Data Archival and Retrieval Enhancement (DARE) Metadata Modeling and Its User Interface

NASA Technical Reports Server (NTRS)

Hyon, Jason J.; Borgen, Rosana B.

1996-01-01

The Defense Nuclear Agency (DNA) has acquired terabytes of valuable data which need to be archived and effectively distributed to the entire nuclear weapons effects community and others...This paper describes the DARE (Data Archival and Retrieval Enhancement) metadata model and explains how it is used as a source for generating HyperText Markup Language (HTML)or Standard Generalized Markup Language (SGML) documents for access through web browsers such as Netscape.

An approach to access control in electronic health record.

PubMed

Sucurovic, Snezana

2010-08-01

OASIS is a non-for-profit consortium that drives the development convergence and adoption of open standards for the global information society. It involves more than 600 organizations and individuals as well as IT leaders Sun, Microsoft, IBM and Oracle. One of its standards is XACML which appeared a few years ago and now there are about 150,000 hits on Google. XACML (eXtensible Access Control Markup Language) is not technology related. Sun published in 2004 open source Sun XACML which is in compliance with XACML 1.0. specification and now works to make it comply with XACML 2.0. The heart of XACML are attributes values of defined type and name that is to be attached to a subject, a resource, an action and an environment in which a subject request action on resource. In that way XACML is to replace Role Based Access Control which dominated for years. The paper examines performances in CEN 13 606 and ISO 22 600 based healthcare system which uses XACML for access control.

A method to implement fine-grained access control for personal health records through standard relational database queries.

PubMed

Sujansky, Walter V; Faus, Sam A; Stone, Ethan; Brennan, Patricia Flatley

2010-10-01

Online personal health records (PHRs) enable patients to access, manage, and share certain of their own health information electronically. This capability creates the need for precise access-controls mechanisms that restrict the sharing of data to that intended by the patient. The authors describe the design and implementation of an access-control mechanism for PHR repositories that is modeled on the eXtensible Access Control Markup Language (XACML) standard, but intended to reduce the cognitive and computational complexity of XACML. The authors implemented the mechanism entirely in a relational database system using ANSI-standard SQL statements. Based on a set of access-control rules encoded as relational table rows, the mechanism determines via a single SQL query whether a user who accesses patient data from a specific application is authorized to perform a requested operation on a specified data object. Testing of this query on a moderately large database has demonstrated execution times consistently below 100ms. The authors include the details of the implementation, including algorithms, examples, and a test database as Supplementary materials. Copyright © 2010 Elsevier Inc. All rights reserved.

Thin client (web browser)-based collaboration for medical imaging and web-enabled data.

PubMed

Le, Tuong Huu; Malhi, Nadeem

2002-01-01

Utilizing thin client software and open source server technology, a collaborative architecture was implemented allowing for sharing of Digital Imaging and Communications in Medicine (DICOM) and non-DICOM images with real-time markup. Using the Web browser as a thin client integrated with standards-based components, such as DHTML (dynamic hypertext markup language), JavaScript, and Java, collaboration was achieved through a Web server/proxy server combination utilizing Java Servlets and Java Server Pages. A typical collaborative session involved the driver, who directed the navigation of the other collaborators, the passengers, and provided collaborative markups of medical and nonmedical images. The majority of processing was performed on the server side, allowing for the client to remain thin and more accessible.

Accessing Electronic Theses: Progress?

ERIC Educational Resources Information Center

Tennant, Roy

2000-01-01

Describes various ways by which universities provide access to their electronic theses and dissertations (ETDs), discussing UMI (University Microfilms International), XML (eXtensible Markup Language), and other formats. Discusses key leaders--national and international--in the ETD effort. Outlines the two main methods for locating ETDs. Presents a…

Converting Optically Scanned Regular or Irregular Tables to a Standardised Markup Format to Be Accessible to Vision-Impaired

ERIC Educational Resources Information Center

Nazemi, Azadeh; Murray, Iain; Fernaando, Chandrika; McMeekin, David A.

2016-01-01

Documents use tables to communicate multidimensional information clearly, summarise and present data in an easy-to-interpret way. Tabular information in scanned PDF due to its nature without further processing is not accessible for vision-impaired people who use assistive technology such as screen readers. The lack of access to table contents…

Resolving Controlled Vocabulary in DITA Markup: A Case Example in Agroforestry

ERIC Educational Resources Information Center

Zschocke, Thomas

2012-01-01

Purpose: This paper aims to address the issue of matching controlled vocabulary on agroforestry from knowledge organization systems (KOS) and incorporating these terms in DITA markup. The paper has been selected for an extended version from MTSR'11. Design/methodology/approach: After a general description of the steps taken to harmonize controlled…

Automating testbed documentation and database access using World Wide Web (WWW) tools

NASA Technical Reports Server (NTRS)

Ames, Charles; Auernheimer, Brent; Lee, Young H.

1994-01-01

A method for providing uniform transparent access to disparate distributed information systems was demonstrated. A prototype testing interface was developed to access documentation and information using publicly available hypermedia tools. The prototype gives testers a uniform, platform-independent user interface to on-line documentation, user manuals, and mission-specific test and operations data. Mosaic was the common user interface, and HTML (Hypertext Markup Language) provided hypertext capability.

Integrating Top-down and Bottom-up Cybersecurity Guidance using XML

PubMed Central

Lubell, Joshua

2016-01-01

This paper describes a markup-based approach for synthesizing disparate information sources and discusses a software implementation of the approach. The implementation makes it easier for people to use two complementary, but differently structured, guidance specifications together: the (top-down) Cybersecurity Framework and the (bottom-up) National Institute of Standards and Technology Special Publication 800-53 security control catalog. An example scenario demonstrates how the software implementation can help a security professional select the appropriate safeguards for restricting unauthorized access to an Industrial Control System. The implementation and example show the benefits of this approach and suggest its potential application to disciplines other than cybersecurity. PMID:27795810

Impact of China's Public Hospital Reform on Healthcare Expenditures and Utilization: A Case Study in ZJ Province

PubMed Central

Zhang, Hao; Hu, Huimei; Wu, Christina; Yu, Hai; Dong, Hengjin

2015-01-01

Background High drug costs due to supplier-induced demand (SID) obstruct healthcare accessibility in China. Drug prescriptions can generate markup-related profits, and the low prices of other medical services can lead to labor-force underestimations; therefore, physicians are keen to prescribe drugs rather than services. Thus, in China, a public hospital reform has been instituted to cancel markups and increase service prices. Methods A retrospective pre/post-reform study was conducted in ZJ province to assess the impact of the reform on healthcare expenditures and utilization, ultimately to inform policy development and decision-making. The main indicators are healthcare expenditures and utilization. Results Post-reform, drug expenditures per visit decreased by 8.2% and 15.36% in outpatient and inpatient care, respectively; service expenditures per visit increased by 23.03% and 27.69% in outpatient and inpatient care, respectively. Drug utilization per visit increased by 5.58% in outpatient care and underwent no significant change in inpatient care. Both were lower than the theoretical drug-utilization level, which may move along the demand curve because of patient-initiated demand (PID); this indicates that SID-promoted drug utilization may decrease. Finally, service utilization per visit increased by 6% in outpatient care and by 13.10% in inpatient care; both were higher than the theoretical level moving along the demand curve, and this indicates that SID-promoted service utilization may increase. Conclusion The reform reduces drug-prescription profits by eliminating drug markups; additionally, it compensates for service costs by increasing service prices. Post-reform, the SID of drug prescriptions decreased, which may reduce drug-resource waste. The SID of services increased, with potentially positive and negative effects: accessibility to services may be promoted when physicians provide more services, but the risk of resource waste may also increase. This warrants further research. It is recommended that comprehensive measures that control SID and promote physician enthusiasm be carried out concurrently. PMID:26588244

Impact of China's Public Hospital Reform on Healthcare Expenditures and Utilization: A Case Study in ZJ Province.

PubMed

Zhang, Hao; Hu, Huimei; Wu, Christina; Yu, Hai; Dong, Hengjin

2015-01-01

High drug costs due to supplier-induced demand (SID) obstruct healthcare accessibility in China. Drug prescriptions can generate markup-related profits, and the low prices of other medical services can lead to labor-force underestimations; therefore, physicians are keen to prescribe drugs rather than services. Thus, in China, a public hospital reform has been instituted to cancel markups and increase service prices. A retrospective pre/post-reform study was conducted in ZJ province to assess the impact of the reform on healthcare expenditures and utilization, ultimately to inform policy development and decision-making. The main indicators are healthcare expenditures and utilization. Post-reform, drug expenditures per visit decreased by 8.2% and 15.36% in outpatient and inpatient care, respectively; service expenditures per visit increased by 23.03% and 27.69% in outpatient and inpatient care, respectively. Drug utilization per visit increased by 5.58% in outpatient care and underwent no significant change in inpatient care. Both were lower than the theoretical drug-utilization level, which may move along the demand curve because of patient-initiated demand (PID); this indicates that SID-promoted drug utilization may decrease. Finally, service utilization per visit increased by 6% in outpatient care and by 13.10% in inpatient care; both were higher than the theoretical level moving along the demand curve, and this indicates that SID-promoted service utilization may increase. The reform reduces drug-prescription profits by eliminating drug markups; additionally, it compensates for service costs by increasing service prices. Post-reform, the SID of drug prescriptions decreased, which may reduce drug-resource waste. The SID of services increased, with potentially positive and negative effects: accessibility to services may be promoted when physicians provide more services, but the risk of resource waste may also increase. This warrants further research. It is recommended that comprehensive measures that control SID and promote physician enthusiasm be carried out concurrently.

Field Markup Language: biological field representation in XML.

PubMed

Chang, David; Lovell, Nigel H; Dokos, Socrates

2007-01-01

With an ever increasing number of biological models available on the internet, a standardized modeling framework is required to allow information to be accessed or visualized. Based on the Physiome Modeling Framework, the Field Markup Language (FML) is being developed to describe and exchange field information for biological models. In this paper, we describe the basic features of FML, its supporting application framework and its ability to incorporate CellML models to construct tissue-scale biological models. As a typical application example, we present a spatially-heterogeneous cardiac pacemaker model which utilizes both FML and CellML to describe and solve the underlying equations of electrical activation and propagation.

Why SGML? Why Now?

ERIC Educational Resources Information Center

Marcoux, Yves; Sevigny, Martin

1997-01-01

Defines Standard Generalized Markup Language (SGML), a format for electronic documents that provides documentary information for efficient accessibility, dissemination, and preservation. Compares SGML to Open Document Architecture (ODA) based on standards by the International Organization for Standardization (ISO), and describes the principles and…

XML in an Adaptive Framework for Instrument Control

NASA Technical Reports Server (NTRS)

Ames, Troy J.

2004-01-01

NASA Goddard Space Flight Center is developing an extensible framework for instrument command and control, known as Instrument Remote Control (IRC), that combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML). A key aspect of the architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). IML is an XML dialect used to describe interfaces to control and monitor the instrument, command sets and command formats, data streams, communication mechanisms, and data processing algorithms.

Designing and Managing Your Digital Library.

ERIC Educational Resources Information Center

Guenther, Kim

2000-01-01

Discusses digital libraries and Web site design issues. Highlights include accessibility issues, including standards, markup languages like HTML and XML, and metadata; building virtual communities; the use of Web portals for customized delivery of information; quality assurance tools, including data mining; and determining user needs, including…

SCOPIC Design and Overview

ERIC Educational Resources Information Center

Barth, Danielle; Evans, Nicholas

2017-01-01

This paper provides an overview of the design and motivation for creating the Social Cognition Parallax Interview Corpus (SCOPIC), an open-ended, accessible corpus that balances the need for language-specific annotation with typologically-calibrated markup. SCOPIC provides richly annotated data, focusing on functional categories relevant to social…

Castles Made of Sand: Building Sustainable Digitized Collections Using XML.

ERIC Educational Resources Information Center

Ragon, Bart

2003-01-01

Describes work at the University of Virginia library to digitize special collections. Discusses the use of XML (Extensible Markup Language); providing access to original source materials; DTD (Document Type Definition); TEI (Text Encoding Initiative); metadata; XSL (Extensible Style Language); and future possibilities. (LRW)

Symmetric Key Services Markup Language (SKSML)

NASA Astrophysics Data System (ADS)

Noor, Arshad

Symmetric Key Services Markup Language (SKSML) is the eXtensible Markup Language (XML) being standardized by the OASIS Enterprise Key Management Infrastructure Technical Committee for requesting and receiving symmetric encryption cryptographic keys within a Symmetric Key Management System (SKMS). This protocol is designed to be used between clients and servers within an Enterprise Key Management Infrastructure (EKMI) to secure data, independent of the application and platform. Building on many security standards such as XML Signature, XML Encryption, Web Services Security and PKI, SKSML provides standards-based capability to allow any application to use symmetric encryption keys, while maintaining centralized control. This article describes the SKSML protocol and its capabilities.

Gene Fusion Markup Language: a prototype for exchanging gene fusion data.

PubMed

Kalyana-Sundaram, Shanker; Shanmugam, Achiraman; Chinnaiyan, Arul M

2012-10-16

An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with more detailed resolution than previously achieved. However, in the excitement and necessity of publishing the observations from this recently developed cutting-edge technology, no community standardization approach has arisen to organize and represent the data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future. Here we propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools. The GFML prototype is made available at http://code.google.com/p/gfml-prototype/. The Gene Fusion Markup Language (GFML) presented here could facilitate the development of a standard format for organizing, integrating and representing the significant features of gene fusion data in an inter-operable and query-able fashion that will enable biologically intuitive access to gene fusion findings and expedite functional characterization. A similar model is envisaged for other NGS data analyses.

Reducing tobacco use and access through strengthened minimum price laws.

PubMed

McLaughlin, Ian; Pearson, Anne; Laird-Metke, Elisa; Ribisl, Kurt

2014-10-01

Higher prices reduce consumption and initiation of tobacco products. A minimum price law that establishes a high statutory minimum price and prohibits the industry's discounting tactics for tobacco products is a promising pricing strategy as an alternative to excise tax increases. Although some states have adopted minimum price laws on the basis of statutorily defined price "markups" over the invoice price, existing state laws have been largely ineffective at increasing the retail price. We analyzed 3 new variations of minimum price laws that hold great potential for raising tobacco prices and reducing consumption: (1) a flat rate minimum price law similar to a recent enactment in New York City, (2) an enhanced markup law, and (3) a law that incorporates both elements.

Applying a Service-Oriented Architecture to Operational Flight Program Development

DTIC Science & Technology

2007-09-01

using two Java 2 Enterprise Edition (J2EE) Web servers. The weapon models were accessed using a SUN Microsystems Java Web Services Development Pack...Oriented Architectures 22 CROSSTALK The Journal of Defense Software Engineering September 2007 tion, and Spring/ Hibernate to provide the data access...tion since a major coding effort was avoided. The majority of the effort was tweaking pre-existing Java source code and editing of eXtensible Markup

Migrating an Online Service to WAP - A Case Study.

ERIC Educational Resources Information Center

Klasen, Lars

2002-01-01

Discusses mobile access via wireless application protocol (WAP) to online services that is offered in Sweden through InfoTorg. Topics include the Swedish online market; filtering HTML data from an Internet/Web server into WML (wireless markup language); mobile phone technology; microbrowsers; WAP protocol; and future possibilities. (LRW)

Hospital markup and operation outcomes in the United States.

PubMed

Gani, Faiz; Ejaz, Aslam; Makary, Martin A; Pawlik, Timothy M

2016-07-01

Although the price hospitals charge for operations has broad financial implications, hospital pricing is not subject to regulation. We sought to characterize national variation in hospital price markup for major cardiothoracic and gastrointestinal operations and to evaluate perioperative outcomes of hospitals relative to hospital price markup. All hospitals in which a patient underwent a cardiothoracic or gastrointestinal procedure were identified using the Nationwide Inpatient Sample for 2012. Markup ratios (ratio of charges to costs) for the total cost of hospitalization were compared across hospitals. Risk-adjusted morbidity, failure-to-rescue, and mortality were calculated using multivariable, hierarchical logistic regression. Among the 3,498 hospitals identified, markup ratios ranged from 0.5-12.2, with a median markup ratio of 2.8 (interquartile range 2.7-3.9). For the 888 hospitals with extreme markup (greatest markup ratio quartile: markup ratio >3.9), the median markup ratio was 4.9 (interquartile range 4.3-6.0), with 10% of these hospitals billing more than 7 times the Medicare-allowable costs (markup ratio ≥7.25). Extreme markup hospitals were more often large (46.3% vs 33.8%, P < .001), urban, nonteaching centers (57.0% vs 37.9%, P < .001), and located in the Southern (46.4% vs 32.8%, P < .001) or Western (27.8% vs 17.6%, P < .001) regions of the United States. Of the 639 investor-owned, for-profit hospitals, 401 hospitals (62.8%) had an extreme markup ratio compared with 19.3% (n = 452) and 6.8% (n = 35) of nonprofit and government hospitals, respectively. Perioperative morbidity (32.7% vs 26.4%, P < .001) was greater at extreme markup hospitals. There is wide variation in hospital markup for cardiothoracic and gastrointestinal procedures, with approximately a quarter of hospital charges being 4 times greater than the actual cost of hospitalization. Hospitals with an extreme markup had greater perioperative morbidity. Copyright © 2016 Elsevier Inc. All rights reserved.

Do state minimum markup/price laws work? Evidence from retail scanner data and TUS-CPS

PubMed Central

Huang, Jidong; Chriqui, Jamie F; DeLong, Hillary; Mirza, Maryam; Diaz, Megan C; Chaloupka, Frank J

2016-01-01

Background Minimum markup/price laws (MPLs) have been proposed as an alternative non-tax pricing strategy to reduce tobacco use and access. However, the empirical evidence on the effectiveness of MPLs in increasing cigarette prices is very limited. This study aims to fill this critical gap by examining the association between MPLs and cigarette prices. Methods State MPLs were compiled from primary legal research databases and were linked to cigarette prices constructed from the Nielsen retail scanner data and the self-reported cigarette prices from the Tobacco Use Supplement to the Current Population Survey. Multivariate regression analyses were conducted to examine the association between MPLs and the major components of MPLs and cigarette prices. Results The presence of MPLs was associated with higher cigarette prices. In addition, cigarette prices were higher, above and beyond the higher prices resulting from MPLs, in states that prohibit below-cost combination sales; do not allow any distributing party to use trade discounts to reduce the base cost of cigarettes; prohibit distributing parties from meeting the price of a competitor, and prohibit distributing below-cost coupons to the consumer. Moreover, states that had total markup rates >24% were associated with significantly higher cigarette prices. Conclusions MPLs are an effective way to increase cigarette prices. The impact of MPLs can be further strengthened by imposing greater markup rates and by prohibiting coupon distribution, competitor price matching, and use of below-cost combination sales and trade discounts. PMID:27697948

A Leaner, Meaner Markup Language.

ERIC Educational Resources Information Center

Online & CD-ROM Review, 1997

1997-01-01

In 1996 a working group of the World Wide Web Consortium developed and released a simpler form of markup language, Extensible Markup Language (XML), combining the flexibility of standard Generalized Markup Language (SGML) and the Web suitability of HyperText Markup Language (HTML). Reviews SGML and discusses XML's suitability for journal…

Gene Fusion Markup Language: a prototype for exchanging gene fusion data

PubMed Central

2012-01-01

Background An avalanche of next generation sequencing (NGS) studies has generated an unprecedented amount of genomic structural variation data. These studies have also identified many novel gene fusion candidates with more detailed resolution than previously achieved. However, in the excitement and necessity of publishing the observations from this recently developed cutting-edge technology, no community standardization approach has arisen to organize and represent the data with the essential attributes in an interchangeable manner. As transcriptome studies have been widely used for gene fusion discoveries, the current non-standard mode of data representation could potentially impede data accessibility, critical analyses, and further discoveries in the near future. Results Here we propose a prototype, Gene Fusion Markup Language (GFML) as an initiative to provide a standard format for organizing and representing the significant features of gene fusion data. GFML will offer the advantage of representing the data in a machine-readable format to enable data exchange, automated analysis interpretation, and independent verification. As this database-independent exchange initiative evolves it will further facilitate the formation of related databases, repositories, and analysis tools. The GFML prototype is made available at http://code.google.com/p/gfml-prototype/. Conclusion The Gene Fusion Markup Language (GFML) presented here could facilitate the development of a standard format for organizing, integrating and representing the significant features of gene fusion data in an inter-operable and query-able fashion that will enable biologically intuitive access to gene fusion findings and expedite functional characterization. A similar model is envisaged for other NGS data analyses. PMID:23072312

So You Wanna Be a Web Author?

ERIC Educational Resources Information Center

Buchanan, Larry

1996-01-01

Defines HyperText Markup Language (HTML) as it relates to the World Wide Web (WWW). Describes steps needed to create HTML files on a UNIX system and to make them accessible via the WWW. Presents a list of basic HTML formatting codes and explains the coding used in the author's personal HTML file. (JMV)

PIML: the Pathogen Information Markup Language.

PubMed

He, Yongqun; Vines, Richard R; Wattam, Alice R; Abramochkin, Georgiy V; Dickerman, Allan W; Eckart, J Dana; Sobral, Bruno W S

2005-01-01

A vast amount of information about human, animal and plant pathogens has been acquired, stored and displayed in varied formats through different resources, both electronically and otherwise. However, there is no community standard format for organizing this information or agreement on machine-readable format(s) for data exchange, thereby hampering interoperation efforts across information systems harboring such infectious disease data. The Pathogen Information Markup Language (PIML) is a free, open, XML-based format for representing pathogen information. XSLT-based visual presentations of valid PIML documents were developed and can be accessed through the PathInfo website or as part of the interoperable web services federation known as ToolBus/PathPort. Currently, detailed PIML documents are available for 21 pathogens deemed of high priority with regard to public health and national biological defense. A dynamic query system allows simple queries as well as comparisons among these pathogens. Continuing efforts are being taken to include other groups' supporting PIML and to develop more PIML documents. All the PIML-related information is accessible from http://www.vbi.vt.edu/pathport/pathinfo/

XML: A Language To Manage the World Wide Web. ERIC Digest.

