenient tool for data searching and solar physics. It is necessary that our data be provided to users via the Web when it is opened to the world. In this presentation, the author describes general design and programming construction of the system. The system will be generated by PHP and MySQL. The author also introduces basic feature of PHP and MySQL.

Optical levitation of a mirror for reaching the standard quantum limit.

PubMed

Michimura, Yuta; Kuwahara, Yuya; Ushiba, Takafumi; Matsumoto, Nobuyuki; Ando, Masaki

2017-06-12

We propose a new method to optically levitate a macroscopic mirror with two vertical Fabry-Pérot cavities linearly aligned. This configuration gives the simplest possible optical levitation in which the number of laser beams used is the minimum of two. We demonstrate that reaching the standard quantum limit (SQL) of a displacement measurement with our system is feasible with current technology. The cavity geometry and the levitated mirror parameters are designed to ensure that the Brownian vibration of the mirror surface is smaller than the SQL. Our scheme provides a promising tool for testing macroscopic quantum mechanics.

Optical levitation of a mirror for reaching the standard quantum limit

NASA Astrophysics Data System (ADS)

Michimura, Yuta; Kuwahara, Yuya; Ushiba, Takafumi; Matsumoto, Nobuyuki; Ando, Masaki

2017-06-01

We propose a new method to optically levitate a macroscopic mirror with two vertical Fabry-P{\\'e}rot cavities linearly aligned. This configuration gives the simplest possible optical levitation in which the number of laser beams used is the minimum of two. We demonstrate that reaching the standard quantum limit (SQL) of a displacement measurement with our system is feasible with current technology. The cavity geometry and the levitated mirror parameters are designed to ensure that the Brownian vibration of the mirror surface is smaller than the SQL. Our scheme provides a promising tool for testing macroscopic quantum mechanics.

A Flexible Online Metadata Editing and Management System

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

Aguilar, Raul; Pan, Jerry Yun; Gries, Corinna

2010-01-01

A metadata editing and management system is being developed employing state of the art XML technologies. A modular and distributed design was chosen for scalability, flexibility, options for customizations, and the possibility to add more functionality at a later stage. The system consists of a desktop design tool or schema walker used to generate code for the actual online editor, a native XML database, and an online user access management application. The design tool is a Java Swing application that reads an XML schema, provides the designer with options to combine input fields into online forms and give the fieldsmore » user friendly tags. Based on design decisions, the tool generates code for the online metadata editor. The code generated is an implementation of the XForms standard using the Orbeon Framework. The design tool fulfills two requirements: First, data entry forms based on one schema may be customized at design time and second data entry applications may be generated for any valid XML schema without relying on custom information in the schema. However, the customized information generated at design time is saved in a configuration file which may be re-used and changed again in the design tool. Future developments will add functionality to the design tool to integrate help text, tool tips, project specific keyword lists, and thesaurus services. Additional styling of the finished editor is accomplished via cascading style sheets which may be further customized and different look-and-feels may be accumulated through the community process. The customized editor produces XML files in compliance with the original schema, however, data from the current page is saved into a native XML database whenever the user moves to the next screen or pushes the save button independently of validity. Currently the system uses the open source XML database eXist for storage and management, which comes with third party online and desktop management tools. However, access to metadata files in the application introduced here is managed in a custom online module, using a MySQL backend accessed by a simple Java Server Faces front end. A flexible system with three grouping options, organization, group and single editing access is provided. Three levels were chosen to distribute administrative responsibilities and handle the common situation of an information manager entering the bulk of the metadata but leave specifics to the actual data provider.« less

Low-cost extrapolation method for maximal LTE radio base station exposure estimation: test and validation.

PubMed

Verloock, Leen; Joseph, Wout; Gati, Azeddine; Varsier, Nadège; Flach, Björn; Wiart, Joe; Martens, Luc

2013-06-01

An experimental validation of a low-cost method for extrapolation and estimation of the maximal electromagnetic-field exposure from long-term evolution (LTE) radio base station installations are presented. No knowledge on downlink band occupation or service characteristics is required for the low-cost method. The method is applicable in situ. It only requires a basic spectrum analyser with appropriate field probes without the need of expensive dedicated LTE decoders. The method is validated both in laboratory and in situ, for a single-input single-output antenna LTE system and a 2×2 multiple-input multiple-output system, with low deviations in comparison with signals measured using dedicated LTE decoders.

PKI Layer Cake: New Collision Attacks against the Global X.509 Infrastructure

NASA Astrophysics Data System (ADS)

Kaminsky, Dan; Patterson, Meredith L.; Sassaman, Len

Research unveiled in December of 2008 [15] showed how MD5's long-known flaws could be actively exploited to attack the real-worldCertification Authority infrastructure. In this paper, we demonstrate two new classes of collision, which will be somewhat trickier to address than previous attacks against X.509: the applicability of MD2 preimage attacks against the primary root certificate for Verisign, and the difficulty of validating X.509 Names contained within PKCS#10 Certificate Requests.We also draw particular attention to two possibly unrecognized vectors for implementation flaws that have been problematic in the past: the ASN.1 BER decoder required to parsePKCS#10, and the potential for SQL injection fromtext contained within its requests. Finally, we explore why the implications of these attacks are broader than some have realized - first, because Client Authentication is sometimes tied to X.509, and second, because Extended Validation certificates were only intended to stop phishing attacks from names similar to trusted brands. As per the work of Adam Barth and Collin Jackson [4], EV does not prevent an attacker who can synthesize or acquire a "low assurance" certificate for a given name from acquiring the "green bar" EV experience.

Standardizing Activation Analysis: New Software for Photon Activation Analysis

NASA Astrophysics Data System (ADS)

Sun, Z. J.; Wells, D.; Segebade, C.; Green, J.

2011-06-01

Photon Activation Analysis (PAA) of environmental, archaeological and industrial samples requires extensive data analysis that is susceptible to error. For the purpose of saving time, manpower and minimizing error, a computer program was designed, built and implemented using SQL, Access 2007 and asp.net technology to automate this process. Based on the peak information of the spectrum and assisted by its PAA library, the program automatically identifies elements in the samples and calculates their concentrations and respective uncertainties. The software also could be operated in browser/server mode, which gives the possibility to use it anywhere the internet is accessible. By switching the nuclide library and the related formula behind, the new software can be easily expanded to neutron activation analysis (NAA), charged particle activation analysis (CPAA) or proton-induced X-ray emission (PIXE). Implementation of this would standardize the analysis of nuclear activation data. Results from this software were compared to standard PAA analysis with excellent agreement. With minimum input from the user, the software has proven to be fast, user-friendly and reliable.

A web-server of cell type discrimination system.

PubMed

Wang, Anyou; Zhong, Yan; Wang, Yanhua; He, Qianchuan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells.

A Web-Server of Cell Type Discrimination System

PubMed Central

Zhong, Yan

2014-01-01

Discriminating cell types is a daily request for stem cell biologists. However, there is not a user-friendly system available to date for public users to discriminate the common cell types, embryonic stem cells (ESCs), induced pluripotent stem cells (iPSCs), and somatic cells (SCs). Here, we develop WCTDS, a web-server of cell type discrimination system, to discriminate the three cell types and their subtypes like fetal versus adult SCs. WCTDS is developed as a top layer application of our recent publication regarding cell type discriminations, which employs DNA-methylation as biomarkers and machine learning models to discriminate cell types. Implemented by Django, Python, R, and Linux shell programming, run under Linux-Apache web server, and communicated through MySQL, WCTDS provides a friendly framework to efficiently receive the user input and to run mathematical models for analyzing data and then to present results to users. This framework is flexible and easy to be expended for other applications. Therefore, WCTDS works as a user-friendly framework to discriminate cell types and subtypes and it can also be expended to detect other cell types like cancer cells. PMID:24578634

Chapter 21: Programmatic Interfaces - STILTS

NASA Astrophysics Data System (ADS)

Fitzpatrick, M. J.

STILTS is the Starlink Tables Infrastructure Library Tool Set developed by Mark Taylor of the former Starlink Project. STILTS is a command-line tool (see the NVOSS_HOME/bin/stilts command) providing access to the same functionality driving the TOPCAT application and can be run using either the STILTS-specific jar file, or the more general TOPCAT jar file (both are available in the NVOSS_HOME/java/lib directory and are included in the default software environment classpath). The heart of both STILTS and TOPCAT is the STIL Java library. STIL is designed to efficiently handle the input, output and processing of very large tabular datasets and the STILTS task interface makes it an ideal tool for the scripting environment. Multiple formats are supported (including FITS Binary Tables, VOTable, CSV, SQL databases and ASCII, amongst others) and while some tools will generically handle all supported formats, others are specific to the VOTable format. Converting a VOTable to a more script-friendly format is the first thing most users will encounter, but there are many other useful tools as well.

[Research and development of medical case database: a novel medical case information system integrating with biospecimen management].

PubMed

Pan, Shiyang; Mu, Yuan; Wang, Hong; Wang, Tong; Huang, Peijun; Ma, Jianfeng; Jiang, Li; Zhang, Jie; Gu, Bing; Yi, Lujiang

2010-04-01

To meet the needs of management of medical case information and biospecimen simultaneously, we developed a novel medical case information system integrating with biospecimen management. The database established by MS SQL Server 2000 covered, basic information, clinical diagnosis, imaging diagnosis, pathological diagnosis and clinical treatment of patient; physicochemical property, inventory management and laboratory analysis of biospecimen; users log and data maintenance. The client application developed by Visual C++ 6.0 was used to implement medical case and biospecimen management, which was based on Client/Server model. This system can perform input, browse, inquest, summary of case and related biospecimen information, and can automatically synthesize case-records based on the database. Management of not only a long-term follow-up on individual, but also of grouped cases organized according to the aim of research can be achieved by the system. This system can improve the efficiency and quality of clinical researches while biospecimens are used coordinately. It realizes synthesized and dynamic management of medical case and biospecimen, which may be considered as a new management platform.

Integrated Budget Office Toolbox

NASA Technical Reports Server (NTRS)

Rushing, Douglas A.; Blakeley, Chris; Chapman, Gerry; Robertson, Bill; Horton, Allison; Besser, Thomas; McCarthy, Debbie

2010-01-01

The Integrated Budget Office Toolbox (IBOT) combines budgeting, resource allocation, organizational funding, and reporting features in an automated, integrated tool that provides data from a single source for Johnson Space Center (JSC) personnel. Using a common interface, concurrent users can utilize the data without compromising its integrity. IBOT tracks planning changes and updates throughout the year using both phasing and POP-related (program-operating-plan-related) budget information for the current year, and up to six years out. Separating lump-sum funds received from HQ (Headquarters) into separate labor, travel, procurement, Center G&A (general & administrative), and servicepool categories, IBOT creates a script that significantly reduces manual input time. IBOT also manages the movement of travel and procurement funds down to the organizational level and, using its integrated funds management feature, helps better track funding at lower levels. Third-party software is used to create integrated reports in IBOT that can be generated for plans, actuals, funds received, and other combinations of data that are currently maintained in the centralized format. Based on Microsoft SQL, IBOT incorporates generic budget processes, is transportable, and is economical to deploy and support.

The CMS DBS query language

NASA Astrophysics Data System (ADS)

Kuznetsov, Valentin; Riley, Daniel; Afaq, Anzar; Sekhri, Vijay; Guo, Yuyi; Lueking, Lee

2010-04-01

The CMS experiment has implemented a flexible and powerful system enabling users to find data within the CMS physics data catalog. The Dataset Bookkeeping Service (DBS) comprises a database and the services used to store and access metadata related to CMS physics data. To this, we have added a generalized query system in addition to the existing web and programmatic interfaces to the DBS. This query system is based on a query language that hides the complexity of the underlying database structure by discovering the join conditions between database tables. This provides a way of querying the system that is simple and straightforward for CMS data managers and physicists to use without requiring knowledge of the database tables or keys. The DBS Query Language uses the ANTLR tool to build the input query parser and tokenizer, followed by a query builder that uses a graph representation of the DBS schema to construct the SQL query sent to underlying database. We will describe the design of the query system, provide details of the language components and overview of how this component fits into the overall data discovery system architecture.

Geoinformatics paves the way for a zoo information system

NASA Astrophysics Data System (ADS)

Michel, Ulrich

2008-10-01

The use of modern electronic media offers new ways of (environmental) knowledge transfer. All kind of information can be made quickly available as well as queryable and can be processed individually. The Institute for Geoinformatics and Remote Sensing (IGF) in collaboration with the Osnabrueck Zoo, is developing a zoo information system, especially for new media (e.g. mobile devices), which provides information about the animals living there, their natural habitat and endangerment status. Thereby multimedia information is being offered to the zoo visitors. The implementation of the 2D/3D components is realized by modern database and Mapserver technologies. Among other technologies, the VRML (Virtual Reality Modeling Language) standard is used for the realization of the 3D visualization so that it can be viewed in every conventional web browser. Also, a mobile information system for Pocket PCs, Smartphones and Ultra Mobile PCs (UMPC) is being developed. All contents, including the coordinates, are stored in a PostgreSQL database. The data input, the processing and other administrative operations are executed by a content management system (CMS).

Surrogates for numerical simulations; optimization of eddy-promoter heat exchangers

NASA Technical Reports Server (NTRS)

Patera, Anthony T.; Patera, Anthony

1993-01-01

Although the advent of fast and inexpensive parallel computers has rendered numerous previously intractable calculations feasible, many numerical simulations remain too resource-intensive to be directly inserted in engineering optimization efforts. An attractive alternative to direct insertion considers models for computational systems: the expensive simulation is evoked only to construct and validate a simplified, input-output model; this simplified input-output model then serves as a simulation surrogate in subsequent engineering optimization studies. A simple 'Bayesian-validated' statistical framework for the construction, validation, and purposive application of static computer simulation surrogates is presented. As an example, dissipation-transport optimization of laminar-flow eddy-promoter heat exchangers are considered: parallel spectral element Navier-Stokes calculations serve to construct and validate surrogates for the flowrate and Nusselt number; these surrogates then represent the originating Navier-Stokes equations in the ensuing design process.

Patient and caregiver perspectives on decision support for symptom and quality of life management during cancer treatment: Implications for eHealth.

PubMed

Cooley, Mary E; Nayak, Manan M; Abrahm, Janet L; Braun, Ilana M; Rabin, Michael S; Brzozowski, Jane; Lathan, Christopher; Berry, Donna L

2017-08-01

Adequate symptom and quality-of-life (SQL) management is a priority during cancer treatment. eHealth is a timely way to enhance patient-engagement, facilitate communication, and improve health outcomes. The objectives of this study were to describe patient and caregivers' perspectives for providing, processing, and managing SQL data to enhance communication and identify desired components for decision support. Data were collected from 64 participants through questionnaires and focus groups. Analysis was conducted using NVivo. Open and axial coding was completed, grouping commonalities and large constructs into nodes to identify and synthesize themes. Face-to-face meetings with clinicians were the prime time to communicate, and patients strove to understand treatment options and the effect on SQL by bringing caregivers to their visits, taking notes, tracking symptoms, and creating portable health records. Patients/caregivers struggled to self-manage their symptoms and were uncertain when to contact clinicians when experiencing uncontrolled symptoms. Most participants identified eHealth solutions for decision support. However, 38% of participants (n = 24) rarely used computers and identified non-eHealth options for decision support. Core components for both eHealth and non-eHealth systems were access to (1) cancer information, (2) medical records, (3) peer support, and (4) improved support and understanding on when to contact clinicians. Patients were faced with an overwhelming amount of information and relied on their caregivers to help navigate the complexities of cancer care and self-manage SQL. Health technologies can provide informational support; however, decision support needs to span multiple venues to avoid increasing disparities caused by a digital divide. Copyright © 2017 John Wiley & Sons, Ltd.

SU-E-T-255: Development of a Michigan Quality Assurance (MQA) Database for Clinical Machine Operations

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

Roberts, D

Purpose: A unified database system was developed to allow accumulation, review and analysis of quality assurance (QA) data for measurement, treatment, imaging and simulation equipment in our department. Recording these data in a database allows a unified and structured approach to review and analysis of data gathered using commercial database tools. Methods: A clinical database was developed to track records of quality assurance operations on linear accelerators, a computed tomography (CT) scanner, high dose rate (HDR) afterloader and imaging systems such as on-board imaging (OBI) and Calypso in our department. The database was developed using Microsoft Access database and visualmore » basic for applications (VBA) programming interface. Separate modules were written for accumulation, review and analysis of daily, monthly and annual QA data. All modules were designed to use structured query language (SQL) as the basis of data accumulation and review. The SQL strings are dynamically re-written at run time. The database also features embedded documentation, storage of documents produced during QA activities and the ability to annotate all data within the database. Tests are defined in a set of tables that define test type, specific value, and schedule. Results: Daily, Monthly and Annual QA data has been taken in parallel with established procedures to test MQA. The database has been used to aggregate data across machines to examine the consistency of machine parameters and operations within the clinic for several months. Conclusion: The MQA application has been developed as an interface to a commercially available SQL engine (JET 5.0) and a standard database back-end. The MQA system has been used for several months for routine data collection.. The system is robust, relatively simple to extend and can be migrated to a commercial SQL server.« less

An SQL query generator for CLIPS

NASA Technical Reports Server (NTRS)

Snyder, James; Chirica, Laurian

1990-01-01

As expert systems become more widely used, their access to large amounts of external information becomes increasingly important. This information exists in several forms such as statistical, tabular data, knowledge gained by experts and large databases of information maintained by companies. Because many expert systems, including CLIPS, do not provide access to this external information, much of the usefulness of expert systems is left untapped. The scope of this paper is to describe a database extension for the CLIPS expert system shell. The current industry standard database language is SQL. Due to SQL standardization, large amounts of information stored on various computers, potentially at different locations, will be more easily accessible. Expert systems should be able to directly access these existing databases rather than requiring information to be re-entered into the expert system environment. The ORACLE relational database management system (RDBMS) was used to provide a database connection within the CLIPS environment. To facilitate relational database access a query generation system was developed as a CLIPS user function. The queries are entered in a CLlPS-like syntax and are passed to the query generator, which constructs and submits for execution, an SQL query to the ORACLE RDBMS. The query results are asserted as CLIPS facts. The query generator was developed primarily for use within the ICADS project (Intelligent Computer Aided Design System) currently being developed by the CAD Research Unit in the California Polytechnic State University (Cal Poly). In ICADS, there are several parallel or distributed expert systems accessing a common knowledge base of facts. Expert system has a narrow domain of interest and therefore needs only certain portions of the information. The query generator provides a common method of accessing this information and allows the expert system to specify what data is needed without specifying how to retrieve it.

14 CFR 417.307 - Support systems.

Code of Federal Regulations, 2010 CFR

2010-01-01

... subsystem, component, and part that can affect the reliability of the support system must have written..., evaluate the data for validity, and provide valid data for display and recording; (3) Perform any... input and processed data at a rate that maintains the validity of the data and at no less than 0.1...

TargetCompare: A web interface to compare simultaneous miRNAs targets

PubMed Central

Moreira, Fabiano Cordeiro; Dustan, Bruno; Hamoy, Igor G; Ribeiro-dos-Santos, André M; dos Santos, Ândrea Ribeiro

2014-01-01

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. Availability http://lghm.ufpa.br/targetcompare PMID:25352731

TargetCompare: A web interface to compare simultaneous miRNAs targets.

PubMed

Moreira, Fabiano Cordeiro; Dustan, Bruno; Hamoy, Igor G; Ribeiro-Dos-Santos, André M; Dos Santos, Andrea Ribeiro

2014-01-01

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue. http://lghm.ufpa.br/targetcompare.

A Relational Encoding of a Conceptual Model with Multiple Temporal Dimensions

NASA Astrophysics Data System (ADS)

Gubiani, Donatella; Montanari, Angelo

The theoretical interest and the practical relevance of a systematic treatment of multiple temporal dimensions is widely recognized in the database and information system communities. Nevertheless, most relational databases have no temporal support at all. A few of them provide a limited support, in terms of temporal data types and predicates, constructors, and functions for the management of time values (borrowed from the SQL standard). One (resp., two) temporal dimensions are supported by historical and transaction-time (resp., bitemporal) databases only. In this paper, we provide a relational encoding of a conceptual model featuring four temporal dimensions, namely, the classical valid and transaction times, plus the event and availability times. We focus our attention on the distinctive technical features of the proposed temporal extension of the relation model. In the last part of the paper, we briefly show how to implement it in a standard DBMS.

Headspace profiling of cocaine samples for intelligence purposes.

PubMed

Dujourdy, Laurence; Besacier, Fabrice

2008-08-06

A method for determination of residual solvents in illicit hydrochloride cocaine samples using static headspace-gas chromatography (HS-GC) associated with a storage computerized procedure is described for the profiling and comparison of seizures. The system involves a gas chromatographic separation of 18 occluded solvents followed by fully automatic data analysis and transfer to a PHP/MySQL database. First, a fractional factorial design was used to evaluate the main effects of some critical method parameters (salt choice, vial agitation intensity, oven temperature, pressurization and loop equilibration) on the results with a minimum of experiments. The method was then validated for tactical intelligence purposes (batch comparison) via several studies: selection of solvents and mathematical comparison tool, reproducibility and "cutting" influence studies. The decision threshold to determine the similarity of two samples was set and false positives and negatives evaluated. Finally, application of the method to distinguish geographical origins is discussed.

BIRS - Bioterrorism Information Retrieval System.

PubMed

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. The database is freely available at http://www.bioterrorism.biowaves.org.

Automated ocean color product validation for the Southern California Bight

NASA Astrophysics Data System (ADS)

Davis, Curtiss O.; Tufillaro, Nicholas; Jones, Burt; Arnone, Robert

2012-06-01

Automated match ups allow us to maintain and improve the products of current satellite ocean color sensors (MODIS, MERIS), and new sensors (VIIRS). As part of the VIIRS mission preparation, we have created a web based automated match up tool that provides access to searchable fields for date, site, and products, and creates match-ups between satellite (MODIS, MERIS, VIIRS), and in-situ measurements (HyperPRO and SeaPRISM). The back end of the system is a 'mySQL' database, and the front end is a `php' web portal with pull down menus for searchable fields. Based on selections, graphics are generated showing match-ups and statistics, and ascii files are created for downloads for the matchup data. Examples are shown for matching the satellite data with the data from Platform Eureka SeaPRISM off L.A. Harbor in the Southern California Bight.

Integration of Evidence Base into a Probabilistic Risk Assessment

NASA Technical Reports Server (NTRS)

Saile, Lyn; Lopez, Vilma; Bickham, Grandin; Kerstman, Eric; FreiredeCarvalho, Mary; Byrne, Vicky; Butler, Douglas; Myers, Jerry; Walton, Marlei

2011-01-01

INTRODUCTION: A probabilistic decision support model such as the Integrated Medical Model (IMM) utilizes an immense amount of input data that necessitates a systematic, integrated approach for data collection, and management. As a result of this approach, IMM is able to forecasts medical events, resource utilization and crew health during space flight. METHODS: Inflight data is the most desirable input for the Integrated Medical Model. Non-attributable inflight data is collected from the Lifetime Surveillance for Astronaut Health study as well as the engineers, flight surgeons, and astronauts themselves. When inflight data is unavailable cohort studies, other models and Bayesian analyses are used, in addition to subject matters experts input on occasion. To determine the quality of evidence of a medical condition, the data source is categorized and assigned a level of evidence from 1-5; the highest level is one. The collected data reside and are managed in a relational SQL database with a web-based interface for data entry and review. The database is also capable of interfacing with outside applications which expands capabilities within the database itself. Via the public interface, customers can access a formatted Clinical Findings Form (CLiFF) that outlines the model input and evidence base for each medical condition. Changes to the database are tracked using a documented Configuration Management process. DISSCUSSION: This strategic approach provides a comprehensive data management plan for IMM. The IMM Database s structure and architecture has proven to support additional usages. As seen by the resources utilization across medical conditions analysis. In addition, the IMM Database s web-based interface provides a user-friendly format for customers to browse and download the clinical information for medical conditions. It is this type of functionality that will provide Exploratory Medicine Capabilities the evidence base for their medical condition list. CONCLUSION: The IMM Database in junction with the IMM is helping NASA aerospace program improve the health care and reduce risk for the astronauts crew. Both the database and model will continue to expand to meet customer needs through its multi-disciplinary evidence based approach to managing data. Future expansion could serve as a platform for a Space Medicine Wiki of medical conditions.

FEMFLOW3D; a finite-element program for the simulation of three-dimensional aquifers; version 1.0

USGS Publications Warehouse

Durbin, Timothy J.; Bond, Linda D.

1998-01-01

This document also includes model validation, source code, and example input and output files. Model validation was performed using four test problems. For each test problem, the results of a model simulation with FEMFLOW3D were compared with either an analytic solution or the results of an independent numerical approach. The source code, written in the ANSI x3.9-1978 FORTRAN standard, and the complete input and output of an example problem are listed in the appendixes.

An algorithm to generate input data from meteorological and space shuttle observations to validate a CH4-CO model

NASA Technical Reports Server (NTRS)

Peters, L. K.; Yamanis, J.

1981-01-01

Objective procedures to analyze data from meteorological and space shuttle observations to validate a three dimensional model were investigated. The transport and chemistry of carbon monoxide and methane in the troposphere were studied. Four aspects were examined: (1) detailed evaluation of the variational calculus procedure, with the equation of continuity as a strong constraint, for adjustment of global tropospheric wind fields; (2) reduction of the National Meteorological Center (NMC) data tapes for data input to the OSTA-1/MAPS Experiment; (3) interpolation of the NMC Data for input to the CH4-CO model; and (4) temporal and spatial interpolation procedures of the CO measurements from the OSTA-1/MAPS Experiment to generate usable contours of the data.

Concept locator: a client-server application for retrieval of UMLS metathesaurus concepts through complex boolean query.

PubMed

Nadkarni, P M

1997-08-01

Concept Locator (CL) is a client-server application that accesses a Sybase relational database server containing a subset of the UMLS Metathesaurus for the purpose of retrieval of concepts corresponding to one or more query expressions supplied to it. CL's query grammar permits complex Boolean expressions, wildcard patterns, and parenthesized (nested) subexpressions. CL translates the query expressions supplied to it into one or more SQL statements that actually perform the retrieval. The generated SQL is optimized by the client to take advantage of the strengths of the server's query optimizer, and sidesteps its weaknesses, so that execution is reasonably efficient.

Astronomical Data Processing Using SciQL, an SQL Based Query Language for Array Data

NASA Astrophysics Data System (ADS)

Zhang, Y.; Scheers, B.; Kersten, M.; Ivanova, M.; Nes, N.

2012-09-01

SciQL (pronounced as ‘cycle’) is a novel SQL-based array query language for scientific applications with both tables and arrays as first class citizens. SciQL lowers the entrance fee of adopting relational DBMS (RDBMS) in scientific domains, because it includes functionality often only found in mathematics software packages. In this paper, we demonstrate the usefulness of SciQL for astronomical data processing using examples from the Transient Key Project of the LOFAR radio telescope. In particular, how the LOFAR light-curve database of all detected sources can be constructed, by correlating sources across the spatial, frequency, time and polarisation domains.

GEOMAGIA50: An archeointensity database with PHP and MySQL

NASA Astrophysics Data System (ADS)

Korhonen, K.; Donadini, F.; Riisager, P.; Pesonen, L. J.

2008-04-01

The GEOMAGIA50 database stores 3798 archeomagnetic and paleomagnetic intensity determinations dated to the past 50,000 years. It also stores details of the measurement setup for each determination, which are used for ranking the data according to prescribed reliability criteria. The ranking system aims to alleviate the data reliability problem inherent in this kind of data. GEOMAGIA50 is based on two popular open source technologies. The MySQL database management system is used for storing the data, whereas the functionality and user interface are provided by server-side PHP scripts. This technical brief gives a detailed description of GEOMAGIA50 from a technical viewpoint.

The MAO NASU Plate Archive Database. Current Status and Perspectives

NASA Astrophysics Data System (ADS)

Pakuliak, L. K.; Sergeeva, T. P.

2006-04-01

The preliminary online version of the database of the MAO NASU plate archive is constructed on the basis of the relational database management system MySQL and permits an easy supplement of database with new collections of astronegatives, provides a high flexibility in constructing SQL-queries for data search optimization, PHP Basic Authorization protected access to administrative interface and wide range of search parameters. The current status of the database will be reported and the brief description of the search engine and means of the database integrity support will be given. Methods and means of the data verification and tasks for the further development will be discussed.

Using career ladders to motivate and retain employees: an implementation success story.

PubMed

Garletts, Joseph A

2002-01-01

In October 2000, Phoenix-based Sonora Quest Laboratories, LLC (SQL), commissioned The Gelfond Group to survey SQL employees. Responding to negative survey scores, SQL developed and implemented an entry-level career ladder for line staff of the specimen management/referral testing department. The program was piloted in February 2001, and was implemented fully shortly thereafter. The ladder was designed to provide job enrichment opportunities through company-conducted training and advancement provisions. It contained requirements for productivity and quality of work performed in addition to increasingly rigorous training and competency documentation. Employees were accountable for their own advancement and for ensuring that all documentation was complete. Advancement was automatic once requirements were completed. Pay increases accompanied each advancement on a predetermined scale. At the end of 12 months, employee turnover dropped from 39% to less than 20% annually. Both productivity and morale improved, and results on a second employee survey indicated dramatic improvement in five key areas. The career ladder concept has been replicated successfully in several other departments, including phlebotomy, and a six-tiered ladder is under development for the clinical laboratory. It will encompass CLA, MLT, and MT positions from entry level to technical coordinator.

Mining the SDSS SkyServer SQL queries log

NASA Astrophysics Data System (ADS)

Hirota, Vitor M.; Santos, Rafael; Raddick, Jordan; Thakar, Ani

2016-05-01

SkyServer, the Internet portal for the Sloan Digital Sky Survey (SDSS) astronomic catalog, provides a set of tools that allows data access for astronomers and scientific education. One of SkyServer data access interfaces allows users to enter ad-hoc SQL statements to query the catalog. SkyServer also presents some template queries that can be used as basis for more complex queries. This interface has logged over 330 million queries submitted since 2001. It is expected that analysis of this data can be used to investigate usage patterns, identify potential new classes of queries, find similar queries, etc. and to shed some light on how users interact with the Sloan Digital Sky Survey data and how scientists have adopted the new paradigm of e-Science, which could in turn lead to enhancements on the user interfaces and experience in general. In this paper we review some approaches to SQL query mining, apply the traditional techniques used in the literature and present lessons learned, namely, that the general text mining approach for feature extraction and clustering does not seem to be adequate for this type of data, and, most importantly, we find that this type of analysis can result in very different queries being clustered together.

NVST Data Archiving System Based On FastBit NoSQL Database

NASA Astrophysics Data System (ADS)

Liu, Ying-bo; Wang, Feng; Ji, Kai-fan; Deng, Hui; Dai, Wei; Liang, Bo

2014-06-01

The New Vacuum Solar Telescope (NVST) is a 1-meter vacuum solar telescope that aims to observe the fine structures of active regions on the Sun. The main tasks of the NVST are high resolution imaging and spectral observations, including the measurements of the solar magnetic field. The NVST has been collecting more than 20 million FITS files since it began routine observations in 2012 and produces a maximum observational records of 120 thousand files in a day. Given the large amount of files, the effective archiving and retrieval of files becomes a critical and urgent problem. In this study, we implement a new data archiving system for the NVST based on the Fastbit Not Only Structured Query Language (NoSQL) database. Comparing to the relational database (i.e., MySQL; My Structured Query Language), the Fastbit database manifests distinctive advantages on indexing and querying performance. In a large scale database of 40 million records, the multi-field combined query response time of Fastbit database is about 15 times faster and fully meets the requirements of the NVST. Our study brings a new idea for massive astronomical data archiving and would contribute to the design of data management systems for other astronomical telescopes.

Integration in PACS of DICOM with TCP/IP, SQL, and X Windows

NASA Astrophysics Data System (ADS)

Reijns, Gerard L.

1994-05-01

The DICOM standard (Digital Imaging and Communications in Medicine) has been developed in order to obtain compatibility at the higher OSI levels. This paper describes the implementation of DICOM into our developed low cost PACS, which uses as much as possible standard software and standard protocols such as SQL, X Windows and TCP/IP. We adopted the requirement that all messages on the communication network have to be DICOM compatible. The translation between DICOM messages and SQL commands, which drive the relational data base, has been accommodated in our PACS supervisor. The translation takes only between 10 and 20 milliseconds. Images, that will be used the current day are stored in a distributed, parallel operating image base for reasons of performance. Extensive use has been made of X Windows to visualize images. A maximum of 12 images can simultaneously be displayed, of which one selected image can be manipulated (e.g., magnified, rotated, etc.), without affecting the other displayed images. The emphasis of the future work will be on performance measurements and modeling of our PACS and bringing the results of both methods in agreement with each other.

Technical Aspects of Interfacing MUMPS to an External SQL Relational Database Management System

PubMed Central

Kuzmak, Peter M.; Walters, Richard F.; Penrod, Gail

1988-01-01

This paper describes an interface connecting InterSystems MUMPS (M/VX) to an external relational DBMS, the SYBASE Database Management System. The interface enables MUMPS to operate in a relational environment and gives the MUMPS language full access to a complete set of SQL commands. MUMPS generates SQL statements as ASCII text and sends them to the RDBMS. The RDBMS executes the statements and returns ASCII results to MUMPS. The interface suggests that the language features of MUMPS make it an attractive tool for use in the relational database environment. The approach described in this paper separates MUMPS from the relational database. Positioning the relational database outside of MUMPS promotes data sharing and permits a number of different options to be used for working with the data. Other languages like C, FORTRAN, and COBOL can access the RDBMS database. Advanced tools provided by the relational database vendor can also be used. SYBASE is an advanced high-performance transaction-oriented relational database management system for the VAX/VMS and UNIX operating systems. SYBASE is designed using a distributed open-systems architecture, and is relatively easy to interface with MUMPS.

Modification and Validation of Conceptual Design Aerodynamic Prediction Method HASC95 With VTXCHN

NASA Technical Reports Server (NTRS)

Albright, Alan E.; Dixon, Charles J.; Hegedus, Martin C.

1996-01-01

A conceptual/preliminary design level subsonic aerodynamic prediction code HASC (High Angle of Attack Stability and Control) has been improved in several areas, validated, and documented. The improved code includes improved methodologies for increased accuracy and robustness, and simplified input/output files. An engineering method called VTXCHN (Vortex Chine) for prediciting nose vortex shedding from circular and non-circular forebodies with sharp chine edges has been improved and integrated into the HASC code. This report contains a summary of modifications, description of the code, user's guide, and validation of HASC. Appendices include discussion of a new HASC utility code, listings of sample input and output files, and a discussion of the application of HASC to buffet analysis.

Simulation models in population breast cancer screening: A systematic review.

PubMed

Koleva-Kolarova, Rositsa G; Zhan, Zhuozhao; Greuter, Marcel J W; Feenstra, Talitha L; De Bock, Geertruida H

2015-08-01

The aim of this review was to critically evaluate published simulation models for breast cancer screening of the general population and provide a direction for future modeling. A systematic literature search was performed to identify simulation models with more than one application. A framework for qualitative assessment which incorporated model type; input parameters; modeling approach, transparency of input data sources/assumptions, sensitivity analyses and risk of bias; validation, and outcomes was developed. Predicted mortality reduction (MR) and cost-effectiveness (CE) were compared to estimates from meta-analyses of randomized control trials (RCTs) and acceptability thresholds. Seven original simulation models were distinguished, all sharing common input parameters. The modeling approach was based on tumor progression (except one model) with internal and cross validation of the resulting models, but without any external validation. Differences in lead times for invasive or non-invasive tumors, and the option for cancers not to progress were not explicitly modeled. The models tended to overestimate the MR (11-24%) due to screening as compared to optimal RCTs 10% (95% CI - 2-21%) MR. Only recently, potential harms due to regular breast cancer screening were reported. Most scenarios resulted in acceptable cost-effectiveness estimates given current thresholds. The selected models have been repeatedly applied in various settings to inform decision making and the critical analysis revealed high risk of bias in their outcomes. Given the importance of the models, there is a need for externally validated models which use systematical evidence for input data to allow for more critical evaluation of breast cancer screening. Copyright © 2015 Elsevier Ltd. All rights reserved.

Program Description: EDIT Program and Vendor Master Update, SWRL Financial System.

ERIC Educational Resources Information Center

Ikeda, Masumi

Computer routines to edit input data for the Southwest Regional Laboratory's (SWRL) Financial System are described. The program is responsible for validating input records, generating records for further system processing, and updating the Vendor Master File--a file containing the information necessary to support the accounts payable and…

Spliceman2: a computational web server that predicts defects in pre-mRNA splicing.

PubMed

Cygan, Kamil Jan; Sanford, Clayton Hendrick; Fairbrother, William Guy

2017-09-15

Most pre-mRNA transcripts in eukaryotic cells must undergo splicing to remove introns and join exons, and splicing elements present a large mutational target for disease-causing mutations. Splicing elements are strongly position dependent with respect to the transcript annotations. In 2012, we presented Spliceman, an online tool that used positional dependence to predict how likely distant mutations around annotated splice sites were to disrupt splicing. Here, we present an improved version of the previous tool that will be more useful for predicting the likelihood of splicing mutations. We have added industry-standard input options (i.e. Spliceman now accepts variant call format files), which allow much larger inputs than previously available. The tool also can visualize the locations-within exons and introns-of sequence variants to be analyzed and the predicted effects on splicing of the pre-mRNA transcript. In addition, Spliceman2 integrates with RNAcompete motif libraries to provide a prediction of which trans -acting factors binding sites are disrupted/created and links out to the UCSC genome browser. In summary, the new features in Spliceman2 will allow scientists and physicians to better understand the effects of single nucleotide variations on splicing. Freely available on the web at http://fairbrother.biomed.brown.edu/spliceman2 . Website implemented in PHP framework-Laravel 5, PostgreSQL, Apache, and Perl, with all major browsers supported. william_fairbrother@brown.edu. Supplementary data are available at Bioinformatics online. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Validating a Conceptual Framework for the Core Concept of "Cell-Cell Communication"

ERIC Educational Resources Information Center

Michael, Joel; Martinkova, Patricia; McFarland, Jenny; Wright, Ann; Cliff, William; Modell, Harold; Wenderoth, Mary Pat

2017-01-01

We have created and validated a conceptual framework for the core physiology concept of "cell-cell communication." The conceptual framework is composed of 51 items arranged in a hierarchy that is, in some instances, four levels deep. We have validated it with input from faculty who teach at a wide variety of institutional types. All…

Optimal test selection for prediction uncertainty reduction

DOE PAGES

Mullins, Joshua; Mahadevan, Sankaran; Urbina, Angel

2016-12-02

Economic factors and experimental limitations often lead to sparse and/or imprecise data used for the calibration and validation of computational models. This paper addresses resource allocation for calibration and validation experiments, in order to maximize their effectiveness within given resource constraints. When observation data are used for model calibration, the quality of the inferred parameter descriptions is directly affected by the quality and quantity of the data. This paper characterizes parameter uncertainty within a probabilistic framework, which enables the uncertainty to be systematically reduced with additional data. The validation assessment is also uncertain in the presence of sparse and imprecisemore » data; therefore, this paper proposes an approach for quantifying the resulting validation uncertainty. Since calibration and validation uncertainty affect the prediction of interest, the proposed framework explores the decision of cost versus importance of data in terms of the impact on the prediction uncertainty. Often, calibration and validation tests may be performed for different input scenarios, and this paper shows how the calibration and validation results from different conditions may be integrated into the prediction. Then, a constrained discrete optimization formulation that selects the number of tests of each type (calibration or validation at given input conditions) is proposed. Furthermore, the proposed test selection methodology is demonstrated on a microelectromechanical system (MEMS) example.« less

Model-Free Primitive-Based Iterative Learning Control Approach to Trajectory Tracking of MIMO Systems With Experimental Validation.

PubMed

Radac, Mircea-Bogdan; Precup, Radu-Emil; Petriu, Emil M

2015-11-01

This paper proposes a novel model-free trajectory tracking of multiple-input multiple-output (MIMO) systems by the combination of iterative learning control (ILC) and primitives. The optimal trajectory tracking solution is obtained in terms of previously learned solutions to simple tasks called primitives. The library of primitives that are stored in memory consists of pairs of reference input/controlled output signals. The reference input primitives are optimized in a model-free ILC framework without using knowledge of the controlled process. The guaranteed convergence of the learning scheme is built upon a model-free virtual reference feedback tuning design of the feedback decoupling controller. Each new complex trajectory to be tracked is decomposed into the output primitives regarded as basis functions. The optimal reference input for the control system to track the desired trajectory is next recomposed from the reference input primitives. This is advantageous because the optimal reference input is computed straightforward without the need to learn from repeated executions of the tracking task. In addition, the optimization problem specific to trajectory tracking of square MIMO systems is decomposed in a set of optimization problems assigned to each separate single-input single-output control channel that ensures a convenient model-free decoupling. The new model-free primitive-based ILC approach is capable of planning, reasoning, and learning. A case study dealing with the model-free control tuning for a nonlinear aerodynamic system is included to validate the new approach. The experimental results are given.

Evaluation of Sub Query Performance in SQL Server

NASA Astrophysics Data System (ADS)

Oktavia, Tanty; Sujarwo, Surya

2014-03-01

The paper explores several sub query methods used in a query and their impact on the query performance. The study uses experimental approach to evaluate the performance of each sub query methods combined with indexing strategy. The sub query methods consist of in, exists, relational operator and relational operator combined with top operator. The experimental shows that using relational operator combined with indexing strategy in sub query has greater performance compared with using same method without indexing strategy and also other methods. In summary, for application that emphasized on the performance of retrieving data from database, it better to use relational operator combined with indexing strategy. This study is done on Microsoft SQL Server 2012.

Version 1.00 programmer`s tools used in constructing the INEL RML/analytical radiochemistry sample tracking database and its user interface

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

Femec, D.A.

This report describes two code-generating tools used to speed design and implementation of relational databases and user interfaces: CREATE-SCHEMA and BUILD-SCREEN. CREATE-SCHEMA produces the SQL commands that actually create and define the database. BUILD-SCREEN takes templates for data entry screens and generates the screen management system routine calls to display the desired screen. Both tools also generate the related FORTRAN declaration statements and precompiled SQL calls. Included with this report is the source code for a number of FORTRAN routines and functions used by the user interface. This code is broadly applicable to a number of different databases.

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

DOE PAGES

Rinke, Christian; Low, Serene; Woodcroft, Ben J.; ...

2016-09-22

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

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

Rinke, Christian; Low, Serene; Woodcroft, Ben J.

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diversemore » Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.« less

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

PubMed Central

Low, Serene; Raina, Jean-Baptiste; Skarshewski, Adam; Le, Xuyen H.; Butler, Margaret K.; Stocker, Roman; Seymour, Justin; Tyson, Gene W.

2016-01-01

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. Here we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (∼100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics. PMID:27688978

Reduced basis ANOVA methods for partial differential equations with high-dimensional random inputs

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

Liao, Qifeng, E-mail: liaoqf@shanghaitech.edu.cn; Lin, Guang, E-mail: guanglin@purdue.edu

2016-07-15

In this paper we present a reduced basis ANOVA approach for partial deferential equations (PDEs) with random inputs. The ANOVA method combined with stochastic collocation methods provides model reduction in high-dimensional parameter space through decomposing high-dimensional inputs into unions of low-dimensional inputs. In this work, to further reduce the computational cost, we investigate spatial low-rank structures in the ANOVA-collocation method, and develop efficient spatial model reduction techniques using hierarchically generated reduced bases. We present a general mathematical framework of the methodology, validate its accuracy and demonstrate its efficiency with numerical experiments.

Experimental observation of spatial quantum noise reduction below the standard quantum limit with bright twin beams of light

NASA Astrophysics Data System (ADS)

Kumar, Ashok; Nunley, Hayden; Marino, Alberto

2016-05-01

Quantum noise reduction (QNR) below the standard quantum limit (SQL) has been a subject of interest for the past two to three decades due to its wide range of applications in quantum metrology and quantum information processing. To date, most of the attention has focused on the study of QNR in the temporal domain. However, many areas in quantum optics, specifically in quantum imaging, could benefit from QNR not only in the temporal domain but also in the spatial domain. With the use of a high quantum efficiency electron multiplier charge coupled device (EMCCD) camera, we have observed spatial QNR below the SQL in bright narrowband twin light beams generated through a four-wave mixing (FWM) process in hot rubidium atoms. Owing to momentum conservation in this process, the twin beams are momentum correlated. This leads to spatial quantum correlations and spatial QNR. Our preliminary results show a spatial QNR of over 2 dB with respect to the SQL. Unlike previous results on spatial QNR with faint and broadband photon pairs from parametric down conversion (PDC), we demonstrate spatial QNR with spectrally and spatially narrowband bright light beams. The results obtained will be useful for atom light interaction based quantum protocols and quantum imaging. Work supported by the W.M. Keck Foundation.

Find the fish: using PROC SQL to build a relational database

USGS Publications Warehouse

Fabrizio, Mary C.; Nelson, Scott N.

1995-01-01

Reliable estimates of abundance and survival, gained through mark-recapture studies, are necessary to better understand how to manage and restore lake trout populations in the Great Lakes. Working with a 24-year data set from a mark-recapture study conducted in Lake Superior, we attempted to disclose information on tag shedding by examining recaptures of double-tagged fish. The data set consisted of 64,288 observations on fish which had been marked with one or more tags; a subset of these fish had been marked with two tags at initial capture. Although DATA and PROC statements could be used to obtain some of the information we sought, these statements could not be used to extract a complete set of results from the double-tagging experiments. We therefore used SQL processing to create three tables representing the same information but in a fully normalized relational structure. In addition, we created indices to efficiently examine complex relationships among the individual capture records. This approach allowed us to obtain all the information necessary to estimate tag retention through subsequent modeling. We believe that our success with SQL was due in large part to its ability to simultaneosly scan the same table more than once and to permit consideration of other tables in sub-queries.

Database constraints applied to metabolic pathway reconstruction tools.

PubMed

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes.

Integrating Radar Image Data with Google Maps

NASA Technical Reports Server (NTRS)

Chapman, Bruce D.; Gibas, Sarah

2010-01-01

A public Web site has been developed as a method for displaying the multitude of radar imagery collected by NASA s Airborne Synthetic Aperture Radar (AIRSAR) instrument during its 16-year mission. Utilizing NASA s internal AIRSAR site, the new Web site features more sophisticated visualization tools that enable the general public to have access to these images. The site was originally maintained at NASA on six computers: one that held the Oracle database, two that took care of the software for the interactive map, and three that were for the Web site itself. Several tasks were involved in moving this complicated setup to just one computer. First, the AIRSAR database was migrated from Oracle to MySQL. Then the back-end of the AIRSAR Web site was updated in order to access the MySQL database. To do this, a few of the scripts needed to be modified; specifically three Perl scripts that query that database. The database connections were then updated from Oracle to MySQL, numerous syntax errors were corrected, and a query was implemented that replaced one of the stored Oracle procedures. Lastly, the interactive map was designed, implemented, and tested so that users could easily browse and access the radar imagery through the Google Maps interface.

Extending SQL to Support Privacy Policies

NASA Astrophysics Data System (ADS)

Ghazinour, Kambiz; Pun, Sampson; Majedi, Maryam; Chinaci, Amir H.; Barker, Ken

Increasing concerns over Internet applications that violate user privacy by exploiting (back-end) database vulnerabilities must be addressed to protect both customer privacy and to ensure corporate strategic assets remain trustworthy. This chapter describes an extension onto database catalogues and Structured Query Language (SQL) for supporting privacy in Internet applications, such as in social networks, e-health, e-governmcnt, etc. The idea is to introduce new predicates to SQL commands to capture common privacy requirements, such as purpose, visibility, generalization, and retention for both mandatory and discretionary access control policies. The contribution is that corporations, when creating the underlying databases, will be able to define what their mandatory privacy policies arc with which all application users have to comply. Furthermore, each application user, when providing their own data, will be able to define their own privacy policies with which other users have to comply. The extension is supported with underlying catalogues and algorithms. The experiments demonstrate a very reasonable overhead for the extension. The result is a low-cost mechanism to create new systems that arc privacy aware and also to transform legacy databases to their privacy-preserving equivalents. Although the examples arc from social networks, one can apply the results to data security and user privacy of other enterprises as well.

Groundwater Model Validation

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

Ahmed E. Hassan

2006-01-24

Models have an inherent uncertainty. The difficulty in fully characterizing the subsurface environment makes uncertainty an integral component of groundwater flow and transport models, which dictates the need for continuous monitoring and improvement. Building and sustaining confidence in closure decisions and monitoring networks based on models of subsurface conditions require developing confidence in the models through an iterative process. The definition of model validation is postulated as a confidence building and long-term iterative process (Hassan, 2004a). Model validation should be viewed as a process not an end result. Following Hassan (2004b), an approach is proposed for the validation process ofmore » stochastic groundwater models. The approach is briefly summarized herein and detailed analyses of acceptance criteria for stochastic realizations and of using validation data to reduce input parameter uncertainty are presented and applied to two case studies. During the validation process for stochastic models, a question arises as to the sufficiency of the number of acceptable model realizations (in terms of conformity with validation data). Using a hierarchical approach to make this determination is proposed. This approach is based on computing five measures or metrics and following a decision tree to determine if a sufficient number of realizations attain satisfactory scores regarding how they represent the field data used for calibration (old) and used for validation (new). The first two of these measures are applied to hypothetical scenarios using the first case study and assuming field data consistent with the model or significantly different from the model results. In both cases it is shown how the two measures would lead to the appropriate decision about the model performance. Standard statistical tests are used to evaluate these measures with the results indicating they are appropriate measures for evaluating model realizations. The use of validation data to constrain model input parameters is shown for the second case study using a Bayesian approach known as Markov Chain Monte Carlo. The approach shows a great potential to be helpful in the validation process and in incorporating prior knowledge with new field data to derive posterior distributions for both model input and output.« less

An Array Library for Microsoft SQL Server with Astrophysical Applications

NASA Astrophysics Data System (ADS)

Dobos, L.; Szalay, A. S.; Blakeley, J.; Falck, B.; Budavári, T.; Csabai, I.

2012-09-01

Today's scientific simulations produce output on the 10-100 TB scale. This unprecedented amount of data requires data handling techniques that are beyond what is used for ordinary files. Relational database systems have been successfully used to store and process scientific data, but the new requirements constantly generate new challenges. Moving terabytes of data among servers on a timely basis is a tough problem, even with the newest high-throughput networks. Thus, moving the computations as close to the data as possible and minimizing the client-server overhead are absolutely necessary. At least data subsetting and preprocessing have to be done inside the server process. Out of the box commercial database systems perform very well in scientific applications from the prospective of data storage optimization, data retrieval, and memory management but lack basic functionality like handling scientific data structures or enabling advanced math inside the database server. The most important gap in Microsoft SQL Server is the lack of a native array data type. Fortunately, the technology exists to extend the database server with custom-written code that enables us to address these problems. We present the prototype of a custom-built extension to Microsoft SQL Server that adds array handling functionality to the database system. With our Array Library, fix-sized arrays of all basic numeric data types can be created and manipulated efficiently. Also, the library is designed to be able to be seamlessly integrated with the most common math libraries, such as BLAS, LAPACK, FFTW, etc. With the help of these libraries, complex operations, such as matrix inversions or Fourier transformations, can be done on-the-fly, from SQL code, inside the database server process. We are currently testing the prototype with two different scientific data sets: The Indra cosmological simulation will use it to store particle and density data from N-body simulations, and the Milky Way Laboratory project will use it to store galaxy simulation data.

A Customizable Dashboarding System for Watershed Model Interpretation

NASA Astrophysics Data System (ADS)

Easton, Z. M.; Collick, A.; Wagena, M. B.; Sommerlot, A.; Fuka, D.

2017-12-01

Stakeholders, including policymakers, agricultural water managers, and small farm managers, can benefit from the outputs of commonly run watershed models. However, the information that each stakeholder needs is be different. While policy makers are often interested in the broader effects that small farm management may have on a watershed during extreme events or over long periods, farmers are often interested in field specific effects at daily or seasonal period. To provide stakeholders with the ability to analyze and interpret data from large scale watershed models, we have developed a framework that can support custom exploration of the large datasets produced. For the volume of data produced by these models, SQL-based data queries are not efficient; thus, we employ a "Not Only SQL" (NO-SQL) query language, which allows data to scale in both quantity and query volumes. We demonstrate a stakeholder customizable Dashboarding system that allows stakeholders to create custom `dashboards' to summarize model output specific to their needs. Dashboarding is a dynamic and purpose-based visual interface needed to display one-to-many database linkages so that the information can be presented for a single time period or dynamically monitored over time and allows a user to quickly define focus areas of interest for their analysis. We utilize a single watershed model that is run four times daily with a combined set of climate projections, which are then indexed, and added to an ElasticSearch datastore. ElasticSearch is a NO-SQL search engine built on top of Apache Lucene, a free and open-source information retrieval software library. Aligned with the ElasticSearch project is the open source visualization and analysis system, Kibana, which we utilize for custom stakeholder dashboarding. The dashboards create a visualization of the stakeholder selected analysis and can be extended to recommend robust strategies to support decision-making.

How to maintain blood supply during computer network breakdown: a manual backup system.

PubMed

Zeiler, T; Slonka, J; Bürgi, H R; Kretschmer, V

2000-12-01

Electronic data management systems using computer network systems and client/server architecture are increasingly used in laboratories and transfusion services. Severe problems arise if there is no network access to the database server and critical functions are not available. We describe a manual backup system (MBS) developed to maintain the delivery of blood products to patients in a hospital transfusion service in case of a computer network breakdown. All data are kept on a central SQL database connected to peripheral workstations in a local area network (LAN). Request entry from wards is performed via machine-readable request forms containing self-adhesive specimen labels with barcodes for test tubes. Data entry occurs on-line by bidirectional automated systems or off-line manually. One of the workstations in the laboratory contains a second SQL database which is frequently and incrementally updated. This workstation is run as a stand-alone, read-only database if the central SQL database is not available. In case of a network breakdown, the time-graded MBS is launched. Patient data, requesting ward and ordered tests/requests, are photocopied through a template from the request forms on special MBS worksheets serving as laboratory journal for manual processing and result report (a copy is left in the laboratory). As soon as the network is running again the data from the off-line period are entered into the primary SQL server. The MBS was successfully used at several occasions. The documentation of a 90-min breakdown period is presented in detail. Additional work resulted from the copy work and the belated manual data entry after restoration of the system. There was no delay in issue of blood products or result reporting. The backup system described has been proven to be simple, quick and safe to maintain urgent blood supply and distribution of laboratory results in case of unexpected network breakdown.

A generic minimization random allocation and blinding system on web.

PubMed

Cai, Hongwei; Xia, Jielai; Xu, Dezhong; Gao, Donghuai; Yan, Yongping

2006-12-01

Minimization is a dynamic randomization method for clinical trials. Although recommended by many researchers, the utilization of minimization has been seldom reported in randomized trials mainly because of the controversy surrounding the validity of conventional analyses and its complexity in implementation. However, both the statistical and clinical validity of minimization were demonstrated in recent studies. Minimization random allocation system integrated with blinding function that could facilitate the implementation of this method in general clinical trials has not been reported. SYSTEM OVERVIEW: The system is a web-based random allocation system using Pocock and Simon minimization method. It also supports multiple treatment arms within a trial, multiple simultaneous trials, and blinding without further programming. This system was constructed with generic database schema design method, Pocock and Simon minimization method and blinding method. It was coded with Microsoft Visual Basic and Active Server Pages (ASP) programming languages. And all dataset were managed with a Microsoft SQL Server database. Some critical programming codes were also provided. SIMULATIONS AND RESULTS: Two clinical trials were simulated simultaneously to test the system's applicability. Not only balanced groups but also blinded allocation results were achieved in both trials. Practical considerations for minimization method, the benefits, general applicability and drawbacks of the technique implemented in this system are discussed. Promising features of the proposed system are also summarized.

Footprint Representation of Planetary Remote Sensing Data

NASA Astrophysics Data System (ADS)

Walter, S. H. G.; Gasselt, S. V.; Michael, G.; Neukum, G.

The geometric outline of remote sensing image data, the so called footprint, can be represented as a number of coordinate tuples. These polygons are associated with according attribute information such as orbit name, ground- and image resolution, solar longitude and illumination conditions to generate a powerful base for classification of planetary experiment data. Speed, handling and extended capabilites are the reasons for using geodatabases to store and access these data types. Techniques for such a spatial database of footprint data are demonstrated using the Relational Database Management System (RDBMS) PostgreSQL, spatially enabled by the PostGIS extension. Exemplary, footprints of the HRSC and OMEGA instruments, both onboard ESA's Mars Express Orbiter, are generated and connected to attribute information. The aim is to provide high-resolution footprints of the OMEGA instrument to the science community for the first time and make them available for web-based mapping applications like the "Planetary Interactive GIS-on-the-Web Analyzable Database" (PIG- WAD), produced by the USGS. Map overlays with HRSC or other instruments like MOC and THEMIS (footprint maps are already available for these instruments and can be integrated into the database) allow on-the-fly intersection and comparison as well as extended statistics of the data. Footprint polygons are generated one by one using standard software provided by the instrument teams. Attribute data is calculated and stored together with the geometric information. In the case of HRSC, the coordinates of the footprints are already available in the VICAR label of each image file. Using the VICAR RTL and PostgreSQL's libpq C library they are loaded into the database using the Well-Known Text (WKT) notation by the Open Geospatial Consortium, Inc. (OGC). For the OMEGA instrument, image data is read using IDL routines developed and distributed by the OMEGA team. Image outlines are exported together with relevant attribute data to the industry standard Shapefile format. These files are translated to a Structured Query Language (SQL) command sequence suitable for insertion into the PostGIS/PostgrSQL database using the shp2pgsql data loader provided by the PostGIS software. PostgreSQL's advanced features such as geometry types, rules, operators and functions allow complex spatial queries and on-the-fly processing of data on DBMS level e.g. generalisation of the outlines. Processing done by the DBMS, visualisation via GIS systems and utilisation for web-based applications like mapservers will be demonstrated.

SU-E-T-206: Improving Radiotherapy Toxicity Based On Artificial Neural Network (ANN) for Head and Neck Cancer Patients

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

Cho, Daniel D; Wernicke, A Gabriella; Nori, Dattatreyudu

Purpose/Objective(s): The aim of this study is to build the estimator of toxicity using artificial neural network (ANN) for head and neck cancer patients Materials/Methods: An ANN can combine variables into a predictive model during training and considered all possible correlations of variables. We constructed an ANN based on the data from 73 patients with advanced H and N cancer treated with external beam radiotherapy and/or chemotherapy at our institution. For the toxicity estimator we defined input data including age, sex, site, stage, pathology, status of chemo, technique of external beam radiation therapy (EBRT), length of treatment, dose of EBRT,more » status of post operation, length of follow-up, the status of local recurrences and distant metastasis. These data were digitized based on the significance and fed to the ANN as input nodes. We used 20 hidden nodes (for the 13 input nodes) to take care of the correlations of input nodes. For training ANN, we divided data into three subsets such as training set, validation set and test set. Finally, we built the estimator for the toxicity from ANN output. Results: We used 13 input variables including the status of local recurrences and distant metastasis and 20 hidden nodes for correlations. 59 patients for training set, 7 patients for validation set and 7 patients for test set and fed the inputs to Matlab neural network fitting tool. We trained the data within 15% of errors of outcome. In the end we have the toxicity estimation with 74% of accuracy. Conclusion: We proved in principle that ANN can be a very useful tool for predicting the RT outcomes for high risk H and N patients. Currently we are improving the results using cross validation.« less

Implementation and Validation of an Impedance Eduction Technique

NASA Technical Reports Server (NTRS)

Watson, Willie R.; Jones, Michael G.; Gerhold, Carl H.