ERIC Educational Resources Information Center

Davis-Tanous, Jennifer R.

This digest provides an overview of XML (Extensible Markup Language), a markup language used to construct World Wide Web pages. Topics addressed include: (1) definition of a markup language, including comparison of XML with SGML (Standard Generalized Markup Language) and HTML (HyperText Markup Language); (2) how XML works, including sample tags,…

Microprocessor-controlled, wide-range streak camera

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

Amy E. Lewis, Craig Hollabaugh

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storagemore » using flash-based storage media. The camera’s user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.« less

Microprocessor-controlled wide-range streak camera

NASA Astrophysics Data System (ADS)

Lewis, Amy E.; Hollabaugh, Craig

2006-08-01

Bechtel Nevada/NSTec recently announced deployment of their fifth generation streak camera. This camera incorporates many advanced features beyond those currently available for streak cameras. The arc-resistant driver includes a trigger lockout mechanism, actively monitors input trigger levels, and incorporates a high-voltage fault interrupter for user safety and tube protection. The camera is completely modular and may deflect over a variable full-sweep time of 15 nanoseconds to 500 microseconds. The camera design is compatible with both large- and small-format commercial tubes from several vendors. The embedded microprocessor offers Ethernet connectivity, and XML [extensible markup language]-based configuration management with non-volatile parameter storage using flash-based storage media. The camera's user interface is platform-independent (Microsoft Windows, Unix, Linux, Macintosh OSX) and is accessible using an AJAX [asynchronous Javascript and XML]-equipped modem browser, such as Internet Explorer 6, Firefox, or Safari. User interface operation requires no installation of client software or browser plug-in technology. Automation software can also access the camera configuration and control using HTTP [hypertext transfer protocol]. The software architecture supports multiple-simultaneous clients, multiple cameras, and multiple module access with a standard browser. The entire user interface can be customized.

Designing a Virtual Classroom for Distance Learning Students through the Internet.

ERIC Educational Resources Information Center

Bradshaw, Allen

Advantages to using the Internet to deliver instruction include the fact that Hypertext Markup Language (HTML) can be accessed on any computer, broadening the student base to anyone with an Internet browser and a PPP (Point-to-Point Protocol) account. In addition, instructions, lectures, and examples can be linked together for use as students need…

Development of the Plate Tectonics and Seismology markup languages with XML

NASA Astrophysics Data System (ADS)

Babaie, H.; Babaei, A.

2003-04-01

The Extensible Markup Language (XML) and its specifications such as the XSD Schema, allow geologists to design discipline-specific vocabularies such as Seismology Markup Language (SeismML) or Plate Tectonics Markup Language (TectML). These languages make it possible to store and interchange structured geological information over the Web. Development of a geological markup language requires mapping geological concepts, such as "Earthquake" or "Plate" into a UML object model, applying a modeling and design environment. We have selected four inter-related geological concepts: earthquake, fault, plate, and orogeny, and developed four XML Schema Definitions (XSD), that define the relationships, cardinalities, hierarchies, and semantics of these concepts. In such a geological concept model, the UML object "Earthquake" is related to one or more "Wave" objects, each arriving to a seismic station at a specific "DateTime", and relating to a specific "Epicenter" object that lies at a unique "Location". The "Earthquake" object occurs along a "Segment" of a "Fault" object, which is related to a specific "Plate" object. The "Fault" has its own associations with such things as "Bend", "Step", and "Segment", and could be of any kind (e.g., "Thrust", "Transform'). The "Plate" is related to many other objects such as "MOR", "Subduction", and "Forearc", and is associated with an "Orogeny" object that relates to "Deformation" and "Strain" and several other objects. These UML objects were mapped into XML Metadata Interchange (XMI) formats, which were then converted into four XSD Schemas. The schemas were used to create and validate the XML instance documents, and to create a relational database hosting the plate tectonics and seismological data in the Microsoft Access format. The SeismML and TectML allow seismologists and structural geologists, among others, to submit and retrieve structured geological data on the Internet. A seismologist, for example, can submit peer-reviewed and reliable data about a specific earthquake to a Java Server Page on our web site hosting the XML application. Other geologists can readily retrieve the submitted data, saved in files or special tables of the designed database, through a search engine designed with J2EE (JSP, servlet, Java Bean) and XML specifications such as XPath, XPointer, and XSLT. When extended to include all the important concepts of seismology and plate tectonics, the two markup languages will make global interchange of geological data a reality.

SGML-Based Markup for Literary Texts: Two Problems and Some Solutions.

ERIC Educational Resources Information Center

Barnard, David; And Others

1988-01-01

Identifies the Standard Generalized Markup Language (SGML) as the best basis for a markup standard for encoding literary texts. Outlines solutions to problems using SGML and discusses the problem of maintaining multiple views of a document. Examines several ways of reducing the burden of markups. (GEA)

iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

PubMed Central

2015-01-01

As the amount of data generated by biomolecular simulations dramatically increases, new tools need to be developed to help manage this data at the individual investigator or small research group level. In this paper, we introduce iBIOMES Lite, a lightweight tool for biomolecular simulation data indexing and summarization. The main goal of iBIOMES Lite is to provide a simple interface to summarize computational experiments in a setting where the user might have limited privileges and limited access to IT resources. A command-line interface allows the user to summarize, publish, and search local simulation data sets. Published data sets are accessible via static hypertext markup language (HTML) pages that summarize the simulation protocols and also display data analysis graphically. The publication process is customized via extensible markup language (XML) descriptors while the HTML summary template is customized through extensible stylesheet language (XSL). iBIOMES Lite was tested on different platforms and at several national computing centers using various data sets generated through classical and quantum molecular dynamics, quantum chemistry, and QM/MM. The associated parsers currently support AMBER, GROMACS, Gaussian, and NWChem data set publication. The code is available at https://github.com/jcvthibault/ibiomes. PMID:24830957

Do state minimum markup/price laws work? Evidence from retail scanner data and TUS-CPS.

PubMed

Huang, Jidong; Chriqui, Jamie F; DeLong, Hillary; Mirza, Maryam; Diaz, Megan C; Chaloupka, Frank J

2016-10-01

Minimum markup/price laws (MPLs) have been proposed as an alternative non-tax pricing strategy to reduce tobacco use and access. However, the empirical evidence on the effectiveness of MPLs in increasing cigarette prices is very limited. This study aims to fill this critical gap by examining the association between MPLs and cigarette prices. State MPLs were compiled from primary legal research databases and were linked to cigarette prices constructed from the Nielsen retail scanner data and the self-reported cigarette prices from the Tobacco Use Supplement to the Current Population Survey. Multivariate regression analyses were conducted to examine the association between MPLs and the major components of MPLs and cigarette prices. The presence of MPLs was associated with higher cigarette prices. In addition, cigarette prices were higher, above and beyond the higher prices resulting from MPLs, in states that prohibit below-cost combination sales; do not allow any distributing party to use trade discounts to reduce the base cost of cigarettes; prohibit distributing parties from meeting the price of a competitor, and prohibit distributing below-cost coupons to the consumer. Moreover, states that had total markup rates >24% were associated with significantly higher cigarette prices. MPLs are an effective way to increase cigarette prices. The impact of MPLs can be further strengthened by imposing greater markup rates and by prohibiting coupon distribution, competitor price matching, and use of below-cost combination sales and trade discounts. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/.

Facilitating NCAR Data Discovery by Connecting Related Resources

NASA Astrophysics Data System (ADS)

Rosati, A.

2012-12-01

Linking datasets, creators, and users by employing the proper standards helps to increase the impact of funded research. In order for users to find a dataset, it must first be named. Data citations play the important role of giving datasets a persistent presence by assigning a formal "name" and location. This project focuses on the next step of the "name-find-use" sequence: enhancing discoverability of NCAR data by connecting related resources on the web. By examining metadata schemas that document datasets, I examined how Semantic Web approaches can help to ensure the widest possible range of data users. The focus was to move from search engine optimization (SEO) to information connectivity. Two main markup types are very visible in the Semantic Web and applicable to scientific dataset discovery: The Open Archives Initiative-Object Reuse and Exchange (OAI-ORE - www.openarchives.org) and Microdata (HTML5 and www.schema.org). My project creates pilot aggregations of related resources using both markup types for three case studies: The North American Regional Climate Change Assessment Program (NARCCAP) dataset and related publications, the Palmer Drought Severity Index (PSDI) animation and image files from NCAR's Visualization Lab (VisLab), and the multidisciplinary data types and formats from the Advanced Cooperative Arctic Data and Information Service (ACADIS). This project documents the differences between these markups and how each creates connectedness on the web. My recommendations point toward the most efficient and effective markup schema for aggregating resources within the three case studies based on the following assessment criteria: ease of use, current state of support and adoption of technology, integration with typical web tools, available vocabularies and geoinformatic standards, interoperability with current repositories and access portals (e.g. ESG, Java), and relation to data citation tools and methods.

HDF-EOS Web Server

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A shell script has been written as a means of automatically making HDF-EOS-formatted data sets available via the World Wide Web. ("HDF-EOS" and variants thereof are defined in the first of the two immediately preceding articles.) The shell script chains together some software tools developed by the Data Usability Group at Goddard Space Flight Center to perform the following actions: Extract metadata in Object Definition Language (ODL) from an HDF-EOS file, Convert the metadata from ODL to Extensible Markup Language (XML), Reformat the XML metadata into human-readable Hypertext Markup Language (HTML), Publish the HTML metadata and the original HDF-EOS file to a Web server and an Open-source Project for a Network Data Access Protocol (OPeN-DAP) server computer, and Reformat the XML metadata and submit the resulting file to the EOS Clearinghouse, which is a Web-based metadata clearinghouse that facilitates searching for, and exchange of, Earth-Science data.

Instrument Remote Control Application Framework

NASA Technical Reports Server (NTRS)

Ames, Troy; Hostetter, Carl F.

2006-01-01

The Instrument Remote Control (IRC) architecture is a flexible, platform-independent application framework that is well suited for the control and monitoring of remote devices and sensors. IRC enables significant savings in development costs by utilizing extensible Markup Language (XML) descriptions to configure the framework for a specific application. The Instrument Markup Language (IML) is used to describe the commands used by an instrument, the data streams produced, the rules for formatting commands and parsing the data, and the method of communication. Often no custom code is needed to communicate with a new instrument or device. An IRC instance can advertise and publish a description about a device or subscribe to another device's description on a network. This simple capability of dynamically publishing and subscribing to interfaces enables a very flexible, self-adapting architecture for monitoring and control of complex instruments in diverse environments.

ScienceCentral: open access full-text archive of scientific journals based on Journal Article Tag Suite regardless of their languages.

PubMed

Huh, Sun

2013-01-01

ScienceCentral, a free or open access, full-text archive of scientific journal literature at the Korean Federation of Science and Technology Societies, was under test in September 2013. Since it is a Journal Article Tag Suite-based full text database, extensible markup language files of all languages can be presented, according to Unicode Transformation Format 8-bit encoding. It is comparable to PubMed Central: however, there are two distinct differences. First, its scope comprises all science fields; second, it accepts all language journals. Launching ScienceCentral is the first step for free access or open access academic scientific journals of all languages to leap to the world, including scientific journals from Croatia.

Variation in markup of general surgical procedures by hospital market concentration.

PubMed

Cerullo, Marcelo; Chen, Sophia Y; Dillhoff, Mary; Schmidt, Carl R; Canner, Joseph K; Pawlik, Timothy M

2018-04-01

Increasing hospital market concentration (with concomitantly decreasing hospital market competition) may be associated with rising hospital prices. Hospital markup - the relative increase in price over costs - has been associated with greater hospital market concentration. Patients undergoing a cardiothoracic or gastrointestinal procedure in the 2008-2011 Nationwide Inpatient Sample (NIS) were identified and linked to Hospital Market Structure Files. The association between market concentration, hospital markup and hospital for-profit status was assessed using mixed-effects log-linear models. A weighted total of 1,181,936 patients were identified. In highly concentrated markets, private for-profit status was associated with an 80.8% higher markup compared to public/private not-for-profit status (95%CI: +69.5% - +96.9%; p < 0.001). However, private for-profit status in highly concentrated markets was associated with only a 62.9% higher markup compared to public/private not-for-profit status in unconcentrated markets (95%CI: +45.4% - +81.1%; p < 0.001). Hospital for-profit status modified the association between hospitals' market concentration and markup. Government and private not-for-profit hospitals employed lower markups in more concentrated markets, whereas private for-profit hospitals employed higher markups in more concentrated markets. Copyright © 2017 Elsevier Inc. All rights reserved.

Digitising legacy zoological taxonomic literature: Processes, products and using the output

PubMed Central

Lyal, Christopher H. C.

2016-01-01

Abstract By digitising legacy taxonomic literature using XML mark-up the contents become accessible to other taxonomic and nomenclatural information systems. Appropriate schemas need to be interoperable with other sectorial schemas, atomise to appropriate content elements and carry appropriate metadata to, for example, enable algorithmic assessment of availability of a name under the Code. Legacy (and new) literature delivered in this fashion will become part of a global taxonomic resource from which users can extract tailored content to meet their particular needs, be they nomenclatural, taxonomic, faunistic or other. To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output of the many efforts has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, the means by which many scientific papers are indexed and located is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising taxonomic names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be searched directly. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original papers and extract target content manually. This opens the door to dynamic linking of new content with extant systems: automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. A means to do this is through marking up content into XML, and the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. We now need to automate this process as far as possible. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying in its production the requirements of the Code, is fit for purpose in the future. PMID:26877659

Interoperability In The New Planetary Science Archive (PSA)

NASA Astrophysics Data System (ADS)

Rios, C.; Barbarisi, I.; Docasal, R.; Macfarlane, A. J.; Gonzalez, J.; Arviset, C.; Grotheer, E.; Besse, S.; Martinez, S.; Heather, D.; De Marchi, G.; Lim, T.; Fraga, D.; Barthelemy, M.

2015-12-01

As the world becomes increasingly interconnected, there is a greater need to provide interoperability with software and applications that are commonly being used globally. For this purpose, the development of the new Planetary Science Archive (PSA), by the European Space Astronomy Centre (ESAC) Science Data Centre (ESDC), is focused on building a modern science archive that takes into account internationally recognised standards in order to provide access to the archive through tools from third parties, for example by the NASA Planetary Data System (PDS), the VESPA project from the Virtual Observatory of Paris as well as other international institutions. The protocols and standards currently being supported by the new Planetary Science Archive at this time are the Planetary Data Access Protocol (PDAP), the EuroPlanet-Table Access Protocol (EPN-TAP) and Open Geospatial Consortium (OGC) standards. The architecture of the PSA consists of a Geoserver (an open-source map server), the goal of which is to support use cases such as the distribution of search results, sharing and processing data through a OGC Web Feature Service (WFS) and a Web Map Service (WMS). This server also allows the retrieval of requested information in several standard output formats like Keyhole Markup Language (KML), Geography Markup Language (GML), shapefile, JavaScript Object Notation (JSON) and Comma Separated Values (CSV), among others. The provision of these various output formats enables end-users to be able to transfer retrieved data into popular applications such as Google Mars and NASA World Wind.

Definition of an XML markup language for clinical laboratory procedures and comparison with generic XML markup.

PubMed

Saadawi, Gilan M; Harrison, James H

2006-10-01

Clinical laboratory procedure manuals are typically maintained as word processor files and are inefficient to store and search, require substantial effort for review and updating, and integrate poorly with other laboratory information. Electronic document management systems could improve procedure management and utility. As a first step toward building such systems, we have developed a prototype electronic format for laboratory procedures using Extensible Markup Language (XML). Representative laboratory procedures were analyzed to identify document structure and data elements. This information was used to create a markup vocabulary, CLP-ML, expressed as an XML Document Type Definition (DTD). To determine whether this markup provided advantages over generic markup, we compared procedures structured with CLP-ML or with the vocabulary of the Health Level Seven, Inc. (HL7) Clinical Document Architecture (CDA) narrative block. CLP-ML includes 124 XML tags and supports a variety of procedure types across different laboratory sections. When compared with a general-purpose markup vocabulary (CDA narrative block), CLP-ML documents were easier to edit and read, less complex structurally, and simpler to traverse for searching and retrieval. In combination with appropriate software, CLP-ML is designed to support electronic authoring, reviewing, distributing, and searching of clinical laboratory procedures from a central repository, decreasing procedure maintenance effort and increasing the utility of procedure information. A standard electronic procedure format could also allow laboratories and vendors to share procedures and procedure layouts, minimizing duplicative word processor editing. Our results suggest that laboratory-specific markup such as CLP-ML will provide greater benefit for such systems than generic markup.

XML syntax for clinical laboratory procedure manuals.

PubMed

Saadawi, Gilan; Harrison, James H

2003-01-01

We have developed a document type description (DTD) in Extensable Markup Language (XML) for clinical laboratory procedures. Our XML syntax can adequately structure a variety of procedure types across different laboratories and is compatible with current procedure standards. The combination of this format with an XML content management system and appropriate style sheets will allow efficient procedure maintenance, distributed access, customized display and effective searching across a large body of test information.

Payao: a community platform for SBML pathway model curation

PubMed Central

Matsuoka, Yukiko; Ghosh, Samik; Kikuchi, Norihiro; Kitano, Hiroaki

2010-01-01

Summary: Payao is a community-based, collaborative web service platform for gene-regulatory and biochemical pathway model curation. The system combines Web 2.0 technologies and online model visualization functions to enable a collaborative community to annotate and curate biological models. Payao reads the models in Systems Biology Markup Language format, displays them with CellDesigner, a process diagram editor, which complies with the Systems Biology Graphical Notation, and provides an interface for model enrichment (adding tags and comments to the models) for the access-controlled community members. Availability and implementation: Freely available for model curation service at http://www.payaologue.org. Web site implemented in Seaser Framework 2.0 with S2Flex2, MySQL 5.0 and Tomcat 5.5, with all major browsers supported. Contact: kitano@sbi.jp PMID:20371497

ScienceCentral: open access full-text archive of scientific journals based on Journal Article Tag Suite regardless of their languages

PubMed Central

Huh, Sun

2013-01-01

ScienceCentral, a free or open access, full-text archive of scientific journal literature at the Korean Federation of Science and Technology Societies, was under test in September 2013. Since it is a Journal Article Tag Suite-based full text database, extensible markup language files of all languages can be presented, according to Unicode Transformation Format 8-bit encoding. It is comparable to PubMed Central: however, there are two distinct differences. First, its scope comprises all science fields; second, it accepts all language journals. Launching ScienceCentral is the first step for free access or open access academic scientific journals of all languages to leap to the world, including scientific journals from Croatia. PMID:24266292

ART-ML: a new markup language for modelling and representation of biological processes in cardiovascular diseases.

PubMed

Karvounis, E C; Exarchos, T P; Fotiou, E; Sakellarios, A I; Iliopoulou, D; Koutsouris, D; Fotiadis, D I

2013-01-01

With an ever increasing number of biological models available on the internet, a standardized modelling framework is required to allow information to be accessed and visualized. In this paper we propose a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of geometry, blood flow, plaque progression and stent modelling, exported by any cardiovascular disease modelling software. ART-ML has been developed and tested using ARTool. ARTool is a platform for the automatic processing of various image modalities of coronary and carotid arteries. The images and their content are fused to develop morphological models of the arteries in 3D representations. All the above described procedures integrate disparate data formats, protocols and tools. ART-ML proposes a representation way, expanding ARTool, for interpretability of the individual resources, creating a standard unified model for the description of data and, consequently, a format for their exchange and representation that is machine independent. More specifically, ARTool platform incorporates efficient algorithms which are able to perform blood flow simulations and atherosclerotic plaque evolution modelling. Integration of data layers between different modules within ARTool are based upon the interchange of information included in the ART-ML model repository. ART-ML provides a markup representation that enables the representation and management of embedded models within the cardiovascular disease modelling platform, the storage and interchange of well-defined information. The corresponding ART-ML model incorporates all relevant information regarding geometry, blood flow, plaque progression and stent modelling procedures. All created models are stored in a model repository database which is accessible to the research community using efficient web interfaces, enabling the interoperability of any cardiovascular disease modelling software models. ART-ML can be used as a reference ML model in multiscale simulations of plaque formation and progression, incorporating all scales of the biological processes.

XML: An Introduction.

ERIC Educational Resources Information Center

Lewis, John D.

1998-01-01

Describes XML (extensible markup language), a new language classification submitted to the World Wide Web Consortium that is defined in terms of both SGML (Standard Generalized Markup Language) and HTML (Hypertext Markup Language), specifically designed for the Internet. Limitations of PDF (Portable Document Format) files for electronic journals…

PathwayAccess: CellDesigner plugins for pathway databases.

PubMed

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

Providing Internet Access to High-Resolution Lunar Images

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2008-01-01

The OnMoon server is a computer program that provides Internet access to high-resolution Lunar images, maps, and elevation data, all suitable for use in geographical information system (GIS) software for generating images, maps, and computational models of the Moon. The OnMoon server implements the Open Geospatial Consortium (OGC) Web Map Service (WMS) server protocol and supports Moon-specific extensions. Unlike other Internet map servers that provide Lunar data using an Earth coordinate system, the OnMoon server supports encoding of data in Moon-specific coordinate systems. The OnMoon server offers access to most of the available high-resolution Lunar image and elevation data. This server can generate image and map files in the tagged image file format (TIFF) or the Joint Photographic Experts Group (JPEG), 8- or 16-bit Portable Network Graphics (PNG), or Keyhole Markup Language (KML) format. Image control is provided by use of the OGC Style Layer Descriptor (SLD) protocol. Full-precision spectral arithmetic processing is also available, by use of a custom SLD extension. This server can dynamically add shaded relief based on the Lunar elevation to any image layer. This server also implements tiled WMS protocol and super-overlay KML for high-performance client application programs.