2011-01-01

Implementation of a pressure gradient method of impedance eduction in two NASA Langley flow ducts is described. The Grazing Flow Impedance Tube only supports plane-wave sources, while the Curved Duct Test Rig supports sources that contain higher-order modes. Multiple exercises are used to validate this new impedance eduction method. First, synthesized data for a hard wall insert and a conventional liner mounted in the Grazing Flow Impedance Tube are used as input to the two impedance eduction methods, the pressure gradient method and a previously validated wall pressure method. Comparisons between the two results are excellent. Next, data measured in the Grazing Flow Impedance Tube are used as input to both methods. Results from the two methods compare quite favorably for sufficiently low Mach numbers but this comparison degrades at Mach 0.5, especially when the hard wall insert is used. Finally, data measured with a hard wall insert mounted in the Curved Duct Test Rig are used as input to the pressure gradient method. Significant deviation from the known solution is observed, which is believed to be largely due to 3-D effects in this flow duct. Potential solutions to this issue are currently being explored.

Development and validation of a new population-based simulation model of osteoarthritis in New Zealand.

PubMed

Wilson, R; Abbott, J H

2018-04-01

To describe the construction and preliminary validation of a new population-based microsimulation model developed to analyse the health and economic burden and cost-effectiveness of treatments for knee osteoarthritis (OA) in New Zealand (NZ). We developed the New Zealand Management of Osteoarthritis (NZ-MOA) model, a discrete-time state-transition microsimulation model of the natural history of radiographic knee OA. In this article, we report on the model structure, derivation of input data, validation of baseline model parameters against external data sources, and validation of model outputs by comparison of the predicted population health loss with previous estimates. The NZ-MOA model simulates both the structural progression of radiographic knee OA and the stochastic development of multiple disease symptoms. Input parameters were sourced from NZ population-based data where possible, and from international sources where NZ-specific data were not available. The predicted distributions of structural OA severity and health utility detriments associated with OA were externally validated against other sources of evidence, and uncertainty resulting from key input parameters was quantified. The resulting lifetime and current population health-loss burden was consistent with estimates of previous studies. The new NZ-MOA model provides reliable estimates of the health loss associated with knee OA in the NZ population. The model structure is suitable for analysis of the effects of a range of potential treatments, and will be used in future work to evaluate the cost-effectiveness of recommended interventions within the NZ healthcare system. Copyright © 2018 Osteoarthritis Research Society International. Published by Elsevier Ltd. All rights reserved.

The effect of long-term changes in plant inputs on soil carbon stocks

NASA Astrophysics Data System (ADS)

Georgiou, K.; Li, Z.; Torn, M. S.

2017-12-01

Soil organic carbon (SOC) is the largest actively-cycling terrestrial reservoir of C and an integral component of thriving natural and managed ecosystems. C input interventions (e.g., litter removal or organic amendments) are common in managed landscapes and present an important decision for maintaining healthy soils in sustainable agriculture and forestry. Furthermore, climate and land-cover change can also affect the amount of plant C inputs that enter the soil through changes in plant productivity, allocation, and rooting depth. Yet, the processes that dictate the response of SOC to such changes in C inputs are poorly understood and inadequately represented in predictive models. Long-term litter manipulations are an invaluable resource for exploring key controls of SOC storage and validating model representations. Here we explore the response of SOC to long-term changes in plant C inputs across a range of biomes and soil types. We synthesize and analyze data from long-term litter manipulation field experiments, and focus our meta-analysis on changes to total SOC stocks, microbial biomass carbon, and mineral-associated (`protected') carbon pools and explore the relative contribution of above- versus below-ground C inputs. Our cross-site data comparison reveals that divergent SOC responses are observed between forest sites, particularly for treatments that increase C inputs to the soil. We explore trends among key variables (e.g., microbial biomass to SOC ratios) that inform soil C model representations. The assembled dataset is an important benchmark for evaluating process-based hypotheses and validating divergent model formulations.

The design and implementation of GML data management information system based on PostgreSQL

NASA Astrophysics Data System (ADS)

Zhang, Aiguo; Wu, Qunyong; Xu, Qifeng

2008-10-01

GML expresses geographic information in text, and it provides an extensible and standard way of spatial information encoding. At the present time, the management of GML data is in terms of document. By this way, the inquiry and update of GML data is inefficient, and it demands high memory when the document is comparatively large. In this respect, the paper put forward a data management of GML based on PostgreSQL. It designs four kinds of inquiries, which are inquiry of metadata, inquiry of geometry based on property, inquiry of property based on spatial information, and inquiry of spatial data based on location. At the same time, it designs and implements the visualization of the inquired WKT data.

A Medical Image Backup Architecture Based on a NoSQL Database and Cloud Computing Services.

PubMed

Santos Simões de Almeida, Luan Henrique; Costa Oliveira, Marcelo

2015-01-01

The use of digital systems for storing medical images generates a huge volume of data. Digital images are commonly stored and managed on a Picture Archiving and Communication System (PACS), under the DICOM standard. However, PACS is limited because it is strongly dependent on the server's physical space. Alternatively, Cloud Computing arises as an extensive, low cost, and reconfigurable resource. However, medical images contain patient information that can not be made available in a public cloud. Therefore, a mechanism to anonymize these images is needed. This poster presents a solution for this issue by taking digital images from PACS, converting the information contained in each image file to a NoSQL database, and using cloud computing to store digital images.

Monitoring SLAC High Performance UNIX Computing Systems

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

Lettsome, Annette K.; /Bethune-Cookman Coll. /SLAC

2005-12-15

Knowledge of the effectiveness and efficiency of computers is important when working with high performance systems. The monitoring of such systems is advantageous in order to foresee possible misfortunes or system failures. Ganglia is a software system designed for high performance computing systems to retrieve specific monitoring information. An alternative storage facility for Ganglia's collected data is needed since its default storage system, the round-robin database (RRD), struggles with data integrity. The creation of a script-driven MySQL database solves this dilemma. This paper describes the process took in the creation and implementation of the MySQL database for use by Ganglia.more » Comparisons between data storage by both databases are made using gnuplot and Ganglia's real-time graphical user interface.« less

Operationalizing Semantic Medline for meeting the information needs at point of care.

PubMed

Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

2015-01-01

Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible.

MaGnET: Malaria Genome Exploration Tool.

PubMed

Sharman, Joanna L; Gerloff, Dietlind L

2013-09-15

The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive 'exploration-style' visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum. MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein-protein interactions and more. Any selection of genes to explore made by the user is easily carried over between the different viewers for different datasets, and can be changed interactively at any point (without returning to a search). Free online use (Java Web Start) or download (Java application archive and MySQL database; requires local MySQL installation) at http://malariagenomeexplorer.org joanna.sharman@ed.ac.uk or dgerloff@ffame.org Supplementary data are available at Bioinformatics online.

Operationalizing Semantic Medline for meeting the information needs at point of care

PubMed Central

Rastegar-Mojarad, Majid; Li, Dingcheng; Liu, Hongfang

2015-01-01

Scientific literature is one of the popular resources for providing decision support at point of care. It is highly desirable to bring the most relevant literature to support the evidence-based clinical decision making process. Motivated by the recent advance in semantically enhanced information retrieval, we have developed a system, which aims to bring semantically enriched literature, Semantic Medline, to meet the information needs at point of care. This study reports our work towards operationalizing the system for real time use. We demonstrate that the migration of a relational database implementation to a NoSQL (Not only SQL) implementation significantly improves the performance and makes the use of Semantic Medline at point of care decision support possible. PMID:26306259

MySQL/PHP web database applications for IPAC proposal submission

NASA Astrophysics Data System (ADS)

Crane, Megan K.; Storrie-Lombardi, Lisa J.; Silbermann, Nancy A.; Rebull, Luisa M.

2008-07-01

The Infrared Processing and Analysis Center (IPAC) is NASA's multi-mission center of expertise for long-wavelength astrophysics. Proposals for various IPAC missions and programs are ingested via MySQL/PHP web database applications. Proposers use web forms to enter coversheet information and upload PDF files related to the proposal. Upon proposal submission, a unique directory is created on the webserver into which all of the uploaded files are placed. The coversheet information is converted into a PDF file using a PHP extension called FPDF. The files are concatenated into one PDF file using the command-line tool pdftk and then forwarded to the review committee. This work was performed at the California Institute of Technology under contract to the National Aeronautics and Space Administration.

Fish Karyome: A karyological information network database of Indian Fishes.

PubMed

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra

2012-01-01

'Fish Karyome', a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.

PELE web server: atomistic study of biomolecular systems at your fingertips.

PubMed

Madadkar-Sobhani, Armin; Guallar, Victor

2013-07-01

PELE, Protein Energy Landscape Exploration, our novel technology based on protein structure prediction algorithms and a Monte Carlo sampling, is capable of modelling the all-atom protein-ligand dynamical interactions in an efficient and fast manner, with two orders of magnitude reduced computational cost when compared with traditional molecular dynamics techniques. PELE's heuristic approach generates trial moves based on protein and ligand perturbations followed by side chain sampling and global/local minimization. The collection of accepted steps forms a stochastic trajectory. Furthermore, several processors may be run in parallel towards a collective goal or defining several independent trajectories; the whole procedure has been parallelized using the Message Passing Interface. Here, we introduce the PELE web server, designed to make the whole process of running simulations easier and more practical by minimizing input file demand, providing user-friendly interface and producing abstract outputs (e.g. interactive graphs and tables). The web server has been implemented in C++ using Wt (http://www.webtoolkit.eu) and MySQL (http://www.mysql.com). The PELE web server, accessible at http://pele.bsc.es, is free and open to all users with no login requirement.

Real-time Geographic Information System (GIS) for Monitoring the Area of Potential Water Level Using Rule Based System

NASA Astrophysics Data System (ADS)

Anugrah, Wirdah; Suryono; Suseno, Jatmiko Endro

2018-02-01

Management of water resources based on Geographic Information System can provide substantial benefits to water availability settings. Monitoring the potential water level is needed in the development sector, agriculture, energy and others. In this research is developed water resource information system using real-time Geographic Information System concept for monitoring the potential water level of web based area by applying rule based system method. GIS consists of hardware, software, and database. Based on the web-based GIS architecture, this study uses a set of computer that are connected to the network, run on the Apache web server and PHP programming language using MySQL database. The Ultrasound Wireless Sensor System is used as a water level data input. It also includes time and geographic location information. This GIS maps the five sensor locations. GIS is processed through a rule based system to determine the level of potential water level of the area. Water level monitoring information result can be displayed on thematic maps by overlaying more than one layer, and also generating information in the form of tables from the database, as well as graphs are based on the timing of events and the water level values.

Software platform for managing the classification of error- related potentials of observers

NASA Astrophysics Data System (ADS)

Asvestas, P.; Ventouras, E.-C.; Kostopoulos, S.; Sidiropoulos, K.; Korfiatis, V.; Korda, A.; Uzunolglu, A.; Karanasiou, I.; Kalatzis, I.; Matsopoulos, G.

2015-09-01

Human learning is partly based on observation. Electroencephalographic recordings of subjects who perform acts (actors) or observe actors (observers), contain a negative waveform in the Evoked Potentials (EPs) of the actors that commit errors and of observers who observe the error-committing actors. This waveform is called the Error-Related Negativity (ERN). Its detection has applications in the context of Brain-Computer Interfaces. The present work describes a software system developed for managing EPs of observers, with the aim of classifying them into observations of either correct or incorrect actions. It consists of an integrated platform for the storage, management, processing and classification of EPs recorded during error-observation experiments. The system was developed using C# and the following development tools and frameworks: MySQL, .NET Framework, Entity Framework and Emgu CV, for interfacing with the machine learning library of OpenCV. Up to six features can be computed per EP recording per electrode. The user can select among various feature selection algorithms and then proceed to train one of three types of classifiers: Artificial Neural Networks, Support Vector Machines, k-nearest neighbour. Next the classifier can be used for classifying any EP curve that has been inputted to the database.

A Dynamic Human Health Risk Assessment System

PubMed Central

Prasad, Umesh; Singh, Gurmit; Pant, A. B.

2012-01-01

An online human health risk assessment system (OHHRAS) has been designed and developed in the form of a prototype database-driven system and made available for the population of India through a website – www.healthriskindia.in. OHHRAS provide the three utilities, that is, health survey, health status, and bio-calculators. The first utility health survey is functional on the basis of database being developed dynamically and gives the desired output to the user on the basis of input criteria entered into the system; the second utility health status is providing the output on the basis of dynamic questionnaire and ticked (selected) answers and generates the health status reports based on multiple matches set as per advise of medical experts and the third utility bio-calculators are very useful for the scientists/researchers as online statistical analysis tool that gives more accuracy and save the time of user. The whole system and database-driven website has been designed and developed by using the software (mainly are PHP, My-SQL, Deamweaver, C++ etc.) and made available publically through a database-driven website (www.healthriskindia.in), which are very useful for researchers, academia, students, and general masses of all sectors. PMID:22778520

Flight instrument and telemetry response and its inversion

NASA Technical Reports Server (NTRS)

Weinberger, M. R.

1971-01-01

Mathematical models of rate gyros, servo accelerometers, pressure transducers, and telemetry systems were derived and their parameters were obtained from laboratory tests. Analog computer simulations were used extensively for verification of the validity for fast and large input signals. An optimal inversion method was derived to reconstruct input signals from noisy output signals and a computer program was prepared.

The Effects of Task Complexity and Input Frequency on the Acquisition of the Past Counterfactual Construction through Recasts

ERIC Educational Resources Information Center

Révész, Andrea; Sachs, Rebecca; Hama, Mika

2014-01-01

This investigation examined two techniques that may help learners focus on second language (L2) constructions when recasts are provided during meaning-based communicative activities: altering the cognitive complexity of tasks and manipulating the input frequency distributions of target constructions. We first independently assessed the validity of…

MURI: Impact of Oceanographic Variability on Acoustic Communications

DTIC Science & Technology

2011-09-01

multiplexing ( OFDM ), multiple- input/multiple-output ( MIMO ) transmissions, and multi-user single-input/multiple-output (SIMO) communications. Lastly... MIMO - OFDM communications: Receiver design for Doppler distorted underwater acoustic channels,” Proc. Asilomar Conf. on Signals, Systems, and... MIMO ) will be of particular interest. Validating experimental data will be obtained during the ONR acoustic communications experiment in summer 2008

Implementation of an Enterprise Information Portal (EIP) in the Loyola University Health System

PubMed Central

Price, Ronald N.; Hernandez, Kim

2001-01-01

Loyola University Chicago Stritch School of Medicine and Loyola University Medical Center have long histories in the development of applications to support the institutions' missions of education, research and clinical care. In late 1998, the institutions' application development group undertook an ambitious program to re-architecture more than 10 years of legacy application development (30+ core applications) into a unified World Wide Web (WWW) environment. The primary project objectives were to construct an environment that would support the rapid development of n-tier, web-based applications while providing standard methods for user authentication/validation, security/access control and definition of a user's organizational context. The project's efforts resulted in Loyola's Enterprise Information Portal (EIP), which meets the aforementioned objectives. This environment: 1) allows access to other vertical Intranet portals (e.g., electronic medical record, patient satisfaction information and faculty effort); 2) supports end-user desktop customization; and 3) provides a means for standardized application “look and feel.” The portal was constructed utilizing readily available hardware and software. Server hardware consists of multiprocessor (Intel Pentium 500Mhz) Compaq 6500 servers with one gigabyte of random access memory and 75 gigabytes of hard disk storage. Microsoft SQL Server was selected to house the portal's internal or security data structures. Netscape Enterprise Server was selected for the web server component of the environment and Allaire's ColdFusion was chosen for access and application tiers. Total costs for the portal environment was less than $40,000. User data storage is accomplished through two Microsoft SQL Servers and an existing SUN Microsystems enterprise server with eight processors, 750 gigabytes of disk storage operating Sybase relational database manager. Total storage capacity for all system exceeds one terabyte. In the past 12 months, the EIP has supported development of more than 88 applications and is utilized by more than 2,200 users.

DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data.

PubMed

Nettling, Martin; Thieme, Nils; Both, Andreas; Grosse, Ivo

2014-02-04

New technologies for analyzing biological samples, like next generation sequencing, are producing a growing amount of data together with quality scores. Moreover, software tools (e.g., for mapping sequence reads), calculating transcription factor binding probabilities, estimating epigenetic modification enriched regions or determining single nucleotide polymorphism increase this amount of position-specific DNA-related data even further. Hence, requesting data becomes challenging and expensive and is often implemented using specialised hardware. In addition, picking specific data as fast as possible becomes increasingly important in many fields of science. The general problem of handling big data sets was addressed by developing specialized databases like HBase, HyperTable or Cassandra. However, these database solutions require also specialized or distributed hardware leading to expensive investments. To the best of our knowledge, there is no database capable of (i) storing billions of position-specific DNA-related records, (ii) performing fast and resource saving requests, and (iii) running on a single standard computer hardware. Here, we present DRUMS (Disk Repository with Update Management and Select option), satisfying demands (i)-(iii). It tackles the weaknesses of traditional databases while handling position-specific DNA-related data in an efficient manner. DRUMS is capable of storing up to billions of records. Moreover, it focuses on optimizing relating single lookups as range request, which are needed permanently for computations in bioinformatics. To validate the power of DRUMS, we compare it to the widely used MySQL database. The test setting considers two biological data sets. We use standard desktop hardware as test environment. DRUMS outperforms MySQL in writing and reading records by a factor of two up to a factor of 10000. Furthermore, it can work with significantly larger data sets. Our work focuses on mid-sized data sets up to several billion records without requiring cluster technology. Storing position-specific data is a general problem and the concept we present here is a generalized approach. Hence, it can be easily applied to other fields of bioinformatics.

MO-F-CAMPUS-T-05: SQL Database Queries to Determine Treatment Planning Resource Usage

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

Fox, C; Gladstone, D

2015-06-15

Purpose: A radiation oncology clinic’s treatment capacity is traditionally thought to be limited by the number of machines in the clinic. As the number of fractions per course decrease and the number of adaptive plans increase, the question of how many treatment plans a clinic can plan becomes increasingly important. This work seeks to lay the ground work for assessing treatment planning resource usage. Methods: Care path templates were created using the Aria 11 care path interface. Care path tasks included key steps in the treatment planning process from the completion of CT simulation through the first radiation treatment. SQLmore » Server Management Studio was used to run SQL queries to extract task completion time stamps along with care path template information and diagnosis codes from the Aria database. 6 months of planning cycles were evaluated. Elapsed time was evaluated in terms of work hours within Monday – Friday, 7am to 5pm. Results: For the 195 validated treatment planning cycles, the average time for planning and MD review was 22.8 hours. Of those cases 33 were categorized as urgent. The average planning time for urgent plans was 5 hours. A strong correlation between diagnosis code and range of elapsed planning time was as well as between elapsed time and select diagnosis codes was observed. It was also observed that tasks were more likely to be completed on the date due than the time that they were due. Follow-up confirmed that most users did not look at the due time. Conclusion: Evaluation of elapsed planning time and other tasks suggest that care paths should be adjusted to allow for different contouring and planning times for certain diagnosis codes and urgent cases. Additional clinic training around task due times vs dates or a structuring of care paths around due dates is also needed.« less

Bayesian nonlinear structural FE model and seismic input identification for damage assessment of civil structures

NASA Astrophysics Data System (ADS)

Astroza, Rodrigo; Ebrahimian, Hamed; Li, Yong; Conte, Joel P.

2017-09-01

A methodology is proposed to update mechanics-based nonlinear finite element (FE) models of civil structures subjected to unknown input excitation. The approach allows to jointly estimate unknown time-invariant model parameters of a nonlinear FE model of the structure and the unknown time histories of input excitations using spatially-sparse output response measurements recorded during an earthquake event. The unscented Kalman filter, which circumvents the computation of FE response sensitivities with respect to the unknown model parameters and unknown input excitations by using a deterministic sampling approach, is employed as the estimation tool. The use of measurement data obtained from arrays of heterogeneous sensors, including accelerometers, displacement sensors, and strain gauges is investigated. Based on the estimated FE model parameters and input excitations, the updated nonlinear FE model can be interrogated to detect, localize, classify, and assess damage in the structure. Numerically simulated response data of a three-dimensional 4-story 2-by-1 bay steel frame structure with six unknown model parameters subjected to unknown bi-directional horizontal seismic excitation, and a three-dimensional 5-story 2-by-1 bay reinforced concrete frame structure with nine unknown model parameters subjected to unknown bi-directional horizontal seismic excitation are used to illustrate and validate the proposed methodology. The results of the validation studies show the excellent performance and robustness of the proposed algorithm to jointly estimate unknown FE model parameters and unknown input excitations.

Automatic helmet-wearing detection for law enforcement using CCTV cameras

NASA Astrophysics Data System (ADS)

Wonghabut, P.; Kumphong, J.; Satiennam, T.; Ung-arunyawee, R.; Leelapatra, W.

2018-04-01

The objective of this research is to develop an application for enforcing helmet wearing using CCTV cameras. The developed application aims to help law enforcement by police, and eventually resulting in changing risk behaviours and consequently reducing the number of accidents and its severity. Conceptually, the application software implemented using C++ language and OpenCV library uses two different angle of view CCTV cameras. Video frames recorded by the wide-angle CCTV camera are used to detect motorcyclists. If any motorcyclist without helmet is found, then the zoomed (narrow-angle) CCTV is activated to capture image of the violating motorcyclist and the motorcycle license plate in real time. Captured images are managed by database implemented using MySQL for ticket issuing. The results show that the developed program is able to detect 81% of motorcyclists on various motorcycle types during daytime and night-time. The validation results reveal that the program achieves 74% accuracy in detecting the motorcyclist without helmet.

STILTS -- Starlink Tables Infrastructure Library Tool Set

NASA Astrophysics Data System (ADS)

Taylor, Mark

STILTS is a set of command-line tools for processing tabular data. It has been designed for, but is not restricted to, use on astronomical data such as source catalogues. It contains both generic (format-independent) table processing tools and tools for processing VOTable documents. Facilities offered include crossmatching, format conversion, format validation, column calculation and rearrangement, row selection, sorting, plotting, statistical calculations and metadata display. Calculations on cell data can be performed using a powerful and extensible expression language. The package is written in pure Java and based on STIL, the Starlink Tables Infrastructure Library. This gives it high portability, support for many data formats (including FITS, VOTable, text-based formats and SQL databases), extensibility and scalability. Where possible the tools are written to accept streamed data so the size of tables which can be processed is not limited by available memory. As well as the tutorial and reference information in this document, detailed on-line help is available from the tools themselves. STILTS is available under the GNU General Public Licence.

BIRS – Bioterrorism Information Retrieval System

PubMed Central

Tewari, Ashish Kumar; Rashi; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Jain, Chakresh Kumar

2013-01-01

Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10 microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources and literature mining in order to provide the user with a comprehensive information system. Availability The database is freely available at http://www.bioterrorism.biowaves.org PMID:23390356

Establishing survey validity and reliability for American Indians through "think aloud" and test-retest methods.

PubMed

Hauge, Cindy Horst; Jacobs-Knight, Jacque; Jensen, Jamie L; Burgess, Katherine M; Puumala, Susan E; Wilton, Georgiana; Hanson, Jessica D

2015-06-01

The purpose of this study was to use a mixed-methods approach to determine the validity and reliability of measurements used within an alcohol-exposed pregnancy prevention program for American Indian women. To develop validity, content experts provided input into the survey measures, and a "think aloud" methodology was conducted with 23 American Indian women. After revising the measurements based on this input, a test-retest was conducted with 79 American Indian women who were randomized to complete either the original measurements or the new, modified measurements. The test-retest revealed that some of the questions performed better for the modified version, whereas others appeared to be more reliable for the original version. The mixed-methods approach was a useful methodology for gathering feedback on survey measurements from American Indian participants and in indicating specific survey questions that needed to be modified for this population. © The Author(s) 2015.

Ensuring the validity of calculated subcritical limits

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

Clark, H.K.

1977-01-01

The care taken at the Savannah River Laboratory and Plant to ensure the validity of calculated subcritical limits is described. Close attention is given to ANSI N16.1-1975, ''Validation of Calculational Methods for Nuclear Criticality Safety.'' The computer codes used for criticality safety computations, which are listed and are briefly described, have been placed in the SRL JOSHUA system to facilitate calculation and to reduce input errors. A driver module, KOKO, simplifies and standardizes input and links the codes together in various ways. For any criticality safety evaluation, correlations of the calculational methods are made with experiment to establish bias. Occasionallymore » subcritical experiments are performed expressly to provide benchmarks. Calculated subcritical limits contain an adequate but not excessive margin to allow for uncertainty in the bias. The final step in any criticality safety evaluation is the writing of a report describing the calculations and justifying the margin.« less

Database Constraints Applied to Metabolic Pathway Reconstruction Tools

PubMed Central

Vilaplana, Jordi; Solsona, Francesc; Teixido, Ivan; Usié, Anabel; Karathia, Hiren; Alves, Rui; Mateo, Jordi

2014-01-01

Our group developed two biological applications, Biblio-MetReS and Homol-MetReS, accessing the same database of organisms with annotated genes. Biblio-MetReS is a data-mining application that facilitates the reconstruction of molecular networks based on automated text-mining analysis of published scientific literature. Homol-MetReS allows functional (re)annotation of proteomes, to properly identify both the individual proteins involved in the process(es) of interest and their function. It also enables the sets of proteins involved in the process(es) in different organisms to be compared directly. The efficiency of these biological applications is directly related to the design of the shared database. We classified and analyzed the different kinds of access to the database. Based on this study, we tried to adjust and tune the configurable parameters of the database server to reach the best performance of the communication data link to/from the database system. Different database technologies were analyzed. We started the study with a public relational SQL database, MySQL. Then, the same database was implemented by a MapReduce-based database named HBase. The results indicated that the standard configuration of MySQL gives an acceptable performance for low or medium size databases. Nevertheless, tuning database parameters can greatly improve the performance and lead to very competitive runtimes. PMID:25202745

Database Reports Over the Internet

NASA Technical Reports Server (NTRS)

Smith, Dean Lance

2002-01-01

Most of the summer was spent developing software that would permit existing test report forms to be printed over the web on a printer that is supported by Adobe Acrobat Reader. The data is stored in a DBMS (Data Base Management System). The client asks for the information from the database using an HTML (Hyper Text Markup Language) form in a web browser. JavaScript is used with the forms to assist the user and verify the integrity of the entered data. Queries to a database are made in SQL (Sequential Query Language), a widely supported standard for making queries to databases. Java servlets, programs written in the Java programming language running under the control of network server software, interrogate the database and complete a PDF form template kept in a file. The completed report is sent to the browser requesting the report. Some errors are sent to the browser in an HTML web page, others are reported to the server. Access to the databases was restricted since the data are being transported to new DBMS software that will run on new hardware. However, the SQL queries were made to Microsoft Access, a DBMS that is available on most PCs (Personal Computers). Access does support the SQL commands that were used, and a database was created with Access that contained typical data for the report forms. Some of the problems and features are discussed below.

Geospatial data sharing, online spatial analysis and processing of Indian Biodiversity data in Internet GIS domain - A case study for raster based online geo-processing

NASA Astrophysics Data System (ADS)

Karnatak, H.; Pandey, K.; Oberai, K.; Roy, A.; Joshi, D.; Singh, H.; Raju, P. L. N.; Krishna Murthy, Y. V. N.

2014-11-01

National Biodiversity Characterization at Landscape Level, a project jointly sponsored by Department of Biotechnology and Department of Space, was implemented to identify and map the potential biodiversity rich areas in India. This project has generated spatial information at three levels viz. Satellite based primary information (Vegetation Type map, spatial locations of road & village, Fire occurrence); geospatially derived or modelled information (Disturbance Index, Fragmentation, Biological Richness) and geospatially referenced field samples plots. The study provides information of high disturbance and high biological richness areas suggesting future management strategies and formulating action plans. The study has generated for the first time baseline database in India which will be a valuable input towards climate change study in the Indian Subcontinent. The spatial data generated during the study is organized as central data repository in Geo-RDBMS environment using PostgreSQL and POSTGIS. The raster and vector data is published as OGC WMS and WFS standard for development of web base geoinformation system using Service Oriented Architecture (SOA). The WMS and WFS based system allows geo-visualization, online query and map outputs generation based on user request and response. This is a typical mashup architecture based geo-information system which allows access to remote web services like ISRO Bhuvan, Openstreet map, Google map etc., with overlay on Biodiversity data for effective study on Bio-resources. The spatial queries and analysis with vector data is achieved through SQL queries on POSTGIS and WFS-T operations. But the most important challenge is to develop a system for online raster based geo-spatial analysis and processing based on user defined Area of Interest (AOI) for large raster data sets. The map data of this study contains approximately 20 GB of size for each data layer which are five in number. An attempt has been to develop system using python, PostGIS and PHP for raster data analysis over the web for Biodiversity conservation and prioritization. The developed system takes inputs from users as WKT, Openlayer based Polygon geometry and Shape file upload as AOI to perform raster based operation using Python and GDAL/OGR. The intermediate products are stored in temporary files and tables which generate XML outputs for web representation. The raster operations like clip-zip-ship, class wise area statistics, single to multi-layer operations, diagrammatic representation and other geo-statistical analysis are performed. This is indigenous geospatial data processing engine developed using Open system architecture for spatial analysis of Biodiversity data sets in Internet GIS environment. The performance of this applications in multi-user environment like Internet domain is another challenging task which is addressed by fine tuning the source code, server hardening, spatial indexing and running the process in load balance mode. The developed system is hosted in Internet domain (http://bis.iirs.gov.in) for user access.

The construction of the spatio-temporal database of the ancient Silk Road within Xinjiang province during the Han and Tang dynasties

NASA Astrophysics Data System (ADS)

Bi, Jiantao; Luo, Guilin; Wang, Xingxing; Zhu, Zuojia

2014-03-01

As the bridge over the Chinese and Western civilization, the ancient Silk Road has made a huge contribution to cultural, economic, political exchanges between China and western countries. In this paper, we treated the historical period of Western Han Dynasty, Eastern Han Dynasty and Tang Dynasty as the research time domain, and the Western Regions' countries that were existed along the Silk Road at the mean time as the research spatial domain. Then we imported these data into the SQL Server database we constructed, from which we could either query the attribute information such as population, military force, the era of the Central Plains empire, the significant events taking place in the country and some related attribute information of these events like the happened calendar year in addition to some related spatial information such as the present location, the coordinates of the capital and the territory by inputting the name of the Western countries. At the same time we could query the significant events, government institution in Central Plains and the existent Western countries at the mean time by inputting the calendar year. Based on the database, associated with GIS, RS, Flex, C# and other related information technology and network technology, we could not only browsing, searching and editing the information of the ancient Silk Road in Xinjiang Province during the Han and Tang Dynasties, but preliminary analysing as well. This is the combination of archaeology and modern information technology, and the database could also be a reference to further study, research and practice in the related fields in the future.