Providing Internet Access to High-Resolution Mars Images

NASA Technical Reports Server (NTRS)

Plesea, Lucian

2008-01-01

The OnMars server is a computer program that provides Internet access to high-resolution Mars images, maps, and elevation data, all suitable for use in geographical information system (GIS) software for generating images, maps, and computational models of Mars. The OnMars server is an implementation of the Open Geospatial Consortium (OGC) Web Map Service (WMS) server. Unlike other Mars Internet map servers that provide Martian data using an Earth coordinate system, the OnMars WMS server supports encoding of data in Mars-specific coordinate systems. The OnMars server offers access to most of the available high-resolution Martian image and elevation data, including an 8-meter-per-pixel uncontrolled mosaic of most of the Mars Global Surveyor (MGS) Mars Observer Camera Narrow Angle (MOCNA) image collection, which is not available elsewhere. This server can generate image and map files in the tagged image file format (TIFF), Joint Photographic Experts Group (JPEG), 8- or 16-bit Portable Network Graphics (PNG), or Keyhole Markup Language (KML) format. Image control is provided by use of the OGC Style Layer Descriptor (SLD) protocol. The OnMars server also implements tiled WMS protocol and super-overlay KML for high-performance client application programs.

Telemetry Attributes Transfer Standard (TMATS) Handbook

DTIC Science & Technology

2015-07-01

Example ......................... 6-1 Appendix A. Extensible Markup Language TMATS Differences ...................................... A-1 Appendix B...return-to-zero - level TG Telemetry Group TM telemetry TMATS Telemetry Attributes Transfer Standard XML eXtensible Markup Language Telemetry... Markup Language) format. The initial version of a standard 1 Range Commanders Council. Telemetry

XML Content Finally Arrives on the Web!

ERIC Educational Resources Information Center

Funke, Susan

1998-01-01

Explains extensible markup language (XML) and how it differs from hypertext markup language (HTML) and standard generalized markup language (SGML). Highlights include features of XML, including better formatting of documents, better searching capabilities, multiple uses for hyperlinking, and an increase in Web applications; Web browsers; and what…

Migration of the Three-dimensional Wind Field (3DWF) Model from Linux to Windows and Mobile Platforms

DTIC Science & Technology

2017-11-01

7 Fig. 10 Build executable code ........................................................................... 8 Fig. 11 3DWF GUI’s main web ...can be designed in any Windows operating system with internet access via Microsoft’s Internet Explorer (IE) web browser. For this particular project...Therefore, it is advised to have network security safeguards in place and operate only in a trusted PC. The GUI’s Hypertext Markup Language (HTML) web

Proof of Concept Integration of a Single-Level Service-Oriented Architecture into a Multi-Domain Secure Environment

DTIC Science & Technology

2008-03-01

Machine [29]. OC4J applications support Java Servlets , Web services, and the following J2EE specific standards: Extensible Markup Language (XML...IMAP Internet Message Access Protocol IP Internet Protocol IT Information Technology xviii J2EE Java Enterprise Environment JSR 168 Java ...LDAP), World Wide Web Distributed Authoring and Versioning (WebDav), Java Specification Request 168 (JSR 168), and Web Services for Remote

An Approach to Dynamic Service Management in Pervasive Computing Systems

DTIC Science & Technology

2005-01-01

standard interface to them that is easily accessible by any user. This paper outlines the design of Centaurus , an infrastructure for presenting...based on Extensi- ble Markup Language (XML) for communication, giving the system a uniform and easily adaptable interface. Centaurus defines a...easy and automatic usage. This is the vision that guides our re- search on the Centaurus system. We define a SmartSpace as a dynamic environment that

48 CFR 552.243-71 - Equitable Adjustments.

Code of Federal Regulations, 2010 CFR

2010-10-01

...) Markups. (3) Change to the time for completion specified in the contract. (e) Direct costs. The Contractor... contract regarding the Contractor's project schedule. (h) Markups. For each firm whose direct costs are... applicable, a bond rate and insurance rate. Markups shall be determined and applied as follows: (1) Overhead...

Competition in the economic crisis: Analysis of procurement auctions.

PubMed

Gugler, Klaus; Weichselbaumer, Michael; Zulehner, Christine

2015-01-01

We study the effects of the recent economic crisis on firms׳ bidding behavior and markups in sealed bid auctions. Using data from Austrian construction procurements, we estimate bidders׳ construction costs within a private value auction model. We find that markups of all bids submitted decrease by 1.5 percentage points in the recent economic crisis, markups of winning bids decrease by 3.3 percentage points. We also find that without the government stimulus package this decrease would have been larger. These two pieces of evidence point to pro-cyclical markups.

The caBIG annotation and image Markup project.

PubMed

Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L

2010-04-01

Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM.

Comparing pharmaceutical pricing and reimbursement policies in Croatia to the European Union Member States.

PubMed

Vogler, Sabine; Habl, Claudia; Bogut, Martina; Voncina, Luka

2011-04-15

To perform a comparative analysis of the pharmaceutical pricing and reimbursement systems in Croatia and the 27 European Union (EU) Member States. Knowledge about the pharmaceutical systems in Croatia and the 27 EU Member States was acquired by literature review and primary research with stakeholders. Pharmaceutical prices are controlled at all levels in Croatia, which is also the case in 21 EU Member States. Like many EU countries, Croatia also applies external price referencing, i.e., compares prices with other countries. While the wholesale remuneration by a statutorily regulated linear mark-up is applied in Croatia and in several EU countries, the pharmacy compensation for dispensing reimbursable medicines in the form of a flat rate service fee in Croatia is rare among EU countries, which usually apply a linear or regressive pharmacy mark-up scheme. Like in most EU countries, the Croatian Social Insurance reimburses specific medicines at 100%, whereas patients are charged co-payments for other reimbursable medicines. Criteria for reimbursement include the medicine's importance from the public health perspective, its therapeutic value, and relative effectiveness. In Croatia and in many EU Member States, reimbursement is based on a reference price system. The Croatian pharmaceutical system is similar to those in the EU Member States. Key policies, like external price referencing and reference price systems, which have increasingly been introduced in EU countries are also applied in Croatia and serve the same purpose: to ensure access to medicines while containing public pharmaceutical expenditure.

Open Access: From Myth to Paradox

ScienceCinema

Ginsparg, Paul [Cornell University, Ithaca, New York, United States

2018-04-19

True open access to scientific publications not only gives readers the possibility to read articles without paying subscription, but also makes the material available for automated ingestion and harvesting by 3rd parties. Once articles and associated data become universally treatable as computable objects, openly available to 3rd party aggregators and value-added services, what new services can we expect, and how will they change the way that researchers interact with their scholarly communications infrastructure? I will discuss straightforward applications of existing ideas and services, including citation analysis, collaborative filtering, external database linkages, interoperability, and other forms of automated markup, and speculate on the sociology of the next generation of users.

Analysis of Content Legibility for Smartphones of Websites of the Korean Urological Association and Other Urological Societies in Korea

PubMed Central

Lee, Joo Yong; Kang, Dong Hyuk; Moon, Hong Sang; Kim, Yong Tae; Yoo, Tag Keun; Choi, Hong Yong; Lee, Tchun Yong

2011-01-01

Purpose We performed an analysis of the smartphone legibility of the websites of the Korean Urological Association (KUA) and other urological societies. Materials and Methods This study was conducted on the websites of the KUA and nine other urological societies. Each website was accessed via iPhone Safari and Android Chrome, respectively, to evaluate the establishment and readability of the mobile web pages. The provision of Really Simple Syndication (RSS) feeds by the websites and whether the websites had Twitter and Facebook accounts were evaluated. In addition, a validation test on the web standards was performed by using the World Wide Web Consortium (W3C®) Markup Validation Service, and subsequently the numbers of errors and warnings that occurred were analyzed. Results When accessed via Safari, two websites were legible, four were somewhat legible, and four were somewhat illegible. When accessed via Chrome, two websites were legible, six were somewhat legible, and two were somewhat illegible. One website provided an RSS feed and two websites managed members via separate Twitter accounts. No website supported mobile web pages. The result of the W3C® Markup Validation test on 10 websites showed a mean error rate of 221.6 (range, 13-1,477) and a mean warning rate of 127.13 (range, 0-655). Conclusions The smartphone legibility level of the websites of urological societies was relatively low. Improved smartphone legibility and web standard compliance of the websites of urological societies are required to keep up with the popularity of smartphones. PMID:21379433

Data Display Markup Language (DDML) Handbook

DTIC Science & Technology

2017-01-31

Moreover, the tendency of T&E is towards a plug-and-play-like data acquisition system that requires standard languages and modules for data displays...Telemetry Group DOCUMENT 127-17 DATA DISPLAY MARKUP LANGUAGE (DDML) HANDBOOK DISTRIBUTION A: APPROVED FOR...DOCUMENT 127-17 DATA DISPLAY MARKUP LANGUAGE (DDML) HANDBOOK January 2017 Prepared by Telemetry Group

A Conversion Tool for Mathematical Expressions in Web XML Files.

ERIC Educational Resources Information Center

Ohtake, Nobuyuki; Kanahori, Toshihiro

2003-01-01

This article discusses the conversion of mathematical equations into Extensible Markup Language (XML) on the World Wide Web for individuals with visual impairments. A program is described that converts the presentation markup style to the content markup style in MathML to allow browsers to render mathematical expressions without other programs.…

Answer Markup Algorithms for Southeast Asian Languages.

ERIC Educational Resources Information Center

Henry, George M.

1991-01-01

Typical markup methods for providing feedback to foreign language learners are not applicable to languages not written in a strictly linear fashion. A modification of Hart's edit markup software is described, along with a second variation based on a simple edit distance algorithm adapted to a general Southeast Asian font system. (10 references)…

An Introduction to the Extensible Markup Language (XML).

ERIC Educational Resources Information Center

Bryan, Martin

1998-01-01

Describes Extensible Markup Language (XML), a subset of the Standard Generalized Markup Language (SGML) that is designed to make it easy to interchange structured documents over the Internet. Topics include Document Type Definition (DTD), components of XML, the use of XML, text and non-text elements, and uses for XML-coded files. (LRW)

Chemical Markup, XML and the World-Wide Web. 8. Polymer Markup Language.

PubMed

Adams, Nico; Winter, Jerry; Murray-Rust, Peter; Rzepa, Henry S

2008-11-01

Polymers are among the most important classes of materials but are only inadequately supported by modern informatics. The paper discusses the reasons why polymer informatics is considerably more challenging than small molecule informatics and develops a vision for the computer-aided design of polymers, based on modern semantic web technologies. The paper then discusses the development of Polymer Markup Language (PML). PML is an extensible language, designed to support the (structural) representation of polymers and polymer-related information. PML closely interoperates with Chemical Markup Language (CML) and overcomes a number of the previously identified challenges.

Data on the interexaminer variation of minutia markup on latent fingerprints.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2016-09-01

The data in this article supports the research paper entitled "Interexaminer variation of minutia markup on latent fingerprints" [1]. The data in this article describes the variability in minutia markup during both analysis of the latents and comparison between latents and exemplars. The data was collected in the "White Box Latent Print Examiner Study," in which each of 170 volunteer latent print examiners provided detailed markup documenting their examinations of latent-exemplar pairs of prints randomly assigned from a pool of 320 pairs. Each examiner examined 22 latent-exemplar pairs; an average of 12 examiners marked each latent.

Network Application Server Using Extensible Mark-Up Language (XML) to Support Distributed Databases and 3D Environments

DTIC Science & Technology

2001-12-01

diides.ncr.disa.mil/xmlreg/user/index.cfm] [ Deitel ] Deitel , H., Deitel , P., Java How to Program 3rd Edition, Prentice Hall, 1999. [DL99...presentation, and data) of information and the programming functionality. The Web framework addressed ability to provide a framework for the distribution...BLANK v ABSTRACT Advances in computer communication technology and an increased awareness of how enhanced information access can lead to improved

Analysis of prices paid by low-income countries - how price sensitive is government demand for medicines?

PubMed

Srivastava, Divya; McGuire, Alistair

2014-07-30

Access to medicines is an important health policy issue. This paper considers demand structures in a selection of low-income countries from the perspective of public authorities as the evidence base is limited. Analysis of the demand for medicines in low-income countries is critical for effective pharmaceutical policy where regulation is less developed, health systems are cash constrained and medicines are not typically subsidised by a public health insurance system This study analyses the demand for medicines in low-income countries from the perspective of the prices paid by public authorities. The analysis draws on a unique dataset from World Health Organization (WHO) and Health Action International (HAI) using 2003 data on procurement prices of medicines across 16 low-income countries covering 48 branded drugs and 18 therapeutic categories. Variation in prices, the mark-ups over marginal costs and estimation of price elasticities allows assessment of whether these elasticities are correlated with a country's national income. Using the Ramsey pricing rule, the study's findings suggest that substantial cross-country variation in prices and mark-ups exist, with price elasticities ranging from -1 to -2, which are weakly correlated with national income. Government demand for medicines thus appears to be price elastic, raising important policy implications aimed at improving access to medicines for patients in low-income countries.

Semantic Markup for Literary Scholars: How Descriptive Markup Affects the Study and Teaching of Literature.

ERIC Educational Resources Information Center

Campbell, D. Grant

2002-01-01

Describes a qualitative study which investigated the attitudes of literary scholars towards the features of semantic markup for primary texts in XML format. Suggests that layout is a vital part of the reading process which implies that the standardization of DTDs (Document Type Definitions) should extend to styling as well. (Author/LRW)

XML Style Guide

DTIC Science & Technology

2015-07-01

Acronyms ASCII American Standard Code for Information Interchange DAU data acquisition unit DDML data display markup language IHAL...Transfer Standard URI uniform resource identifier W3C World Wide Web Consortium XML extensible markup language XSD XML schema definition XML Style...Style Guide, RCC 125-15, July 2015 1 Introduction The next generation of telemetry systems will rely heavily on extensible markup language (XML

DDML Schema Validation

DTIC Science & Technology

2016-02-08

Data Display Markup Language HUD heads-up display IRIG Inter-Range Instrumentation Group RCC Range Commanders Council SVG Scalable Vector Graphics...T&E test and evaluation TMATS Telemetry Attributes Transfer Standard XML eXtensible Markup Language DDML Schema Validation, RCC 126-16, February...2016 viii This page intentionally left blank. DDML Schema Validation, RCC 126-16, February 2016 1 1. Introduction This Data Display Markup

77 FR 47896 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-10

... that it is appropriate to charge a markup with respect to directed orders to reflect the costs of offering routing services and the value of such services. Notably, in all instances NASDAQ charges a markup... that it does not currently charge a markup with respect to non-directed orders that are routed to PSX...

Application of whole slide image markup and annotation for pathologist knowledge capture.

PubMed

Campbell, Walter S; Foster, Kirk W; Hinrichs, Steven H

2013-01-01

The ability to transfer image markup and annotation data from one scanned image of a slide to a newly acquired image of the same slide within a single vendor platform was investigated. The goal was to study the ability to use image markup and annotation data files as a mechanism to capture and retain pathologist knowledge without retaining the entire whole slide image (WSI) file. Accepted mathematical principles were investigated as a method to overcome variations in scans of the same glass slide and to accurately associate image markup and annotation data across different WSI of the same glass slide. Trilateration was used to link fixed points within the image and slide to the placement of markups and annotations of the image in a metadata file. Variation in markup and annotation placement between WSI of the same glass slide was reduced from over 80 μ to less than 4 μ in the x-axis and from 17 μ to 6 μ in the y-axis (P < 0.025). This methodology allows for the creation of a highly reproducible image library of histopathology images and interpretations for educational and research use.

Application of whole slide image markup and annotation for pathologist knowledge capture

PubMed Central

Campbell, Walter S.; Foster, Kirk W.; Hinrichs, Steven H.

2013-01-01

Objective: The ability to transfer image markup and annotation data from one scanned image of a slide to a newly acquired image of the same slide within a single vendor platform was investigated. The goal was to study the ability to use image markup and annotation data files as a mechanism to capture and retain pathologist knowledge without retaining the entire whole slide image (WSI) file. Methods: Accepted mathematical principles were investigated as a method to overcome variations in scans of the same glass slide and to accurately associate image markup and annotation data across different WSI of the same glass slide. Trilateration was used to link fixed points within the image and slide to the placement of markups and annotations of the image in a metadata file. Results: Variation in markup and annotation placement between WSI of the same glass slide was reduced from over 80 μ to less than 4 μ in the x-axis and from 17 μ to 6 μ in the y-axis (P < 0.025). Conclusion: This methodology allows for the creation of a highly reproducible image library of histopathology images and interpretations for educational and research use. PMID:23599902

Modeling track access charge to enhance railway industry performance

NASA Astrophysics Data System (ADS)

Berawi, Mohammed Ali; Miraj, Perdana; Berawi, Abdur Rohim Boy; Susantono, Bambang; Leviakangas, Pekka; Radiansyah, Hendra

2017-11-01

Indonesia attempts to improve nation's competitiveness by increasing the quality and the availability of railway network. However, the infrastructure improperly managed by the operator in terms of the technical issue. One of the reasons for this problem is an unbalanced value of infrastructure charge. In 2000's track access charge and infrastructure maintenance and operation for Indonesia railways are equal and despite current formula of the infrastructure charge, issues of transparency and accountability still in question. This research aims to produce an alternative scheme of track access charge by considering marginal cost plus markup (MC+) approach. The research combines qualitative and quantitative method through an in-depth interview and financial analysis. The result will generate alternative formula of infrastructure charge in Indonesia's railway industry. The simulation also conducted to estimate track access charge for the operator and to forecast government support in terms of subsidy. The result is expected to enhance railway industry performance and competitiveness.

Optimality of profit-including prices under ideal planning.

PubMed

Samuelson, P A

1973-07-01

Although prices calculated by a constant percentage markup on all costs (nonlabor as well as direct-labor) are usually admitted to be more realistic for a competitive capitalistic model, the view is often expressed that, for optimal planning purposes, the "values" model of Marx's Capital, Volume I, is to be preferred. It is shown here that an optimal-control model that maximizes discounted social utility of consumption per capita and that ultimately approaches a steady state must ultimately have optimal pricing that involves equal rates of steady-state profit in all industries; and such optimal pricing will necessarily deviate from Marx's model of equal rates of surplus value (markups on direct-labor only) in all industries.

Optimality of Profit-Including Prices Under Ideal Planning

PubMed Central

Samuelson, Paul A.

1973-01-01

Although prices calculated by a constant percentage markup on all costs (nonlabor as well as direct-labor) are usually admitted to be more realistic for a competitive capitalistic model, the view is often expressed that, for optimal planning purposes, the “values” model of Marx's Capital, Volume I, is to be preferred. It is shown here that an optimal-control model that maximizes discounted social utility of consumption per capita and that ultimately approaches a steady state must ultimately have optimal pricing that involves equal rates of steady-state profit in all industries; and such optimal pricing will necessarily deviate from Marx's model of equal rates of surplus value (markups on direct-labor only) in all industries. PMID:16592102

Open Access: From Myth to Paradox

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

Ginsparg, Paul

2009-05-06

True open access to scientific publications not only gives readers the possibility to read articles without paying subscription, but also makes the material available for automated ingestion and harvesting by 3rd parties. Once articles and associated data become universally treatable as computable objects, openly available to 3rd party aggregators and value-added services, what new services can we expect, and how will they change the way that researchers interact with their scholarly communications infrastructure? I will discuss straightforward applications of existing ideas and services, including citation analysis, collaborative filtering, external database linkages, interoperability, and other forms of automated markup, and speculatemore » on the sociology of the next generation of users.« less

Training Joint, Interagency, Intergovernmental, and Multinational (JIIM) Participants for Stability Operations

DTIC Science & Technology

2012-09-01

boxes) using a third-party commercial software component. When creating version 1, it was necessary to enter raw Hypertext Markup Language (HTML) tags...Markup Language (HTML) web page. Figure 12. Authors create procedures using the Procedure Editor. Users run procedures using the...step presents instructions to the user using formatted text and graphics specified using the Hypertext Markup Language (HTML). Instructions can

TMATS/ IHAL/ DDML Schema Validation

DTIC Science & Technology

2017-02-01

task was to create a method for performing IRIG eXtensible Markup Language (XML) schema validation. As opposed to XML instance document validation...TMATS / IHAL / DDML Schema Validation, RCC 126-17, February 2017 vii Acronyms DDML Data Display Markup Language HUD heads-up display iNET...system XML eXtensible Markup Language TMATS / IHAL / DDML Schema Validation, RCC 126-17, February 2017 viii This page intentionally left blank

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.

An object-oriented approach for harmonization of multimedia markup languages

NASA Astrophysics Data System (ADS)

Chen, Yih-Feng; Kuo, May-Chen; Sun, Xiaoming; Kuo, C.-C. Jay

2003-12-01

An object-oriented methodology is proposed to harmonize several different markup languages in this research. First, we adopt the Unified Modelling Language (UML) as the data model to formalize the concept and the process of the harmonization process between the eXtensible Markup Language (XML) applications. Then, we design the Harmonization eXtensible Markup Language (HXML) based on the data model and formalize the transformation between the Document Type Definitions (DTDs) of the original XML applications and HXML. The transformation between instances is also discussed. We use the harmonization of SMIL and X3D as an example to demonstrate the proposed methodology. This methodology can be generalized to various application domains.

Managing and Querying Image Annotation and Markup in XML.

PubMed

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid.

Development of clinical contents model markup language for electronic health records.

PubMed

Yun, Ji-Hyun; Ahn, Sun-Ju; Kim, Yoon

2012-09-01

To develop dedicated markup language for clinical contents models (CCM) to facilitate the active use of CCM in electronic health record systems. Based on analysis of the structure and characteristics of CCM in the clinical domain, we designed extensible markup language (XML) based CCM markup language (CCML) schema manually. CCML faithfully reflects CCM in both the syntactic and semantic aspects. As this language is based on XML, it can be expressed and processed in computer systems and can be used in a technology-neutral way. CCML HAS THE FOLLOWING STRENGTHS: it is machine-readable and highly human-readable, it does not require a dedicated parser, and it can be applied for existing electronic health record systems.

Managing and Querying Image Annotation and Markup in XML

PubMed Central

Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

2010-01-01

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid. PMID:21218167

Comparing pharmaceutical pricing and reimbursement policies in Croatia to the European Union Member States

PubMed Central

Vogler, Sabine; Habl, Claudia; Bogut, Martina; Vončina, Luka

2011-01-01

Aim To perform a comparative analysis of the pharmaceutical pricing and reimbursement systems in Croatia and the 27 European Union (EU) Member States. Methods Knowledge about the pharmaceutical systems in Croatia and the 27 EU Member States was acquired by literature review and primary research with stakeholders. Results Pharmaceutical prices are controlled at all levels in Croatia, which is also the case in 21 EU Member States. Like many EU countries, Croatia also applies external price referencing, ie, compares prices with other countries. While the wholesale remuneration by a statutorily regulated linear mark-up is applied in Croatia and in several EU countries, the pharmacy compensation for dispensing reimbursable medicines in the form of a flat rate service fee in Croatia is rare among EU countries, which usually apply a linear or regressive pharmacy mark-up scheme. Like in most EU countries, the Croatian Social Insurance reimburses specific medicines at 100%, whereas patients are charged co-payments for other reimbursable medicines. Criteria for reimbursement include the medicine’s importance from the public health perspective, its therapeutic value, and relative effectiveness. In Croatia and in many EU Member States, reimbursement is based on a reference price system. Conclusion The Croatian pharmaceutical system is similar to those in the EU Member States. Key policies, like external price referencing and reference price systems, which have increasingly been introduced in EU countries are also applied in Croatia and serve the same purpose: to ensure access to medicines while containing public pharmaceutical expenditure. PMID:21495202

Interexaminer variation of minutia markup on latent fingerprints.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2016-07-01

Latent print examiners often differ in the number of minutiae they mark during analysis of a latent, and also during comparison of a latent with an exemplar. Differences in minutia counts understate interexaminer variability: examiners' markups may have similar minutia counts but differ greatly in which specific minutiae were marked. We assessed variability in minutia markup among 170 volunteer latent print examiners. Each provided detailed markup documenting their examinations of 22 latent-exemplar pairs of prints randomly assigned from a pool of 320 pairs. An average of 12 examiners marked each latent. The primary factors associated with minutia reproducibility were clarity, which regions of the prints examiners chose to mark, and agreement on value or comparison determinations. In clear areas (where the examiner was "certain of the location, presence, and absence of all minutiae"), median reproducibility was 82%; in unclear areas, median reproducibility was 46%. Differing interpretations regarding which regions should be marked (e.g., when there is ambiguity in the continuity of a print) contributed to variability in minutia markup: especially in unclear areas, marked minutiae were often far from the nearest minutia marked by a majority of examiners. Low reproducibility was also associated with differences in value or comparison determinations. Lack of standardization in minutia markup and unfamiliarity with test procedures presumably contribute to the variability we observed. We have identified factors accounting for interexaminer variability; implementing standards for detailed markup as part of documentation and focusing future training efforts on these factors may help to facilitate transparency and reduce subjectivity in the examination process. Published by Elsevier Ireland Ltd.

Development of Clinical Contents Model Markup Language for Electronic Health Records

PubMed Central

Yun, Ji-Hyun; Kim, Yoon

2012-01-01

Objectives To develop dedicated markup language for clinical contents models (CCM) to facilitate the active use of CCM in electronic health record systems. Methods Based on analysis of the structure and characteristics of CCM in the clinical domain, we designed extensible markup language (XML) based CCM markup language (CCML) schema manually. Results CCML faithfully reflects CCM in both the syntactic and semantic aspects. As this language is based on XML, it can be expressed and processed in computer systems and can be used in a technology-neutral way. Conclusions CCML has the following strengths: it is machine-readable and highly human-readable, it does not require a dedicated parser, and it can be applied for existing electronic health record systems. PMID:23115739

Networking observers and observatories with remote telescope markup language

NASA Astrophysics Data System (ADS)

Hessman, Frederic V.; Tuparev, Georg; Allan, Alasdair

2006-06-01

Remote Telescope Markup Language (RTML) is an XML-based protocol for the transport of the high-level description of a set of observations to be carried out on a remote, robotic or service telescope. We describe how RTML is being used in a wide variety of contexts: the transport of service and robotic observing requests in the Hands-On Universe TM, ACP, eSTAR, and MONET networks; how RTML is easily combined with other XML protocols for more localized control of telescopes; RTML as a secondary observation report format for the IVOA's VOEvent protocol; the input format for a general-purpose observation simulator; and the observatory-independent means for carrying out request transactions for the international Heterogeneous Telescope Network (HTN).

Variation in Emergency Department vs Internal Medicine Excess Charges in the United States.

PubMed

Xu, Tim; Park, Angela; Bai, Ge; Joo, Sarah; Hutfless, Susan M; Mehta, Ambar; Anderson, Gerard F; Makary, Martin A

2017-08-01

Uninsured and insured but out-of-network emergency department (ED) patients are often billed hospital chargemaster prices, which exceed amounts typically paid by insurers. To examine the variation in excess charges for services provided by emergency medicine and internal medicine physicians. Retrospective analysis was conducted of professional fee payment claims made by the Centers for Medicare & Medicaid Services for all services provided to Medicare Part B fee-for-service beneficiaries in calendar year 2013. Data analysis was conducted from January 1 to July 31, 2016. Markup ratios for ED and internal medicine professional services, defined as the charges submitted by the hospital divided by the Medicare allowable amount. Our analysis included 12 337 emergency medicine physicians from 2707 hospitals and 57 607 internal medicine physicians from 3669 hospitals in all 50 states. Services provided by emergency medicine physicians had an overall markup ratio of 4.4 (340% excess charges), which was greater than the markup ratio of 2.1 (110% excess charges) for all services performed by internal medicine physicians. Markup ratios for all ED services ranged by hospital from 1.0 to 12.6 (median, 4.2; interquartile range [IQR], 3.3-5.8); markup ratios for all internal medicine services ranged by hospital from 1.0 to 14.1 (median, 2.0; IQR, 1.7-2.5). The median markup ratio by hospital for ED evaluation and management procedure codes varied between 4.0 and 5.0. Among the most common ED services, laceration repair had the highest median markup ratio (7.0); emergency medicine physician review of a head computed tomographic scan had the greatest interhospital variation (range, 1.6-27.7). Across hospitals, markups in the ED were often substantially higher than those in the internal medicine department for the same services. Higher ED markup ratios were associated with hospital for-profit ownership (median, 5.7; IQR, 4.0-7.1), a greater percentage of uninsured patients seen (median, 5.0; IQR, 3.5-6.7 for ≥20% uninsured), and location (median, 5.3; IQR, 3.8-6.8 for the southeastern United States). Across hospitals, there is wide variation in excess charges on ED services, which are often priced higher than internal medicine services. Our results inform policy efforts to protect uninsured and out-of-network patients from highly variable pricing.

A quality assessment tool for markup-based clinical guidelines.

PubMed

Shalom, Erez; Shahar, Yuval; Taieb-Maimon, Meirav; Lunenfeld, Eitan

2008-11-06

We introduce a tool for quality assessment of procedural and declarative knowledge. We developed this tool for evaluating the specification of mark-up-based clinical GLs. Using this graphical tool, the expert physician and knowledge engineer collaborate to perform scoring, using pre-defined scoring scale, each of the knowledge roles of the mark-ups, comparing it to a gold standard. The tool enables scoring the mark-ups simultaneously at different sites by different users at different locations.

Changes in latent fingerprint examiners' markup between analysis and comparison.

PubMed

Ulery, Bradford T; Hicklin, R Austin; Roberts, Maria Antonia; Buscaglia, JoAnn

2015-02-01

After the initial analysis of a latent print, an examiner will sometimes revise the assessment during comparison with an exemplar. Changes between analysis and comparison may indicate that the initial analysis of the latent was inadequate, or that confirmation bias may have affected the comparison. 170 volunteer latent print examiners, each randomly assigned 22 pairs of prints from a pool of 320 total pairs, provided detailed markup documenting their interpretations of the prints and the bases for their comparison conclusions. We describe changes in value assessments and markup of features and clarity. When examiners individualized, they almost always added or deleted minutiae (90.3% of individualizations); every examiner revised at least some markups. For inconclusive and exclusion determinations, changes were less common, and features were added more frequently when the image pair was mated (same source). Even when individualizations were based on eight or fewer corresponding minutiae, in most cases some of those minutiae had been added during comparison. One erroneous individualization was observed: the markup changes were notably extreme, and almost all of the corresponding minutiae had been added during comparison. Latents assessed to be of value for exclusion only (VEO) during analysis were often individualized when compared to a mated exemplar (26%); in our previous work, where examiners were not required to provide markup of features, VEO individualizations were much less common (1.8%). Published by Elsevier Ireland Ltd.

17 CFR 240.15c2-7 - Identification of quotations.

Code of Federal Regulations, 2010 CFR

2010-04-01

..., guarantee of profit, guarantee against loss, commission, markup, markdown, indication of interest and... account, guarantee of profit, guarantee against loss, commission, markup, markdown, indication of interest...

Records and history of the United States Geological Survey

USGS Publications Warehouse

Nelson, Clifford M.

2000-01-01

This publication contains two presentations in Portable Document Format (PDF). The first is Renee M. Jaussaud's inventory of the documents accessioned by the end of 1997 into Record Group 57 (Geological Survey) at the National Archives and Records Administration's (NARA) Archives II facility in College Park, Md., but not the materials in NARA's regional archives. The second is Mary C. Rabbitt's 'The United States Geological Survey 1879-1989,' which appeared in 1989 as USGS Circular 1050. Additionally, USGS Circular 1050 is also presented in Hyper Text Markup Language (HTML) format.

U.S. EPAs Geospatial Data Access Project

EPA Pesticide Factsheets

To improve public health and the environment, the United States Environmental Protection Agency (EPA) collects information about facilities, sites, or places subject to environmental regulation or of environmental interest. Through the Geospatial Data Download Service, the public is now able to download the EPA Geodata Shapefile, Feature Class or extensible markup language (XML) file containing facility and site information from EPA's national program systems. The files are Internet accessible from the Envirofacts Web site (https://www3.epa.gov/enviro/). The data may be used with geospatial mapping applications. (Note: The files omit facilities without latitude/longitude coordinates.) The EPA Geospatial Data contains the name, location (latitude/longitude), and EPA program information about specific facilities and sites. In addition, the files contain a Uniform Resource Locator (URL), which allows mapping applications to present an option to users to access additional EPA data resources on a specific facility or site.

XML Based Markup Languages for Specific Domains

NASA Astrophysics Data System (ADS)

Varde, Aparna; Rundensteiner, Elke; Fahrenholz, Sally

A challenging area in web based support systems is the study of human activities in connection with the web, especially with reference to certain domains. This includes capturing human reasoning in information retrieval, facilitating the exchange of domain-specific knowledge through a common platform and developing tools for the analysis of data on the web from a domain expert's angle. Among the techniques and standards related to such work, we have XML, the eXtensible Markup Language. This serves as a medium of communication for storing and publishing textual, numeric and other forms of data seamlessly. XML tag sets are such that they preserve semantics and simplify the understanding of stored information by users. Often domain-specific markup languages are designed using XML, with a user-centric perspective. Standardization bodies and research communities may extend these to include additional semantics of areas within and related to the domain. This chapter outlines the issues to be considered in developing domain-specific markup languages: the motivation for development, the semantic considerations, the syntactic constraints and other relevant aspects, especially taking into account human factors. Illustrating examples are provided from domains such as Medicine, Finance and Materials Science. Particular emphasis in these examples is on the Materials Markup Language MatML and the semantics of one of its areas, namely, the Heat Treating of Materials. The focus of this chapter, however, is not the design of one particular language but rather the generic issues concerning the development of domain-specific markup languages.

Impact of the zero-markup drug policy on hospitalisation expenditure in western rural China: an interrupted time series analysis.

PubMed

Yang, Caijun; Shen, Qian; Cai, Wenfang; Zhu, Wenwen; Li, Zongjie; Wu, Lina; Fang, Yu

2017-02-01

To assess the long-term effects of the introduction of China's zero-markup drug policy on hospitalisation expenditure and hospitalisation expenditures after reimbursement. An interrupted time series was used to evaluate the impact of the zero-markup drug policy on hospitalisation expenditure and hospitalisation expenditure after reimbursement at primary health institutions in Fufeng County of Shaanxi Province, western China. Two regression models were developed. Monthly average hospitalisation expenditure and monthly average hospitalisation expenditure after reimbursement in primary health institutions were analysed covering the period 2009 through to 2013. For the monthly average hospitalisation expenditure, the increasing trend was slowed down after the introduction of the zero-markup drug policy (coefficient = -16.49, P = 0.009). For the monthly average hospitalisation expenditure after reimbursement, the increasing trend was slowed down after the introduction of the zero-markup drug policy (coefficient = -10.84, P = 0.064), and a significant decrease in the intercept was noted after the second intervention of changes in reimbursement schemes of the new rural cooperative medical insurance (coefficient = -220.64, P < 0.001). A statistically significant absolute decrease in the level or trend of monthly average hospitalisation expenditure and monthly average hospitalisation expenditure after reimbursement was detected after the introduction of the zero-markup drug policy in western China. However, hospitalisation expenditure and hospitalisation expenditure after reimbursement were still increasing. More effective policies are needed to prevent these costs from continuing to rise. © 2016 John Wiley & Sons Ltd.

Data Integration Using SOAP in the VSO

NASA Astrophysics Data System (ADS)

Tian, K. Q.; Bogart, R. S.; Davey, A.; Dimitoglou, G.; Gurman, J. B.; Hill, F.; Martens, P. C.; Wampler, S.

2003-05-01

The Virtual Solar Observatory (VSO) project has implemented a time interval search for all four participating data archives. The back-end query services are implemented as web services, and are accessible via SOAP. SOAP (Simple Object Access Protocol) defines an RPC (Remote Procedure Call) mechanism that employs HTTP as its transport and encodes the client-server interactions (request and response messages) in XML (eXtensible Markup Language) documents. In addition to its core function of identifying relevant datasets in the local archive, the SOAP server at each data provider acts as a "wrapper" that maps descriptions in an abstract data model to those in the provider-specific data model, and vice versa. It is in this way that VSO integrates heterogeneous data services and allows access to them using a common interface. Our experience with SOAP has been fruitful. It has proven to be a better alternative to traditional web access methods, namely POST and GET, because of its flexibility and interoperability.

Variation in Emergency Department vs Internal Medicine Excess Charges in the United States

PubMed Central

Park, Angela; Bai, Ge; Joo, Sarah; Hutfless, Susan M.; Mehta, Ambar; Anderson, Gerard F.; Makary, Martin A.

2017-01-01

Importance Uninsured and insured but out-of-network emergency department (ED) patients are often billed hospital chargemaster prices, which exceed amounts typically paid by insurers. Objective To examine the variation in excess charges for services provided by emergency medicine and internal medicine physicians. Design, Setting, and Participants Retrospective analysis was conducted of professional fee payment claims made by the Centers for Medicare & Medicaid Services for all services provided to Medicare Part B fee-for-service beneficiaries in calendar year 2013. Data analysis was conducted from January 1 to July 31, 2016. Main Outcomes and Measures Markup ratios for ED and internal medicine professional services, defined as the charges submitted by the hospital divided by the Medicare allowable amount. Results Our analysis included 12 337 emergency medicine physicians from 2707 hospitals and 57 607 internal medicine physicians from 3669 hospitals in all 50 states. Services provided by emergency medicine physicians had an overall markup ratio of 4.4 (340% excess charges), which was greater than the markup ratio of 2.1 (110% excess charges) for all services performed by internal medicine physicians. Markup ratios for all ED services ranged by hospital from 1.0 to 12.6 (median, 4.2; interquartile range [IQR], 3.3-5.8); markup ratios for all internal medicine services ranged by hospital from 1.0 to 14.1 (median, 2.0; IQR, 1.7-2.5). The median markup ratio by hospital for ED evaluation and management procedure codes varied between 4.0 and 5.0. Among the most common ED services, laceration repair had the highest median markup ratio (7.0); emergency medicine physician review of a head computed tomographic scan had the greatest interhospital variation (range, 1.6-27.7). Across hospitals, markups in the ED were often substantially higher than those in the internal medicine department for the same services. Higher ED markup ratios were associated with hospital for-profit ownership (median, 5.7; IQR, 4.0-7.1), a greater percentage of uninsured patients seen (median, 5.0; IQR, 3.5-6.7 for ≥20% uninsured), and location (median, 5.3; IQR, 3.8-6.8 for the southeastern United States). Conclusions and Relevance Across hospitals, there is wide variation in excess charges on ED services, which are often priced higher than internal medicine services. Our results inform policy efforts to protect uninsured and out-of-network patients from highly variable pricing. PMID:28558093

WaterML: an XML Language for Communicating Water Observations Data

NASA Astrophysics Data System (ADS)

Maidment, D. R.; Zaslavsky, I.; Valentine, D.

2007-12-01

One of the great impediments to the synthesis of water information is the plethora of formats used to publish such data. Each water agency uses its own approach. XML (eXtended Markup Languages) are generalizations of Hypertext Markup Language to communicate specific kinds of information via the internet. WaterML is an XML language for water observations data - streamflow, water quality, groundwater levels, climate, precipitation and aquatic biology data, recorded at fixed, point locations as a function of time. The Hydrologic Information System project of the Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI) has defined WaterML and prepared a set of web service functions called WaterOneFLow that use WaterML to provide information about observation sites, the variables measured there and the values of those measurments. WaterML has been submitted to the Open GIS Consortium for harmonization with its standards for XML languages. Academic investigators at a number of testbed locations in the WATERS network are providing data in WaterML format using WaterOneFlow web services. The USGS and other federal agencies are also working with CUAHSI to similarly provide access to their data in WaterML through WaterOneFlow services.

SuML: A Survey Markup Language for Generalized Survey Encoding

PubMed Central

Barclay, MW; Lober, WB; Karras, BT

2002-01-01

There is a need in clinical and research settings for a sophisticated, generalized, web based survey tool that supports complex logic, separation of content and presentation, and computable guidelines. There are many commercial and open source survey packages available that provide simple logic; few provide sophistication beyond “goto” statements; none support the use of guidelines. These tools are driven by databases, static web pages, and structured documents using markup languages such as eXtensible Markup Language (XML). We propose a generalized, guideline aware language and an implementation architecture using open source standards.

Using XML and Java for Astronomical Instrumentation Control

NASA Technical Reports Server (NTRS)

Ames, Troy; Koons, Lisa; Sall, Ken; Warsaw, Craig

2000-01-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). ]ML is used to describe graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, and communication mechanisms. Although the current effort is targeted for the High-resolution Airborne Wideband Camera, a first-light instrument of the Stratospheric Observatory for Infrared Astronomy, the framework is designed to be generic and extensible so that it can be applied to any instrument.

Prices and mark-ups on antimalarials: evidence from nationally representative studies in six malaria-endemic countries

PubMed Central

Palafox, Benjamin; Patouillard, Edith; Tougher, Sarah; Goodman, Catherine; Hanson, Kara; Kleinschmidt, Immo; Torres Rueda, Sergio; Kiefer, Sabine; O’Connell, Kate; Zinsou, Cyprien; Phok, Sochea; Akulayi, Louis; Arogundade, Ekundayo; Buyungo, Peter; Mpasela, Felton; Poyer, Stephen; Chavasse, Desmond

2016-01-01

The private for-profit sector is an important source of treatment for malaria. However, private patients face high prices for the recommended treatment for uncomplicated malaria, artemisinin combination therapies (ACTs), which makes them more likely to receive cheaper, less effective non-artemisinin therapies (nATs). This study seeks to better understand consumer antimalarial prices by documenting and exploring the pricing behaviour of retailers and wholesalers. Using data collected in 2009–10, we present survey estimates of antimalarial retail prices, and wholesale- and retail-level price mark-ups from six countries (Benin, Cambodia, the Democratic Republic of Congo, Nigeria, Uganda and Zambia), along with qualitative findings on factors affecting pricing decisions. Retail prices were lowest for nATs, followed by ACTs and artemisinin monotherapies (AMTs). Retailers applied the highest percentage mark-ups on nATs (range: 40% in Nigeria to 100% in Cambodia and Zambia), whereas mark-ups on ACTs (range: 22% in Nigeria to 71% in Zambia) and AMTs (range: 22% in Nigeria to 50% in Uganda) were similar in magnitude, but lower than those applied to nATs. Wholesale mark-ups were generally lower than those at retail level, and were similar across antimalarial categories in most countries. When setting prices wholesalers and retailers commonly considered supplier prices, prevailing market prices, product availability, product characteristics and the costs related to transporting goods, staff salaries and maintaining a property. Price discounts were regularly used to encourage sales and were sometimes used by wholesalers to reward long-term customers. Pricing constraints existed only in Benin where wholesaler and retailer mark-ups are regulated; however, unlicensed drug vendors based in open-air markets did not adhere to the pricing regime. These findings indicate that mark-ups on antimalarials are reasonable. Therefore, improving ACT affordability would be most readily achieved by interventions that reduce commodity prices for retailers, such as ACT subsidies, pooled purchasing mechanisms and cost-effective strategies to increase the distribution coverage area of wholesalers. PMID:25944705

Descriptive Metadata: Emerging Standards.

ERIC Educational Resources Information Center

Ahronheim, Judith R.