Development of a Stochastically-driven, Forward Predictive Performance Model for PEMFCs

NASA Astrophysics Data System (ADS)

Harvey, David Benjamin Paul

A one-dimensional multi-scale coupled, transient, and mechanistic performance model for a PEMFC membrane electrode assembly has been developed. The model explicitly includes each of the 5 layers within a membrane electrode assembly and solves for the transport of charge, heat, mass, species, dissolved water, and liquid water. Key features of the model include the use of a multi-step implementation of the HOR reaction on the anode, agglomerate catalyst sub-models for both the anode and cathode catalyst layers, a unique approach that links the composition of the catalyst layer to key properties within the agglomerate model and the implementation of a stochastic input-based approach for component material properties. The model employs a new methodology for validation using statistically varying input parameters and statistically-based experimental performance data; this model represents the first stochastic input driven unit cell performance model. The stochastic input driven performance model was used to identify optimal ionomer content within the cathode catalyst layer, demonstrate the role of material variation in potential low performing MEA materials, provide explanation for the performance of low-Pt loaded MEAs, and investigate the validity of transient-sweep experimental diagnostic methods.

Numerical Electromagnetic Code (NEC)-Basic Scattering Code. Part I. User’s Manual.

DTIC Science & Technology

1979-09-01

Command RT : 29 I. Command PG: 32 J. Command GP: 35 K. Command CG: 36 L. Command SG: 39 M. Command AM: 44 N. Conumand PR: 48 0. Command NP: 49 P...these points and con- firm the validity of the solution. 1 0 1 -.- ’----.- ... The source presently considered in the computer code is an Plec - tric...Range Input 28 * RT : Translate and/or Rotate Coordinates 29 SG: Source Geometry Input IQ TO: Test Data Generation Options 17 [IN: Units of Input U)S

New Directions in the NOAO Observing Proposal System

NASA Astrophysics Data System (ADS)

Gasson, David; Bell, Dave

For the past eight years NOAO has been refining its on-line observing proposal system. Virtually all related processes are now handled electronically. Members of the astronomical community can submit proposals through email, web form, or via the Gemini Phase I Tool. NOAO staff can use the system to do administrative tasks, scheduling, and compilation of various statistics. In addition, all information relevant to the TAC process is made available on-line, including the proposals themselves (in HTML, PDF and PostScript) and technical comments. Grades and TAC comments are entered and edited through web forms, and can be sorted and filtered according to specified criteria. Current developments include a move away from proprietary solutions, toward open standards such as SQL (in the form of the MySQL relational database system), Perl, PHP and XML.

The unified database for the fixed target experiment BM@N

NASA Astrophysics Data System (ADS)

Gertsenberger, K. V.

2016-09-01

The article describes the developed database designed as comprehensive data storage of the fixed target experiment BM@N [1] at Joint Institute for Nuclear Research (JINR) in Dubna. The structure and purposes of the BM@N facility will be briefly presented. The scheme of the unified database and its parameters will be described in detail. The use of the BM@N database implemented on the PostgreSQL database management system (DBMS) allows one to provide user access to the actual information of the experiment. Also the interfaces developed for the access to the database will be presented. One was implemented as the set of C++ classes to access the data without SQL statements, the other-Web-interface being available on the Web page of the BM@N experiment.

ExplorEnz: the primary source of the IUBMB enzyme list

PubMed Central

McDonald, Andrew G.; Boyce, Sinéad; Tipton, Keith F.

2009-01-01

ExplorEnz is the MySQL database that is used for the curation and dissemination of the International Union of Biochemistry and Molecular Biology (IUBMB) Enzyme Nomenclature. A simple web-based query interface is provided, along with an advanced search engine for more complex Boolean queries. The WWW front-end is accessible at http://www.enzyme-database.org, from where downloads of the database as SQL and XML are also available. An associated form-based curatorial application has been developed to facilitate the curation of enzyme data as well as the internal and public review processes that occur before an enzyme entry is made official. Suggestions for new enzyme entries, or modifications to existing ones, can be made using the forms provided at http://www.enzyme-database.org/forms.php. PMID:18776214

DataBase on Demand

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, R.; Gomez, D.; Coterillo Coz, I.; Wojcik, D.

2012-12-01

At CERN a number of key database applications are running on user-managed MySQL database services. The database on demand project was born out of an idea to provide the CERN user community with an environment to develop and run database services outside of the actual centralised Oracle based database services. The Database on Demand (DBoD) empowers the user to perform certain actions that had been traditionally done by database administrators, DBA's, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently open community version of MySQL and single instance Oracle database server. This article describes a technology approach to face this challenge, a service level agreement, the SLA that the project provides, and an evolution of possible scenarios.

Ontology-oriented retrieval of putative microRNAs in Vitis vinifera via GrapeMiRNA: a web database of de novo predicted grape microRNAs.

PubMed

Lazzari, Barbara; Caprera, Andrea; Cestaro, Alessandro; Merelli, Ivan; Del Corvo, Marcello; Fontana, Paolo; Milanesi, Luciano; Velasco, Riccardo; Stella, Alessandra

2009-06-29

Two complete genome sequences are available for Vitis vinifera Pinot noir. Based on the sequence and gene predictions produced by the IASMA, we performed an in silico detection of putative microRNA genes and of their targets, and collected the most reliable microRNA predictions in a web database. The application is available at http://www.itb.cnr.it/ptp/grapemirna/. The program FindMiRNA was used to detect putative microRNA genes in the grape genome. A very high number of predictions was retrieved, calling for validation. Nine parameters were calculated and, based on the grape microRNAs dataset available at miRBase, thresholds were defined and applied to FindMiRNA predictions having targets in gene exons. In the resulting subset, predictions were ranked according to precursor positions and sequence similarity, and to target identity. To further validate FindMiRNA predictions, comparisons to the Arabidopsis genome, to the grape Genoscope genome, and to the grape EST collection were performed. Results were stored in a MySQL database and a web interface was prepared to query the database and retrieve predictions of interest. The GrapeMiRNA database encompasses 5,778 microRNA predictions spanning the whole grape genome. Predictions are integrated with information that can be of use in selection procedures. Tools added in the web interface also allow to inspect predictions according to gene ontology classes and metabolic pathways of targets. The GrapeMiRNA database can be of help in selecting candidate microRNA genes to be validated.

Analytic uncertainty and sensitivity analysis of models with input correlations

NASA Astrophysics Data System (ADS)

Zhu, Yueying; Wang, Qiuping A.; Li, Wei; Cai, Xu

2018-03-01

Probabilistic uncertainty analysis is a common means of evaluating mathematical models. In mathematical modeling, the uncertainty in input variables is specified through distribution laws. Its contribution to the uncertainty in model response is usually analyzed by assuming that input variables are independent of each other. However, correlated parameters are often happened in practical applications. In the present paper, an analytic method is built for the uncertainty and sensitivity analysis of models in the presence of input correlations. With the method, it is straightforward to identify the importance of the independence and correlations of input variables in determining the model response. This allows one to decide whether or not the input correlations should be considered in practice. Numerical examples suggest the effectiveness and validation of our analytic method in the analysis of general models. A practical application of the method is also proposed to the uncertainty and sensitivity analysis of a deterministic HIV model.

Current Source Logic Gate

NASA Technical Reports Server (NTRS)

Krasowski, Michael J. (Inventor); Prokop, Norman F. (Inventor)

2017-01-01

A current source logic gate with depletion mode field effect transistor ("FET") transistors and resistors may include a current source, a current steering switch input stage, and a resistor divider level shifting output stage. The current source may include a transistor and a current source resistor. The current steering switch input stage may include a transistor to steer current to set an output stage bias point depending on an input logic signal state. The resistor divider level shifting output stage may include a first resistor and a second resistor to set the output stage point and produce valid output logic signal states. The transistor of the current steering switch input stage may function as a switch to provide at least two operating points.

Approach for Uncertainty Propagation and Robust Design in CFD Using Sensitivity Derivatives

NASA Technical Reports Server (NTRS)

Putko, Michele M.; Newman, Perry A.; Taylor, Arthur C., III; Green, Lawrence L.

2001-01-01

This paper presents an implementation of the approximate statistical moment method for uncertainty propagation and robust optimization for a quasi 1-D Euler CFD (computational fluid dynamics) code. Given uncertainties in statistically independent, random, normally distributed input variables, a first- and second-order statistical moment matching procedure is performed to approximate the uncertainty in the CFD output. Efficient calculation of both first- and second-order sensitivity derivatives is required. In order to assess the validity of the approximations, the moments are compared with statistical moments generated through Monte Carlo simulations. The uncertainties in the CFD input variables are also incorporated into a robust optimization procedure. For this optimization, statistical moments involving first-order sensitivity derivatives appear in the objective function and system constraints. Second-order sensitivity derivatives are used in a gradient-based search to successfully execute a robust optimization. The approximate methods used throughout the analyses are found to be valid when considering robustness about input parameter mean values.

A Pro-active Real-time Forecasting and Decision Support System for Daily Management of Marine Works

NASA Astrophysics Data System (ADS)

Bollen, Mark; Leyssen, Gert; Smets, Steven; De Wachter, Tom

2016-04-01

Marine Works involving turbidity generating activities (eg. dredging, dredge spoil placement) can generate environmental stress in and around a project area in the form of sediment plumes causing light reduction and sedimentation. If these works are situated near sensitive habitats like sea-grass beds, coral reefs or sensitive human activities eg. aquaculture farms or water intakes, or if contaminants are present in the water soil environmental scrutiny is advised. Environmental Regulations can impose limitations to these activities in the form of turbidity thresholds, spill budgets, contaminant levels. Breaching environmental regulations can result in increased monitoring, adaptation of the works planning and production rates and ultimately in a (temporary) stop of activities all of which entail time and cost impacts for a contractor and/or client. Sediment plume behaviour is governed by the dredging process, soil properties and ambient conditions (currents, water depth) and can be modelled. Usually this is done during the preparatory EIA phase of a project, for estimation of environmental impact based on climatic scenarios. An operational forecasting tool is developed to adapt marine work schedules to the real-time circumstances and thus evade exceedance of critical threshold levels at sensitive areas. The forecasting system is based on a Python-based workflow manager with a MySQL database and a Django frontend web tool for user interaction and visualisation of the model results. The core consists of a numerical hydrodynamic model with sediment transport module (Mike21 from DHI). This model is driven by space and time varying wind fields and wave boundary conditions, and turbidity inputs (suspended sediment source terms) based on marine works production rates and soil properties. The resulting threshold analysis allows the operator to indicate potential impact at the sensitive areas and instigate an adaption of the marine work schedule if needed. In order to use this toolbox in real-time situations and facilitate forecasting of impacts of planned dredge works, the following operational online functionalities are implemented: • Automated fetch and preparation of the input data, including 7 day forecast wind and wave fields and real-time measurements, and user defined the turbidity inputs based on scheduled marine works. • Generate automated forecasts and running user configurable scenarios at the same time in parallel. • Export and convert the model results, time series and maps, into a standardized format (netcdf). • Automatic analysis and processing of model results, including the calculation of indicator turbidity values and the exceedance analysis of threshold levels at the different sensitive areas. Data assimilation with the real time on site turbidity measurements is implemented in this threshold analysis. • Pre-programmed generation of animated sediment plumes, specific charts and pdf reports to allow a rapid interpretation of the model results by the operators and facilitating decision making in the operational planning. The performed marine works, resulting from the marine work schedule proposed by the forecasting system, are evaluated by a threshold analysis on the validated turbidity measurements on the sensitive sites. This machine learning loop allows a check of the system in order to evaluate forecast and model uncertainties.

Orchestrating TRANSP Simulations for Interpretative and Predictive Tokamak Modeling with OMFIT

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

Grierson, B. A.; Yuan, X.; Gorelenkova, M.

TRANSP simulations are being used in the OMFIT work- flow manager to enable a machine independent means of experimental analysis, postdictive validation, and predictive time dependent simulations on the DIII-D, NSTX, JET and C-MOD tokamaks. The procedures for preparing the input data from plasma profile diagnostics and equilibrium reconstruction, as well as processing of the time-dependent heating and current drive sources and assumptions about the neutral recycling, vary across machines, but are streamlined by using a common workflow manager. Settings for TRANSP simulation fidelity are incorporated into the OMFIT framework, contrasting between-shot analysis, power balance, and fast-particle simulations. A previouslymore » established series of data consistency metrics are computed such as comparison of experimental vs. calculated neutron rate, equilibrium stored energy vs. total stored energy from profile and fast-ion pressure, and experimental vs. computed surface loop voltage. Discrepancies between data consistency metrics can indicate errors in input quantities such as electron density profile or Zeff, or indicate anomalous fast-particle transport. Measures to assess the sensitivity of the verification metrics to input quantities are provided by OMFIT, including scans of the input profiles and standardized post-processing visualizations. For predictive simulations, TRANSP uses GLF23 or TGLF to predict core plasma profiles, with user defined boundary conditions in the outer region of the plasma. ITPA validation metrics are provided in post-processing to assess the transport model validity. By using OMFIT to orchestrate the steps for experimental data preparation, selection of operating mode, submission, post-processing and visualization, we have streamlined and standardized the usage of TRANSP.« less

Orchestrating TRANSP Simulations for Interpretative and Predictive Tokamak Modeling with OMFIT

DOE PAGES

Grierson, B. A.; Yuan, X.; Gorelenkova, M.; ...

2018-02-21

TRANSP simulations are being used in the OMFIT work- flow manager to enable a machine independent means of experimental analysis, postdictive validation, and predictive time dependent simulations on the DIII-D, NSTX, JET and C-MOD tokamaks. The procedures for preparing the input data from plasma profile diagnostics and equilibrium reconstruction, as well as processing of the time-dependent heating and current drive sources and assumptions about the neutral recycling, vary across machines, but are streamlined by using a common workflow manager. Settings for TRANSP simulation fidelity are incorporated into the OMFIT framework, contrasting between-shot analysis, power balance, and fast-particle simulations. A previouslymore » established series of data consistency metrics are computed such as comparison of experimental vs. calculated neutron rate, equilibrium stored energy vs. total stored energy from profile and fast-ion pressure, and experimental vs. computed surface loop voltage. Discrepancies between data consistency metrics can indicate errors in input quantities such as electron density profile or Zeff, or indicate anomalous fast-particle transport. Measures to assess the sensitivity of the verification metrics to input quantities are provided by OMFIT, including scans of the input profiles and standardized post-processing visualizations. For predictive simulations, TRANSP uses GLF23 or TGLF to predict core plasma profiles, with user defined boundary conditions in the outer region of the plasma. ITPA validation metrics are provided in post-processing to assess the transport model validity. By using OMFIT to orchestrate the steps for experimental data preparation, selection of operating mode, submission, post-processing and visualization, we have streamlined and standardized the usage of TRANSP.« less

Building the Ferretome

PubMed Central

Sukhinin, Dmitrii I.; Engel, Andreas K.; Manger, Paul; Hilgetag, Claus C.

2016-01-01

Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (https://bams1.org), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the computational modeling of the human brain. Another animal model that is widely used in electrophysiological or developmental studies is the ferret; however, no systematic compilation of brain connectivity is currently available for this species. Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain, the Ferret(connect)ome, www.Ferretome.org. The Ferretome database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model. This data model was simplified and extended in order to accommodate new data modalities that were not represented previously, such as the cytoarchitecture of brain areas. The Ferretome uses a semantic parcellation of brain regions as well as a logical brain map transformation algorithm (objective relational transformation, ORT). The ORT algorithm was also adopted for the transformation of architecture data. The database is being developed in MySQL and has been populated with literature reports on tract-tracing observations in the ferret brain using a custom-designed web interface that allows efficient and validated simultaneous input and proofreading by multiple curators. The database is equipped with a non-specialist web interface. This interface can be extended to produce connectivity matrices in several formats, including a graphical representation superimposed on established ferret brain maps. An important feature of the Ferretome database is the possibility to trace back entries in connectivity matrices to the original studies archived in the system. Currently, the Ferretome contains 50 reports on connections comprising 20 injection reports with more than 150 labeled source and target areas, the majority reflecting connectivity of subcortical nuclei and 15 descriptions of regional brain architecture. We hope that the Ferretome database will become a useful resource for neuroinformatics and neural modeling, and will support studies of the ferret brain as well as facilitate advances in comparative studies of mesoscopic brain connectivity. PMID:27242503

Building the Ferretome.

PubMed

Sukhinin, Dmitrii I; Engel, Andreas K; Manger, Paul; Hilgetag, Claus C

2016-01-01

Databases of structural connections of the mammalian brain, such as CoCoMac (cocomac.g-node.org) or BAMS (https://bams1.org), are valuable resources for the analysis of brain connectivity and the modeling of brain dynamics in species such as the non-human primate or the rodent, and have also contributed to the computational modeling of the human brain. Another animal model that is widely used in electrophysiological or developmental studies is the ferret; however, no systematic compilation of brain connectivity is currently available for this species. Thus, we have started developing a database of anatomical connections and architectonic features of the ferret brain, the Ferret(connect)ome, www.Ferretome.org. The Ferretome database has adapted essential features of the CoCoMac methodology and legacy, such as the CoCoMac data model. This data model was simplified and extended in order to accommodate new data modalities that were not represented previously, such as the cytoarchitecture of brain areas. The Ferretome uses a semantic parcellation of brain regions as well as a logical brain map transformation algorithm (objective relational transformation, ORT). The ORT algorithm was also adopted for the transformation of architecture data. The database is being developed in MySQL and has been populated with literature reports on tract-tracing observations in the ferret brain using a custom-designed web interface that allows efficient and validated simultaneous input and proofreading by multiple curators. The database is equipped with a non-specialist web interface. This interface can be extended to produce connectivity matrices in several formats, including a graphical representation superimposed on established ferret brain maps. An important feature of the Ferretome database is the possibility to trace back entries in connectivity matrices to the original studies archived in the system. Currently, the Ferretome contains 50 reports on connections comprising 20 injection reports with more than 150 labeled source and target areas, the majority reflecting connectivity of subcortical nuclei and 15 descriptions of regional brain architecture. We hope that the Ferretome database will become a useful resource for neuroinformatics and neural modeling, and will support studies of the ferret brain as well as facilitate advances in comparative studies of mesoscopic brain connectivity.

A Neuroimaging Web Services Interface as a Cyber Physical System for Medical Imaging and Data Management in Brain Research: Design Study

PubMed Central

2018-01-01

Background Structural and functional brain images are essential imaging modalities for medical experts to study brain anatomy. These images are typically visually inspected by experts. To analyze images without any bias, they must be first converted to numeric values. Many software packages are available to process the images, but they are complex and difficult to use. The software packages are also hardware intensive. The results obtained after processing vary depending on the native operating system used and its associated software libraries; data processed in one system cannot typically be combined with data on another system. Objective The aim of this study was to fulfill the neuroimaging community’s need for a common platform to store, process, explore, and visualize their neuroimaging data and results using Neuroimaging Web Services Interface: a series of processing pipelines designed as a cyber physical system for neuroimaging and clinical data in brain research. Methods Neuroimaging Web Services Interface accepts magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and functional magnetic resonance imaging. These images are processed using existing and custom software packages. The output is then stored as image files, tabulated files, and MySQL tables. The system, made up of a series of interconnected servers, is password-protected and is securely accessible through a Web interface and allows (1) visualization of results and (2) downloading of tabulated data. Results All results were obtained using our processing servers in order to maintain data validity and consistency. The design is responsive and scalable. The processing pipeline started from a FreeSurfer reconstruction of Structural magnetic resonance imaging images. The FreeSurfer and regional standardized uptake value ratio calculations were validated using Alzheimer’s Disease Neuroimaging Initiative input images, and the results were posted at the Laboratory of Neuro Imaging data archive. Notable leading researchers in the field of Alzheimer’s Disease and epilepsy have used the interface to access and process the data and visualize the results. Tabulated results with unique visualization mechanisms help guide more informed diagnosis and expert rating, providing a truly unique multimodal imaging platform that combines magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and resting state functional magnetic resonance imaging. A quality control component was reinforced through expert visual rating involving at least 2 experts. Conclusions To our knowledge, there is no validated Web-based system offering all the services that Neuroimaging Web Services Interface offers. The intent of Neuroimaging Web Services Interface is to create a tool for clinicians and researchers with keen interest on multimodal neuroimaging. More importantly, Neuroimaging Web Services Interface significantly augments the Alzheimer’s Disease Neuroimaging Initiative data, especially since our data contain a large cohort of Hispanic normal controls and Alzheimer’s Disease patients. The obtained results could be scrutinized visually or through the tabulated forms, informing researchers on subtle changes that characterize the different stages of the disease. PMID:29699962

A design approach for ultrareliable real-time systems

NASA Technical Reports Server (NTRS)

Lala, Jaynarayan H.; Harper, Richard E.; Alger, Linda S.

1991-01-01

A design approach developed over the past few years to formalize redundancy management and validation is described. Redundant elements are partitioned into individual fault-containment regions (FCRs). An FCR is a collection of components that operates correctly regardless of any arbitrary logical or electrical fault outside the region. Conversely, a fault in an FCR cannot cause hardware outside the region to fail. The outputs of all channels are required to agree bit-for-bit under no-fault conditions (exact bitwise consensus). Synchronization, input agreement, and input validity conditions are discussed. The Advanced Information Processing System (AIPS), which is a fault-tolerant distributed architecture based on this approach, is described. A brief overview of recent applications of these systems and current research is presented.

Software Independent Verification and Validation (SIV&V) Simplified

DTIC Science & Technology

2006-12-01

Configuration Item I/O Input/Output I2V2 Independent Integrated Verification and Validation IBM International Business Machines ICD Interface...IPT Integrated Product Team IRS Interface Requirements Specification ISD Integrated System Diagram ITD Integrated Test Description ITP ...programming languages such as COBOL (Common Business Oriented Language) (Codasyl committee 1960), and FORTRAN (FORmula TRANslator) ( IBM 1952) (Robat 11

PACSY, a relational database management system for protein structure and chemical shift analysis.

PubMed

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

2012-10-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists

PubMed Central

Wiley, Laura K.; Sivley, R. Michael; Bush, William S.

2013-01-01

Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks. Database URL: https://github.com/bushlab/mynclist PMID:23894185

Rapid storage and retrieval of genomic intervals from a relational database system using nested containment lists.

PubMed

Wiley, Laura K; Sivley, R Michael; Bush, William S

2013-01-01

Efficient storage and retrieval of genomic annotations based on range intervals is necessary, given the amount of data produced by next-generation sequencing studies. The indexing strategies of relational database systems (such as MySQL) greatly inhibit their use in genomic annotation tasks. This has led to the development of stand-alone applications that are dependent on flat-file libraries. In this work, we introduce MyNCList, an implementation of the NCList data structure within a MySQL database. MyNCList enables the storage, update and rapid retrieval of genomic annotations from the convenience of a relational database system. Range-based annotations of 1 million variants are retrieved in under a minute, making this approach feasible for whole-genome annotation tasks. Database URL: https://github.com/bushlab/mynclist.

MaGnET: Malaria Genome Exploration Tool

PubMed Central

Sharman, Joanna L.; Gerloff, Dietlind L.

2013-01-01

Summary: The Malaria Genome Exploration Tool (MaGnET) is a software tool enabling intuitive ‘exploration-style’ visualization of functional genomics data relating to the malaria parasite, Plasmodium falciparum. MaGnET provides innovative integrated graphic displays for different datasets, including genomic location of genes, mRNA expression data, protein–protein interactions and more. Any selection of genes to explore made by the user is easily carried over between the different viewers for different datasets, and can be changed interactively at any point (without returning to a search). Availability and Implementation: Free online use (Java Web Start) or download (Java application archive and MySQL database; requires local MySQL installation) at http://malariagenomeexplorer.org Contact: joanna.sharman@ed.ac.uk or dgerloff@ffame.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23894142

A SQL-Database Based Meta-CASE System and its Query Subsystem

NASA Astrophysics Data System (ADS)

Eessaar, Erki; Sgirka, Rünno

Meta-CASE systems simplify the creation of CASE (Computer Aided System Engineering) systems. In this paper, we present a meta-CASE system that provides a web-based user interface and uses an object-relational database system (ORDBMS) as its basis. The use of ORDBMSs allows us to integrate different parts of the system and simplify the creation of meta-CASE and CASE systems. ORDBMSs provide powerful query mechanism. The proposed system allows developers to use queries to evaluate and gradually improve artifacts and calculate values of software measures. We illustrate the use of the systems by using SimpleM modeling language and discuss the use of SQL in the context of queries about artifacts. We have created a prototype of the meta-CASE system by using PostgreSQL™ ORDBMS and PHP scripting language.

Database on Demand: insight how to build your own DBaaS

NASA Astrophysics Data System (ADS)

Gaspar Aparicio, Ruben; Coterillo Coz, Ignacio

2015-12-01

At CERN, a number of key database applications are running on user-managed MySQL, PostgreSQL and Oracle database services. The Database on Demand (DBoD) project was born out of an idea to provide CERN user community with an environment to develop and run database services as a complement to the central Oracle based database service. The Database on Demand empowers the user to perform certain actions that had been traditionally done by database administrators, providing an enterprise platform for database applications. It also allows the CERN user community to run different database engines, e.g. presently three major RDBMS (relational database management system) vendors are offered. In this article we show the actual status of the service after almost three years of operations, some insight of our new redesign software engineering and near future evolution.

WebBio, a web-based management and analysis system for patient data of biological products in hospital.

PubMed

Lu, Ying-Hao; Kuo, Chen-Chun; Huang, Yaw-Bin

2011-08-01

We selected HTML, PHP and JavaScript as the programming languages to build "WebBio", a web-based system for patient data of biological products and used MySQL as database. WebBio is based on the PHP-MySQL suite and is run by Apache server on Linux machine. WebBio provides the functions of data management, searching function and data analysis for 20 kinds of biological products (plasma expanders, human immunoglobulin and hematological products). There are two particular features in WebBio: (1) pharmacists can rapidly find out whose patients used contaminated products for medication safety, and (2) the statistics charts for a specific product can be automatically generated to reduce pharmacist's work loading. WebBio has successfully turned traditional paper work into web-based data management.

A Comparison of Different Database Technologies for the CMS AsyncStageOut Transfer Database

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

Ciangottini, D.; Balcas, J.; Mascheroni, M.

AsyncStageOut (ASO) is the component of the CMS distributed data analysis system (CRAB) that manages users transfers in a centrally controlled way using the File Transfer System (FTS3) at CERN. It addresses a major weakness of the previous, decentralized model, namely that the transfer of the user’s output data to a single remote site was part of the job execution, resulting in inefficient use of job slots and an unacceptable failure rate. Currently ASO manages up to 600k files of various sizes per day from more than 500 users per month, spread over more than 100 sites. ASO uses amore » NoSQL database (CouchDB) as internal bookkeeping and as way to communicate with other CRAB components. Since ASO/CRAB were put in production in 2014, the number of transfers constantly increased up to a point where the pressure to the central CouchDB instance became critical, creating new challenges for the system scalability, performance, and monitoring. This forced a re-engineering of the ASO application to increase its scalability and lowering its operational effort. In this contribution we present a comparison of the performance of the current NoSQL implementation and a new SQL implementation, and how their different strengths and features influenced the design choices and operational experience. We also discuss other architectural changes introduced in the system to handle the increasing load and latency in delivering output to the user.« less

A comparison of different database technologies for the CMS AsyncStageOut transfer database

NASA Astrophysics Data System (ADS)

Ciangottini, D.; Balcas, J.; Mascheroni, M.; Rupeika, E. A.; Vaandering, E.; Riahi, H.; Silva, J. M. D.; Hernandez, J. M.; Belforte, S.; Ivanov, T. T.

2017-10-01

AsyncStageOut (ASO) is the component of the CMS distributed data analysis system (CRAB) that manages users transfers in a centrally controlled way using the File Transfer System (FTS3) at CERN. It addresses a major weakness of the previous, decentralized model, namely that the transfer of the user’s output data to a single remote site was part of the job execution, resulting in inefficient use of job slots and an unacceptable failure rate. Currently ASO manages up to 600k files of various sizes per day from more than 500 users per month, spread over more than 100 sites. ASO uses a NoSQL database (CouchDB) as internal bookkeeping and as way to communicate with other CRAB components. Since ASO/CRAB were put in production in 2014, the number of transfers constantly increased up to a point where the pressure to the central CouchDB instance became critical, creating new challenges for the system scalability, performance, and monitoring. This forced a re-engineering of the ASO application to increase its scalability and lowering its operational effort. In this contribution we present a comparison of the performance of the current NoSQL implementation and a new SQL implementation, and how their different strengths and features influenced the design choices and operational experience. We also discuss other architectural changes introduced in the system to handle the increasing load and latency in delivering output to the user.

HbA1c values calculated from blood glucose levels using truncated Fourier series and implementation in standard SQL database language.

PubMed

Temsch, W; Luger, A; Riedl, M

2008-01-01

This article presents a mathematical model to calculate HbA1c values based on self-measured blood glucose and past HbA1c levels, thereby enabling patients to monitor diabetes therapy between scheduled checkups. This method could help physicians to make treatment decisions if implemented in a system where glucose data are transferred to a remote server. The method, however, cannot replace HbA1c measurements; past HbA1c values are needed to gauge the method. The mathematical model of HbA1c formation was developed based on biochemical principles. Unlike an existing HbA1c formula, the new model respects the decreasing contribution of older glucose levels to current HbA1c values. About 12 standard SQL statements embedded in a php program were used to perform Fourier transform. Regression analysis was used to gauge results with previous HbA1c values. The method can be readily implemented in any SQL database. The predicted HbA1c values thus obtained were in accordance with measured values. They also matched the results of the HbA1c formula in the elevated range. By contrast, the formula was too "optimistic" in the range of better glycemic control. Individual analysis of two subjects improved the accuracy of values and reflected the bias introduced by different glucometers and individual measurement habits.

Improved oilfield GHG accounting using a global oilfield database

NASA Astrophysics Data System (ADS)

Roberts, S.; Brandt, A. R.; Masnadi, M.