1998-01-01

Discusses metadata, digital resources, cross-disciplinary activity, and standards. Highlights include Standard Generalized Markup Language (SGML); Extensible Markup Language (XML); Dublin Core; Resource Description Framework (RDF); Text Encoding Initiative (TEI); Encoded Archival Description (EAD); art and cultural-heritage metadata initiatives;…

Improving Interoperability by Incorporating UnitsML Into Markup Languages

PubMed Central

Celebi, Ismet; Dragoset, Robert A.; Olsen, Karen J.; Schaefer, Reinhold; Kramer, Gary W.

2010-01-01

Maintaining the integrity of analytical data over time is a challenge. Years ago, data were recorded on paper that was pasted directly into a laboratory notebook. The digital age has made maintaining the integrity of data harder. Nowadays, digitized analytical data are often separated from information about how the sample was collected and prepared for analysis and how the data were acquired. The data are stored on digital media, while the related information about the data may be written in a paper notebook or stored separately in other digital files. Sometimes the connection between this “scientific meta-data” and the analytical data is lost, rendering the spectrum or chromatogram useless. We have been working with ASTM Subcommittee E13.15 on Analytical Data to create the Analytical Information Markup Language or AnIML—a new way to interchange and store spectroscopy and chromatography data based on XML (Extensible Markup Language). XML is a language for describing what data are by enclosing them in computer-useable tags. Recording the units associated with the analytical data and metadata is an essential issue for any data representation scheme that must be addressed by all domain-specific markup languages. As scientific markup languages proliferate, it is very desirable to have a single scheme for handling units to facilitate moving information between different data domains. At NIST, we have been developing a general markup language just for units that we call UnitsML. This presentation will describe how UnitsML is used and how it is being incorporated into AnIML. PMID:27134778

Improving Interoperability by Incorporating UnitsML Into Markup Languages.

PubMed

Celebi, Ismet; Dragoset, Robert A; Olsen, Karen J; Schaefer, Reinhold; Kramer, Gary W

2010-01-01

Maintaining the integrity of analytical data over time is a challenge. Years ago, data were recorded on paper that was pasted directly into a laboratory notebook. The digital age has made maintaining the integrity of data harder. Nowadays, digitized analytical data are often separated from information about how the sample was collected and prepared for analysis and how the data were acquired. The data are stored on digital media, while the related information about the data may be written in a paper notebook or stored separately in other digital files. Sometimes the connection between this "scientific meta-data" and the analytical data is lost, rendering the spectrum or chromatogram useless. We have been working with ASTM Subcommittee E13.15 on Analytical Data to create the Analytical Information Markup Language or AnIML-a new way to interchange and store spectroscopy and chromatography data based on XML (Extensible Markup Language). XML is a language for describing what data are by enclosing them in computer-useable tags. Recording the units associated with the analytical data and metadata is an essential issue for any data representation scheme that must be addressed by all domain-specific markup languages. As scientific markup languages proliferate, it is very desirable to have a single scheme for handling units to facilitate moving information between different data domains. At NIST, we have been developing a general markup language just for units that we call UnitsML. This presentation will describe how UnitsML is used and how it is being incorporated into AnIML.

The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation model.

PubMed

Mongkolwat, Pattanasak; Kleper, Vladimir; Talbot, Skip; Rubin, Daniel

2014-12-01

Knowledge contained within in vivo imaging annotated by human experts or computer programs is typically stored as unstructured text and separated from other associated information. The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation information model is an evolution of the National Institute of Health's (NIH) National Cancer Institute's (NCI) Cancer Bioinformatics Grid (caBIG®) AIM model. The model applies to various image types created by various techniques and disciplines. It has evolved in response to the feedback and changing demands from the imaging community at NCI. The foundation model serves as a base for other imaging disciplines that want to extend the type of information the model collects. The model captures physical entities and their characteristics, imaging observation entities and their characteristics, markups (two- and three-dimensional), AIM statements, calculations, image source, inferences, annotation role, task context or workflow, audit trail, AIM creator details, equipment used to create AIM instances, subject demographics, and adjudication observations. An AIM instance can be stored as a Digital Imaging and Communications in Medicine (DICOM) structured reporting (SR) object or Extensible Markup Language (XML) document for further processing and analysis. An AIM instance consists of one or more annotations and associated markups of a single finding along with other ancillary information in the AIM model. An annotation describes information about the meaning of pixel data in an image. A markup is a graphical drawing placed on the image that depicts a region of interest. This paper describes fundamental AIM concepts and how to use and extend AIM for various imaging disciplines.

Using XML and Java for Astronomical Instrument Control

NASA Astrophysics Data System (ADS)

Koons, L.; Ames, T.; Evans, R.; Warsaw, C.; Sall, K.

1999-12-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests. Instrument description is too tightly coupled with details of implementation. NASA/Goddard Space Flight Center and AppNet, Inc. are developing a very general and highly extensible framework that applies to virtually any kind of instrument that can be controlled by a computer (e.g., telescopes, microscopes and printers). A key aspect of the object-oriented architecture, implemented in Java, involves software that is driven by an instrument description. The Astronomical Instrument Markup Language (AIML) is a domain-specific implementation of the more generalized Instrument Markup Language (IML). The software architecture combines the platform-independent processing capabilities of Java with the vendor-independent data description syntax of Extensible Markup Language (XML), a human-readable and machine-understandable way to describe structured data. IML is used to describe command sets (including parameters, datatypes, and constraints) and their associated formats, telemetry, and communication mechanisms. The software uses this description to present graphical user interfaces to control and monitor the instrument. Recent efforts have extended to command procedures (scripting) and representation of data pipeline inputs, outputs, and connections. Near future efforts are likely to include an XML description of data visualizations, as well as the potential use of XSL (Extensible Stylesheet Language) to permit astronomers to customize the user interface on several levels: per user, instrument, subsystem, or observatory-wide. Our initial prototyping effort was targeted for HAWC (High-resolution Airborne Wideband Camera), a first-light instrument of SOFIA (the Stratospheric Observatory for Infrared Astronomy). A production-level application of this technology is for one of the three candidate detectors of SPIRE (Spectral and Photometric Imaging REceiver), a focal plane instrument proposed for the European Space Agency's Far Infrared Space Telescope. The detectors are being developed by the Infrared Astrophysics Branch of NASA/GSFC.

NAVAIR Portable Source Initiative (NPSI) Data Preparation Standard V2.2: NPSI DPS V2.2

DTIC Science & Technology

2012-05-22

Keyhole Markup Language (file format) KMZ ............................................................................. Keyhole Markup...required for the geo-specific texture may differ within the database depending on the mission parameters. When operating close to the ground (e.g

TumorML: Concept and requirements of an in silico cancer modelling markup language.

PubMed

Johnson, David; Cooper, Jonathan; McKeever, Steve

2011-01-01

This paper describes the initial groundwork carried out as part of the European Commission funded Transatlantic Tumor Model Repositories project, to develop a new markup language for computational cancer modelling, TumorML. In this paper we describe the motivations for such a language, arguing that current state-of-the-art biomodelling languages are not suited to the cancer modelling domain. We go on to describe the work that needs to be done to develop TumorML, the conceptual design, and a description of what existing markup languages will be used to compose the language specification.

Building and evaluating an ontology-based tool for reasoning about consent permission

PubMed Central

Grando, Adela; Schwab, Richard

2013-01-01

Given the lack of mechanisms for specifying, sharing and checking the compliance of consent permissions, we focus on building and testing novel approaches to address this gap. In our previous work, we introduced a “permission ontology” to capture in a precise, machine-interpretable form informed consent permissions in research studies. Here we explain how we built and evaluated a framework for specifying subject’s permissions and checking researcher’s resource request in compliance with those permissions. The framework is proposed as an extension of an existing policy engine based on the eXtensible Access Control Markup Language (XACML), incorporating ontology-based reasoning. The framework is evaluated in the context of the UCSD Moores Cancer Center biorepository, modeling permissions from an informed consent and a HIPAA form. The resulting permission ontology and mechanisms to check subject’s permission are implementation and institution independent, and therefore offer the potential to be reusable in other biorepositories and data warehouses. PMID:24551354

SGML Authoring Tools for Technical Communication.

ERIC Educational Resources Information Center

Davidson, W. J.

1993-01-01

Explains that structured authoring systems designed for the creation of generically encoded reusable information have context-sensitive application of markup, markup suppression, queing and automated formatting, structural navigation, and self-validation features. Maintains that they are a real alternative to conventional publishing systems. (SR)

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Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... rates. In effect, the Exchange is obtaining wholesale rates from the carriers and then charging a markup... a markup to allow the Exchange to cover its administrative costs and to earn a profit on its...

SGML by Evolution.

ERIC Educational Resources Information Center

Ensign, Chet

1993-01-01

Describes how the change to Standard Generalized Markup Language at Information Builders began with the use of SGML-like markup in text because it solved a specific problem. Notes that many additional unexpected benefits led to an investigation of converting to formal SGML-based electronic publishing. (SR)

Automation and integration of components for generalized semantic markup of electronic medical texts.

PubMed

Dugan, J M; Berrios, D C; Liu, X; Kim, D K; Kaizer, H; Fagan, L M

1999-01-01

Our group has built an information retrieval system based on a complex semantic markup of medical textbooks. We describe the construction of a set of web-based knowledge-acquisition tools that expedites the collection and maintenance of the concepts required for text markup and the search interface required for information retrieval from the marked text. In the text markup system, domain experts (DEs) identify sections of text that contain one or more elements from a finite set of concepts. End users can then query the text using a predefined set of questions, each of which identifies a subset of complementary concepts. The search process matches that subset of concepts to relevant points in the text. The current process requires that the DE invest significant time to generate the required concepts and questions. We propose a new system--called ACQUIRE (Acquisition of Concepts and Queries in an Integrated Retrieval Environment)--that assists a DE in two essential tasks in the text-markup process. First, it helps her to develop, edit, and maintain the concept model: the set of concepts with which she marks the text. Second, ACQUIRE helps her to develop a query model: the set of specific questions that end users can later use to search the marked text. The DE incorporates concepts from the concept model when she creates the questions in the query model. The major benefit of the ACQUIRE system is a reduction in the time and effort required for the text-markup process. We compared the process of concept- and query-model creation using ACQUIRE to the process used in previous work by rebuilding two existing models that we previously constructed manually. We observed a significant decrease in the time required to build and maintain the concept and query models.

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2011-02-15

..., thereby maintaining the $0.0002 markup that exists in the current fee schedule. \\4\\ SR-PHLX-2011-11... recent pricing changes by that venue, and allows NASDAQ to maintain the current markup of $0.0002 per...

XML and E-Journals: The State of Play.

ERIC Educational Resources Information Center

Wusteman, Judith

2003-01-01

Discusses the introduction of the use of XML (Extensible Markup Language) in publishing electronic journals. Topics include standards, including DTDs (Document Type Definition), or document type definitions; aggregator requirements; SGML (Standard Generalized Markup Language); benefits of XML for e-journals; XML metadata; the possibility of…

76 FR 70184 - Self-Regulatory Organizations; NASDAQ OMX BX, Inc.; Notice of Filing of Proposed Rule Change To...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... rates. In effect, the Exchange is obtaining wholesale rates from the carriers and then charging a markup... a markup to allow the Exchange to cover its administrative costs and to earn a profit on its...

76 FR 70199 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-10

... rates. In effect, the Exchange is obtaining wholesale rates from the carriers and then charging a markup... a markup to allow the Exchange to cover its administrative costs and to earn a profit on its...

Semi-automated XML markup of biosystematic legacy literature with the GoldenGATE editor.

PubMed

Sautter, Guido; Böhm, Klemens; Agosti, Donat

2007-01-01

Today, digitization of legacy literature is a big issue. This also applies to the domain of biosystematics, where this process has just started. Digitized biosystematics literature requires a very precise and fine grained markup in order to be useful for detailed search, data linkage and mining. However, manual markup on sentence level and below is cumbersome and time consuming. In this paper, we present and evaluate the GoldenGATE editor, which is designed for the special needs of marking up OCR output with XML. It is built in order to support the user in this process as far as possible: Its functionality ranges from easy, intuitive tagging through markup conversion to dynamic binding of configurable plug-ins provided by third parties. Our evaluation shows that marking up an OCR document using GoldenGATE is three to four times faster than with an off-the-shelf XML editor like XML-Spy. Using domain-specific NLP-based plug-ins, these numbers are even higher.

AAS Publishing News: Preparing Your Manuscript Just Got Easier

NASA Astrophysics Data System (ADS)

Kohler, Susanna

2016-03-01

Watermarking using the command watermark{DRAFT, v2}.Are you an astronomer considering submitting a paper to an AAS journal (i.e., AJ, ApJ, ApJ Letters, or ApJ Supplements)? If so, this post is for you! Read on to find out about the exciting new things you can do with the AASs newest LaTeX class file, available for download now.Why the Update?AAS publishing has maintained a consistent class file for LaTeX manuscript preparation for the past decade. But academic publishing is changing rapidly in todays era of electronic journals! Since its journals went fully electronic, the AAS has been continuously adding new publishing capabilities based on the recommendations of the Journals Task Force and the needs and requests of AAS authors. The AASs manuscript preparation tools are now being updated accordingly.Whats New in AASTex 6.0?There are many exciting new features and capabilities in AASTex 6.0. Here are just a few:Tracking options for author revisions include added{text}, deleted{text}, replaced{old}{new}, and explain{text}.Based on emulateapjDo you use the popular class file emulateapj to prepare your manuscripts? AASTex 6.0 is based on emulateapj, rather than on the older AASTex 5.2 (though 5.2 is still supported). This means that it is easy to produce a double-columned, single-spaced, and astro-ph-ready manuscript. Since two thirds of the AAS journals authors use emulateapj, this transition was designed to make manuscript preparation and sharing an easier and more seamless process.Tools for collaborationsDo you work in a large collaboration? AASTex now includes new tools to make preparing a manuscript within a collaboration easier. Drafts can now be watermarked to differentiate between versions. New markup for large author lists streamlines the display so that readers can access article information immediately, yet they can still access the full author list and affiliations at the end of the paper. And author revision markup allows members of a collaboration to track their edits within a manuscript, for clearer organization of versions and edits.An example figure set, which the reader can download as a .tar.gz high-resolution set or as PowerPoint slides.Additional figure supportDo you have a lot of similar figures that youd like associated with the electronic journal article but dont all need to be included in the article pdf? New support is now available for figure sets, which allow readers efficient access to the full set of images without slowing down their ability to read your article. In addition, AASTex 6.0 now offers new markup for displaying figures in a grid, providing authors with more control over figure placement.New features for tablesDo you frequently work with large data tables? You might be especially happy with the changes in table-handling in AASTex 6.0. Now you can automatically number columns, hide columns with a single command, specify math mode automatically for a designated column, control decimal alignment, and even split wide tables into multiple parts.Example use of the new software command.Software citation supportDo you want to cite software and third-party repositories within your articles? With AASTex 6.0, theres now a software command that can be used to highlight and link to software that you used in your work. In addition, the ApJ BibTeX style file has been updated to support software citation.Where Can You Get More Information?Learn more about AASTex 6.0Watch a video presentation about AASTex 6.0 by AAS Data Scientist Greg SchwarzDownload AASTex 6.0Wishing for still more improvements?The AAS publishing team would love your input! You can contact them at aastex-help@aas.org with additional suggestions or ideas for the next iteration of AASTex.

Prices and mark-ups on antimalarials: evidence from nationally representative studies in six malaria-endemic countries.

PubMed

Palafox, Benjamin; Patouillard, Edith; Tougher, Sarah; Goodman, Catherine; Hanson, Kara; Kleinschmidt, Immo; Torres Rueda, Sergio; Kiefer, Sabine; O'Connell, Kate; Zinsou, Cyprien; Phok, Sochea; Akulayi, Louis; Arogundade, Ekundayo; Buyungo, Peter; Mpasela, Felton; Poyer, Stephen; Chavasse, Desmond

2016-03-01

The private for-profit sector is an important source of treatment for malaria. However, private patients face high prices for the recommended treatment for uncomplicated malaria, artemisinin combination therapies (ACTs), which makes them more likely to receive cheaper, less effective non-artemisinin therapies (nATs). This study seeks to better understand consumer antimalarial prices by documenting and exploring the pricing behaviour of retailers and wholesalers. Using data collected in 2009-10, we present survey estimates of antimalarial retail prices, and wholesale- and retail-level price mark-ups from six countries (Benin, Cambodia, the Democratic Republic of Congo, Nigeria, Uganda and Zambia), along with qualitative findings on factors affecting pricing decisions. Retail prices were lowest for nATs, followed by ACTs and artemisinin monotherapies (AMTs). Retailers applied the highest percentage mark-ups on nATs (range: 40% in Nigeria to 100% in Cambodia and Zambia), whereas mark-ups on ACTs (range: 22% in Nigeria to 71% in Zambia) and AMTs (range: 22% in Nigeria to 50% in Uganda) were similar in magnitude, but lower than those applied to nATs. Wholesale mark-ups were generally lower than those at retail level, and were similar across antimalarial categories in most countries. When setting prices wholesalers and retailers commonly considered supplier prices, prevailing market prices, product availability, product characteristics and the costs related to transporting goods, staff salaries and maintaining a property. Price discounts were regularly used to encourage sales and were sometimes used by wholesalers to reward long-term customers. Pricing constraints existed only in Benin where wholesaler and retailer mark-ups are regulated; however, unlicensed drug vendors based in open-air markets did not adhere to the pricing regime. These findings indicate that mark-ups on antimalarials are reasonable. Therefore, improving ACT affordability would be most readily achieved by interventions that reduce commodity prices for retailers, such as ACT subsidies, pooled purchasing mechanisms and cost-effective strategies to increase the distribution coverage area of wholesalers. © The Author 2015. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Public accessibility of biomedical articles from PubMed Central reduces journal readership--retrospective cohort analysis.

PubMed

Davis, Philip M

2013-07-01

Does PubMed Central--a government-run digital archive of biomedical articles--compete with scientific society journals? A longitudinal, retrospective cohort analysis of 13,223 articles (5999 treatment, 7224 control) published in 14 society-run biomedical research journals in nutrition, experimental biology, physiology, and radiology between February 2008 and January 2011 reveals a 21.4% reduction in full-text hypertext markup language (HTML) article downloads and a 13.8% reduction in portable document format (PDF) article downloads from the journals' websites when U.S. National Institutes of Health-sponsored articles (treatment) become freely available from the PubMed Central repository. In addition, the effect of PubMed Central on reducing PDF article downloads is increasing over time, growing at a rate of 1.6% per year. There was no longitudinal effect for full-text HTML downloads. While PubMed Central may be providing complementary access to readers traditionally underserved by scientific journals, the loss of article readership from the journal website may weaken the ability of the journal to build communities of interest around research papers, impede the communication of news and events to scientific society members and journal readers, and reduce the perceived value of the journal to institutional subscribers.

The "New Oxford English Dictionary" Project.

ERIC Educational Resources Information Center

Fawcett, Heather

1993-01-01

Describes the conversion of the 22,000-page Oxford English Dictionary to an electronic version incorporating a modified Standard Generalized Markup Language (SGML) syntax. Explains that the database designers chose structured markup because it supports users' data searching needs, allows textual components to be extracted or modified, and allows…

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Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-10

... believes that it is reasonable to charge a $0.0001 per share markup on such routed orders as a means of..., and accordingly, it is equitable for NASDAQ to charge members a markup for making use of NASDAQ's...

Using the eXtensible Markup Language (XML) in a regional electronic patient record for patients with malignant diseases.

PubMed

Wolff, A C; Mludek, V; van der Haak, M; Bork, W; Bülzebruck, H; Drings, P; Schmücker, P; Wannenmacher, M; Haux, R

2001-01-01

Communication between different institutions which are responsible for the treatment of the same patient is of outstanding significance, especially in the field of tumor diseases. Regional electronic patient records could support the co-operation of different institutions by providing ac-cess to all necessary information whether it belongs to the own institution or to a partner. The Department of Medical Informatics, University of Heidelberg is performing a project in co-operation with the Thoraxclinic-Heidelberg and the Department of Clinical Radiology, University of Heidelberg with the goal: to define an architectural concept for interlinking the electronic patient record of the two clinical institutions to build a common virtual electronic patient record and carry out an exemplary implementation, to examine composition, structure and content of medical documents for tumor patients with the aim of defining an XML-based markup language allowing summarizing overviews and suitable granularities, and to integrate clinical practice guidelines and other external knowledge with the electronic patient record using XML-technologies to support the physician in the daily decision process. This paper will show, how a regional electronic patient record could be built on an architectural level and describe elementary steps towards a on content-oriented structuring of medical records.

The markup is the model: reasoning about systems biology models in the Semantic Web era.

PubMed

Kell, Douglas B; Mendes, Pedro

2008-06-07

Metabolic control analysis, co-invented by Reinhart Heinrich, is a formalism for the analysis of biochemical networks, and is a highly important intellectual forerunner of modern systems biology. Exchanging ideas and exchanging models are part of the international activities of science and scientists, and the Systems Biology Markup Language (SBML) allows one to perform the latter with great facility. Encoding such models in SBML allows their distributed analysis using loosely coupled workflows, and with the advent of the Internet the various software modules that one might use to analyze biochemical models can reside on entirely different computers and even on different continents. Optimization is at the core of many scientific and biotechnological activities, and Reinhart made many major contributions in this area, stimulating our own activities in the use of the methods of evolutionary computing for optimization.

Designing Multimedia for the Hypertext Markup Language.

ERIC Educational Resources Information Center

Schwier, Richard A.; Misanchuk, Earl R.