2016-12-01

The definition of oil is shifting in considerable ways. Conventional oil resources are declining as oil sands, heavy oils, and others emerge. Technological advances mean that these unconventional hydrocarbons are now viable resources. Meanwhile, scientific evidence is mounting that climate change is occurring. The oil sector is responsible for 35% of global greenhouse gas (GHG) emissions, but the climate impacts of these new unconventional oils are not well understood. As such, the Oil Climate Index (OCI) project has been an international effort to evaluate the total life-cycle environmental GHG emissions of different oil fields globally. Over the course of the first and second phases of the project, 30 and 75 global oil fields have been investigated, respectively. The 75 fields account for about 25% of global oil production. For the third phase of the project, it is aimed to expand the OCI to contain closing to 100% of global oil production; leading to the analysis of 8000 fields. To accomplish this, a robust database system is required to handle and manipulate the data. Therefore, the integration of the data into the computer science language SQL (Structured Query Language) was performed. The implementation of SQL allows users to process the data more efficiently than would be possible by using the previously established program (Microsoft Excel). Next, a graphic user interface (gui) was implemented, in the computer science language of C#, in order to make the data interactive; enabling people to update the database without prior knowledge of SQL being necessary.

An Approach to Comprehensive and Sustainable Solar Wind Model Validation

NASA Astrophysics Data System (ADS)

Rastaetter, L.; MacNeice, P. J.; Mays, M. L.; Boblitt, J. M.; Wiegand, C.

2017-12-01

The number of models of the corona and inner heliosphere and of their updates and upgrades grows steadily, as does the number and character of the model inputs. Maintaining up to date validation of these models, in the face of this constant model evolution, is a necessary but very labor intensive activity. In the last year alone, both NASA's LWS program and the CCMC's ongoing support of model forecasting activities at NOAA SWPC have sought model validation reports on the quality of all aspects of the community's coronal and heliospheric models, including both ambient and CME related wind solutions at L1. In this presentation I will give a brief review of the community's previous model validation results of L1 wind representation. I will discuss the semi-automated web based system we are constructing at the CCMC to present comparative visualizations of all interesting aspects of the solutions from competing models.This system is designed to be easily queried to provide the essential comprehensive inputs to repeat andupdate previous validation studies and support extensions to them. I will illustrate this by demonstrating how the system is being used to support the CCMC/LWS Model Assessment Forum teams focused on the ambient and time dependent corona and solar wind, including CME arrival time and IMF Bz.I will also discuss plans to extend the system to include results from the Forum teams addressing SEP model validation.

Correcting ligands, metabolites, and pathways

PubMed Central

Ott, Martin A; Vriend, Gert

2006-01-01

Background A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metabolic network reconstruction, and systems biology. Most available databases, however, treat chemical structures more as illustrations than as a datafield in its own right. Lack of chemical accuracy impedes progress in the areas mentioned above. We present a database of metabolites called BioMeta that augments the existing pathway databases by explicitly assessing the validity, correctness, and completeness of chemical structure and reaction information. Description The main bulk of the data in BioMeta were obtained from the KEGG Ligand database. We developed a tool for chemical structure validation which assesses the chemical validity and stereochemical completeness of a molecule description. The validation tool was used to examine the compounds in BioMeta, showing that a relatively small number of compounds had an incorrect constitution (connectivity only, not considering stereochemistry) and that a considerable number (about one third) had incomplete or even incorrect stereochemistry. We made a large effort to correct the errors and to complete the structural descriptions. A total of 1468 structures were corrected and/or completed. We also established the reaction balance of the reactions in BioMeta and corrected 55% of the unbalanced (stoichiometrically incorrect) reactions in an automatic procedure. The BioMeta database was implemented in PostgreSQL and provided with a web-based interface. Conclusion We demonstrate that the validation of metabolite structures and reactions is a feasible and worthwhile undertaking, and that the validation results can be used to trigger corrections and improvements to BioMeta, our metabolite database. BioMeta provides some tools for rational drug design, reaction searches, and visualization. It is freely available at provided that the copyright notice of all original data is cited. The database will be useful for querying and browsing biochemical pathways, and to obtain reference information for identifying compounds. However, these applications require that the underlying data be correct, and that is the focus of BioMeta. PMID:17132165

STK Integrated Message Production List Editor (SIMPLE) for CEO Operations

NASA Technical Reports Server (NTRS)

Trenchard, Mike; Heydorn, James

2014-01-01

Late in fiscal year 2011, the Crew Earth Observations (CEO) team was tasked to upgrade and replace its mission planning and mission operations software systems, which were developed in the Space Shuttle era of the 1980s and 1990s. The impetuses for this change were the planned transition of all workstations to the Windows 7 64-bit operating system and the desire for more efficient and effective use of Satellite Tool Kit (STK) software required for reliable International Space Station (ISS) Earth location tracking. An additional requirement of this new system was the use of the same SQL database of CEO science sites from the SMMS, which was also being developed. STK Integrated Message Production List Editor (SIMPLE) is the essential, all-in-one tool now used by CEO staff to perform daily ISS mission planning to meet its requirement to acquire astronaut photography of specific sites on Earth. The sites are part of a managed, long-term database that has been defined and developed for scientific, educational, and public interest. SIMPLE's end product is a set of basic time and location data computed for an operator-selected set of targets that the ISS crew will be asked to photograph (photography is typically planned 12 to 36 hours out). The CEO operator uses SIMPLE to (a) specify a payload operations planning period; (b) acquire and validate the best available ephemeris data (vectors) for the ISS during the planning period; (c) ingest and display mission-specific site information from the CEO database; (d) identify and display potential current dynamic event targets as map features; (e) compute and display time and location information for each target; (f) screen and select targets based on known crew availability constraints, obliquity constraints, and real-time evaluated constraints to target visibility due to illumination (sun elevation) and atmospheric conditions (weather); and finally (g) incorporate basic, computed time and location information for each selected target into the daily CEO Target List product (message) for submission to ISS payload planning and integration teams for their review and approval prior to uplink. SIMPLE requires and uses the following resources: an ISS mission planning period Greenwich Mean Time start date/time and end date/time), the best available ISS mission ephemeris data (vectors) for that planning period, the STK software package configured for the ISS, and an ISS mission-specific subset of the CEO sites database. The primary advantages realized by the development and implementation of SIMPLE into the CEO payload operations support activity are a smooth transition to the Windows 7 operating system upon scheduled workstation refresh; streamlining of the input and verification of the current ISS ephemeris (vector data); seamless incorporation of selected contents of the SQL database of science sites; the ability to tag and display potential dynamic event opportunities on orbit track maps; simplification of the display and selection of encountered sites based on crew availability, illumination, obliquity, and weather constraints; the incorporation of high-quality mapping of the Earth with various satellite-based datasets for use in describing targets; and the ability to encapsulate and export the essential selected target elements in XML format for use by onboard Earth-location systems, such as Worldmap. SIMPLE is a carefully designed and crafted in-house software package that includes detailed help files for the user and meticulous internal documentation for future modifications. It was delivered in February 2012 for test and evaluation. Following acceptance, it was implemented for CEO mission operations support in May 2012.

Möglichkeiten und Grenzen der Validierung flächenhaft modellierter Nitrateinträge ins Grundwasser mit der N2/Ar-Methode

NASA Astrophysics Data System (ADS)

Eschenbach, Wolfram; Budziak, Dörte; Elbracht, Jörg; Höper, Heinrich; Krienen, Lisa; Kunkel, Ralf; Meyer, Knut; Well, Reinhard; Wendland, Frank

2018-06-01

Valid models for estimating nitrate emissions from agriculture to groundwater are an indispensable forecasting tool. A major challenge for model validation is the spatial and temporal inconsistency between data from groundwater monitoring points and modelled nitrate inputs into groundwater, and the fact that many existing groundwater monitoring wells cannot be used for validation. With the help of the N2/Ar-method, groundwater monitoring wells in areas with reduced groundwater can now be used for model validation. For this purpose, 484 groundwater monitoring wells were sampled in Lower Saxony. For the first time, modelled potential nitrate concentrations in groundwater recharge (from the DENUZ model) were compared with nitrate input concentrations, which were calculated using the N2/Ar method. The results show a good agreement between both methods for glacial outwash plains and moraine deposits. Although the nitrate degradation processes in groundwater and soil merge seamlessly in areas with a shallow groundwater table, the DENUZ model only calculates denitrification in the soil zone. The DENUZ model thus predicts 27% higher nitrate emissions into the groundwater than the N2/Ar method in such areas. To account for high temporal and spatial variability of nitrate emissions into groundwater, a large number of groundwater monitoring points must be investigated for model validation.

Bayesian cross-entropy methodology for optimal design of validation experiments

NASA Astrophysics Data System (ADS)

Jiang, X.; Mahadevan, S.

2006-07-01

An important concern in the design of validation experiments is how to incorporate the mathematical model in the design in order to allow conclusive comparisons of model prediction with experimental output in model assessment. The classical experimental design methods are more suitable for phenomena discovery and may result in a subjective, expensive, time-consuming and ineffective design that may adversely impact these comparisons. In this paper, an integrated Bayesian cross-entropy methodology is proposed to perform the optimal design of validation experiments incorporating the computational model. The expected cross entropy, an information-theoretic distance between the distributions of model prediction and experimental observation, is defined as a utility function to measure the similarity of two distributions. A simulated annealing algorithm is used to find optimal values of input variables through minimizing or maximizing the expected cross entropy. The measured data after testing with the optimum input values are used to update the distribution of the experimental output using Bayes theorem. The procedure is repeated to adaptively design the required number of experiments for model assessment, each time ensuring that the experiment provides effective comparison for validation. The methodology is illustrated for the optimal design of validation experiments for a three-leg bolted joint structure and a composite helicopter rotor hub component.

On the Role of L1 Markedness and L2 Input Robustness in Determining Potentially Fossilizable Language Forms in Iranian EFL Learners' Writing

ERIC Educational Resources Information Center

Nushi, Musa

2016-01-01

Han's (2009, 2013) selective fossilization hypothesis (SFH) claims that L1 markedness and L2 input robustness determine the fossilizability (and learnability) of an L2 feature. To test the validity of the model, a pseudo-longitudinal study was designed in which the errors in the argumentative essays of 52 Iranian EFL learners were identified and…

Sierra Structural Dynamics User's Notes

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

Reese, Garth M.

2015-10-19

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

Computation and Validation of the Dynamic Response Index (DRI)

DTIC Science & Technology

2013-08-06

matplotlib plotting library. • Executed from command line. • Allows several optional arguments. • Runs on Windows, Linux, UNIX, and Mac OS X. 10... vs . Time: Triangular pulse input data with given time duration and peak acceleration: Time (s) EARTH Code: Motivation • Error Assessment of...public release • ARC provided electrothermal battery model example: • Test vs . simulation data for terminal voltage. • EARTH input parameters

Sierra/SD User's Notes.

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

Munday, Lynn Brendon; Day, David M.; Bunting, Gregory

Sierra/SD provides a massively parallel implementation of structural dynamics finite element analysis, required for high fidelity, validated models used in modal, vibration, static and shock analysis of weapons systems. This document provides a users guide to the input for Sierra/SD. Details of input specifications for the different solution types, output options, element types and parameters are included. The appendices contain detailed examples, and instructions for running the software on parallel platforms.

Environmental Loss Characterization of an Advanced Stirling Convertor (ASC-E2) Insulation Package Using a Mock Heater Head

NASA Technical Reports Server (NTRS)

Schifer, Nicholas A.; Briggs, Maxwell H.

2012-01-01

The U.S. Department of Energy (DOE) and Lockheed Martin Space Systems Company (LMSSC) have been developing the Advanced Stirling Radioisotope Generator (ASRG) for use as a power system for space science missions. This generator would use two highefficiency Advanced Stirling Convertors (ASCs), developed by Sunpower Inc. and NASA Glenn Research Center (GRC). As part of ground testing of these ASCs, different operating conditions are used to simulate expected mission conditions. These conditions require achieving a specified electrical power output for a given net heat input. While electrical power output can be precisely quantified, thermal power input to the Stirling cycle cannot be directly measured. In an effort to improve net heat input predictions, the Mock Heater Head was developed with the same relative thermal paths as a convertor using a conducting rod to represent the Stirling cycle and tested to provide a direct comparison to numerical and empirical models used to predict convertor net heat input. The Mock Heater Head also served as the pathfinder for a higher fidelity version of validation test hardware, known as the Thermal Standard. This paper describes how the Mock Heater Head was tested and utilized to validate a process for the Thermal Standard.

Astronomical databases of Nikolaev Observatory

NASA Astrophysics Data System (ADS)

Protsyuk, Y.; Mazhaev, A.

2008-07-01

Several astronomical databases were created at Nikolaev Observatory during the last years. The databases are built by using MySQL search engine and PHP scripts. They are available on NAO web-site http://www.mao.nikolaev.ua.

A Comparative Reference Study for the Validation of HLA-Matching Algorithms in the Search for Allogeneic Hematopoietic Stem Cell Donors and Cord Blood Units

DTIC Science & Technology

2016-08-15

HLA ISSN 2059-2302 A comparative reference study for the validation of HLA-matching algorithms in the search for allogeneic hematopoietic stem cell...from different inter- national donor registries by challenging them with simulated input data and subse- quently comparing the output. This experiment...original work is properly cited, the use is non-commercial and no modifications or adaptations are made. Comparative reference validation of HLA

Validation Results for LEWICE 2.0. [Supplement

NASA Technical Reports Server (NTRS)

Wright, William B.; Rutkowski, Adam

1999-01-01

Two CD-ROMs contain experimental ice shapes and code prediction used for validation of LEWICE 2.0 (see NASA/CR-1999-208690, CASI ID 19990021235). The data include ice shapes for both experiment and for LEWICE, all of the input and output files for the LEWICE cases, JPG files of all plots generated, an electronic copy of the text of the validation report, and a Microsoft Excel(R) spreadsheet containing all of the quantitative measurements taken. The LEWICE source code and executable are not contained on the discs.

Development of Innovative Design Processor

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

Park, Y.S.; Park, C.O.

2004-07-01

The nuclear design analysis requires time-consuming and erroneous model-input preparation, code run, output analysis and quality assurance process. To reduce human effort and improve design quality and productivity, Innovative Design Processor (IDP) is being developed. Two basic principles of IDP are the document-oriented design and the web-based design. The document-oriented design is that, if the designer writes a design document called active document and feeds it to a special program, the final document with complete analysis, table and plots is made automatically. The active documents can be written with ordinary HTML editors or created automatically on the web, which ismore » another framework of IDP. Using the proper mix-up of server side and client side programming under the LAMP (Linux/Apache/MySQL/PHP) environment, the design process on the web is modeled as a design wizard style so that even a novice designer makes the design document easily. This automation using the IDP is now being implemented for all the reload design of Korea Standard Nuclear Power Plant (KSNP) type PWRs. The introduction of this process will allow large reduction in all reload design efforts of KSNP and provide a platform for design and R and D tasks of KNFC. (authors)« less

The Royal Society of Chemistry and the delivery of chemistry data repositories for the community.

PubMed

Williams, Antony; Tkachenko, Valery

2014-10-01

Since 2009 the Royal Society of Chemistry (RSC) has been delivering access to chemistry data and cheminformatics tools via the ChemSpider database and has garnered a significant community following in terms of usage and contribution to the platform. ChemSpider has focused only on those chemical entities that can be represented as molecular connection tables or, to be more specific, the ability to generate an InChI from the input structure. As a structure centric hub ChemSpider is built around the molecular structure with other data and links being associated with this structure. As a result the platform has been limited in terms of the types of data that can be managed, and the flexibility of its searches, and it is constrained by the data model. New technologies and approaches, specifically taking into account a shift from relational to NoSQL databases, and the growing importance of the semantic web, has motivated RSC to rearchitect and create a more generic data repository utilizing these new technologies. This article will provide an overview of our activities in delivering data sharing platforms for the chemistry community including the development of the new data repository expanding into more extensive domains of chemistry data.

Vi-da: vitiligo diagnostic assistance mobile application

NASA Astrophysics Data System (ADS)

Nugraha, G. A.; Nurhudatiana, A.; Bahana, R.

2018-03-01

Vitiligo is a skin disorder in which white patches of depigmentation appear on different parts of the body. Usually, patients come to hospitals or clinics to have their vitiligo conditions assessed. This can be very tiring to the patients, as vitiligo treatments usually take a relatively long period of time, which can range from months to years. To address this challenge, we present in this paper a prototype of an Android-based mobile application called Vi-DA, which stands for Vitiligo Diagnostic Assistance. Vi-DA consists of three subsystems, which are user sign-up subsystem, camera and image analysis subsystem, and progress report subsystem. The mobile application was developed in Java programming language and uses MySQL as the database system. Vi-DA adopts a vitiligo segmentation algorithm to segment input image into normal skin area, vitiligo skin area, and non-skin area. Results showed that Vi-DA gave comparable results to the previous system implemented in Matlab. User acceptance testing results also showed that all respondents agreed on the usefulness of the system and agreed to use Vi-DA again in the future. Vi-DA benefits both dermatologists and patients as not only a computer-aided diagnosis (CAD) tool but also as a smart application that can be used for self-assessment at home.

The Royal Society of Chemistry and the delivery of chemistry data repositories for the community

NASA Astrophysics Data System (ADS)

Williams, Antony; Tkachenko, Valery

2014-10-01

Since 2009 the Royal Society of Chemistry (RSC) has been delivering access to chemistry data and cheminformatics tools via the ChemSpider database and has garnered a significant community following in terms of usage and contribution to the platform. ChemSpider has focused only on those chemical entities that can be represented as molecular connection tables or, to be more specific, the ability to generate an InChI from the input structure. As a structure centric hub ChemSpider is built around the molecular structure with other data and links being associated with this structure. As a result the platform has been limited in terms of the types of data that can be managed, and the flexibility of its searches, and it is constrained by the data model. New technologies and approaches, specifically taking into account a shift from relational to NoSQL databases, and the growing importance of the semantic web, has motivated RSC to rearchitect and create a more generic data repository utilizing these new technologies. This article will provide an overview of our activities in delivering data sharing platforms for the chemistry community including the development of the new data repository expanding into more extensive domains of chemistry data.

MALINA: a web service for visual analytics of human gut microbiota whole-genome metagenomic reads.

PubMed

Tyakht, Alexander V; Popenko, Anna S; Belenikin, Maxim S; Altukhov, Ilya A; Pavlenko, Alexander V; Kostryukova, Elena S; Selezneva, Oksana V; Larin, Andrei K; Karpova, Irina Y; Alexeev, Dmitry G

2012-12-07

MALINA is a web service for bioinformatic analysis of whole-genome metagenomic data obtained from human gut microbiota sequencing. As input data, it accepts metagenomic reads of various sequencing technologies, including long reads (such as Sanger and 454 sequencing) and next-generation (including SOLiD and Illumina). It is the first metagenomic web service that is capable of processing SOLiD color-space reads, to authors' knowledge. The web service allows phylogenetic and functional profiling of metagenomic samples using coverage depth resulting from the alignment of the reads to the catalogue of reference sequences which are built into the pipeline and contain prevalent microbial genomes and genes of human gut microbiota. The obtained metagenomic composition vectors are processed by the statistical analysis and visualization module containing methods for clustering, dimension reduction and group comparison. Additionally, the MALINA database includes vectors of bacterial and functional composition for human gut microbiota samples from a large number of existing studies allowing their comparative analysis together with user samples, namely datasets from Russian Metagenome project, MetaHIT and Human Microbiome Project (downloaded from http://hmpdacc.org). MALINA is made freely available on the web at http://malina.metagenome.ru. The website is implemented in JavaScript (using Ext JS), Microsoft .NET Framework, MS SQL, Python, with all major browsers supported.

Expanded all-optical programmable logic array based on multi-input/output canonical logic units.

PubMed

Lei, Lei; Dong, Jianji; Zou, Bingrong; Wu, Zhao; Dong, Wenchan; Zhang, Xinliang

2014-04-21

We present an expanded all-optical programmable logic array (O-PLA) using multi-input and multi-output canonical logic units (CLUs) generation. Based on four-wave mixing (FWM) in highly nonlinear fiber (HNLF), two-input and three-input CLUs are simultaneously achieved in five different channels with an operation speed of 40 Gb/s. Clear temporal waveforms and wide open eye diagrams are successfully observed. The effectiveness of the scheme is validated by extinction ratio and optical signal-to-noise ratio measurements. The computing capacity, defined as the total amount of logic functions achieved by the O-PLA, is discussed in detail. For a three-input O-PLA, the computing capacity of the expanded CLUs-PLA is more than two times as large as that of the standard CLUs-PLA, and this multiple will increase to more than three and a half as the idlers are individually independent.

Aircraft signal definition for flight safety system monitoring system

NASA Technical Reports Server (NTRS)

Gibbs, Michael (Inventor); Omen, Debi Van (Inventor)

2003-01-01

A system and method compares combinations of vehicle variable values against known combinations of potentially dangerous vehicle input signal values. Alarms and error messages are selectively generated based on such comparisons. An aircraft signal definition is provided to enable definition and monitoring of sets of aircraft input signals to customize such signals for different aircraft. The input signals are compared against known combinations of potentially dangerous values by operational software and hardware of a monitoring function. The aircraft signal definition is created using a text editor or custom application. A compiler receives the aircraft signal definition to generate a binary file that comprises the definition of all the input signals used by the monitoring function. The binary file also contains logic that specifies how the inputs are to be interpreted. The file is then loaded into the monitor function, where it is validated and used to continuously monitor the condition of the aircraft.

Experimental Validation of a Closed Brayton Cycle System Transient Simulation

NASA Technical Reports Server (NTRS)

Johnson, Paul K.; Hervol, David S.

2006-01-01

The Brayton Power Conversion Unit (BPCU) located at NASA Glenn Research Center (GRC) in Cleveland, Ohio was used to validate the results of a computational code known as Closed Cycle System Simulation (CCSS). Conversion system thermal transient behavior was the focus of this validation. The BPCU was operated at various steady state points and then subjected to transient changes involving shaft rotational speed and thermal energy input. These conditions were then duplicated in CCSS. Validation of the CCSS BPCU model provides confidence in developing future Brayton power system performance predictions, and helps to guide high power Brayton technology development.

A New Local Bipolar Autoassociative Memory Based on External Inputs of Discrete Recurrent Neural Networks With Time Delay.

PubMed

Zhou, Caigen; Zeng, Xiaoqin; Luo, Chaomin; Zhang, Huaguang

In this paper, local bipolar auto-associative memories are presented based on discrete recurrent neural networks with a class of gain type activation function. The weight parameters of neural networks are acquired by a set of inequalities without the learning procedure. The global exponential stability criteria are established to ensure the accuracy of the restored patterns by considering time delays and external inputs. The proposed methodology is capable of effectively overcoming spurious memory patterns and achieving memory capacity. The effectiveness, robustness, and fault-tolerant capability are validated by simulated experiments.In this paper, local bipolar auto-associative memories are presented based on discrete recurrent neural networks with a class of gain type activation function. The weight parameters of neural networks are acquired by a set of inequalities without the learning procedure. The global exponential stability criteria are established to ensure the accuracy of the restored patterns by considering time delays and external inputs. The proposed methodology is capable of effectively overcoming spurious memory patterns and achieving memory capacity. The effectiveness, robustness, and fault-tolerant capability are validated by simulated experiments.

Toxicity ForeCaster (ToxCast™) Data

EPA Pesticide Factsheets

Data is organized into different data sets and includes descriptions of ToxCast chemicals and assays and files summarizing the screening results, a MySQL database, chemicals screened through Tox21, and available data generated from animal toxicity studies.

76 FR 26729 - Ceridian Corporation; Analysis of Proposed Consent Order to Aid Public Comment

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-09

... result of these failures, hackers executed an SQL injection attack on the Powerpay Web site and Web application. Through this attack, the hackers found personal information stored in Powerpay on Ceridian's...

Similarity extraction mechanism concerning historical personalities based on SQL queries in an RDBMS environment

NASA Astrophysics Data System (ADS)

Barouchou, Alexandra; Dendrinos, Markos

2015-02-01

An interesting issue in the domain of history of science and ideas is the concept of similarity of historical personalities. Similar objects of research of philosophers and scientists indicate prospective influences, caused either from one another's reading or meetings, communication or even cooperation. Key methodological role in the surfacing of the sought similarities play the keywords extracted from their works as well as their placement in a philosophical and scientific term taxonomy. The case study examined in the framework of this paper concerns scientists and philosophers, who lived in ancient Greece or Renaissance periods and dealt, in at least one work, with the subject God. All the available data (scientists, studies, recorded relations between scientists, keywords, and thematic hierarchy) have been organized in an RDBMS environment, aiming at the emergence of similarities and influences between scientists through properly created SQL queries based on date and thematic hierarchy criteria.

STINGRAY: system for integrated genomic resources and analysis.

PubMed

Wagner, Glauber; Jardim, Rodrigo; Tschoeke, Diogo A; Loureiro, Daniel R; Ocaña, Kary A C S; Ribeiro, Antonio C B; Emmel, Vanessa E; Probst, Christian M; Pitaluga, André N; Grisard, Edmundo C; Cavalcanti, Maria C; Campos, Maria L M; Mattoso, Marta; Dávila, Alberto M R

2014-03-07

The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/.

Evaluation of the performance of open-source RDBMS and triplestores for storing medical data over a web service.

PubMed

Kilintzis, Vassilis; Beredimas, Nikolaos; Chouvarda, Ioanna

2014-01-01

An integral part of a system that manages medical data is the persistent storage engine. For almost twenty five years Relational Database Management Systems(RDBMS) were considered the obvious decision, yet today new technologies have emerged that require our attention as possible alternatives. Triplestores store information in terms of RDF triples without necessarily binding to a specific predefined structural model. In this paper we present an attempt to compare the performance of Apache JENA-Fuseki and the Virtuoso Universal Server 6 triplestores with that of MySQL 5.6 RDBMS for storing and retrieving medical information that it is communicated as RDF/XML ontology instances over a RESTful web service. The results show that the performance, calculated as average time of storing and retrieving instances, is significantly better using Virtuoso Server while MySQL performed better than Fuseki.

Data Processing on Database Management Systems with Fuzzy Query

NASA Astrophysics Data System (ADS)

Şimşek, Irfan; Topuz, Vedat

In this study, a fuzzy query tool (SQLf) for non-fuzzy database management systems was developed. In addition, samples of fuzzy queries were made by using real data with the tool developed in this study. Performance of SQLf was tested with the data about the Marmara University students' food grant. The food grant data were collected in MySQL database by using a form which had been filled on the web. The students filled a form on the web to describe their social and economical conditions for the food grant request. This form consists of questions which have fuzzy and crisp answers. The main purpose of this fuzzy query is to determine the students who deserve the grant. The SQLf easily found the eligible students for the grant through predefined fuzzy values. The fuzzy query tool (SQLf) could be used easily with other database system like ORACLE and SQL server.

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity

PubMed Central

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping). PMID:29065644

PACSY, a relational database management system for protein structure and chemical shift analysis

PubMed Central

Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo

2012-01-01

PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu. PMID:22903636

Vulnerability Assessment of IPv6 Websites to SQL Injection and Other Application Level Attacks

PubMed Central

Cho, Ying-Chiang; Pan, Jen-Yi

2013-01-01

Given the proliferation of internet connected devices, IPv6 has been proposed to replace IPv4. Aside from providing a larger address space which can be assigned to internet enabled devices, it has been suggested that the IPv6 protocol offers increased security due to the fact that with the large number of addresses available, standard IP scanning attacks will no longer become feasible. However, given the interest in attacking organizations rather than individual devices, most initial points of entry onto an organization's network and their attendant devices are visible and reachable through web crawling techniques, and, therefore, attacks on the visible application layer may offer ways to compromise the overall network. In this evaluation, we provide a straightforward implementation of a web crawler in conjunction with a benign black box penetration testing system and analyze the ease at which SQL injection attacks can be carried out. PMID:24574863

A UML Profile for Developing Databases that Conform to the Third Manifesto

NASA Astrophysics Data System (ADS)

Eessaar, Erki

The Third Manifesto (TTM) presents the principles of a relational database language that is free of deficiencies and ambiguities of SQL. There are database management systems that are created according to TTM. Developers need tools that support the development of databases by using these database management systems. UML is a widely used visual modeling language. It provides built-in extension mechanism that makes it possible to extend UML by creating profiles. In this paper, we introduce a UML profile for designing databases that correspond to the rules of TTM. We created the first version of the profile by translating existing profiles of SQL database design. After that, we extended and improved the profile. We implemented the profile by using UML CASE system StarUML™. We present an example of using the new profile. In addition, we describe problems that occurred during the profile development.

Development of noSQL data storage for the ATLAS PanDA Monitoring System

NASA Astrophysics Data System (ADS)

Potekhin, M.; ATLAS Collaboration

2012-06-01

For several years the PanDA Workload Management System has been the basis for distributed production and analysis for the ATLAS experiment at the LHC. Since the start of data taking PanDA usage has ramped up steadily, typically exceeding 500k completed jobs/day by June 2011. The associated monitoring data volume has been rising as well, to levels that present a new set of challenges in the areas of database scalability and monitoring system performance and efficiency. These challenges are being met with a R&D effort aimed at implementing a scalable and efficient monitoring data storage based on a noSQL solution (Cassandra). We present our motivations for using this technology, as well as data design and the techniques used for efficient indexing of the data. We also discuss the hardware requirements as they were determined by testing with actual data and realistic loads.

A DBTechNet course module on database SQL transactions for VET teachers training and higher education informatics education

NASA Astrophysics Data System (ADS)

Dervos, D. A.; Skourlas, C.; Laiho, M.

2015-02-01

"DBTech VET Teachers" project is Leonardo da Vinci Multilateral Transfer of Innovation Project co-financed by the European Commission's Lifelong Learning Programme. The aim of the project is to renew the teaching of database technologies in VET (Vocational Education and Training) institutes, on the basis of the current and real needs of ICT industry in Europe. Training of the VET teachers is done with the systems used in working life and they are taught to guide students to learning by verifying. In this framework, a course module on SQL transactions is prepared and offered. In this paper we present and briefly discuss some qualitative/quantitative data collected from its first pilot offering to an international audience in Greece during May-June 2013. The questionnaire/evaluation results, and the types of participants who have attended the course offering, are presented. Conclusions are also presented.

GEOmetadb: powerful alternative search engine for the Gene Expression Omnibus

PubMed Central

Zhu, Yuelin; Davis, Sean; Stephens, Robert; Meltzer, Paul S.; Chen, Yidong

2008-01-01

The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data in GEO can be challenging. We have developed GEOmetadb in an attempt to make querying the GEO metadata both easier and more powerful. All GEO metadata records as well as the relationships between them are parsed and stored in a local MySQL database. A powerful, flexible web search interface with several convenient utilities provides query capabilities not available via NCBI tools. In addition, a Bioconductor package, GEOmetadb that utilizes a SQLite export of the entire GEOmetadb database is also available, rendering the entire GEO database accessible with full power of SQL-based queries from within R. Availability: The web interface and SQLite databases available at http://gbnci.abcc.ncifcrf.gov/geo/. The Bioconductor package is available via the Bioconductor project. The corresponding MATLAB implementation is also available at the same website. Contact: yidong@mail.nih.gov PMID:18842599

STINGRAY: system for integrated genomic resources and analysis

PubMed Central

2014-01-01

Background The STINGRAY system has been conceived to ease the tasks of integrating, analyzing, annotating and presenting genomic and expression data from Sanger and Next Generation Sequencing (NGS) platforms. Findings STINGRAY includes: (a) a complete and integrated workflow (more than 20 bioinformatics tools) ranging from functional annotation to phylogeny; (b) a MySQL database schema, suitable for data integration and user access control; and (c) a user-friendly graphical web-based interface that makes the system intuitive, facilitating the tasks of data analysis and annotation. Conclusion STINGRAY showed to be an easy to use and complete system for analyzing sequencing data. While both Sanger and NGS platforms are supported, the system could be faster using Sanger data, since the large NGS datasets could potentially slow down the MySQL database usage. STINGRAY is available at http://stingray.biowebdb.org and the open source code at http://sourceforge.net/projects/stingray-biowebdb/. PMID:24606808

Vulnerability assessment of IPv6 websites to SQL injection and other application level attacks.

PubMed

Cho, Ying-Chiang; Pan, Jen-Yi

2013-01-01

Given the proliferation of internet connected devices, IPv6 has been proposed to replace IPv4. Aside from providing a larger address space which can be assigned to internet enabled devices, it has been suggested that the IPv6 protocol offers increased security due to the fact that with the large number of addresses available, standard IP scanning attacks will no longer become feasible. However, given the interest in attacking organizations rather than individual devices, most initial points of entry onto an organization's network and their attendant devices are visible and reachable through web crawling techniques, and, therefore, attacks on the visible application layer may offer ways to compromise the overall network. In this evaluation, we provide a straightforward implementation of a web crawler in conjunction with a benign black box penetration testing system and analyze the ease at which SQL injection attacks can be carried out.

Abstraction of the Relational Model from a Department of Veterans Affairs DHCP Database: Bridging Theory and Working Application

PubMed Central

Levy, C.; Beauchamp, C.

1996-01-01

This poster describes the methods used and working prototype that was developed from an abstraction of the relational model from the VA's hierarchical DHCP database. Overlaying the relational model on DHCP permits multiple user views of the physical data structure, enhances access to the database by providing a link to commercial (SQL based) software, and supports a conceptual managed care data model based on primary and longitudinal patient care. The goal of this work was to create a relational abstraction of the existing hierarchical database; to construct, using SQL data definition language, user views of the database which reflect the clinical conceptual view of DHCP, and to allow the user to work directly with the logical view of the data using GUI based commercial software of their choosing. The workstation is intended to serve as a platform from which a managed care information model could be implemented and evaluated.

Hosting and pulishing astronomical data in SQL databases

NASA Astrophysics Data System (ADS)

Galkin, Anastasia; Klar, Jochen; Riebe, Kristin; Matokevic, Gal; Enke, Harry

2017-04-01

In astronomy, terabytes and petabytes of data are produced by ground instruments, satellite missions and simulations. At Leibniz-Institute for Astrophysics Potsdam (AIP) we host and publish terabytes of cosmological simulation and observational data. The public archive at AIP has now reached a size of 60TB and growing and helps to produce numerous scientific papers. The web framework Daiquiri offers a dedicated web interface for each of the hosted scientific databases. Scientists all around the world run SQL queries which include specific astrophysical functions and get their desired data in reasonable time. Daiquiri supports the scientific projects by offering a number of administration tools such as database and user management, contact messages to the staff and support for organization of meetings and workshops. The webpages can be customized and the Wordpress integration supports the participating scientists in maintaining the documentation and the projects' news sections.

Computer-Aided Clinical Trial Recruitment Based on Domain-Specific Language Translation: A Case Study of Retinopathy of Prematurity.

PubMed

Zhang, Yinsheng; Zhang, Guoming; Shang, Qian

2017-01-01

Reusing the data from healthcare information systems can effectively facilitate clinical trials (CTs). How to select candidate patients eligible for CT recruitment criteria is a central task. Related work either depends on DBA (database administrator) to convert the recruitment criteria to native SQL queries or involves the data mapping between a standard ontology/information model and individual data source schema. This paper proposes an alternative computer-aided CT recruitment paradigm, based on syntax translation between different DSLs (domain-specific languages). In this paradigm, the CT recruitment criteria are first formally represented as production rules. The referenced rule variables are all from the underlying database schema. Then the production rule is translated to an intermediate query-oriented DSL (e.g., LINQ). Finally, the intermediate DSL is directly mapped to native database queries (e.g., SQL) automated by ORM (object-relational mapping).

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

Khalili, Farid; Danilishin, Stefan; Mueller-Ebhardt, Helge

We consider enhancing the sensitivity of future gravitational-wave detectors by using double optical spring. When the power, detuning and bandwidth of the two carriers are chosen appropriately, the effect of the double optical spring can be described as a 'negative inertia', which cancels the positive inertia of the test masses and thus increases their response to gravitational waves. This allows us to surpass the free-mass standard quantum limit (SQL) over a broad frequency band, through signal amplification, rather than noise cancellation, which has been the case for all broadband SQL-beating schemes so far considered for gravitational-wave detectors. The merit ofmore » such signal amplification schemes lies in the fact that they are less susceptible to optical losses than noise-cancellation schemes. We show that it is feasible to demonstrate such an effect with the Gingin High Optical Power Test Facility, and it can eventually be implemented in future advanced GW detectors.« less

Practical input optimization for aircraft parameter estimation experiments. Ph.D. Thesis, 1990

NASA Technical Reports Server (NTRS)

Morelli, Eugene A.

1993-01-01

The object of this research was to develop an algorithm for the design of practical, optimal flight test inputs for aircraft parameter estimation experiments. A general, single pass technique was developed which allows global optimization of the flight test input design for parameter estimation using the principles of dynamic programming with the input forms limited to square waves only. Provision was made for practical constraints on the input, including amplitude constraints, control system dynamics, and selected input frequency range exclusions. In addition, the input design was accomplished while imposing output amplitude constraints required by model validity and considerations of safety during the flight test. The algorithm has multiple input design capability, with optional inclusion of a constraint that only one control move at a time, so that a human pilot can implement the inputs. It is shown that the technique can be used to design experiments for estimation of open loop model parameters from closed loop flight test data. The report includes a new formulation of the optimal input design problem, a description of a new approach to the solution, and a summary of the characteristics of the algorithm, followed by three example applications of the new technique which demonstrate the quality and expanded capabilities of the input designs produced by the new technique. In all cases, the new input design approach showed significant improvement over previous input design methods in terms of achievable parameter accuracies.

Global sensitivity analysis for fuzzy inputs based on the decomposition of fuzzy output entropy

NASA Astrophysics Data System (ADS)

Shi, Yan; Lu, Zhenzhou; Zhou, Yicheng

2018-06-01

To analyse the component of fuzzy output entropy, a decomposition method of fuzzy output entropy is first presented. After the decomposition of fuzzy output entropy, the total fuzzy output entropy can be expressed as the sum of the component fuzzy entropy contributed by fuzzy inputs. Based on the decomposition of fuzzy output entropy, a new global sensitivity analysis model is established for measuring the effects of uncertainties of fuzzy inputs on the output. The global sensitivity analysis model can not only tell the importance of fuzzy inputs but also simultaneously reflect the structural composition of the response function to a certain degree. Several examples illustrate the validity of the proposed global sensitivity analysis, which is a significant reference in engineering design and optimization of structural systems.

VSDMIP: virtual screening data management on an integrated platform

NASA Astrophysics Data System (ADS)

Gil-Redondo, Rubén; Estrada, Jorge; Morreale, Antonio; Herranz, Fernando; Sancho, Javier; Ortiz, Ángel R.

2009-03-01

A novel software (VSDMIP) for the virtual screening (VS) of chemical libraries integrated within a MySQL relational database is presented. Two main features make VSDMIP clearly distinguishable from other existing computational tools: (i) its database, which stores not only ligand information but also the results from every step in the VS process, and (ii) its modular and pluggable architecture, which allows customization of the VS stages (such as the programs used for conformer generation or docking), through the definition of a detailed workflow employing user-configurable XML files. VSDMIP, therefore, facilitates the storage and retrieval of VS results, easily adapts to the specific requirements of each method and tool used in the experiments, and allows the comparison of different VS methodologies. To validate the usefulness of VSDMIP as an automated tool for carrying out VS several experiments were run on six protein targets (acetylcholinesterase, cyclin-dependent kinase 2, coagulation factor Xa, estrogen receptor alpha, p38 MAP kinase, and neuraminidase) using nine binary (actives/inactive) test sets. The performance of several VS configurations was evaluated by means of enrichment factors and receiver operating characteristic plots.

Provenance for Runtime Workflow Steering and Validation in Computational Seismology

NASA Astrophysics Data System (ADS)

Spinuso, A.; Krischer, L.; Krause, A.; Filgueira, R.; Magnoni, F.; Muraleedharan, V.; David, M.

2014-12-01

Provenance systems may be offered by modern workflow engines to collect metadata about the data transformations at runtime. If combined with effective visualisation and monitoring interfaces, these provenance recordings can speed up the validation process of an experiment, suggesting interactive or automated interventions with immediate effects on the lifecycle of a workflow run. For instance, in the field of computational seismology, if we consider research applications performing long lasting cross correlation analysis and high resolution simulations, the immediate notification of logical errors and the rapid access to intermediate results, can produce reactions which foster a more efficient progress of the research. These applications are often executed in secured and sophisticated HPC and HTC infrastructures, highlighting the need for a comprehensive framework that facilitates the extraction of fine grained provenance and the development of provenance aware components, leveraging the scalability characteristics of the adopted workflow engines, whose enactment can be mapped to different technologies (MPI, Storm clusters, etc). This work looks at the adoption of W3C-PROV concepts and data model within a user driven processing and validation framework for seismic data, supporting also computational and data management steering. Validation needs to balance automation with user intervention, considering the scientist as part of the archiving process. Therefore, the provenance data is enriched with community-specific metadata vocabularies and control messages, making an experiment reproducible and its description consistent with the community understandings. Moreover, it can contain user defined terms and annotations. The current implementation of the system is supported by the EU-Funded VERCE (http://verce.eu). It provides, as well as the provenance generation mechanisms, a prototypal browser-based user interface and a web API built on top of a NoSQL storage technology, experimenting ways to ensure a rapid and flexible access to the lineage traces. It supports the users with the visualisation of graphical products and offers combined operations to access and download the data which may be selectively stored at runtime, into dedicated data archives.

Shape Optimization by Bayesian-Validated Computer-Simulation Surrogates

NASA Technical Reports Server (NTRS)

Patera, Anthony T.

1997-01-01

A nonparametric-validated, surrogate approach to optimization has been applied to the computational optimization of eddy-promoter heat exchangers and to the experimental optimization of a multielement airfoil. In addition to the baseline surrogate framework, a surrogate-Pareto framework has been applied to the two-criteria, eddy-promoter design problem. The Pareto analysis improves the predictability of the surrogate results, preserves generality, and provides a means to rapidly determine design trade-offs. Significant contributions have been made in the geometric description used for the eddy-promoter inclusions as well as to the surrogate framework itself. A level-set based, geometric description has been developed to define the shape of the eddy-promoter inclusions. The level-set technique allows for topology changes (from single-body,eddy-promoter configurations to two-body configurations) without requiring any additional logic. The continuity of the output responses for input variations that cross the boundary between topologies has been demonstrated. Input-output continuity is required for the straightforward application of surrogate techniques in which simplified, interpolative models are fitted through a construction set of data. The surrogate framework developed previously has been extended in a number of ways. First, the formulation for a general, two-output, two-performance metric problem is presented. Surrogates are constructed and validated for the outputs. The performance metrics can be functions of both outputs, as well as explicitly of the inputs, and serve to characterize the design preferences. By segregating the outputs and the performance metrics, an additional level of flexibility is provided to the designer. The validated outputs can be used in future design studies and the error estimates provided by the output validation step still apply, and require no additional appeals to the expensive analysis. Second, a candidate-based a posteriori error analysis capability has been developed which provides probabilistic error estimates on the true performance for a design randomly selected near the surrogate-predicted optimal design.

Visualization of Vgi Data Through the New NASA Web World Wind Virtual Globe

NASA Astrophysics Data System (ADS)

Brovelli, M. A.; Kilsedar, C. E.; Zamboni, G.

2016-06-01

GeoWeb 2.0, laying the foundations of Volunteered Geographic Information (VGI) systems, has led to platforms where users can contribute to the geographic knowledge that is open to access. Moreover, as a result of the advancements in 3D visualization, virtual globes able to visualize geographic data even on browsers emerged. However the integration of VGI systems and virtual globes has not been fully realized. The study presented aims to visualize volunteered data in 3D, considering also the ease of use aspects for general public, using Free and Open Source Software (FOSS). The new Application Programming Interface (API) of NASA, Web World Wind, written in JavaScript and based on Web Graphics Library (WebGL) is cross-platform and cross-browser, so that the virtual globe created using this API can be accessible through any WebGL supported browser on different operating systems and devices, as a result not requiring any installation or configuration on the client-side, making the collected data more usable to users, which is not the case with the World Wind for Java as installation and configuration of the Java Virtual Machine (JVM) is required. Furthermore, the data collected through various VGI platforms might be in different formats, stored in a traditional relational database or in a NoSQL database. The project developed aims to visualize and query data collected through Open Data Kit (ODK) platform and a cross-platform application, where data is stored in a relational PostgreSQL and NoSQL CouchDB databases respectively.

Two interpenetrating Cu{sup II}/Ni{sup II}-coordinated polymers based on an unsymmetrical bifunctional N/O-tectonic: Syntheses, structures and magnetic properties

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

Liu, Yong-Liang; Department of Chemistry and Chemical Engineering, Shaanxi Key Laboratory of Comprehensive Utilization of Tailings Resources, Shang Luo University, Shang Luo 726000; Wu, Ya-Pan

2015-03-15

Two new interpenetrating Cu{sup II}/Ni{sup II} coordination polymers, based on a unsymmetrical bifunctional N/O-tectonic 3-(pyrid-4′-yl)-5-(4″-carbonylphenyl)-1,2,4-triazolyl (H{sub 2}pycz), ([Cu-(Hpycz){sub 2}]·2H{sub 2}O){sub n} (1) and ([Ni(Hpycz){sub 2}]·H{sub 2}O){sub n} (2), have been solvothermally synthesized and structure characterization. Single crystal X-ray analysis indicates that compound 1 shows 2-fold parallel interpenetrated 4{sup 4}-sql layers with the same handedness. The overall structure of 1 is achiral—in each layer of doubly interpenetrating nets, the two individual nets have the opposite handedness to the corresponding nets in the adjoining layers—while 2 features a rare 8-fold interpenetrating 6{sup 6}-dia network that belongs to class IIIa interpenetration. In addition,more » compounds 1 and 2 both show similar paramagnetic characteristic properties. - Graphical abstract: Two new Cu(II)/Ni(II) coordination polymers present 2D parallel 2-fold interpenetrated 4{sup 4}-sql layers and a rare 3D 8-fold interpenetrating 6{sup 6}-dia network. In addition, magnetic susceptibility measurements show similar paramagnetic characteristic for two complexes. - Highlights: • A new unsymmetrical bifunctional N/O-tectonic as 4-connected spacer. • A 2-fold parallel interpenetrated sql layer with the same handedness. • A rare 8-fold interpenetrating dia network (class IIIa)« less

Can Simulation Credibility Be Improved Using Sensitivity Analysis to Understand Input Data Effects on Model Outcome?

NASA Technical Reports Server (NTRS)

Myers, Jerry G.; Young, M.; Goodenow, Debra A.; Keenan, A.; Walton, M.; Boley, L.

2015-01-01

Model and simulation (MS) credibility is defined as, the quality to elicit belief or trust in MS results. NASA-STD-7009 [1] delineates eight components (Verification, Validation, Input Pedigree, Results Uncertainty, Results Robustness, Use History, MS Management, People Qualifications) that address quantifying model credibility, and provides guidance to the model developers, analysts, and end users for assessing the MS credibility. Of the eight characteristics, input pedigree, or the quality of the data used to develop model input parameters, governing functions, or initial conditions, can vary significantly. These data quality differences have varying consequences across the range of MS application. NASA-STD-7009 requires that the lowest input data quality be used to represent the entire set of input data when scoring the input pedigree credibility of the model. This requirement provides a conservative assessment of model inputs, and maximizes the communication of the potential level of risk of using model outputs. Unfortunately, in practice, this may result in overly pessimistic communication of the MS output, undermining the credibility of simulation predictions to decision makers. This presentation proposes an alternative assessment mechanism, utilizing results parameter robustness, also known as model input sensitivity, to improve the credibility scoring process for specific simulations.

Data Association Algorithms for Tracking Satellites

DTIC Science & Technology

2013-03-27

validation of the new tools. The description provided here includes the mathematical back ground and description of the models implemented, as well as a...simulation development. This work includes the addition of higher-fidelity models in CU-TurboProp and validation of the new tools. The description...ode45(), used in Ananke, and (3) provide the necessary inputs to the bidirectional reflectance distribution function ( BRDF ) model provided by Pacific

Sample selection via angular distance in the space of the arguments of an artificial neural network

NASA Astrophysics Data System (ADS)

Fernández Jaramillo, J. M.; Mayerle, R.

2018-05-01

In the construction of an artificial neural network (ANN) a proper data splitting of the available samples plays a major role in the training process. This selection of subsets for training, testing and validation affects the generalization ability of the neural network. Also the number of samples has an impact in the time required for the design of the ANN and the training. This paper introduces an efficient and simple method for reducing the set of samples used for training a neural network. The method reduces the required time to calculate the network coefficients, while keeping the diversity and avoiding overtraining the ANN due the presence of similar samples. The proposed method is based on the calculation of the angle between two vectors, each one representing one input of the neural network. When the angle formed among samples is smaller than a defined threshold only one input is accepted for the training. The accepted inputs are scattered throughout the sample space. Tidal records are used to demonstrate the proposed method. The results of a cross-validation show that with few inputs the quality of the outputs is not accurate and depends on the selection of the first sample, but as the number of inputs increases the accuracy is improved and differences among the scenarios with a different starting sample have and important reduction. A comparison with the K-means clustering algorithm shows that for this application the proposed method with a smaller number of samples is producing a more accurate network.

Vulnerabilities in Bytecode Removed by Analysis, Nuanced Confinement and Diversification (VIBRANCE)

DTIC Science & Technology

2015-06-01

VIBRANCE tool starts with a vulnerable Java application and automatically hardens it against SQL injection, OS command injection, file path traversal...7 2.2 Java Front End...7 2.2.2 Java Byte Code Parser

Transition metal coordination polymers based on tetrabromoterephthalic and bis(imidazole) ligands: Syntheses, structures, topological analysis and photoluminescence properties

NASA Astrophysics Data System (ADS)

Zhang, Xiaowei; Xing, Peiqi; Geng, Xiujuan; Sun, Daofeng; Xiao, Zhenyu; Wang, Lei

2015-09-01

Eight new coordination polymers (CPs), namely, [Zn(1,2-mbix)(tbtpa)]n (1), [Co(1,2-mbix)(tbtpa)]n (2), [CdCl(1,2-mbix)(tbtpa)0.5]n (3), {[Cd(1,2-bix)(tbtpa)]·H2O}n (4), {[Cd0.5(1,2-bix)(tbtpa)0.5]·H2O}n (5), {[Co0.5(1,2-bix)(tbtpa)0.5]·2H2O}n (6), {[Co(1,2-bix)(tbtpa)]·H2O}n (7) and {[Co(1,2-bix)(tbtpa)]·Diox·2H2O}n (8), were synthesized under solvothermal conditions based on mix-ligand strategy (H2tbtpa=tetrabromoterephthalic acid and 1,2-mbix=1,2-bis((2-methyl-1H-imidazol-1-yl)methyl)benzene, 1,2-bix=1,2-bis(imidazol-1-ylmethyl)benzene). All of the CPs have been structurally characterized by single-crystal X-ray diffraction analyses and further characterized by elemental analyses, IR spectroscopy, powder X-ray diffraction (PXRD), and thermogravimetric analyses (TGA). X-ray diffraction analyses show that 1 and 2 are isotypics which have 2D highly undulated networks with (4,4)-sql topology with the existence of C-H ⋯Br interactions; for 3, it has a 2D planar network with (4,4)-sql topology with the occurrence of C-H ⋯Cl interactions other than C-H ⋯Br interactions; 4 shows a 3D 2-fold interpenetrated nets with rare 65·8-mok topology which has a self-catention property. As the same case as 1 and 2, 5 and 6 are also isostructural with planar layers with 44-sql topology which further assembled into 3D supramolecular structure through the interdigitated stacking fashion and the C-Br ⋯Cph interactions. As for 7, it has a 2D slightly undulated networks with (4,4)-sql topology which has one dimension channel. While 8 has a 2-fold interpenetrated networks with (3,4)-connect jeb topology with point symbol {63}{65·8}. And their structures can be tuned by conformations of bis(imidazol) ligands and solvent mixture. Besides, the TGA properties for all compounds and the luminescent properties for 1, 3, 4, 5 are discussed in detail.

Enhancing SAMOS Data Access in DOMS via a Neo4j Property Graph Database.

NASA Astrophysics Data System (ADS)

Stallard, A. P.; Smith, S. R.; Elya, J. L.

2016-12-01

The Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative provides routine access to high-quality marine meteorological and near-surface oceanographic observations from research vessels. The Distributed Oceanographic Match-Up Service (DOMS) under development is a centralized service that allows researchers to easily match in situ and satellite oceanographic data from distributed sources to facilitate satellite calibration, validation, and retrieval algorithm development. The service currently uses Apache Solr as a backend search engine on each node in the distributed network. While Solr is a high-performance solution that facilitates creation and maintenance of indexed data, it is limited in the sense that its schema is fixed. The property graph model escapes this limitation by creating relationships between data objects. The authors will present the development of the SAMOS Neo4j property graph database including new search possibilities that take advantage of the property graph model, performance comparisons with Apache Solr, and a vision for graph databases as a storage tool for oceanographic data. The integration of the SAMOS Neo4j graph into DOMS will also be described. Currently, Neo4j contains spatial and temporal records from SAMOS which are modeled into a time tree and r-tree using Graph Aware and Spatial plugin tools for Neo4j. These extensions provide callable Java procedures within CYPHER (Neo4j's query language) that generate in-graph structures. Once generated, these structures can be queried using procedures from these libraries, or directly via CYPHER statements. Neo4j excels at performing relationship and path-based queries, which challenge relational-SQL databases because they require memory intensive joins due to the limitation of their design. Consider a user who wants to find records over several years, but only for specific months. If a traditional database only stores timestamps, this type of query would be complex and likely prohibitively slow. Using the time tree model, one can specify a path from the root to the data which restricts resolutions to certain timeframes (e.g., months). This query can be executed without joins, unions, or other compute-intensive operations, putting Neo4j at a computational advantage to the SQL database alternative.

DRUMS: Disk Repository with Update Management and Select option for high throughput sequencing data

PubMed Central

2014-01-01

Background New technologies for analyzing biological samples, like next generation sequencing, are producing a growing amount of data together with quality scores. Moreover, software tools (e.g., for mapping sequence reads), calculating transcription factor binding probabilities, estimating epigenetic modification enriched regions or determining single nucleotide polymorphism increase this amount of position-specific DNA-related data even further. Hence, requesting data becomes challenging and expensive and is often implemented using specialised hardware. In addition, picking specific data as fast as possible becomes increasingly important in many fields of science. The general problem of handling big data sets was addressed by developing specialized databases like HBase, HyperTable or Cassandra. However, these database solutions require also specialized or distributed hardware leading to expensive investments. To the best of our knowledge, there is no database capable of (i) storing billions of position-specific DNA-related records, (ii) performing fast and resource saving requests, and (iii) running on a single standard computer hardware. Results Here, we present DRUMS (Disk Repository with Update Management and Select option), satisfying demands (i)-(iii). It tackles the weaknesses of traditional databases while handling position-specific DNA-related data in an efficient manner. DRUMS is capable of storing up to billions of records. Moreover, it focuses on optimizing relating single lookups as range request, which are needed permanently for computations in bioinformatics. To validate the power of DRUMS, we compare it to the widely used MySQL database. The test setting considers two biological data sets. We use standard desktop hardware as test environment. Conclusions DRUMS outperforms MySQL in writing and reading records by a factor of two up to a factor of 10000. Furthermore, it can work with significantly larger data sets. Our work focuses on mid-sized data sets up to several billion records without requiring cluster technology. Storing position-specific data is a general problem and the concept we present here is a generalized approach. Hence, it can be easily applied to other fields of bioinformatics. PMID:24495746

A new interpretation and validation of variance based importance measures for models with correlated inputs

NASA Astrophysics Data System (ADS)

Hao, Wenrui; Lu, Zhenzhou; Li, Luyi

2013-05-01

In order to explore the contributions by correlated input variables to the variance of the output, a novel interpretation framework of importance measure indices is proposed for a model with correlated inputs, which includes the indices of the total correlated contribution and the total uncorrelated contribution. The proposed indices accurately describe the connotations of the contributions by the correlated input to the variance of output, and they can be viewed as the complement and correction of the interpretation about the contributions by the correlated inputs presented in "Estimation of global sensitivity indices for models with dependent variables, Computer Physics Communications, 183 (2012) 937-946". Both of them contain the independent contribution by an individual input. Taking the general form of quadratic polynomial as an illustration, the total correlated contribution and the independent contribution by an individual input are derived analytically, from which the components and their origins of both contributions of correlated input can be clarified without any ambiguity. In the special case that no square term is included in the quadratic polynomial model, the total correlated contribution by the input can be further decomposed into the variance contribution related to the correlation of the input with other inputs and the independent contribution by the input itself, and the total uncorrelated contribution can be further decomposed into the independent part by interaction between the input and others and the independent part by the input itself. Numerical examples are employed and their results demonstrate that the derived analytical expressions of the variance-based importance measure are correct, and the clarification of the correlated input contribution to model output by the analytical derivation is very important for expanding the theory and solutions of uncorrelated input to those of the correlated one.

Modeling and validation of autoinducer-mediated bacterial gene expression in microfluidic environments

PubMed Central

Austin, Caitlin M.; Stoy, William; Su, Peter; Harber, Marie C.; Bardill, J. Patrick; Hammer, Brian K.; Forest, Craig R.

2014-01-01

Biosensors exploiting communication within genetically engineered bacteria are becoming increasingly important for monitoring environmental changes. Currently, there are a variety of mathematical models for understanding and predicting how genetically engineered bacteria respond to molecular stimuli in these environments, but as sensors have miniaturized towards microfluidics and are subjected to complex time-varying inputs, the shortcomings of these models have become apparent. The effects of microfluidic environments such as low oxygen concentration, increased biofilm encapsulation, diffusion limited molecular distribution, and higher population densities strongly affect rate constants for gene expression not accounted for in previous models. We report a mathematical model that accurately predicts the biological response of the autoinducer N-acyl homoserine lactone-mediated green fluorescent protein expression in reporter bacteria in microfluidic environments by accommodating these rate constants. This generalized mass action model considers a chain of biomolecular events from input autoinducer chemical to fluorescent protein expression through a series of six chemical species. We have validated this model against experimental data from our own apparatus as well as prior published experimental results. Results indicate accurate prediction of dynamics (e.g., 14% peak time error from a pulse input) and with reduced mean-squared error with pulse or step inputs for a range of concentrations (10 μM–30 μM). This model can help advance the design of genetically engineered bacteria sensors and molecular communication devices. PMID:25379076

Dynamic causal modelling of brain-behaviour relationships.

PubMed

Rigoux, L; Daunizeau, J

2015-08-15

In this work, we expose a mathematical treatment of brain-behaviour relationships, which we coin behavioural Dynamic Causal Modelling or bDCM. This approach aims at decomposing the brain's transformation of stimuli into behavioural outcomes, in terms of the relative contribution of brain regions and their connections. In brief, bDCM places the brain at the interplay between stimulus and behaviour: behavioural outcomes arise from coordinated activity in (hidden) neural networks, whose dynamics are driven by experimental inputs. Estimating neural parameters that control network connectivity and plasticity effectively performs a neurobiologically-constrained approximation to the brain's input-outcome transform. In other words, neuroimaging data essentially serves to enforce the realism of bDCM's decomposition of input-output relationships. In addition, post-hoc artificial lesions analyses allow us to predict induced behavioural deficits and quantify the importance of network features for funnelling input-output relationships. This is important, because this enables one to bridge the gap with neuropsychological studies of brain-damaged patients. We demonstrate the face validity of the approach using Monte-Carlo simulations, and its predictive validity using empirical fMRI/behavioural data from an inhibitory control task. Lastly, we discuss promising applications of this work, including the assessment of functional degeneracy (in the healthy brain) and the prediction of functional recovery after lesions (in neurological patients). Copyright © 2015 Elsevier Inc. All rights reserved.

Estimating pesticide runoff in small streams.