Dynamic discussions have begun to emerge concerning style of presentation on world wide web sites. Some hypertext markup language (HTML) designers seek an intimate and chatty ambience, while others want to project a more professional image. Evaluators see many sites as overdecorated and indecipherable. This paper offers suggestions on selecting…

106-17 Telemetry Standards Metadata Configuration Chapter 23

DTIC Science & Technology

2017-07-01

23-1 23.2 Metadata Description Language ...Chapter 23, July 2017 iii Acronyms HTML Hypertext Markup Language MDL Metadata Description Language PCM pulse code modulation TMATS Telemetry...Attributes Transfer Standard W3C World Wide Web Consortium XML eXtensible Markup Language XSD XML schema document Telemetry Network Standard

DAVE-ML Utility Programs

NASA Technical Reports Server (NTRS)

Jackson, Bruce

2006-01-01

DAVEtools is a set of Java archives that embodies tools for manipulating flight-dynamics models that have been encoded in dynamic aerospace vehicle exchange markup language (DAVE-ML). [DAVE-ML is an application program, written in Extensible Markup Language (XML), for encoding complete computational models of the dynamics of aircraft and spacecraft.

An Introduction to the Resource Description Framework.

ERIC Educational Resources Information Center

Miller, Eric

1998-01-01

Explains the Resource Description Framework (RDF), an infrastructure developed under the World Wide Web Consortium that enables the encoding, exchange, and reuse of structured metadata. It is an application of Extended Markup Language (XML), which is a subset of Standard Generalized Markup Language (SGML), and helps with expressing semantics.…

XML: A Publisher's Perspective.

ERIC Educational Resources Information Center

Andrews, Timothy M.

1999-01-01

Explains eXtensible Markup Language (XML) and describes how Dow Jones Interactive is using it to improve the news-gathering and dissemination process through intranets and the World Wide Web. Discusses benefits of using XML, the relationship to HyperText Markup Language (HTML), lack of available software tools and industry support, and future…

Access to Paediatric Essential Medicines: A Survey of Prices, Availability, Affordability and Price Components in Shaanxi Province, China

PubMed Central

Wang, Xiao; Fang, Yu; Yang, Shimin; Jiang, Minghuan; Yan, Kangkang; Wu, Lina; Lv, Bing; Shen, Qian

2014-01-01

Objective To evaluate the prices and availability of paediatric essential medicines in Shaanxi Province, China. Methods Price and availability data for 28 paediatric essential medicines were collected from 60 public hospitals and 60 retail pharmacies in six areas of Shaanxi Province using a standardised methodology developed by the World Health Organization and Health Action International, during November to December 2012. Affordability was measured as the number of days’ wages required for the lowest-paid unskilled government worker to purchase standard treatments for common conditions. Data on medicine price components were collected from hospitals, wholesalers and distributors to obtain price mark-ups. Findings The mean availabilities of originator brands (OBs) and lowest-priced generics (LPGs) were 10.8% and 27.3% in the public hospitals and 11.9% and 20.6% in the private pharmacies. The public procurement and retail prices were 2.25 and 2.59 times the international reference prices (IRPs) for three OBs, and 0.52 and 0.93 times for 20 LPGs. In the private sector, the final prices for OBs and LPGs were 3.89 and 1.25 times their IRPs. The final price in the private sector was 2.7% lower than in the public sector for OBs, and 14.1% higher for LPGs. Generally, standard treatments cost less than 1 day’s wages in both sectors. Distribution mark-ups applied to brand salbutamol in Xi'an was 65.5%, and up to 185.3% for generic. Cumulative mark-ups for LPGs in Ankang were also high, from 33% to 50%. The manufacturer’s selling price is the largest contributor to the final price in both areas. Conclusions The government should approve a list of national paediatric essential medicines. The availability, price and affordability of these should be improved in both public hospitals and private pharmacies to enable children to obtain effective treatment. Measures should be taken to improve the efficiency of the centralised medicine purchasing system. PMID:24595099

Access to paediatric essential medicines: a survey of prices, availability, affordability and price components in Shaanxi Province, China.

PubMed

Wang, Xiao; Fang, Yu; Yang, Shimin; Jiang, Minghuan; Yan, Kangkang; Wu, Lina; Lv, Bing; Shen, Qian

2014-01-01

To evaluate the prices and availability of paediatric essential medicines in Shaanxi Province, China. Price and availability data for 28 paediatric essential medicines were collected from 60 public hospitals and 60 retail pharmacies in six areas of Shaanxi Province using a standardised methodology developed by the World Health Organization and Health Action International, during November to December 2012. Affordability was measured as the number of days' wages required for the lowest-paid unskilled government worker to purchase standard treatments for common conditions. Data on medicine price components were collected from hospitals, wholesalers and distributors to obtain price mark-ups. The mean availabilities of originator brands (OBs) and lowest-priced generics (LPGs) were 10.8% and 27.3% in the public hospitals and 11.9% and 20.6% in the private pharmacies. The public procurement and retail prices were 2.25 and 2.59 times the international reference prices (IRPs) for three OBs, and 0.52 and 0.93 times for 20 LPGs. In the private sector, the final prices for OBs and LPGs were 3.89 and 1.25 times their IRPs. The final price in the private sector was 2.7% lower than in the public sector for OBs, and 14.1% higher for LPGs. Generally, standard treatments cost less than 1 day's wages in both sectors. Distribution mark-ups applied to brand salbutamol in Xi'an was 65.5%, and up to 185.3% for generic. Cumulative mark-ups for LPGs in Ankang were also high, from 33% to 50%. The manufacturer's selling price is the largest contributor to the final price in both areas. The government should approve a list of national paediatric essential medicines. The availability, price and affordability of these should be improved in both public hospitals and private pharmacies to enable children to obtain effective treatment. Measures should be taken to improve the efficiency of the centralised medicine purchasing system.

Overview of the World Wide Web Consortium (W3C) (SIGs IA, USE).

ERIC Educational Resources Information Center

Daly, Janet

2000-01-01

Provides an overview of a planned session to describe the work of the World Wide Web Consortium, including technical specifications for HTML (Hypertext Markup Language), XML (Extensible Markup Language), CSS (Cascading Style Sheets), and over 20 other Web standards that address graphics, multimedia, privacy, metadata, and other technologies. (LRW)

HyperText MARCup: A Conceptualization for Encoding, De-Constructing, Searching, Retrieving, and Using Traditional Knowledge Tools.

ERIC Educational Resources Information Center

Wall, C. Edward; And Others

1995-01-01

Discusses the integration of Standard General Markup Language, Hypertext Markup Language, and MARC format to parse classified analytical bibliographies. Use of the resulting electronic knowledge constructs in local library systems as maps of a specified subset of resources is discussed, and an example is included. (LRW)

An Electronic Finding Aid Using Extensible Markup Language (XML) and Encoded Archival Description (EAD).

ERIC Educational Resources Information Center

Chang, May

2000-01-01

Describes the development of electronic finding aids for archives at the University of Illinois, Urbana-Champaign that used XML (extensible markup language) and EAD (encoded archival description) to enable more flexible information management and retrieval than using MARC or a relational database management system. EAD template is appended.…

Automated Text Markup for Information Retrieval from an Electronic Textbook of Infectious Disease

PubMed Central

Berrios, Daniel C.; Kehler, Andrew; Kim, David K.; Yu, Victor L.; Fagan, Lawrence M.

1998-01-01

The information needs of practicing clinicians frequently require textbook or journal searches. Making these sources available in electronic form improves the speed of these searches, but precision (i.e., the fraction of relevant to total documents retrieved) remains low. Improving the traditional keyword search by transforming search terms into canonical concepts does not improve search precision greatly. Kim et al. have designed and built a prototype system (MYCIN II) for computer-based information retrieval from a forthcoming electronic textbook of infectious disease. The system requires manual indexing by experts in the form of complex text markup. However, this mark-up process is time consuming (about 3 person-hours to generate, review, and transcribe the index for each of 218 chapters). We have designed and implemented a system to semiautomate the markup process. The system, information extraction for semiautomated indexing of documents (ISAID), uses query models and existing information-extraction tools to provide support for any user, including the author of the source material, to mark up tertiary information sources quickly and accurately.

Automation and integration of components for generalized semantic markup of electronic medical texts.

PubMed Central

Dugan, J. M.; Berrios, D. C.; Liu, X.; Kim, D. K.; Kaizer, H.; Fagan, L. M.

1999-01-01

Our group has built an information retrieval system based on a complex semantic markup of medical textbooks. We describe the construction of a set of web-based knowledge-acquisition tools that expedites the collection and maintenance of the concepts required for text markup and the search interface required for information retrieval from the marked text. In the text markup system, domain experts (DEs) identify sections of text that contain one or more elements from a finite set of concepts. End users can then query the text using a predefined set of questions, each of which identifies a subset of complementary concepts. The search process matches that subset of concepts to relevant points in the text. The current process requires that the DE invest significant time to generate the required concepts and questions. We propose a new system--called ACQUIRE (Acquisition of Concepts and Queries in an Integrated Retrieval Environment)--that assists a DE in two essential tasks in the text-markup process. First, it helps her to develop, edit, and maintain the concept model: the set of concepts with which she marks the text. Second, ACQUIRE helps her to develop a query model: the set of specific questions that end users can later use to search the marked text. The DE incorporates concepts from the concept model when she creates the questions in the query model. The major benefit of the ACQUIRE system is a reduction in the time and effort required for the text-markup process. We compared the process of concept- and query-model creation using ACQUIRE to the process used in previous work by rebuilding two existing models that we previously constructed manually. We observed a significant decrease in the time required to build and maintain the concept and query models. Images Figure 1 Figure 2 Figure 4 Figure 5 PMID:10566457

Modularization and Structured Markup for Learning Content in an Academic Environment

ERIC Educational Resources Information Center

Schluep, Samuel; Bettoni, Marco; Schar, Sissel Guttormsen

2006-01-01

This article aims to present a flexible component model for modular, web-based learning content, and a simple structured markup schema for the separation of content and presentation. The article will also contain an overview of the dynamic Learning Content Management System (dLCMS) project, which implements these concepts. Content authors are a…

The Adoption of Mark-Up Tools in an Interactive e-Textbook Reader

ERIC Educational Resources Information Center

Van Horne, Sam; Russell, Jae-eun; Schuh, Kathy L.

2016-01-01

Researchers have more often examined whether students prefer using an e-textbook over a paper textbook or whether e-textbooks provide a better resource for learning than paper textbooks, but students' adoption of mark-up tools has remained relatively unexamined. Drawing on the concept of Innovation Diffusion Theory, we used educational data mining…

A methodology for evaluation of a markup-based specification of clinical guidelines.

PubMed

Shalom, Erez; Shahar, Yuval; Taieb-Maimon, Meirav; Lunenfeld, Eitan

2008-11-06

We introduce a three-phase, nine-step methodology for specification of clinical guidelines (GLs) by expert physicians, clinical editors, and knowledge engineers, and for quantitative evaluation of the specification's quality. We applied this methodology to a particular framework for incremental GL structuring (mark-up) and to GLs in three clinical domains with encouraging results.

Extensible Markup Language: How Might It Alter the Software Documentation Process and the Role of the Technical Communicator?

ERIC Educational Resources Information Center

Battalio, John T.

2002-01-01

Describes the influence that Extensible Markup Language (XML) will have on the software documentation process and subsequently on the curricula of advanced undergraduate and master's programs in technical communication. Recommends how curricula of advanced undergraduate and master's programs in technical communication ought to change in order to…

Astronomical Instrumentation System Markup Language

NASA Astrophysics Data System (ADS)

Goldbaum, Jesse M.

2016-05-01

The Astronomical Instrumentation System Markup Language (AISML) is an Extensible Markup Language (XML) based file format for maintaining and exchanging information about astronomical instrumentation. The factors behind the need for an AISML are first discussed followed by the reasons why XML was chosen as the format. Next it's shown how XML also provides the framework for a more precise definition of an astronomical instrument and how these instruments can be combined to form an Astronomical Instrumentation System (AIS). AISML files for several instruments as well as one for a sample AIS are provided. The files demonstrate how AISML can be utilized for various tasks from web page generation and programming interface to instrument maintenance and quality management. The advantages of widespread adoption of AISML are discussed.

Web-based X-ray quality control documentation.

PubMed

David, George; Burnett, Lou Ann; Schenkel, Robert

2003-01-01

The department of radiology at the Medical College of Georgia Hospital and Clinics has developed an equipment quality control web site. Our goal is to provide immediate access to virtually all medical physics survey data. The web site is designed to assist equipment engineers, department management and technologists. By improving communications and access to equipment documentation, we believe productivity is enhanced. The creation of the quality control web site was accomplished in three distinct steps. First, survey data had to be placed in a computer format. The second step was to convert these various computer files to a format supported by commercial web browsers. Third, a comprehensive home page had to be designed to provide convenient access to the multitude of surveys done in the various x-ray rooms. Because we had spent years previously fine-tuning the computerization of the medical physics quality control program, most survey documentation was already in spreadsheet or database format. A major technical decision was the method of conversion of survey spreadsheet and database files into documentation appropriate for the web. After an unsatisfactory experience with a HyperText Markup Language (HTML) converter (packaged with spreadsheet and database software), we tried creating Portable Document Format (PDF) files using Adobe Acrobat software. This process preserves the original formatting of the document and takes no longer than conventional printing; therefore, it has been very successful. Although the PDF file generated by Adobe Acrobat is a proprietary format, it can be displayed through a conventional web browser using the freely distributed Adobe Acrobat Reader program that is available for virtually all platforms. Once a user installs the software, it is automatically invoked by the web browser whenever the user follows a link to a file with a PDF extension. Although no confidential patient information is available on the web site, our legal department recommended that we secure the site in order to keep out those wishing to make mischief. Our interim solution has not been to password protect the page, which we feared would hinder access for occasional legitimate users, but also not to provide links to it from other hospital and department pages. Utility and productivity were improved and time and money were saved by making radiological equipment quality control documentation instantly available on-line.

77 FR 5265 - Eastern Band of Cherokee Indians-Cherokee Code Chapter 18B, Regulation of Alcoholic Beverages

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-02

... exclusively from the North Carolina Alcoholic Beverage Control Commission at the same price and on the same... issuance and enforcement of ABC permits; (5) Administer an annual budget with said budget to be approved... price as published by North Carolina 18B-804. Where a tax or markup is imposed in this section, the...

Automatic Configuration of Programmable Logic Controller Emulators

DTIC Science & Technology

2015-03-01

25 11 Example tree generated using UPGMA [Edw13] . . . . . . . . . . . . . . . . . . . . 33 12 Example sequence alignment for two... UPGMA Unweighted Pair Group Method with Arithmetic Mean URL uniform resource locator VM virtual machine XML Extensible Markup Language xx List of...appearance in the ses- sion, and then they are clustered again using Unweighted Pair Group Method with Arithmetic Mean ( UPGMA ) with a distance matrix based

Using Extensible Markup Language (XML) for the Single Source Delivery of Educational Resources by Print and Online: A Case Study

ERIC Educational Resources Information Center

Walsh, Lucas

2007-01-01

This article seeks to provide an introduction to Extensible Markup Language (XML) by looking at its use in a single source publishing approach to the provision of teaching resources in both hardcopy and online. Using the development of the International Baccalaureate Organisation's online Economics Subject Guide as a practical example, this…

A Practical Introduction to the XML, Extensible Markup Language, by Way of Some Useful Examples

ERIC Educational Resources Information Center

Snyder, Robin

2004-01-01

XML, Extensible Markup Language, is important as a way to represent and encapsulate the structure of underlying data in a portable way that supports data exchange regardless of the physical storage of the data. This paper (and session) introduces some useful and practical aspects of XML technology for sharing information in a educational setting…

Knowledge Provenance in Semantic Wikis

NASA Astrophysics Data System (ADS)

Ding, L.; Bao, J.; McGuinness, D. L.

2008-12-01

Collaborative online environments with a technical Wiki infrastructure are becoming more widespread. One of the strengths of a Wiki environment is that it is relatively easy for numerous users to contribute original content and modify existing content (potentially originally generated by others). As more users begin to depend on informational content that is evolving by Wiki communities, it becomes more important to track the provenance of the information. Semantic Wikis expand upon traditional Wiki environments by adding some computationally understandable encodings of some of the terms and relationships in Wikis. We have developed a semantic Wiki environment that expands a semantic Wiki with provenance markup. Provenance of original contributions as well as modifications is encoded using the provenance markup component of the Proof Markup Language. The Wiki environment provides the provenance markup automatically, thus users are not required to make specific encodings of author, contribution date, and modification trail. Further, our Wiki environment includes a search component that understands the provenance primitives and thus can be used to provide a provenance-aware search facility. We will describe the knowledge provenance infrastructure of our Semantic Wiki and show how it is being used as the foundation of our group web site as well as a number of project web sites.

Building Community Around Hydrologic Data Models Within CUAHSI

NASA Astrophysics Data System (ADS)

Maidment, D.

2007-12-01

The Consortium of Universities for the Advancement of Hydrologic Science, Inc (CUAHSI) has a Hydrologic Information Systems project which aims to provide better data access and capacity for data synthesis for the nation's water information, both that collected by academic investigators and that collected by water agencies. These data include observations of streamflow, water quality, groundwater levels, weather and climate and aquatic biology. Each water agency or research investigator has a unique method of formatting their data (syntactic heterogeneity) and describing their variables (semantic heterogeneity). The result is a large agglomeration of data in many formats and descriptions whose full content is hard to interpret and analyze. CUAHSI is helping to resolve syntactic heterogeneity through the development of WaterML, a standard XML markup language for communicating water observations data through web services, and a standard relational database structure for archiving data called the Observations Data Model. Variables in these data archiving and communicating systems are indexed against a controlled vocabulary of descriptive terms to provide the capacity to synthesize common data types from disparate data sources.

jmzIdentML API: A Java interface to the mzIdentML standard for peptide and protein identification data.

PubMed

Reisinger, Florian; Krishna, Ritesh; Ghali, Fawaz; Ríos, Daniel; Hermjakob, Henning; Vizcaíno, Juan Antonio; Jones, Andrew R

2012-03-01

We present a Java application programming interface (API), jmzIdentML, for the Human Proteome Organisation (HUPO) Proteomics Standards Initiative (PSI) mzIdentML standard for peptide and protein identification data. The API combines the power of Java Architecture of XML Binding (JAXB) and an XPath-based random-access indexer to allow a fast and efficient mapping of extensible markup language (XML) elements to Java objects. The internal references in the mzIdentML files are resolved in an on-demand manner, where the whole file is accessed as a random-access swap file, and only the relevant piece of XMLis selected for mapping to its corresponding Java object. The APIis highly efficient in its memory usage and can handle files of arbitrary sizes. The APIfollows the official release of the mzIdentML (version 1.1) specifications and is available in the public domain under a permissive licence at http://www.code.google.com/p/jmzidentml/. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Combining computational models, semantic annotations and simulation experiments in a graph database

PubMed Central

Henkel, Ron; Wolkenhauer, Olaf; Waltemath, Dagmar

2015-01-01

Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems. However, their storage concepts support only restricted types of queries and not all data inside the repositories can be retrieved. In this article we present a storage concept that meets this challenge. It grounds on a graph database, reflects the models’ structure, incorporates semantic annotations and simulation descriptions and ultimately connects different types of model-related data. The connections between heterogeneous model-related data and bio-ontologies enable efficient search via biological facts and grant access to new model features. The introduced concept notably improves the access of computational models and associated simulations in a model repository. This has positive effects on tasks such as model search, retrieval, ranking, matching and filtering. Furthermore, our work for the first time enables CellML- and Systems Biology Markup Language-encoded models to be effectively maintained in one database. We show how these models can be linked via annotations and queried. Database URL: https://sems.uni-rostock.de/projects/masymos/ PMID:25754863

A New Method of Viewing Attachment Document of eMail on Various Mobile Devices

NASA Astrophysics Data System (ADS)

Ko, Heeae; Seo, Changwoo; Lim, Yonghwan

As the computing power of the mobile devices is improving rapidly, many kinds of web services are also available in mobile devices just as Email service. Mobile Mail Service began early, but this service is mostly limited in some specified mobile devices such as Smart Phone. That is a limitation that users have to purchase specified phone to be benefited from Mobile Mail Service. In this paper, it uses DIDL (digital item declaration language) markup type defined in MPEG-21 and MobileGate Server, and solved this problem. DIDL could be converted to other markup types which are displayed by mobile devices. By transforming PC Web Mail contents including attachment document to DIDL markup through MobileGate Server, the Mobile Mail Service could be available for all kinds of mobile devices.

Producing a Data Dictionary from an Extensible Markup Language (XML) Schemain the Global Force Management Data Initiative

DTIC Science & Technology

2017-02-01

entity relationship (diagram) EwID Enterprise-wide Identifier FMID Force Management Identifier GFM Global Force Management HTML Hypertext Markup Language... Management Data Initiative by Frederick S Brundick Approved for public release; distribution is unlimited. NOTICES Disclaimers The findings in this report...Schema in the Global Force Management Data Initiative by Frederick S Brundick Computing and Information Sciences Directorate, ARL Approved for public

RTML: remote telescope markup language and you

NASA Astrophysics Data System (ADS)

Hessman, F. V.

2001-12-01

In order to coordinate the use of robotic and remotely operated telescopes in networks -- like Göttingen's MOnitoring NEtwork of Telescopes (MONET) -- a standard format for the exchange of observing requests and reports is needed. I describe the benefits of Remote Telescope Markup Language (RTML), an XML-based protocol originally developed by the Hands-On Universe Project, which is being used and further developed by several robotic telescope projects and firms.

Development of Markup Language for Medical Record Charting: A Charting Language.

PubMed

Jung, Won-Mo; Chae, Younbyoung; Jang, Bo-Hyoung

2015-01-01

Nowadays a lot of trials for collecting electronic medical records (EMRs) exist. However, structuring data format for EMR is an especially labour-intensive task for practitioners. Here we propose a new mark-up language for medical record charting (called Charting Language), which borrows useful properties from programming languages. Thus, with Charting Language, the text data described in dynamic situation can be easily used to extract information.