PubMed

Schriever, Carola A; von der Ohe, Peter C; Liess, Matthias

2007-08-01

Surface runoff is one of the most important pathways for pesticides to enter surface waters. Mathematical models are employed to characterize its spatio-temporal variability within landscapes, but they must be simple owing to the limited availability and low resolution of data at this scale. This study aimed to validate a simplified spatially-explicit model that is developed for the regional scale to calculate the runoff potential (RP). The RP is a generic indicator of the magnitude of pesticide inputs into streams via runoff. The underlying runoff model considers key environmental factors affecting runoff (precipitation, topography, land use, and soil characteristics), but predicts losses of a generic substance instead of any one pesticide. We predicted and evaluated RP for 20 small streams. RP input data were extracted from governmental databases. Pesticide measurements from a triennial study were used for validation. Measured pesticide concentrations were standardized by the applied mass per catchment and the water solubility of the relevant compounds. The maximum standardized concentration per site and year (runoff loss, R(Loss)) provided a generalized measure of observed pesticide inputs into the streams. Average RP explained 75% (p<0.001) of the variance in R(Loss). Our results imply that the generic indicator can give an adequate estimate of runoff inputs into small streams, wherever data of similar resolution are available. Therefore, we suggest RP for a first quick and cost-effective location of potential runoff hot spots at the landscape level.

47 CFR 11.33 - EAS Decoder.

Code of Federal Regulations, 2011 CFR

2011-10-01

... time periods expire. (4) Display and logging. A visual message shall be developed from any valid header... input. (8) Decoder Programming. Access to decoder programming shall be protected by a lock or other...

Time series modeling of human operator dynamics in manual control tasks

NASA Technical Reports Server (NTRS)

Biezad, D. J.; Schmidt, D. K.

1984-01-01

A time-series technique is presented for identifying the dynamic characteristics of the human operator in manual control tasks from relatively short records of experimental data. Control of system excitation signals used in the identification is not required. The approach is a multi-channel identification technique for modeling multi-input/multi-output situations. The method presented includes statistical tests for validity, is designed for digital computation, and yields estimates for the frequency responses of the human operator. A comprehensive relative power analysis may also be performed for validated models. This method is applied to several sets of experimental data; the results are discussed and shown to compare favorably with previous research findings. New results are also presented for a multi-input task that has not been previously modeled to demonstrate the strengths of the method.

Time Series Modeling of Human Operator Dynamics in Manual Control Tasks

NASA Technical Reports Server (NTRS)

Biezad, D. J.; Schmidt, D. K.

1984-01-01

A time-series technique is presented for identifying the dynamic characteristics of the human operator in manual control tasks from relatively short records of experimental data. Control of system excitation signals used in the identification is not required. The approach is a multi-channel identification technique for modeling multi-input/multi-output situations. The method presented includes statistical tests for validity, is designed for digital computation, and yields estimates for the frequency response of the human operator. A comprehensive relative power analysis may also be performed for validated models. This method is applied to several sets of experimental data; the results are discussed and shown to compare favorably with previous research findings. New results are also presented for a multi-input task that was previously modeled to demonstrate the strengths of the method.

Statistical validation and an empirical model of hydrogen production enhancement found by utilizing passive flow disturbance in the steam-reformation process

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

Erickson, Paul A.; Liao, Chang-hsien

2007-11-15

A passive flow disturbance has been proven to enhance the conversion of fuel in a methanol-steam reformer. This study presents a statistical validation of the experiment based on a standard 2{sup k} factorial experiment design and the resulting empirical model of the enhanced hydrogen producing process. A factorial experiment design was used to statistically analyze the effects and interactions of various input factors in the experiment. Three input factors, including the number of flow disturbers, catalyst size, and reactant flow rate were investigated for their effects on the fuel conversion in the steam-reformation process. Based on the experimental results, anmore » empirical model was developed and further evaluated with an uncertainty analysis and interior point data. (author)« less

VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets.

PubMed

Qureshi, Abid; Thakur, Nishant; Monga, Isha; Thakur, Anamika; Kumar, Manoj

2014-01-01

Viral microRNAs (miRNAs) regulate gene expression of viral and/or host genes to benefit the virus. Hence, miRNAs play a key role in host-virus interactions and pathogenesis of viral diseases. Lately, miRNAs have also shown potential as important targets for the development of novel antiviral therapeutics. Although several miRNA and their target repositories are available for human and other organisms in literature, but a dedicated resource on viral miRNAs and their targets are lacking. Therefore, we have developed a comprehensive viral miRNA resource harboring information of 9133 entries in three subdatabases. This includes 1308 experimentally validated miRNA sequences with their isomiRs encoded by 44 viruses in viral miRNA ' VIRMIRNA: ' and 7283 of their target genes in ' VIRMIRTAR': . Additionally, there is information of 542 antiviral miRNAs encoded by the host against 24 viruses in antiviral miRNA ' AVIRMIR': . The web interface was developed using Linux-Apache-MySQL-PHP (LAMP) software bundle. User-friendly browse, search, advanced search and useful analysis tools are also provided on the web interface. VIRmiRNA is the first specialized resource of experimentally proven virus-encoded miRNAs and their associated targets. This database would enhance the understanding of viral/host gene regulation and may also prove beneficial in the development of antiviral therapeutics. Database URL: http://crdd.osdd.net/servers/virmirna. © The Author(s) 2014. Published by Oxford University Press.

Flight Test of Orthogonal Square Wave Inputs for Hybrid-Wing-Body Parameter Estimation

NASA Technical Reports Server (NTRS)

Taylor, Brian R.; Ratnayake, Nalin A.

2011-01-01

As part of an effort to improve emissions, noise, and performance of next generation aircraft, it is expected that future aircraft will use distributed, multi-objective control effectors in a closed-loop flight control system. Correlation challenges associated with parameter estimation will arise with this expected aircraft configuration. The research presented in this paper focuses on addressing the correlation problem with an appropriate input design technique in order to determine individual control surface effectiveness. This technique was validated through flight-testing an 8.5-percent-scale hybrid-wing-body aircraft demonstrator at the NASA Dryden Flight Research Center (Edwards, California). An input design technique that uses mutually orthogonal square wave inputs for de-correlation of control surfaces is proposed. Flight-test results are compared with prior flight-test results for a different maneuver style.

Impact of Cross-Axis Structural Dynamics on Validation of Linear Models for Space Launch System

NASA Technical Reports Server (NTRS)

Pei, Jing; Derry, Stephen D.; Zhou Zhiqiang; Newsom, Jerry R.

2014-01-01

A feasibility study was performed to examine the advisability of incorporating a set of Programmed Test Inputs (PTIs) during the Space Launch System (SLS) vehicle flight. The intent of these inputs is to provide validation to the preflight models for control system stability margins, aerodynamics, and structural dynamics. During October 2009, Ares I-X program was successful in carrying out a series of PTI maneuvers which provided a significant amount of valuable data for post-flight analysis. The resulting data comparisons showed excellent agreement with the preflight linear models across the frequency spectrum of interest. However unlike Ares I-X, the structural dynamics associated with the SLS boost phase configuration are far more complex and highly coupled in all three axes. This presents a challenge when implementing this similar system identification technique to SLS. Preliminary simulation results show noticeable mismatches between PTI validation and analytical linear models in the frequency range of the structural dynamics. An alternate approach was examined which demonstrates the potential for better overall characterization of the system frequency response as well as robustness of the control design.

Field measurement of moisture-buffering model inputs for residential buildings

DOE PAGES

Woods, Jason; Winkler, Jon

2016-02-05

Moisture adsorption and desorption in building materials impact indoor humidity. This effect should be included in building-energy simulations, particularly when humidity is being investigated or controlled. Several models can calculate this moisture-buffering effect, but accurate ones require model inputs that are not always known to the user of the building-energy simulation. This research developed an empirical method to extract whole-house model inputs for the effective moisture penetration depth (EMPD) model. The experimental approach was to subject the materials in the house to a square-wave relative-humidity profile, measure all of the moisture-transfer terms (e.g., infiltration, air-conditioner condensate), and calculate the onlymore » unmeasured term—the moisture sorption into the materials. We validated this method with laboratory measurements, which we used to measure the EMPD model inputs of two houses. After deriving these inputs, we measured the humidity of the same houses during tests with realistic latent and sensible loads and demonstrated the accuracy of this approach. Furthermore, these results show that the EMPD model, when given reasonable inputs, is an accurate moisture-buffering model.« less

Input-output mapping reconstruction of spike trains at dorsal horn evoked by manual acupuncture

NASA Astrophysics Data System (ADS)

Wei, Xile; Shi, Dingtian; Yu, Haitao; Deng, Bin; Lu, Meili; Han, Chunxiao; Wang, Jiang

2016-12-01

In this study, a generalized linear model (GLM) is used to reconstruct mapping from acupuncture stimulation to spike trains driven by action potential data. The electrical signals are recorded in spinal dorsal horn after manual acupuncture (MA) manipulations with different frequencies being taken at the “Zusanli” point of experiment rats. Maximum-likelihood method is adopted to estimate the parameters of GLM and the quantified value of assumed model input. Through validating the accuracy of firings generated from the established GLM, it is found that the input-output mapping of spike trains evoked by acupuncture can be successfully reconstructed for different frequencies. Furthermore, via comparing the performance of several GLMs based on distinct inputs, it suggests that input with the form of half-sine with noise can well describe the generator potential induced by acupuncture mechanical action. Particularly, the comparison of reproducing the experiment spikes for five selected inputs is in accordance with the phenomenon found in Hudgkin-Huxley (H-H) model simulation, which indicates the mapping from half-sine with noise input to experiment spikes meets the real encoding scheme to some extent. These studies provide us a new insight into coding processes and information transfer of acupuncture.

VERAIn

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

Simunovic, Srdjan

2015-02-16

CASL's modeling and simulation technology, the Virtual Environment for Reactor Applications (VERA), incorporates coupled physics and science-based models, state-of-the-art numerical methods, modern computational science, integrated uncertainty quantification (UQ) and validation against data from operating pressurized water reactors (PWRs), single-effect experiments, and integral tests. The computational simulation component of VERA is the VERA Core Simulator (VERA-CS). The core simulator is the specific collection of multi-physics computer codes used to model and deplete a LWR core over multiple cycles. The core simulator has a single common input file that drives all of the different physics codes. The parser code, VERAIn, converts VERAmore » Input into an XML file that is used as input to different VERA codes.« less

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

Chinthavali, Madhu Sudhan; Campbell, Steven L

This paper presents an analytical model for wireless power transfer system used in electric vehicle application. The equivalent circuit model for each major component of the system is described, including the input voltage source, resonant network, transformer, nonlinear diode rectifier load, etc. Based on the circuit model, the primary side compensation capacitance, equivalent input impedance, active / reactive power are calculated, which provides a guideline for parameter selection. Moreover, the voltage gain curve from dc output to dc input is derived as well. A hardware prototype with series-parallel resonant stage is built to verify the developed model. The experimental resultsmore » from the hardware are compared with the model predicted results to show the validity of the model.« less

Statistical inference, the bootstrap, and neural-network modeling with application to foreign exchange rates.

PubMed

White, H; Racine, J

2001-01-01

We propose tests for individual and joint irrelevance of network inputs. Such tests can be used to determine whether an input or group of inputs "belong" in a particular model, thus permitting valid statistical inference based on estimated feedforward neural-network models. The approaches employ well-known statistical resampling techniques. We conduct a small Monte Carlo experiment showing that our tests have reasonable level and power behavior, and we apply our methods to examine whether there are predictable regularities in foreign exchange rates. We find that exchange rates do appear to contain information that is exploitable for enhanced point prediction, but the nature of the predictive relations evolves through time.

Development of Finer Spatial Resolution Optical Properties from MODIS

DTIC Science & Technology

2008-02-04

infrared (SWIR) channels at 1240 nm and 2130 run. The increased resolution spectral Rrs channels are input into bio-optical algorithms (Quasi...processes. Additionally, increased resolution is required for validation of ocean color products in coastal regions due to the shorter spatial scales of...with in situ Rrs data to determine the "best" method in coastal regimes. We demonstrate that finer resolution is required for validation of coastal

Testing-Based Compiler Validation for Synchronous Languages

NASA Technical Reports Server (NTRS)

Garoche, Pierre-Loic; Howar, Falk; Kahsai, Temesghen; Thirioux, Xavier

2014-01-01

In this paper we present a novel lightweight approach to validate compilers for synchronous languages. Instead of verifying a compiler for all input programs or providing a fixed suite of regression tests, we extend the compiler to generate a test-suite with high behavioral coverage and geared towards discovery of faults for every compiled artifact. We have implemented and evaluated our approach using a compiler from Lustre to C.

A Validation Metrics Framework for Safety-Critical Software-Intensive Systems

DTIC Science & Technology

2009-03-01

so does its definition, tools, and techniques, including means for measuring the validation activity, its outputs, and impact on development...independent of the SDLP. When considering the above SDLPs from the safety engineering team’s perspective, there are also large impacts on the way... impact . Interpretation of any actionable metric data will need to be undertaken in the context of the SDLP. 2. Safety Input The software safety

Catchment-scale Validation of a Physically-based, Post-fire Runoff and Erosion Model

NASA Astrophysics Data System (ADS)

Quinn, D.; Brooks, E. S.; Robichaud, P. R.; Dobre, M.; Brown, R. E.; Wagenbrenner, J.

2017-12-01

The cascading consequences of fire-induced ecological changes have profound impacts on both natural and managed forest ecosystems. Forest managers tasked with implementing post-fire mitigation strategies need robust tools to evaluate the effectiveness of their decisions, particularly those affecting hydrological recovery. Various hillslope-scale interfaces of the physically-based Water Erosion Prediction Project (WEPP) model have been successfully validated for this purpose using fire-effected plot experiments, however these interfaces are explicitly designed to simulate single hillslopes. Spatially-distributed, catchment-scale WEPP interfaces have been developed over the past decade, however none have been validated for post-fire simulations, posing a barrier to adoption for forest managers. In this validation study, we compare WEPP simulations with pre- and post-fire hydrological records for three forested catchments (W. Willow, N. Thomas, and S. Thomas) that burned in the 2011 Wallow Fire in Northeastern Arizona, USA. Simulations were conducted using two approaches; the first using automatically created inputs from an online, spatial, post-fire WEPP interface, and the second using manually created inputs which incorporate the spatial variability of fire effects observed in the field. Both approaches were compared to five years of observed post-fire sediment and flow data to assess goodness of fit.

A clinical reasoning model focused on clients' behaviour change with reference to physiotherapists: its multiphase development and validation.

PubMed

Elvén, Maria; Hochwälder, Jacek; Dean, Elizabeth; Söderlund, Anne

2015-05-01

A biopsychosocial approach and behaviour change strategies have long been proposed to serve as a basis for addressing current multifaceted health problems. This emphasis has implications for clinical reasoning of health professionals. This study's aim was to develop and validate a conceptual model to guide physiotherapists' clinical reasoning focused on clients' behaviour change. Phase 1 consisted of the exploration of existing research and the research team's experiences and knowledge. Phases 2a and 2b consisted of validation and refinement of the model based on input from physiotherapy students in two focus groups (n = 5 per group) and from experts in behavioural medicine (n = 9). Phase 1 generated theoretical and evidence bases for the first version of a model. Phases 2a and 2b established the validity and value of the model. The final model described clinical reasoning focused on clients' behaviour change as a cognitive, reflective, collaborative and iterative process with multiple interrelated levels that included input from the client and physiotherapist, a functional behavioural analysis of the activity-related target behaviour and the selection of strategies for behaviour change. This unique model, theory- and evidence-informed, has been developed to help physiotherapists to apply clinical reasoning systematically in the process of behaviour change with their clients.

Properties of Syntactic Foam for Simulation of Mechanical Insults.

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

Hubbard, Neal Benson; Haulenbeek, Kimberly K.; Spletzer, Matthew A.

Syntactic foam encapsulation protects sensitive components. The energy mitigated by the foam is calculated with numerical simulations. The properties of a syntactic foam consisting of a mixture of an epoxy-rubber adduct and glass microballoons are obtained from published literature and test results. The conditions and outcomes of the tests are discussed. The method for converting published properties and test results to input for finite element models is described. Simulations of the test conditions are performed to validate the inputs.

Automated validation of a computer operating system

NASA Technical Reports Server (NTRS)

Dervage, M. M.; Milberg, B. A.

1970-01-01

Programs apply selected input/output loads to complex computer operating system and measure performance of that system under such loads. Technique lends itself to checkout of computer software designed to monitor automated complex industrial systems.

49 CFR 1104.3 - Copies.

Code of Federal Regulations, 2011 CFR

2011-10-01

... Microsoft Open Database Connectivity (ODBC) standard. ODBC is a Windows technology that allows a database software package to import data from a database created using a different software package. We currently...-compatible format. All databases must be supported with adequate documentation on data attributes, SQL...

SAMSON Technology Demonstrator

DTIC Science & Technology

2014-06-01

requested. The SAMSON TD was testing with two different policy engines: 1. A custom XACML-based element matching engine using a MySQL database for...performed during the course of the event. Full information protection across the sphere of access management, information protection and auditing was in...

Business Demands for Web-Related Skills as Compared to Other Computer Skills.

ERIC Educational Resources Information Center

Groneman, Nancy

2000-01-01

Analysis of 23,704 want ads for computer-related jobs revealed that the most frequently mentioned skills were UNIX, SQL programming, and computer security. Curriculum implications were derived from the most desired and less frequently mentioned skills. (SK)

Scale-Independent Relational Query Processing

DTIC Science & Technology

2013-10-04

source options are also available, including Postgresql, MySQL , and SQLite. These mod- ern relational databases are generally very complex software systems...and Their Application to Data Stream Management. IGI Global, 2010. [68] George Reese. Database Programming with JDBC and Java , Second Edition. Ed. by

Methods, Knowledge Support, and Experimental Tools for Modeling

DTIC Science & Technology

2006-10-01

open source software entities: the PostgreSQL relational database management system (http://www.postgres.org), the Apache web server (http...past. The revision control system allows the program to capture disagreements, and allows users to explore the history of such disagreements by

Dem Local Accuracy Patterns in Land-Use/Land-Cover Classification

NASA Astrophysics Data System (ADS)

Katerji, Wassim; Farjas Abadia, Mercedes; Morillo Balsera, Maria del Carmen

2016-01-01

Global and nation-wide DEM do not preserve the same height accuracy throughout the area of study. Instead of assuming a single RMSE value for the whole area, this study proposes a vario-model that divides the area into sub-regions depending on the land-use / landcover (LULC) classification, and assigns a local accuracy per each zone, as these areas share similar terrain formation and roughness, and tend to have similar DEM accuracies. A pilot study over Lebanon using the SRTM and ASTER DEMs, combined with a set of 1,105 randomly distributed ground control points (GCPs) showed that even though the inputDEMs have different spatial and temporal resolution, and were collected using difierent techniques, their accuracy varied similarly when changing over difierent LULC classes. Furthermore, validating the generated vario-models proved that they provide a closer representation of the accuracy to the validating GCPs than the conventional RMSE, by 94% and 86% for the SRTMand ASTER respectively. Geostatistical analysis of the input and output datasets showed that the results have a normal distribution, which support the generalization of the proven hypothesis, making this finding applicable to other input datasets anywhere around the world.

Adaptive model reduction for continuous systems via recursive rational interpolation

NASA Technical Reports Server (NTRS)

Lilly, John H.

1994-01-01

A method for adaptive identification of reduced-order models for continuous stable SISO and MIMO plants is presented. The method recursively finds a model whose transfer function (matrix) matches that of the plant on a set of frequencies chosen by the designer. The algorithm utilizes the Moving Discrete Fourier Transform (MDFT) to continuously monitor the frequency-domain profile of the system input and output signals. The MDFT is an efficient method of monitoring discrete points in the frequency domain of an evolving function of time. The model parameters are estimated from MDFT data using standard recursive parameter estimation techniques. The algorithm has been shown in simulations to be quite robust to additive noise in the inputs and outputs. A significant advantage of the method is that it enables a type of on-line model validation. This is accomplished by simultaneously identifying a number of models and comparing each with the plant in the frequency domain. Simulations of the method applied to an 8th-order SISO plant and a 10-state 2-input 2-output plant are presented. An example of on-line model validation applied to the SISO plant is also presented.

Application of a rat hindlimb model: a prediction of force spaces reachable through stimulation of nerve fascicles.

PubMed

Johnson, Will L; Jindrich, Devin L; Zhong, Hui; Roy, Roland R; Edgerton, V Reggie

2011-12-01

A device to generate standing or locomotion through chronically placed electrodes has not been fully developed due in part to limitations of clinical experimentation and the high number of muscle activation inputs of the leg. We investigated the feasibility of functional electrical stimulation paradigms that minimize the input dimensions for controlling the limbs by stimulating at nerve fascicles, utilizing a model of the rat hindlimb, which combined previously collected morphological data with muscle physiological parameters presented herein. As validation of the model, we investigated the suitability of a lumped-parameter model for the prediction of muscle activation during dynamic tasks. Using the validated model, we found that the space of forces producible through activation of muscle groups sharing common nerve fascicles was nonlinearly dependent on the number of discrete muscle groups that could be individually activated (equivalently, the neuroanatomical level of activation). Seven commonly innervated muscle groups were sufficient to produce 78% of the force space producible through individual activation of the 42 modeled hindlimb muscles. This novel, neuroanatomically derived reduction in input dimension emphasizes the potential to simplify controllers for functional electrical stimulation to improve functional recovery after a neuromuscular injury.

Application of a Rat Hindlimb Model: A Prediction of Force Spaces Reachable Through Stimulation of Nerve Fascicles

PubMed Central

Johnson, Will L.; Jindrich, Devin L.; Zhong, Hui; Roy, Roland R.

2011-01-01

A device to generate standing or locomotion through chronically placed electrodes has not been fully developed due in part to limitations of clinical experimentation and the high number of muscle activation inputs of the leg. We investigated the feasibility of functional electrical stimulation paradigms that minimize the input dimensions for controlling the limbs by stimulating at nerve fascicles, utilizing a model of the rat hindlimb which combined previously collected morphological data with muscle physiological parameters presented herein. As validation of the model we investigated the suitability of a lumped-parameter model for prediction of muscle activation during dynamic tasks. Using the validated model we found that the space of forces producible through activation of muscle groups sharing common nerve fascicles was nonlinearly dependent on the number of discrete muscle groups that could be individually activated (equivalently, the neuroanatomical level of activation). Seven commonly innervated muscle groups were sufficient to produce 78% of the force space producible through individual activation of the 42 modeled hindlimb muscles. This novel, neuroanatomically derived reduction in input dimension emphasizes the potential to simplify controllers for functional electrical stimulation to improve functional recovery after a neuromuscular injury. PMID:21244999

Validation analysis of probabilistic models of dietary exposure to food additives.

PubMed

Gilsenan, M B; Thompson, R L; Lambe, J; Gibney, M J

2003-10-01

The validity of a range of simple conceptual models designed specifically for the estimation of food additive intakes using probabilistic analysis was assessed. Modelled intake estimates that fell below traditional conservative point estimates of intake and above 'true' additive intakes (calculated from a reference database at brand level) were considered to be in a valid region. Models were developed for 10 food additives by combining food intake data, the probability of an additive being present in a food group and additive concentration data. Food intake and additive concentration data were entered as raw data or as a lognormal distribution, and the probability of an additive being present was entered based on the per cent brands or the per cent eating occasions within a food group that contained an additive. Since the three model components assumed two possible modes of input, the validity of eight (2(3)) model combinations was assessed. All model inputs were derived from the reference database. An iterative approach was employed in which the validity of individual model components was assessed first, followed by validation of full conceptual models. While the distribution of intake estimates from models fell below conservative intakes, which assume that the additive is present at maximum permitted levels (MPLs) in all foods in which it is permitted, intake estimates were not consistently above 'true' intakes. These analyses indicate the need for more complex models for the estimation of food additive intakes using probabilistic analysis. Such models should incorporate information on market share and/or brand loyalty.

Airport Remote Tower Sensor Systems

NASA Technical Reports Server (NTRS)

Maluf, David A.; Gawdiak, Yuri; Leidichj, Christopher; Papasin, Richard; Tran, Peter B.; Bass, Kevin

2006-01-01

Networks of video cameras, meteorological sensors, and ancillary electronic equipment are under development in collaboration among NASA Ames Research Center, the Federal Aviation Administration (FAA), and the National Oceanic Atmospheric Administration (NOAA). These networks are to be established at and near airports to provide real-time information on local weather conditions that affect aircraft approaches and landings. The prototype network is an airport-approach-zone camera system (AAZCS), which has been deployed at San Francisco International Airport (SFO) and San Carlos Airport (SQL). The AAZCS includes remotely controlled color video cameras located on top of SFO and SQL air-traffic control towers. The cameras are controlled by the NOAA Center Weather Service Unit located at the Oakland Air Route Traffic Control Center and are accessible via a secure Web site. The AAZCS cameras can be zoomed and can be panned and tilted to cover a field of view 220 wide. The NOAA observer can see the sky condition as it is changing, thereby making possible a real-time evaluation of the conditions along the approach zones of SFO and SQL. The next-generation network, denoted a remote tower sensor system (RTSS), will soon be deployed at the Half Moon Bay Airport and a version of it will eventually be deployed at Los Angeles International Airport. In addition to remote control of video cameras via secure Web links, the RTSS offers realtime weather observations, remote sensing, portability, and a capability for deployment at remote and uninhabited sites. The RTSS can be used at airports that lack control towers, as well as at major airport hubs, to provide synthetic augmentation of vision for both local and remote operations under what would otherwise be conditions of low or even zero visibility.

ClimateSpark: An In-memory Distributed Computing Framework for Big Climate Data Analytics

NASA Astrophysics Data System (ADS)

Hu, F.; Yang, C. P.; Duffy, D.; Schnase, J. L.; Li, Z.

2016-12-01

Massive array-based climate data is being generated from global surveillance systems and model simulations. They are widely used to analyze the environment problems, such as climate changes, natural hazards, and public health. However, knowing the underlying information from these big climate datasets is challenging due to both data- and computing- intensive issues in data processing and analyzing. To tackle the challenges, this paper proposes ClimateSpark, an in-memory distributed computing framework to support big climate data processing. In ClimateSpark, the spatiotemporal index is developed to enable Apache Spark to treat the array-based climate data (e.g. netCDF4, HDF4) as native formats, which are stored in Hadoop Distributed File System (HDFS) without any preprocessing. Based on the index, the spatiotemporal query services are provided to retrieve dataset according to a defined geospatial and temporal bounding box. The data subsets will be read out, and a data partition strategy will be applied to equally split the queried data to each computing node, and store them in memory as climateRDDs for processing. By leveraging Spark SQL and User Defined Function (UDFs), the climate data analysis operations can be conducted by the intuitive SQL language. ClimateSpark is evaluated by two use cases using the NASA Modern-Era Retrospective Analysis for Research and Applications (MERRA) climate reanalysis dataset. One use case is to conduct the spatiotemporal query and visualize the subset results in animation; the other one is to compare different climate model outputs using Taylor-diagram service. Experimental results show that ClimateSpark can significantly accelerate data query and processing, and enable the complex analysis services served in the SQL-style fashion.

An anaesthesia information management system as a tool for a quality assurance program: 10years of experience.

PubMed

Motamed, Cyrus; Bourgain, Jean Louis

2016-06-01

Anaesthesia Information Management Systems (AIMS) generate large amounts of data, which might be useful for quality assurance programs. This study was designed to highlight the multiple contributions of our AIMS system in extracting quality indicators over a period of 10years. The study was conducted from 2002 to 2011. Two methods were used to extract anaesthesia indicators: the manual extraction of individual files for monitoring neuromuscular relaxation and structured query language (SQL) extraction for other indicators which were postoperative nausea and vomiting (PONV), pain, sedation scores, pain-related medications, scores and postoperative hypothermia. For each indicator, a program of information/meetings and adaptation/suggestions for operating room and PACU personnel was initiated to improve quality assurance, while data were extracted each year. The study included 77,573 patients. The mean overall completeness of data for the initial years ranged from 55 to 85% and was indicator-dependent, which then improved to 95% completeness for the last 5years. The incidence of neuromuscular monitoring was initially 67% and then increased to 95% (P<0.05). The rate of pharmacological reversal remained around 53% throughout the study. Regarding SQL data, an improvement of severe postoperative pain and PONV scores was observed throughout the study, while mild postoperative hypothermia remained a challenge, despite efforts for improvement. The AIMS system permitted the follow-up of certain indicators through manual sampling and many more via SQL extraction in a sustained and non-time-consuming way across years. However, it requires competent and especially dedicated resources to handle the database. Copyright © 2016 Société française d'anesthésie et de réanimation (Sfar). Published by Elsevier Masson SAS. All rights reserved.

WebDB Component Builder - Lessons Learned

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

Macedo, C.

2000-02-15

Oracle WebDB is the easiest way to produce web enabled lightweight and enterprise-centric applications. This concept from Oracle has tantalized our taste for simplistic web development by using a purely web based tool that lives nowhere else but in the database. The use of online wizards, templates, and query builders, which produces PL/SQL behind the curtains, can be used straight ''out of the box'' by both novice and seasoned developers. The topic of this presentation will introduce lessons learned by developing and deploying applications built using the WebDB Component Builder in conjunction with custom PL/SQL code to empower a hybridmore » application. There are two kinds of WebDB components: those that display data to end users via reporting, and those that let end users update data in the database via entry forms. The presentation will also discuss various methods within the Component Builder to enhance the applications pushed to the desktop. The demonstrated example is an application entitled HOME (Helping Other's More Effectively) that was built to manage a yearly United Way Campaign effort. Our task was to build an end to end application which could manage approximately 900 non-profit agencies, an average of 4,100 individual contributions, and $1.2 million dollars. Using WebDB, the shell of the application was put together in a matter of a few weeks. However, we did encounter some hurdles that WebDB, in it's stage of infancy (v2.0), could not solve for us directly. Together with custom PL/SQL, WebDB's Component Builder became a powerful tool that enabled us to produce a very flexible hybrid application.« less

Dielectrophoretic trapping of multilayer DNA origami nanostructures and DNA origami-induced local destruction of silicon dioxide.

PubMed

Shen, Boxuan; Linko, Veikko; Dietz, Hendrik; Toppari, J Jussi

2015-01-01

DNA origami is a widely used method for fabrication of custom-shaped nanostructures. However, to utilize such structures, one needs to controllably position them on nanoscale. Here we demonstrate how different types of 3D scaffolded multilayer origamis can be accurately anchored to lithographically fabricated nanoelectrodes on a silicon dioxide substrate by DEP. Straight brick-like origami structures, constructed both in square (SQL) and honeycomb lattices, as well as curved "C"-shaped and angular "L"-shaped origamis were trapped with nanoscale precision and single-structure accuracy. We show that the positioning and immobilization of all these structures can be realized with or without thiol-linkers. In general, structural deformations of the origami during the DEP trapping are highly dependent on the shape and the construction of the structure. The SQL brick turned out to be the most robust structure under the high DEP forces, and accordingly, its single-structure trapping yield was also highest. In addition, the electrical conductivity of single immobilized plain brick-like structures was characterized. The electrical measurements revealed that the conductivity is negligible (insulating behavior). However, we observed that the trapping process of the SQL brick equipped with thiol-linkers tended to induce an etched "nanocanyon" in the silicon dioxide substrate. The nanocanyon was formed exactly between the electrodes, that is, at the location of the DEP-trapped origami. The results show that the demonstrated DEP-trapping technique can be readily exploited in assembling and arranging complex multilayered origami geometries. In addition, DNA origamis could be utilized in DEP-assisted deformation of the substrates onto which they are attached. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

An improved resource management model based on MDS

NASA Astrophysics Data System (ADS)

Yuan, Man; Sun, Changying; Li, Pengfei; Sun, Yongdong; He, Rui

2005-11-01

GRID technology provides a kind of convenient method for managing GRID resources. This service is so-called monitoring, discovering service. This method is proposed by Globus Alliance, in this GRID environment, all kinds of resources, such as computational resources, storage resources and other resources can be organized by MDS specifications. However, this MDS is a theory framework, particularly, in a small world intranet, in the case of limit of resources, the MDS has its own limitation. Based on MDS, an improved light method for managing corporation computational resources and storage resources is proposed in intranet(IMDS). Firstly, in MDS, all kinds of resource description information is stored in LDAP, it is well known although LDAP is a light directory access protocol, in practice, programmers rarely master how to access and store resource information into LDAP store, in such way, it limits MDS to be used. So, in intranet, these resources' description information can be stored in RDBMS, programmers and users can access this information by standard SQL. Secondly, in MDS, how to monitor all kinds of resources in GRID is not transparent for programmers and users. In such way, it limits its application scope, in general, resource monitoring method base on SNMP is widely employed in intranet, therefore, a kind of resource monitoring method based on SNMP is integrated into MDS. Finally, all kinds of resources in the intranet can be described by XML, and all kinds of resources' description information is stored in RDBMS, such as MySql, and retrieved by standard SQL, dynamic information for all kinds of resources can be sent to resource storage by SNMP, A prototype resource description, monitoring is designed and implemented in intranet.

Changes in Exercise Data Management

NASA Technical Reports Server (NTRS)

Buxton, R. E.; Kalogera, K. L.; Hanson, A. M.

2018-01-01

The suite of exercise hardware aboard the International Space Station (ISS) generates an immense amount of data. The data collected from the treadmill, cycle ergometer, and resistance strength training hardware are basic exercise parameters (time, heart rate, speed, load, etc.). The raw data are post processed in the laboratory and more detailed parameters are calculated from each exercise data file. Updates have recently been made to how this valuable data are stored, adding an additional level of data security, increasing data accessibility, and resulting in overall increased efficiency of medical report delivery. Questions regarding exercise performance or how exercise may influence other variables of crew health frequently arise within the crew health care community. Inquiries over the health of the exercise hardware often need quick analysis and response to ensure the exercise system is operable on a continuous basis. Consolidating all of the exercise system data in a single repository enables a quick response to both the medical and engineering communities. A SQL server database is currently in use, and provides a secure location for all of the exercise data starting at ISS Expedition 1 - current day. The database has been structured to update derived metrics automatically, making analysis and reporting available within minutes of dropping the inflight data it into the database. Commercial tools were evaluated to help aggregate and visualize data from the SQL database. The Tableau software provides manageable interface, which has improved the laboratory's output time of crew reports by 67%. Expansion of the SQL database to be inclusive of additional medical requirement metrics, addition of 'app-like' tools for mobile visualization, and collaborative use (e.g. operational support teams, research groups, and International Partners) of the data system is currently being explored.

A Neuroimaging Web Services Interface as a Cyber Physical System for Medical Imaging and Data Management in Brain Research: Design Study.

PubMed

Lizarraga, Gabriel; Li, Chunfei; Cabrerizo, Mercedes; Barker, Warren; Loewenstein, David A; Duara, Ranjan; Adjouadi, Malek

2018-04-26

Structural and functional brain images are essential imaging modalities for medical experts to study brain anatomy. These images are typically visually inspected by experts. To analyze images without any bias, they must be first converted to numeric values. Many software packages are available to process the images, but they are complex and difficult to use. The software packages are also hardware intensive. The results obtained after processing vary depending on the native operating system used and its associated software libraries; data processed in one system cannot typically be combined with data on another system. The aim of this study was to fulfill the neuroimaging community’s need for a common platform to store, process, explore, and visualize their neuroimaging data and results using Neuroimaging Web Services Interface: a series of processing pipelines designed as a cyber physical system for neuroimaging and clinical data in brain research. Neuroimaging Web Services Interface accepts magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and functional magnetic resonance imaging. These images are processed using existing and custom software packages. The output is then stored as image files, tabulated files, and MySQL tables. The system, made up of a series of interconnected servers, is password-protected and is securely accessible through a Web interface and allows (1) visualization of results and (2) downloading of tabulated data. All results were obtained using our processing servers in order to maintain data validity and consistency. The design is responsive and scalable. The processing pipeline started from a FreeSurfer reconstruction of Structural magnetic resonance imaging images. The FreeSurfer and regional standardized uptake value ratio calculations were validated using Alzheimer’s Disease Neuroimaging Initiative input images, and the results were posted at the Laboratory of Neuro Imaging data archive. Notable leading researchers in the field of Alzheimer’s Disease and epilepsy have used the interface to access and process the data and visualize the results. Tabulated results with unique visualization mechanisms help guide more informed diagnosis and expert rating, providing a truly unique multimodal imaging platform that combines magnetic resonance imaging, positron emission tomography, diffusion tensor imaging, and resting state functional magnetic resonance imaging. A quality control component was reinforced through expert visual rating involving at least 2 experts. To our knowledge, there is no validated Web-based system offering all the services that Neuroimaging Web Services Interface offers. The intent of Neuroimaging Web Services Interface is to create a tool for clinicians and researchers with keen interest on multimodal neuroimaging. More importantly, Neuroimaging Web Services Interface significantly augments the Alzheimer’s Disease Neuroimaging Initiative data, especially since our data contain a large cohort of Hispanic normal controls and Alzheimer’s Disease patients. The obtained results could be scrutinized visually or through the tabulated forms, informing researchers on subtle changes that characterize the different stages of the disease. ©Gabriel Lizarraga, Chunfei Li, Mercedes Cabrerizo, Warren Barker, David A Loewenstein, Ranjan Duara, Malek Adjouadi. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 26.04.2018.

An open tool for input function estimation and quantification of dynamic PET FDG brain scans.

PubMed

Bertrán, Martín; Martínez, Natalia; Carbajal, Guillermo; Fernández, Alicia; Gómez, Álvaro

2016-08-01

Positron emission tomography (PET) analysis of clinical studies is mostly restricted to qualitative evaluation. Quantitative analysis of PET studies is highly desirable to be able to compute an objective measurement of the process of interest in order to evaluate treatment response and/or compare patient data. But implementation of quantitative analysis generally requires the determination of the input function: the arterial blood or plasma activity which indicates how much tracer is available for uptake in the brain. The purpose of our work was to share with the community an open software tool that can assist in the estimation of this input function, and the derivation of a quantitative map from the dynamic PET study. Arterial blood sampling during the PET study is the gold standard method to get the input function, but is uncomfortable and risky for the patient so it is rarely used in routine studies. To overcome the lack of a direct input function, different alternatives have been devised and are available in the literature. These alternatives derive the input function from the PET image itself (image-derived input function) or from data gathered from previous similar studies (population-based input function). In this article, we present ongoing work that includes the development of a software tool that integrates several methods with novel strategies for the segmentation of blood pools and parameter estimation. The tool is available as an extension to the 3D Slicer software. Tests on phantoms were conducted in order to validate the implemented methods. We evaluated the segmentation algorithms over a range of acquisition conditions and vasculature size. Input function estimation algorithms were evaluated against ground truth of the phantoms, as well as on their impact over the final quantification map. End-to-end use of the tool yields quantification maps with [Formula: see text] relative error in the estimated influx versus ground truth on phantoms. The main contribution of this article is the development of an open-source, free to use tool that encapsulates several well-known methods for the estimation of the input function and the quantification of dynamic PET FDG studies. Some alternative strategies are also proposed and implemented in the tool for the segmentation of blood pools and parameter estimation. The tool was tested on phantoms with encouraging results that suggest that even bloodless estimators could provide a viable alternative to blood sampling for quantification using graphical analysis. The open tool is a promising opportunity for collaboration among investigators and further validation on real studies.

Evaluation of limited blood sampling population input approaches for kinetic quantification of [18F]fluorothymidine PET data.

PubMed

Contractor, Kaiyumars B; Kenny, Laura M; Coombes, Charles R; Turkheimer, Federico E; Aboagye, Eric O; Rosso, Lula

2012-03-24

Quantification of kinetic parameters of positron emission tomography (PET) imaging agents normally requires collecting arterial blood samples which is inconvenient for patients and difficult to implement in routine clinical practice. The aim of this study was to investigate whether a population-based input function (POP-IF) reliant on only a few individual discrete samples allows accurate estimates of tumour proliferation using [18F]fluorothymidine (FLT). Thirty-six historical FLT-PET data with concurrent arterial sampling were available for this study. A population average of baseline scans blood data was constructed using leave-one-out cross-validation for each scan and used in conjunction with individual blood samples. Three limited sampling protocols were investigated including, respectively, only seven (POP-IF7), five (POP-IF5) and three (POP-IF3) discrete samples of the historical dataset. Additionally, using the three-point protocol, we derived a POP-IF3M, the only input function which was not corrected for the fraction of radiolabelled metabolites present in blood. The kinetic parameter for net FLT retention at steady state, Ki, was derived using the modified Patlak plot and compared with the original full arterial set for validation. Small percentage differences in the area under the curve between all the POP-IFs and full arterial sampling IF was found over 60 min (4.2%-5.7%), while there were, as expected, larger differences in the peak position and peak height.A high correlation between Ki values calculated using the original arterial input function and all the population-derived IFs was observed (R2 = 0.85-0.98). The population-based input showed good intra-subject reproducibility of Ki values (R2 = 0.81-0.94) and good correlation (R2 = 0.60-0.85) with Ki-67. Input functions generated using these simplified protocols over scan duration of 60 min estimate net PET-FLT retention with reasonable accuracy.

Online decision support based on modeling with the aim of increased irrigation efficiency

NASA Astrophysics Data System (ADS)

Dövényi-Nagy, Tamás; Bakó, Károly; Molnár, Krisztina; Rácz, Csaba; Vasvári, Gyula; Nagy, János; Dobos, Attila

2015-04-01

The significant changes in the structure of ownership and control of irrigation infrastructure in the past decades resultted in the decrease of total irrigable and irrigated area (Szilárd, 1999). In this paper, the development of a model-based online service is described whose aim is to aid reasonable irrigation practice and increase water use efficiency. In order to establish a scientific background for irrigation, an agrometeorological station network has been built up by the Agrometeorological and Agroecological Monitoring Centre. A website has been launched in order to provide direct access for local agricultural producers to both the measured weather parameters and results of model based calculations. The public site provides information for general use, registered partners get a handy model based toolkit for decision support at the plot level concerning irrigation, plant protection or frost forecast. The agrometeorological reference station network was established in the recent years by the Agrometeorological and Agroecological Monitoring Centre and is distributed to cover most of the irrigated cropland areas of Hungary. From the spatial aspect, the stations have been deployed mainly in Eastern Hungary with concentrated irrigation infrastructure. The meteorological stations' locations have been carefully chosen to represent their environment in terms of soil, climatic and topographic factors, thereby assuring relevant and up-to-date input data for the models. The measured parameters range from classic meteorological data (air temperature, relative humidity, solar irradiation, wind speed etc.) to specific data which are not available from other services in the region, such as soil temperature, soil water content in multiple depths and leaf wetness. In addition to the basic grid of reference stations, specific stations under irrigated conditions have been deployed to calibrate and validate the models. A specific modeling framework (MetAgro) has been developed to allow the integration of several public available models and algorithms adapted to local climate (Rácz et al., 2013). The service, the server side framework, scripts and the front-end, providing access to the measured and modeled data, are based on own developments or free available and/or open source softwares and services like Apache, PHP, MySQL and Google Maps API. MetAgro intends to accomplish functionalities of three different areas of usage: research, education and practice. The members differ in educational background, knowledge of models and possibilities to access relevant input data. The system and interfaces must reflect these differences that is accomplished by the degradation of modeling: choosing the place of the farm and the crop already gives some general results, but with every additional parameter given the results are more reliable. The system 'MetAgro' provides a basis for improved decision-making with regard to irrigation on cropland. Based on experiences and feedback, the online application was proved to be useful in the design and practice of reasonable irrigation. In addition to its use in irrigation practice, MetAgro is also a valuable tool for research and education.

System Identification Methods for Aircraft Flight Control Development and Validation

DOT National Transportation Integrated Search

1995-10-01

System-identification methods compose a mathematical model, or series of models, : from measurements of inputs and outputs of dynamic systems. This paper : discusses the use of frequency-domain system-identification methods for the : development and ...

Relational Algebra and SQL: Better Together

ERIC Educational Resources Information Center

McMaster, Kirby; Sambasivam, Samuel; Hadfield, Steven; Wolthuis, Stuart

2013-01-01

In this paper, we describe how database instructors can teach Relational Algebra and Structured Query Language together through programming. Students write query programs consisting of sequences of Relational Algebra operations vs. Structured Query Language SELECT statements. The query programs can then be run interactively, allowing students to…

Ontological Approach to Military Knowledge Modeling and Management

DTIC Science & Technology

2004-03-01

federated search mechanism has to reformulate user queries (expressed using the ontology) in the query languages of the different sources (e.g. SQL...ontologies as a common terminology – Unified query to perform federated search • Query processing – Ontology mapping to sources reformulate queries

tcpl: The ToxCast Pipeline for High-Throughput Screening Data

EPA Science Inventory

Motivation: The large and diverse high-throughput chemical screening efforts carried out by the US EPAToxCast program requires an efficient, transparent, and reproducible data pipeline.Summary: The tcpl R package and its associated MySQL database provide a generalized platform fo...

An OAIS-Based Hospital Information System on the Cloud: Analysis of a NoSQL Column-Oriented Approach.

PubMed

Celesti, Antonio; Fazio, Maria; Romano, Agata; Bramanti, Alessia; Bramanti, Placido; Villari, Massimo

2018-05-01

The Open Archive Information System (OAIS) is a reference model for organizing people and resources in a system, and it is already adopted in care centers and medical systems to efficiently manage clinical data, medical personnel, and patients. Archival storage systems are typically implemented using traditional relational database systems, but the relation-oriented technology strongly limits the efficiency in the management of huge amount of patients' clinical data, especially in emerging cloud-based, that are distributed. In this paper, we present an OAIS healthcare architecture useful to manage a huge amount of HL7 clinical documents in a scalable way. Specifically, it is based on a NoSQL column-oriented Data Base Management System deployed in the cloud, thus to benefit from a big tables and wide rows available over a virtual distributed infrastructure. We developed a prototype of the proposed architecture at the IRCCS, and we evaluated its efficiency in a real case of study.

A MySQL Based EPICS Archiver

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

Christopher Slominski

2009-10-01

Archiving a large fraction of the EPICS signals within the Jefferson Lab (JLAB) Accelerator control system is vital for postmortem and real-time analysis of the accelerator performance. This analysis is performed on a daily basis by scientists, operators, engineers, technicians, and software developers. Archiving poses unique challenges due to the magnitude of the control system. A MySQL Archiving system (Mya) was developed to scale to the needs of the control system; currently archiving 58,000 EPICS variables, updating at a rate of 11,000 events per second. In addition to the large collection rate, retrieval of the archived data must also bemore » fast and robust. Archived data retrieval clients obtain data at a rate over 100,000 data points per second. Managing the data in a relational database provides a number of benefits. This paper describes an archiving solution that uses an open source database and standard off the shelf hardware to reach high performance archiving needs. Mya has been in production at Jefferson Lab since February of 2007.« less

Computerized database management system for breast cancer patients.

PubMed

Sim, Kok Swee; Chong, Sze Siang; Tso, Chih Ping; Nia, Mohsen Esmaeili; Chong, Aun Kee; Abbas, Siti Fathimah

2014-01-01

Data analysis based on breast cancer risk factors such as age, race, breastfeeding, hormone replacement therapy, family history, and obesity was conducted on breast cancer patients using a new enhanced computerized database management system. My Structural Query Language (MySQL) is selected as the application for database management system to store the patient data collected from hospitals in Malaysia. An automatic calculation tool is embedded in this system to assist the data analysis. The results are plotted automatically and a user-friendly graphical user interface is developed that can control the MySQL database. Case studies show breast cancer incidence rate is highest among Malay women, followed by Chinese and Indian. The peak age for breast cancer incidence is from 50 to 59 years old. Results suggest that the chance of developing breast cancer is increased in older women, and reduced with breastfeeding practice. The weight status might affect the breast cancer risk differently. Additional studies are needed to confirm these findings.

Techniques of Photometry and Astrometry with APASS, Gaia, and Pan-STARRs Results (Abstract)

NASA Astrophysics Data System (ADS)

Green, W.

2017-12-01

(Abstract only) The databases with the APASS DR9, Gaia DR1, and the Pan-STARRs 3pi DR1 data releases are publicly available for use. There is a bit of data-mining involved to download and manage these reference stars. This paper discusses the use of these databases to acquire accurate photometric references as well as techniques for improving results. Images are prepared in the usual way: zero, dark, flat-fields, and WCS solutions with Astrometry.net. Images are then processed with Sextractor to produce an ASCII table of identifying photometric features. The database manages photometics catalogs and images converted to ASCII tables. Scripts convert the files into SQL and assimilate them into database tables. Using SQL techniques, each image star is merged with reference data to produce publishable results. The VYSOS has over 13,000 images of the ONC5 field to process with roughly 100 total fields in the campaign. This paper provides the overview for this daunting task.

Fill factor in organic solar cells can exceed the Shockley-Queisser limit

NASA Astrophysics Data System (ADS)

Trukhanov, Vasily A.; Bruevich, Vladimir V.; Paraschuk, Dmitry Yu.

2015-06-01

The ultimate efficiency of organic solar cells (OSC) is under active debate. The solar cell efficiency is calculated from the current-voltage characteristic as a product of the open-circuit voltage (VOC), short-circuit current (JSC), and the fill factor (FF). While the factors limiting VOC and JSC for OSC were extensively studied, the ultimate FF for OSC is scarcely explored. Using numerical drift-diffusion modeling, we have found that the FF in OSC can exceed the Shockley-Queisser limit (SQL) established for inorganic p-n junction solar cells. Comparing charge generation and recombination in organic donor-acceptor bilayer heterojunction and inorganic p-n junction, we show that such distinctive properties of OSC as interface charge generation and heterojunction facilitate high FF, but the necessary condition for FF exceeding the SQL in OSC is field-dependence of charge recombination at the donor-acceptor interface. These findings can serve as a guideline for further improvement of OSC.

A JEE RESTful service to access Conditions Data in ATLAS

NASA Astrophysics Data System (ADS)

Formica, Andrea; Gallas, E. J.

2015-12-01

Usage of condition data in ATLAS is extensive for offline reconstruction and analysis (e.g. alignment, calibration, data quality). The system is based on the LCG Conditions Database infrastructure, with read and write access via an ad hoc C++ API (COOL), a system which was developed before Run 1 data taking began. The infrastructure dictates that the data is organized into separate schemas (assigned to subsystems/groups storing distinct and independent sets of conditions), making it difficult to access information from several schemas at the same time. We have thus created PL/SQL functions containing queries to provide content extraction at multi-schema level. The PL/SQL API has been exposed to external clients by means of a Java application providing DB access via REST services, deployed inside an application server (JBoss WildFly). The services allow navigation over multiple schemas via simple URLs. The data can be retrieved either in XML or JSON formats, via simple clients (like curl or Web browsers).

Constructing a Graph Database for Semantic Literature-Based Discovery.

PubMed

Hristovski, Dimitar; Kastrin, Andrej; Dinevski, Dejan; Rindflesch, Thomas C

2015-01-01

Literature-based discovery (LBD) generates discoveries, or hypotheses, by combining what is already known in the literature. Potential discoveries have the form of relations between biomedical concepts; for example, a drug may be determined to treat a disease other than the one for which it was intended. LBD views the knowledge in a domain as a network; a set of concepts along with the relations between them. As a starting point, we used SemMedDB, a database of semantic relations between biomedical concepts extracted with SemRep from Medline. SemMedDB is distributed as a MySQL relational database, which has some problems when dealing with network data. We transformed and uploaded SemMedDB into the Neo4j graph database, and implemented the basic LBD discovery algorithms with the Cypher query language. We conclude that storing the data needed for semantic LBD is more natural in a graph database. Also, implementing LBD discovery algorithms is conceptually simpler with a graph query language when compared with standard SQL.

NoSQL Based 3D City Model Management System

NASA Astrophysics Data System (ADS)

Mao, B.; Harrie, L.; Cao, J.; Wu, Z.; Shen, J.

2014-04-01

To manage increasingly complicated 3D city models, a framework based on NoSQL database is proposed in this paper. The framework supports import and export of 3D city model according to international standards such as CityGML, KML/COLLADA and X3D. We also suggest and implement 3D model analysis and visualization in the framework. For city model analysis, 3D geometry data and semantic information (such as name, height, area, price and so on) are stored and processed separately. We use a Map-Reduce method to deal with the 3D geometry data since it is more complex, while the semantic analysis is mainly based on database query operation. For visualization, a multiple 3D city representation structure CityTree is implemented within the framework to support dynamic LODs based on user viewpoint. Also, the proposed framework is easily extensible and supports geoindexes to speed up the querying. Our experimental results show that the proposed 3D city management system can efficiently fulfil the analysis and visualization requirements.

Incremental Query Rewriting with Resolution

NASA Astrophysics Data System (ADS)

Riazanov, Alexandre; Aragão, Marcelo A. T.

We address the problem of semantic querying of relational databases (RDB) modulo knowledge bases using very expressive knowledge representation formalisms, such as full first-order logic or its various fragments. We propose to use a resolution-based first-order logic (FOL) reasoner for computing schematic answers to deductive queries, with the subsequent translation of these schematic answers to SQL queries which are evaluated using a conventional relational DBMS. We call our method incremental query rewriting, because an original semantic query is rewritten into a (potentially infinite) series of SQL queries. In this chapter, we outline the main idea of our technique - using abstractions of databases and constrained clauses for deriving schematic answers, and provide completeness and soundness proofs to justify the applicability of this technique to the case of resolution for FOL without equality. The proposed method can be directly used with regular RDBs, including legacy databases. Moreover, we propose it as a potential basis for an efficient Web-scale semantic search technology.

An experiment in big data: storage, querying and visualisation of data taken from the Liverpool Telescope's wide field cameras

NASA Astrophysics Data System (ADS)

Barnsley, R. M.; Steele, Iain A.; Smith, R. J.; Mawson, Neil R.

2014-07-01

The Small Telescopes Installed at the Liverpool Telescope (STILT) project has been in operation since March 2009, collecting data with three wide field unfiltered cameras: SkycamA, SkycamT and SkycamZ. To process the data, a pipeline was developed to automate source extraction, catalogue cross-matching, photometric calibration and database storage. In this paper, modifications and further developments to this pipeline will be discussed, including a complete refactor of the pipeline's codebase into Python, migration of the back-end database technology from MySQL to PostgreSQL, and changing the catalogue used for source cross-matching from USNO-B1 to APASS. In addition to this, details will be given relating to the development of a preliminary front-end to the source extracted database which will allow a user to perform common queries such as cone searches and light curve comparisons of catalogue and non-catalogue matched objects. Some next steps and future ideas for the project will also be presented.

StreptomycesInforSys: A web-enabled information repository

PubMed Central

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. Availability www.sis.biowaves.org PMID:23275736

A Web-based Tool for SDSS and 2MASS Database Searches

NASA Astrophysics Data System (ADS)

Hendrickson, M. A.; Uomoto, A.; Golimowski, D. A.

We have developed a web site using HTML, Php, Python, and MySQL that extracts, processes, and displays data from the Sloan Digital Sky Survey (SDSS) and the Two-Micron All-Sky Survey (2MASS). The goal is to locate brown dwarf candidates in the SDSS database by looking at color cuts; however, this site could also be useful for targeted searches of other databases as well. MySQL databases are created from broad searches of SDSS and 2MASS data. Broad queries on the SDSS and 2MASS database servers are run weekly so that observers have the most up-to-date information from which to select candidates for observation. Observers can look at detailed information about specific objects including finding charts, images, and available spectra. In addition, updates from previous observations can be added by any collaborators; this format makes observational collaboration simple. Observers can also restrict the database search, just before or during an observing run, to select objects of special interest.

Image query and indexing for digital x rays

NASA Astrophysics Data System (ADS)

Long, L. Rodney; Thoma, George R.

1998-12-01

The web-based medical information retrieval system (WebMIRS) allows interned access to databases containing 17,000 digitized x-ray spine images and associated text data from National Health and Nutrition Examination Surveys (NHANES). WebMIRS allows SQL query of the text, and viewing of the returned text records and images using a standard browser. We are now working (1) to determine utility of data directly derived from the images in our databases, and (2) to investigate the feasibility of computer-assisted or automated indexing of the images to support image retrieval of images of interest to biomedical researchers in the field of osteoarthritis. To build an initial database based on image data, we are manually segmenting a subset of the vertebrae, using techniques from vertebral morphometry. From this, we will derive and add to the database vertebral features. This image-derived data will enhance the user's data access capability by enabling the creation of combined SQL/image-content queries.

StreptomycesInforSys: A web-enabled information repository.

PubMed

Jain, Chakresh Kumar; Gupta, Vidhi; Gupta, Ashvarya; Gupta, Sanjay; Wadhwa, Gulshan; Sharma, Sanjeev Kumar; Sarethy, Indira P

2012-01-01

Members of Streptomyces produce 70% of natural bioactive products. There is considerable amount of information available based on polyphasic approach for classification of Streptomyces. However, this information based on phenotypic, genotypic and bioactive component production profiles is crucial for pharmacological screening programmes. This is scattered across various journals, books and other resources, many of which are not freely accessible. The designed database incorporates polyphasic typing information using combinations of search options to aid in efficient screening of new isolates. This will help in the preliminary categorization of appropriate groups. It is a free relational database compatible with existing operating systems. A cross platform technology with XAMPP Web server has been used to develop, manage, and facilitate the user query effectively with database support. Employment of PHP, a platform-independent scripting language, embedded in HTML and the database management software MySQL will facilitate dynamic information storage and retrieval. The user-friendly, open and flexible freeware (PHP, MySQL and Apache) is foreseen to reduce running and maintenance cost. www.sis.biowaves.org.

Universal modal radiation laws for all thermal emitters

PubMed Central

Zhu, Linxiao; Fan, Shanhui

2017-01-01

We derive four laws relating the absorptivity and emissivity of thermal emitters. Unlike the original Kirchhoff radiation law derivations, these derivations include diffraction, and so are valid also for small objects, and can also cover nonreciprocal objects. The proofs exploit two recent approaches. First, we express all fields in terms of the mode-converter basis sets of beams; these sets, which can be uniquely established for any linear optical object, give orthogonal input beams that are coupled one-by-one to orthogonal output beams. Second, we consider thought experiments using universal linear optical machines, which allow us to couple appropriate beams and black bodies. Two of these laws can be regarded as rigorous extensions of previously known laws: One gives a modal version of a radiation law for reciprocal objects—the absorptivity of any input beam equals the emissivity into the “backward” (i.e., phase-conjugated) version of that beam; another gives the overall equality of the sums of the emissivities and the absorptivities for any object, including nonreciprocal ones. The other two laws, valid for reciprocal and nonreciprocal objects, are quite different from previous relations. One shows universal equivalence of the absorptivity of each mode-converter input beam and the emissivity into its corresponding scattered output beam. The other gives unexpected equivalences of absorptivity and emissivity for broad classes of beams. Additionally, we prove these orthogonal mode-converter sets of input and output beams are the ones that maximize absorptivities and emissivities, respectively, giving these beams surprising additional physical meaning. PMID:28396436

Analytical and experimental comparisons of electromechanical vibration response of a piezoelectric bimorph beam for power harvesting

NASA Astrophysics Data System (ADS)

Lumentut, M. F.; Howard, I. M.

2013-03-01

Power harvesters that extract energy from vibrating systems via piezoelectric transduction show strong potential for powering smart wireless sensor devices in applications of health condition monitoring of rotating machinery and structures. This paper presents an analytical method for modelling an electromechanical piezoelectric bimorph beam with tip mass under two input base transverse and longitudinal excitations. The Euler-Bernoulli beam equations were used to model the piezoelectric bimorph beam. The polarity-electric field of the piezoelectric element is excited by the strain field caused by base input excitation, resulting in electrical charge. The governing electromechanical dynamic equations were derived analytically using the weak form of the Hamiltonian principle to obtain the constitutive equations. Three constitutive electromechanical dynamic equations based on independent coefficients of virtual displacement vectors were formulated and then further modelled using the normalised Ritz eigenfunction series. The electromechanical formulations include both the series and parallel connections of the piezoelectric bimorph. The multi-mode frequency response functions (FRFs) under varying electrical load resistance were formulated using Laplace transformation for the multi-input mechanical vibrations to provide the multi-output dynamic displacement, velocity, voltage, current and power. The experimental and theoretical validations reduced for the single mode system were shown to provide reasonable predictions. The model results from polar base excitation for off-axis input motions were validated with experimental results showing the change to the electrical power frequency response amplitude as a function of excitation angle, with relevance for practical implementation.