Visualization Development of the Ballistic Threat Geospatial Optimization

DTIC Science & Technology

2015-07-01

topographic globes, Keyhole Markup Language (KML), and Collada files. World Wind gives the user the ability to import 3-D models and navigate...present. After the first person view window is closed , the images stored in memory are then converted to a QuickTime movie (.MOV). The video will be...processing unit HPC high-performance computing JOGL Java implementation of OpenGL KML Keyhole Markup Language NASA National Aeronautics and Space

Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML vocabulary for spectral data.

PubMed

Kuhn, Stefan; Helmus, Tobias; Lancashire, Robert J; Murray-Rust, Peter; Rzepa, Henry S; Steinbeck, Christoph; Willighagen, Egon L

2007-01-01

CMLSpect is an extension of Chemical Markup Language (CML) for managing spectral and other analytical data. It is designed to be flexible enough to contain a wide variety of spectral data. The paper describes the CMLElements used and gives practical examples for common types of spectra. In addition it demonstrates how different views of the data can be expressed and what problems still exist.

A comprehensive strategy for designing a Web-based medical curriculum.

PubMed Central

Zucker, J.; Chase, H.; Molholt, P.; Bean, C.; Kahn, R. M.

1996-01-01

In preparing for a full featured online curriculum, it is necessary to develop scaleable strategies for software design that will support the pedagogical goals of the curriculum and which will address the issues of acquisition and updating of materials, of robust content-based linking, and of integration of the online materials into other methods of learning. A complete online curriculum, as distinct from an individual computerized module, must provide dynamic updating of both content and structure and an easy pathway from the professor's notes to the finished online product. At the College of Physicians and Surgeons, we are developing such strategies including a scripted text conversion process that uses the Hypertext Markup Language (HTML) as structural markup rather than as display markup, automated linking by the use of relational databases and the Unified Medical Language System (UMLS), integration of text, images, and multimedia along with interface designs which promote multiple contexts and collaborative study. PMID:8947624

Computer support for physiological cell modelling using an ontology on cell physiology.

PubMed

Takao, Shimayoshi; Kazuhiro, Komurasaki; Akira, Amano; Takeshi, Iwashita; Masanori, Kanazawa; Tetsuya, Matsuda

2006-01-01

The development of electrophysiological whole cell models to support the understanding of biological mechanisms is increasing rapidly. Due to the complexity of biological systems, comprehensive cell models, which are composed of many imported sub-models of functional elements, can get quite complicated as well, making computer modification difficult. Here, we propose a computer support to enhance structural changes of cell models, employing the markup languages CellML and our original PMSML (physiological model structure markup language), in addition to a new ontology for cell physiological modelling. In particular, a method to make references from CellML files to the ontology and a method to assist manipulation of model structures using markup languages together with the ontology are reported. Using these methods three software utilities, including a graphical model editor, are implemented. Experimental results proved that these methods are effective for the modification of electrophysiological models.

Distributed framework for dyanmic telescope and instrument control

NASA Astrophysics Data System (ADS)

Ames, Troy J.; Case, Lynne

2003-02-01

Traditionally, instrument command and control systems have been developed specifically for a single instrument. Such solutions are frequently expensive and are inflexible to support the next instrument development effort. NASA Goddard Space Flight Center is developing an extensible framework, known as Instrument Remote Control (IRC) that applies to any kind of instrument that can be controlled by a computer. IRC combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML). A key aspect of the architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). IML is an XML dialect used to describe graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, communication mechanisms, and data processing algorithms. The IRC framework provides the ability to communicate to components anywhere on a network using the JXTA protocol for dynamic discovery of distributed components. JXTA (see http://www.jxta.org) is a generalized protocol that allows any devices connected by a network to communicate in a peer-to-peer manner. IRC uses JXTA to advertise a devices IML and discover devices of interest on the network. Devices can join or leave the network and thus join or leave the instrument control environment of IRC. Currently, several astronomical instruments are working with the IRC development team to develop custom components for IRC to control their instruments. These instruments include: High resolution Airborne Wideband Camera (HAWC), a first light instrument for the Stratospheric Observatory for Infrared Astronomy (SOFIA); Submillimeter And Far Infrared Experiment (SAFIRE), a Principal Investigator instrument for SOFIA; and Fabry-Perot Interferometer Bolometer Research Experiment (FIBRE), a prototype of the SAFIRE instrument, used at the Caltech Submillimeter Observatory (CSO). Most recently, we have been working with the Submillimetre High

Utilizing Internet Technologies in Observatory Control Systems

NASA Astrophysics Data System (ADS)

Cording, Dean

2002-12-01

The 'Internet boom' of the past few years has spurred the development of a number of technologies to provide services such as secure communications, reliable messaging, information publishing and application distribution for commercial applications. Over the same period, a new generation of computer languages have also developed to provide object oriented design and development, improved reliability, and cross platform compatibility. Whilst the business models of the 'dot.com' era proved to be largely unviable, the technologies that they were based upon have survived and have matured to the point were they can now be utilized to build secure, robust and complete observatory control control systems. This paper will describe how Electro Optic Systems has utilized these technologies in the development of its third generation Robotic Observatory Control System (ROCS). ROCS provides an extremely flexible configuration capability within a control system structure to provide truly autonomous robotic observatory operation including observation scheduling. ROCS was built using Internet technologies such as Java, Java Messaging Service (JMS), Lightweight Directory Access Protocol (LDAP), Secure Sockets Layer (SSL), eXtendible Markup Language (XML), Hypertext Transport Protocol (HTTP) and Java WebStart. ROCS was designed to be capable of controlling all aspects of an observatory and be able to be reconfigured to handle changing equipment configurations or user requirements without the need for an expert computer programmer. ROCS consists of many small components, each designed to perform a specific task, with the configuration of the system specified using a simple meta language. The use of small components facilitates testing and makes it possible to prove that the system is correct.

Representing Information in Patient Reports Using Natural Language Processing and the Extensible Markup Language

PubMed Central

Friedman, Carol; Hripcsak, George; Shagina, Lyuda; Liu, Hongfang

1999-01-01

Objective: To design a document model that provides reliable and efficient access to clinical information in patient reports for a broad range of clinical applications, and to implement an automated method using natural language processing that maps textual reports to a form consistent with the model. Methods: A document model that encodes structured clinical information in patient reports while retaining the original contents was designed using the extensible markup language (XML), and a document type definition (DTD) was created. An existing natural language processor (NLP) was modified to generate output consistent with the model. Two hundred reports were processed using the modified NLP system, and the XML output that was generated was validated using an XML validating parser. Results: The modified NLP system successfully processed all 200 reports. The output of one report was invalid, and 199 reports were valid XML forms consistent with the DTD. Conclusions: Natural language processing can be used to automatically create an enriched document that contains a structured component whose elements are linked to portions of the original textual report. This integrated document model provides a representation where documents containing specific information can be accurately and efficiently retrieved by querying the structured components. If manual review of the documents is desired, the salient information in the original reports can also be identified and highlighted. Using an XML model of tagging provides an additional benefit in that software tools that manipulate XML documents are readily available. PMID:9925230

Biological data integration: wrapping data and tools.

PubMed

Lacroix, Zoé

2002-06-01

Nowadays scientific data is inevitably digital and stored in a wide variety of formats in heterogeneous systems. Scientists need to access an integrated view of remote or local heterogeneous data sources with advanced data accessing, analyzing, and visualization tools. Building a digital library for scientific data requires accessing and manipulating data extracted from flat files or databases, documents retrieved from the Web as well as data generated by software. We present an approach to wrapping web data sources, databases, flat files, or data generated by tools through a database view mechanism. Generally, a wrapper has two tasks: it first sends a query to the source to retrieve data and, second builds the expected output with respect to the virtual structure. Our wrappers are composed of a retrieval component based on an intermediate object view mechanism called search views mapping the source capabilities to attributes, and an eXtensible Markup Language (XML) engine, respectively, to perform these two tasks. The originality of the approach consists of: 1) a generic view mechanism to access seamlessly data sources with limited capabilities and 2) the ability to wrap data sources as well as the useful specific tools they may provide. Our approach has been developed and demonstrated as part of the multidatabase system supporting queries via uniform object protocol model (OPM) interfaces.

An Overview of Genomic Sequence Variation Markup Language (GSVML)

PubMed Central

Nakaya, Jun; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Kimura, Michio

2006-01-01

Internationally accumulated genomic sequence variation data on human requires the interoperable data exchanging format. We developed the GSVML as the data exchanging format. The GSVML is human health oriented and has three categories. Analyses on the use case in human health domain and the investigation on the databases and markup languages were conducted. An interface ability to Health Level Seven Genotype Model was examined. GSVML provides a sharable platform for both clinical and research applications.

MYCIN II: design and implementation of a therapy reference with complex content-based indexing.

PubMed Central

Kim, D. K.; Fagan, L. M.; Jones, K. T.; Berrios, D. C.; Yu, V. L.

1998-01-01

We describe the construction of MYCIN II, a prototype system that provides for content-based markup and search of a forthcoming clinical therapeutics textbook, Antimicrobial Therapy and Vaccines. Existing commercial search technology for digital references utilizes generic tools such as textword-based searches with geographical or statistical refinements. We suggest that the drawbacks of such systems significantly restrict their use in everyday clinical practice. This is in spite of the fact that there is a great need for the information contained within these same references. The system we describe is intended to supplement keyword searching so that certain important questions can be asked easily and can be answered reliably (in terms of precision and recall). Our method attacks this problem in a restricted domain of knowledge-clinical infectious disease. For example, we would like to be able to answer the class of questions exemplified by the following query: "What antimicrobial agents can be used to treat endocarditis caused by Eikenella corrodens?" We have compiled and analyzed a list of such questions to develop a concept-based markup scheme. This scheme was then applied within an HTML markup to electronically "highlight" passages from three textbook chapters. We constructed a functioning web-based search interface. Our system also provides semi-automated querying of PubMed using our concept markup and the user's actions as a guide. PMID:9929205

MYCIN II: design and implementation of a therapy reference with complex content-based indexing.

PubMed

Kim, D K; Fagan, L M; Jones, K T; Berrios, D C; Yu, V L

1998-01-01

We describe the construction of MYCIN II, a prototype system that provides for content-based markup and search of a forthcoming clinical therapeutics textbook, Antimicrobial Therapy and Vaccines. Existing commercial search technology for digital references utilizes generic tools such as textword-based searches with geographical or statistical refinements. We suggest that the drawbacks of such systems significantly restrict their use in everyday clinical practice. This is in spite of the fact that there is a great need for the information contained within these same references. The system we describe is intended to supplement keyword searching so that certain important questions can be asked easily and can be answered reliably (in terms of precision and recall). Our method attacks this problem in a restricted domain of knowledge-clinical infectious disease. For example, we would like to be able to answer the class of questions exemplified by the following query: "What antimicrobial agents can be used to treat endocarditis caused by Eikenella corrodens?" We have compiled and analyzed a list of such questions to develop a concept-based markup scheme. This scheme was then applied within an HTML markup to electronically "highlight" passages from three textbook chapters. We constructed a functioning web-based search interface. Our system also provides semi-automated querying of PubMed using our concept markup and the user's actions as a guide.

Computerization of guidelines: towards a "guideline markup language".

PubMed

Dart, T; Xu, Y; Chatellier, G; Degoulet, P

2001-01-01

Medical decision making is one of the most difficult daily tasks for physicians. Guidelines have been designed to reduce variance between physicians in daily practice, to improve patient outcomes and to control costs. In fact, few physicians use guidelines in daily practice. A way to ease the use of guidelines is to implement computerised guidelines (computer reminders). We present in this paper a method of computerising guidelines. Our objectives were: 1) to propose a generic model that can be instantiated for any specific guidelines; 2) to use eXtensible Markup Language (XML) as a guideline representation language to instantiate the generic model for a specific guideline. Our model is an object representation of a clinical algorithm, it has been validated by running two different guidelines issued by a French official Agency. In spite of some limitations, we found that this model is expressive enough to represent complex guidelines devoted to diabetes and hypertension management. We conclude that XML can be used as a description format to structure guidelines and as an interface between paper-based guidelines and computer applications.

OneGeology: Making the World’s Geological Map Data Accessible Online

NASA Astrophysics Data System (ADS)

Broome, H.; Jackson, I.; Robida, F.; Thorleifson, H.

2009-12-01

OneGeology (http://onegeology.org) is a successful international initiative of the geological surveys of the world and the flagship project of the ‘International Year of Planet Earth’. Its aim is to provide dynamic web access to geological map data covering the world, creating a focus for accessing geological information for everyone. Thanks to the enthusiasm and support of participating nations the initiative has progressed rapidly and geological surveys and the many users of their data are excited about this ground-breaking project. Currently 10 international geoscience organizations have endorsed the initiative and more than 109 countries have agreed to participate. OneGeology works with whatever digital format is available in each country. The target scale is 1:1 million, but the project is pragmatic and accepts a range of scales and the best available data. The initiative recognizes that different nations have differing abilities to participate and transfer of know-how to those who need it is a key aspect of the approach. A key contributor to the success of OneGeology has been its utilization of the latest new web technology and an emerging data exchange standard for geological map data called GeoSciML. GeoSciML (GeoScience Markup Language) is a schema written in GML (Geography Markup Language) for geological data. GeoSciML has the ability to represent both the geography (geometries e.g. polygons, lines and points) and geological attribution in a clear and structured format. OneGeology was launched March 2007 at the inaugural workshop in Brighton England. At that workshop the 43 participating nations developed a declaration of a common objective and principles called the “Brighton Accord” (http://onegeology.org/what_is/accord.html) . Work was initiated immediately and the resulting OneGeology Portal was launched at the International Geological Congress in Oslo in August 2008 by Simon Winchester, author of “The Map that Changed the World”. Since the successful launch, OneGeology participants have continued working both to increase national participation and content, and to put in place a more formal governance structure to oversee the long term evolution of the initiative. OneGeology is an example of collaboration in action and is both multilateral and multinational. In 2007, a group of motivated geoscientists and data managers identified an opportunity and took the initiative to engage their peers to work in concert to achieve a shared objective. OneGeology has facilitated collaborative development of an Internet site that provides unprecedented online access to global geological map data.

Effects on the medical revenue of comprehensive pricing reform in Chinese urban public hospitals after removing drug markups: case of Nanjing.

PubMed

Tang, Wenxi; Xie, Jing; Lu, Yijuan; Liu, Qizhi; Malone, Daniel; Ma, Aixia

2018-04-01

The State Council of China requires that all urban public hospitals must eliminate drug markups by September 2017, and that hospital drugs must be sold at the purchase price. Nanjing-one of the first provincial capital cities to implement the reform-is studied to evaluate the effects of the comprehensive reform on drug prices in public hospitals, and to explore differential compensation plans. Sixteen hospitals were selected, and financial data were collected over the 48-month period before the reform and for 12 months after the reform. An analysis was carried out using a simple linear interrupted time series model. The average difference ratio of drug surplus fell 13.39% after the reform, and the drug markups were basically eliminated. Revenue from medical services showed a net growth of 28.25%. The overall compensation received from government financial budget and medical service revenue growth was 103.69% for the loss from policy-permitted 15% markup sales, and 116.48% for the net loss. However, there were large differences in compensation levels at different hospitals, ranging from -21.92% to 413.74% by medical services revenue growth, causing the combined rate of both financial and service compensation to vary from 28.87-413.74%, There was a significant positive correlation between the services compensation rate and the proportion of medical service revenue (p < .001), and the compensation rate increased by 8% for every 1% increase in the proportion of services revenue. Nanjing's pricing and compensation reform has basically achieved the policy targets of eliminating the drug markups, promoting the growth of medical services revenue, and adjusting the structure of medical revenue. However, the growth rate of service revenue of hospitals varied significantly from one another. Nanjing's reform represents successful pricing and compensation reform in Chinese urban public hospitals. It is recommended that a differentiated and dynamic compensation plan should be established in accordance with the revenue structure of different hospitals.

Automating Information Assurance for Cyber Situational Awareness within a Smart Cloud System of Systems

DTIC Science & Technology

2014-03-01

Humanitarian Assistance and Disaster Relief HTML HyperText Markup Language IA Information Assurance IAI Israel Aerospace Industries IASA Information ...decision maker at the Command and Control “mini cloud” was of upmost interest . This discussion not only confirmed the need to have information ...2) monitoring for specific cyber attacks on a specified system, (3) alerting information of interest to an operator, and finally (4) allowing the

Importing MAGE-ML format microarray data into BioConductor.

PubMed

Durinck, Steffen; Allemeersch, Joke; Carey, Vincent J; Moreau, Yves; De Moor, Bart

2004-12-12

The microarray gene expression markup language (MAGE-ML) is a widely used XML (eXtensible Markup Language) standard for describing and exchanging information about microarray experiments. It can describe microarray designs, microarray experiment designs, gene expression data and data analysis results. We describe RMAGEML, a new Bioconductor package that provides a link between cDNA microarray data stored in MAGE-ML format and the Bioconductor framework for preprocessing, visualization and analysis of microarray experiments. http://www.bioconductor.org. Open Source.

Chemical markup, XML, and the World Wide Web. 5. Applications of chemical metadata in RSS aggregators.

PubMed

Murray-Rust, Peter; Rzepa, Henry S; Williamson, Mark J; Willighagen, Egon L

2004-01-01

Examples of the use of the RSS 1.0 (RDF Site Summary) specification together with CML (Chemical Markup Language) to create a metadata based alerting service termed CMLRSS for molecular content are presented. CMLRSS can be viewed either using generic software or with modular opensource chemical viewers and editors enhanced with CMLRSS modules. We discuss the more automated use of CMLRSS as a component of a World Wide Molecular Matrix of semantically rich chemical information.

Distributing Data to Hand-Held Devices in a Wireless Network

NASA Technical Reports Server (NTRS)

Hodges, Mark; Simmons, Layne

2008-01-01

ADROIT is a developmental computer program for real-time distribution of complex data streams for display on Web-enabled, portable terminals held by members of an operational team of a spacecraft-command-and-control center who may be located away from the center. Examples of such terminals include personal data assistants, laptop computers, and cellular telephones. ADROIT would make it unnecessary to equip each terminal with platform- specific software for access to the data streams or with software that implements the information-sharing protocol used to deliver telemetry data to clients in the center. ADROIT is a combination of middleware plus software specific to the center. (Middleware enables one application program to communicate with another by performing such functions as conversion, translation, consolidation, and/or integration.) ADROIT translates a data stream (voice, video, or alphanumerical data) from the center into Extensible Markup Language, effectuates a subscription process to determine who gets what data when, and presents the data to each user in real time. Thus, ADROIT is expected to enable distribution of operations and to reduce the cost of operations by reducing the number of persons required to be in the center.

Data-Driven Software Framework for Web-Based ISS Telescience

NASA Technical Reports Server (NTRS)

Tso, Kam S.

2005-01-01

Software that enables authorized users to monitor and control scientific payloads aboard the International Space Station (ISS) from diverse terrestrial locations equipped with Internet connections is undergoing development. This software reflects a data-driven approach to distributed operations. A Web-based software framework leverages prior developments in Java and Extensible Markup Language (XML) to create portable code and portable data, to which one can gain access via Web-browser software on almost any common computer. Open-source software is used extensively to minimize cost; the framework also accommodates enterprise-class server software to satisfy needs for high performance and security. To accommodate the diversity of ISS experiments and users, the framework emphasizes openness and extensibility. Users can take advantage of available viewer software to create their own client programs according to their particular preferences, and can upload these programs for custom processing of data, generation of views, and planning of experiments. The same software system, possibly augmented with a subset of data and additional software tools, could be used for public outreach by enabling public users to replay telescience experiments, conduct their experiments with simulated payloads, and create their own client programs and other custom software.

Evolution of a Structure-Searchable Database into a Prototype for a High-Fidelity SmartPhone App for 62 Common Pesticides Used in Delaware.

PubMed

D'Souza, Malcolm J; Barile, Benjamin; Givens, Aaron F

2015-05-01

Synthetic pesticides are widely used in the modern world for human benefit. They are usually classified according to their intended pest target. In Delaware (DE), approximately 42 percent of the arable land is used for agriculture. In order to manage insectivorous and herbaceous pests (such as insects, weeds, nematodes, and rodents), pesticides are used profusely to biologically control the normal pest's life stage. In this undergraduate project, we first created a usable relational database containing 62 agricultural pesticides that are common in Delaware. Chemically pertinent quantitative and qualitative information was first stored in Bio-Rad's KnowItAll® Informatics System. Next, we extracted the data out of the KnowItAll® system and created additional sections on a Microsoft® Excel spreadsheet detailing pesticide use(s) and safety and handling information. Finally, in an effort to promote good agricultural practices, to increase efficiency in business decisions, and to make pesticide data globally accessible, we developed a mobile application for smartphones that displayed the pesticide database using Appery.io™; a cloud-based HyperText Markup Language (HTML5), jQuery Mobile and Hybrid Mobile app builder.

Dynamic assessment of microbial ecology (DAME): a web app for interactive analysis and visualization of microbial sequencing data.

PubMed

Piccolo, Brian D; Wankhade, Umesh D; Chintapalli, Sree V; Bhattacharyya, Sudeepa; Chunqiao, Luo; Shankar, Kartik

2018-03-15

Dynamic assessment of microbial ecology (DAME) is a Shiny-based web application for interactive analysis and visualization of microbial sequencing data. DAME provides researchers not familiar with R programming the ability to access the most current R functions utilized for ecology and gene sequencing data analyses. Currently, DAME supports group comparisons of several ecological estimates of α-diversity and β-diversity, along with differential abundance analysis of individual taxa. Using the Shiny framework, the user has complete control of all aspects of the data analysis, including sample/experimental group selection and filtering, estimate selection, statistical methods and visualization parameters. Furthermore, graphical and tabular outputs are supported by R packages using D3.js and are fully interactive. DAME was implemented in R but can be modified by Hypertext Markup Language (HTML), Cascading Style Sheets (CSS), and JavaScript. It is freely available on the web at https://acnc-shinyapps.shinyapps.io/DAME/. Local installation and source code are available through Github (https://github.com/bdpiccolo/ACNC-DAME). Any system with R can launch DAME locally provided the shiny package is installed. bdpiccolo@uams.edu.

Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.

PubMed

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

XML — an opportunity for data standards in the geosciences

NASA Astrophysics Data System (ADS)

Houlding, Simon W.

2001-08-01

Extensible markup language (XML) is a recently introduced meta-language standard on the Web. It provides the rules for development of metadata (markup) standards for information transfer in specific fields. XML allows development of markup languages that describe what information is rather than how it should be presented. This allows computer applications to process the information in intelligent ways. In contrast hypertext markup language (HTML), which fuelled the initial growth of the Web, is a metadata standard concerned exclusively with presentation of information. Besides its potential for revolutionizing Web activities, XML provides an opportunity for development of meaningful data standards in specific application fields. The rapid endorsement of XML by science, industry and e-commerce has already spawned new metadata standards in such fields as mathematics, chemistry, astronomy, multi-media and Web micro-payments. Development of XML-based data standards in the geosciences would significantly reduce the effort currently wasted on manipulating and reformatting data between different computer platforms and applications and would ensure compatibility with the new generation of Web browsers. This paper explores the evolution, benefits and status of XML and related standards in the more general context of Web activities and uses this as a platform for discussion of its potential for development of data standards in the geosciences. Some of the advantages of XML are illustrated by a simple, browser-compatible demonstration of XML functionality applied to a borehole log dataset. The XML dataset and the associated stylesheet and schema declarations are available for FTP download.

Applying Energy Conservation Retrofits to Standard Army Buildings: Data Analysis and Recommendations

DTIC Science & Technology

1990-09-01

than mechanical. The line titled "Mechanical" includes all line items related to electrical work, HVAC work, and controls. A 25 pet..ctit mark-up is...criteria specify a life of 15 years for HVAC retrofits and a 25-year life for weatherization, calculations were performed for both lifetimes for...circulation pump was serviced. "• Smaller sized steam valves and actuators were installed in the hot water converters. "* New pneumatic heating reset

Reducing Tobacco Use and Access Through Strengthened Minimum Price Laws

PubMed Central

Pearson, Anne; Laird-Metke, Elisa; Ribisl, Kurt

2014-01-01

Higher prices reduce consumption and initiation of tobacco products. A minimum price law that establishes a high statutory minimum price and prohibits the industry’s discounting tactics for tobacco products is a promising pricing strategy as an alternative to excise tax increases. Although some states have adopted minimum price laws on the basis of statutorily defined price “markups” over the invoice price, existing state laws have been largely ineffective at increasing the retail price. We analyzed 3 new variations of minimum price laws that hold great potential for raising tobacco prices and reducing consumption: (1) a flat rate minimum price law similar to a recent enactment in New York City, (2) an enhanced markup law, and (3) a law that incorporates both elements. PMID:25121820

Experimental Applications of Automatic Test Markup Language (ATML)

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; McCartney, Patrick; Gorringe, Chris

2012-01-01

The authors describe challenging use-cases for Automatic Test Markup Language (ATML), and evaluate solutions. The first case uses ATML Test Results to deliver active features to support test procedure development and test flow, and bridging mixed software development environments. The second case examines adding attributes to Systems Modelling Language (SysML) to create a linkage for deriving information from a model to fill in an ATML document set. Both cases are outside the original concept of operations for ATML but are typical when integrating large heterogeneous systems with modular contributions from multiple disciplines.

Analysis of the Effect of Environmental Conditions in Conducting Amphibious Assaults Using a Ship Simulator/Vessel-Response Model Proof-of-Concept Study

DTIC Science & Technology

2017-05-01

Center ESRI Environmental Systems Research Institute GIS Geographic Information System HTML Hyper -Text Markup Language LCAC Landing Craft Air... loop .” The ship simulator bridge is generic in that its layout is similar to that found in a variety of ships. As shown in Figures 17 and 18, the...information stored in the geodatabases. The Hyper -Text Markup Language (HTML) capability built into ArcMap permits a planner to click on a vessel track and

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development.

PubMed

Swat, M J; Moodie, S; Wimalaratne, S M; Kristensen, N R; Lavielle, M; Mari, A; Magni, P; Smith, M K; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, A C; Kaye, R; Keizer, R; Kloft, C; Kok, J N; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, H B; Parra-Guillen, Z P; Plan, E; Ribba, B; Smith, G; Trocóniz, I F; Yvon, F; Milligan, P A; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

2015-06-01

The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps.

Pharmacometrics Markup Language (PharmML): Opening New Perspectives for Model Exchange in Drug Development

PubMed Central

Swat, MJ; Moodie, S; Wimalaratne, SM; Kristensen, NR; Lavielle, M; Mari, A; Magni, P; Smith, MK; Bizzotto, R; Pasotti, L; Mezzalana, E; Comets, E; Sarr, C; Terranova, N; Blaudez, E; Chan, P; Chard, J; Chatel, K; Chenel, M; Edwards, D; Franklin, C; Giorgino, T; Glont, M; Girard, P; Grenon, P; Harling, K; Hooker, AC; Kaye, R; Keizer, R; Kloft, C; Kok, JN; Kokash, N; Laibe, C; Laveille, C; Lestini, G; Mentré, F; Munafo, A; Nordgren, R; Nyberg, HB; Parra-Guillen, ZP; Plan, E; Ribba, B; Smith, G; Trocóniz, IF; Yvon, F; Milligan, PA; Harnisch, L; Karlsson, M; Hermjakob, H; Le Novère, N

2015-01-01

The lack of a common exchange format for mathematical models in pharmacometrics has been a long-standing problem. Such a format has the potential to increase productivity and analysis quality, simplify the handling of complex workflows, ensure reproducibility of research, and facilitate the reuse of existing model resources. Pharmacometrics Markup Language (PharmML), currently under development by the Drug Disease Model Resources (DDMoRe) consortium, is intended to become an exchange standard in pharmacometrics by providing means to encode models, trial designs, and modeling steps. PMID:26225259

Geospatial Data Management Platform for Urban Groundwater

NASA Astrophysics Data System (ADS)

Gaitanaru, D.; Priceputu, A.; Gogu, C. R.

2012-04-01

Due to the large amount of civil work projects and research studies, large quantities of geo-data are produced for the urban environments. These data are usually redundant as well as they are spread in different institutions or private companies. Time consuming operations like data processing and information harmonisation represents the main reason to systematically avoid the re-use of data. The urban groundwater data shows the same complex situation. The underground structures (subway lines, deep foundations, underground parkings, and others), the urban facility networks (sewer systems, water supply networks, heating conduits, etc), the drainage systems, the surface water works and many others modify continuously. As consequence, their influence on groundwater changes systematically. However, these activities provide a large quantity of data, aquifers modelling and then behaviour prediction can be done using monitored quantitative and qualitative parameters. Due to the rapid evolution of technology in the past few years, transferring large amounts of information through internet has now become a feasible solution for sharing geoscience data. Furthermore, standard platform-independent means to do this have been developed (specific mark-up languages like: GML, GeoSciML, WaterML, GWML, CityML). They allow easily large geospatial databases updating and sharing through internet, even between different companies or between research centres that do not necessarily use the same database structures. For Bucharest City (Romania) an integrated platform for groundwater geospatial data management is developed under the framework of a national research project - "Sedimentary media modeling platform for groundwater management in urban areas" (SIMPA) financed by the National Authority for Scientific Research of Romania. The platform architecture is based on three components: a geospatial database, a desktop application (a complex set of hydrogeological and geological analysis tools) and a front-end geoportal service. The SIMPA platform makes use of mark-up transfer standards to provide a user-friendly application that can be accessed through internet to query, analyse, and visualise geospatial data related to urban groundwater. The platform holds the information within the local groundwater geospatial databases and the user is able to access this data through a geoportal service. The database architecture allows storing accurate and very detailed geological, hydrogeological, and infrastructure information that can be straightforwardly generalized and further upscaled. The geoportal service offers the possibility of querying a dataset from the spatial database. The query is coded in a standard mark-up language, and sent to the server through a standard Hyper Text Transfer Protocol (http) to be processed by the local application. After the validation of the query, the results are sent back to the user to be displayed by the geoportal application. The main advantage of the SIMPA platform is that it offers to the user the possibility to make a primary multi-criteria query, which results in a smaller set of data to be analysed afterwards. This improves both the transfer process parameters and the user's means of creating the desired query.

SBMLeditor: effective creation of models in the Systems Biology Markup Language (SBML)

PubMed Central

Rodriguez, Nicolas; Donizelli, Marco; Le Novère, Nicolas

2007-01-01

Background The need to build a tool to facilitate the quick creation and editing of models encoded in the Systems Biology Markup language (SBML) has been growing with the number of users and the increased complexity of the language. SBMLeditor tries to answer this need by providing a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file. Results SBMLeditor is written in JAVA using JCompneur, a library providing interfaces to easily display an XML document as a tree. This decreases dramatically the development time for a new XML editor. The possibility to include custom dialogs for different tags allows a lot of freedom for the editing and validation of the document. In addition to Xerces, SBMLeditor uses libSBML to check the validity and consistency of SBML files. A graphical equation editor allows an easy manipulation of MathML. SBMLeditor can be used as a module of the Systems Biology Workbench. Conclusion SBMLeditor contains many improvements compared to a generic XML editor, and allow users to create an SBML model quickly and without syntactic errors. PMID:17341299

SBMLeditor: effective creation of models in the Systems Biology Markup language (SBML).

PubMed

Rodriguez, Nicolas; Donizelli, Marco; Le Novère, Nicolas

2007-03-06

The need to build a tool to facilitate the quick creation and editing of models encoded in the Systems Biology Markup language (SBML) has been growing with the number of users and the increased complexity of the language. SBMLeditor tries to answer this need by providing a very simple, low level editor of SBML files. Users can create and remove all the necessary bits and pieces of SBML in a controlled way, that maintains the validity of the final SBML file. SBMLeditor is written in JAVA using JCompneur, a library providing interfaces to easily display an XML document as a tree. This decreases dramatically the development time for a new XML editor. The possibility to include custom dialogs for different tags allows a lot of freedom for the editing and validation of the document. In addition to Xerces, SBMLeditor uses libSBML to check the validity and consistency of SBML files. A graphical equation editor allows an easy manipulation of MathML. SBMLeditor can be used as a module of the Systems Biology Workbench. SBMLeditor contains many improvements compared to a generic XML editor, and allow users to create an SBML model quickly and without syntactic errors.

Update of KDBI: Kinetic Data of Bio-molecular Interaction database

PubMed Central

Kumar, Pankaj; Han, B. C.; Shi, Z.; Jia, J.; Wang, Y. P.; Zhang, Y. T.; Liang, L.; Liu, Q. F.; Ji, Z. L.; Chen, Y. Z.

2009-01-01

Knowledge of the kinetics of biomolecular interactions is important for facilitating the study of cellular processes and underlying molecular events, and is essential for quantitative study and simulation of biological systems. Kinetic Data of Bio-molecular Interaction database (KDBI) has been developed to provide information about experimentally determined kinetic data of protein–protein, protein–nucleic acid, protein–ligand, nucleic acid–ligand binding or reaction events described in the literature. To accommodate increasing demand for studying and simulating biological systems, numerous improvements and updates have been made to KDBI, including new ways to access data by pathway and molecule names, data file in System Biology Markup Language format, more efficient search engine, access to published parameter sets of simulation models of 63 pathways, and 2.3-fold increase of data (19 263 entries of 10 532 distinctive biomolecular binding and 11 954 interaction events, involving 2635 proteins/protein complexes, 847 nucleic acids, 1603 small molecules and 45 multi-step processes). KDBI is publically available at http://bidd.nus.edu.sg/group/kdbi/kdbi.asp. PMID:18971255

MITRE-Bedford: Description of the ALEMBIC System as Used for MUC-4

DTIC Science & Technology

1992-01-01

of control, and its corresponding encoding in SGML, consider the first paragraph of message TST2- MUC4 -0048 : SALVADORAN PRESIDENT-ELECT ALFREDO...markup simply encodes th e templates that the system has produced, e .g . , <p><template> <slotname>0 . MESSAGE :ID</slotname> <slotval>TST2- MUC4 -0048...verb in TST2- MUC4 -0048), this includes the active voice (e .g ., "Cristiani . condemned the terrorist killing"), the passive voice, and ancillary forms

Impact of cigarette minimum price laws on the retail price of cigarettes in the USA.

PubMed

Tynan, Michael A; Ribisl, Kurt M; Loomis, Brett R

2013-05-01

Cigarette price increases prevent youth initiation, reduce cigarette consumption and increase the number of smokers who quit. Cigarette minimum price laws (MPLs), which typically require cigarette wholesalers and retailers to charge a minimum percentage mark-up for cigarette sales, have been identified as an intervention that can potentially increase cigarette prices. 24 states and the District of Columbia have cigarette MPLs. Using data extracted from SCANTRACK retail scanner data from the Nielsen company, average cigarette prices were calculated for designated market areas in states with and without MPLs in three retail channels: grocery stores, drug stores and convenience stores. Regression models were estimated using the average cigarette pack price in each designated market area and calendar quarter in 2009 as the outcome variable. The average difference in cigarette pack prices are 46 cents in the grocery channel, 29 cents in the drug channel and 13 cents in the convenience channel, with prices being lower in states with MPLs for all three channels. The findings that MPLs do not raise cigarette prices could be the result of a lack of compliance and enforcement by the state or could be attributed to the minimum state mark-up being lower than the free-market mark-up for cigarettes. Rather than require a minimum mark-up, which can be nullified by promotional incentives and discounts, states and countries could strengthen MPLs by setting a simple 'floor price' that is the true minimum price for all cigarettes or could prohibit discounts to consumers and retailers.

Retail sector distribution chains for malaria treatment in the developing world: a review of the literature.

PubMed

Patouillard, Edith; Hanson, Kara G; Goodman, Catherine A

2010-02-11

In many low-income countries, the retail sector plays an important role in the treatment of malaria and is increasingly being considered as a channel for improving medicine availability. Retailers are the last link in a distribution chain and their supply sources are likely to have an important influence on the availability, quality and price of malaria treatment. This article presents the findings of a systematic literature review on the retail sector distribution chain for malaria treatment in low and middle-income countries. Publication databases were searched using key terms relevant to the distribution chain serving all types of anti-malarial retailers. Organizations involved in malaria treatment and distribution chain related activities were contacted to identify unpublished studies. A total of 32 references distributed across 12 developing countries were identified. The distribution chain had a pyramid shape with numerous suppliers at the bottom and fewer at the top. The chain supplying rural and less-formal outlets was made of more levels than that serving urban and more formal outlets. Wholesale markets tended to be relatively concentrated, especially at the top of the chain where few importers accounted for most of the anti-malarial volumes sold. Wholesale price mark-ups varied across chain levels, ranging from 27% to 99% at the top of the chain, 8% at intermediate level (one study only) and 2% to 67% at the level supplying retailers directly. Retail mark-ups tended to be higher, and varied across outlet types, ranging from 3% to 566% in pharmacies, 29% to 669% in drug shops and 100% to 233% in general shops. Information on pricing determinants was very limited. Evidence on the distribution chain for retail sector malaria treatment was mainly descriptive and lacked representative data on a national scale. These are important limitations in the advent of the Affordable Medicine Facility for Malaria, which aims to increase consumer access to artemisinin-based combination therapy (ACT), through a subsidy introduced at the top of the distribution chain. This review calls for rigorous distribution chain analysis, notably on the factors that influence ACT availability and prices in order to contribute to efforts towards improved access to effective malaria treatment.

Distributed Framework for Dynamic Telescope and Instrument Control

NASA Astrophysics Data System (ADS)

Ames, Troy J.; Case, Lynne

2002-12-01

Traditionally, instrument command and control systems have been developed specifically for a single instrument. Such solutions are frequently expensive and are inflexible to support the next instrument development effort. NASA Goddard Space Flight Center is developing an extensible framework, known as Instrument Remote Control (IRC) that applies to any kind of instrument that can be controlled by a computer. IRC combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML). A key aspect of the architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). IML is an XML dialect used to describe graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, communication mechanisms, and data processing algorithms. The IRC framework provides the ability to communicate to components anywhere on a network using the JXTA protocol for dynamic discovery of distributed components. JXTA (see http://www.jxta.org) is a generalized protocol that allows any devices connected by a network to communicate in a peer-to-peer manner. IRC uses JXTA to advertise a device?s IML and discover devices of interest on the network. Devices can join or leave the network and thus join or leave the instrument control environment of IRC. Currently, several astronomical instruments are working with the IRC development team to develop custom components for IRC to control their instruments. These instruments include: High resolution Airborne Wideband Camera (HAWC), a first light instrument for the Stratospheric Observatory for Infrared Astronomy (SOFIA); Submillimeter And Far Infrared Experiment (SAFIRE), a principal investigator instrument for SOFIA; and Fabry-Perot Interferometer Bolometer Research Experiment (FIBRE), a prototype of the SAFIRE instrument, used at the Caltech Submillimeter Observatory (CSO). Most recently, we have been working with the Submillimetre High Angular Resolution Camera IInd Generation (SHARCII) at the CSO to investigate using IRC capabilities with the SHARC instrument.

Distributed Framework for Dynamic Telescope and Instrument Control

NASA Technical Reports Server (NTRS)

Ames, Troy J.; Case, Lynne

2002-01-01

Traditionally, instrument command and control systems have been developed specifically for a single instrument. Such solutions are frequently expensive and are inflexible to support the next instrument development effort. NASA Goddard Space Flight Center is developing an extensible framework, known as Instrument Remote Control (IRC) that applies to any kind of instrument that can be controlled by a computer. IRC combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML). A key aspect of the architecture is software that is driven by an instrument description, written using the Instrument Markup Language (IML). IML is an XML dialect used to describe graphical user interfaces to control and monitor the instrument, command sets and command formats, data streams, communication mechanisms, and data processing algorithms. The IRC framework provides the ability to communicate to components anywhere on a network using the JXTA protocol for dynamic discovery of distributed components. JXTA (see httD://www.jxta.org,) is a generalized protocol that allows any devices connected by a network to communicate in a peer-to-peer manner. IRC uses JXTA to advertise a device's IML and discover devices of interest on the network. Devices can join or leave the network and thus join or leave the instrument control environment of IRC. Currently, several astronomical instruments are working with the IRC development team to develop custom components for IRC to control their instruments. These instruments include: High resolution Airborne Wideband Camera (HAWC), a first light instrument for the Stratospheric Observatory for Infrared Astronomy (SOFIA); Submillimeter And Far Infrared Experiment (SAFIRE), a Principal Investigator instrument for SOFIA; and Fabry-Perot Interferometer Bolometer Research Experiment (FIBRE), a prototype of the SAFIRE instrument, used at the Caltech Submillimeter Observatory (CSO). Most recently, we have been working with the Submillimetre High Angular Resolution Camera IInd Generation (SHARCII) at the CSO to investigate using IRC capabilities with the SHARC instrument.

Information persistence using XML database technology

NASA Astrophysics Data System (ADS)

Clark, Thomas A.; Lipa, Brian E. G.; Macera, Anthony R.; Staskevich, Gennady R.

2005-05-01

The Joint Battlespace Infosphere (JBI) Information Management (IM) services provide information exchange and persistence capabilities that support tailored, dynamic, and timely access to required information, enabling near real-time planning, control, and execution for DoD decision making. JBI IM services will be built on a substrate of network centric core enterprise services and when transitioned, will establish an interoperable information space that aggregates, integrates, fuses, and intelligently disseminates relevant information to support effective warfighter business processes. This virtual information space provides individual users with information tailored to their specific functional responsibilities and provides a highly tailored repository of, or access to, information that is designed to support a specific Community of Interest (COI), geographic area or mission. Critical to effective operation of JBI IM services is the implementation of repositories, where data, represented as information, is represented and persisted for quick and easy retrieval. This paper will address information representation, persistence and retrieval using existing database technologies to manage structured data in Extensible Markup Language (XML) format as well as unstructured data in an IM services-oriented environment. Three basic categories of database technologies will be compared and contrasted: Relational, XML-Enabled, and Native XML. These technologies have diverse properties such as maturity, performance, query language specifications, indexing, and retrieval methods. We will describe our application of these evolving technologies within the context of a JBI Reference Implementation (RI) by providing some hopefully insightful anecdotes and lessons learned along the way. This paper will also outline future directions, promising technologies and emerging COTS products that can offer more powerful information management representations, better persistence mechanisms and improved retrieval techniques.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M.; Le Novére, Nicolas; Myers, Chris J.; Olivier, Brett G.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Waltemath, Dagmar; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528569

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data

PubMed Central

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H. L.; Onami, Shuichi

2015-01-01

Motivation: Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. Results: We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. Availability and implementation: A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Contact: sonami@riken.jp Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:25414366

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core

PubMed Central

Hucka, Michael; Bergmann, Frank T.; Hoops, Stefan; Keating, Sarah M.; Sahle, Sven; Schaff, James C.; Smith, Lucian P.; Wilkinson, Darren J.

2017-01-01

Summary Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/. PMID:26528564

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-09-04

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Hoops, Stefan; Keating, Sarah M; Sahle, Sven; Schaff, James C; Smith, Lucian P; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Systems Biology Markup Language (SBML) Level 2 Version 5: Structures and Facilities for Model Definitions.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2015-06-01

Computational models can help researchers to interpret data, understand biological function, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that can be exchanged between different software systems. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 5 of SBML Level 2. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project web site, http://sbml.org/.

Biological Dynamics Markup Language (BDML): an open format for representing quantitative biological dynamics data.

PubMed

Kyoda, Koji; Tohsato, Yukako; Ho, Kenneth H L; Onami, Shuichi

2015-04-01

Recent progress in live-cell imaging and modeling techniques has resulted in generation of a large amount of quantitative data (from experimental measurements and computer simulations) on spatiotemporal dynamics of biological objects such as molecules, cells and organisms. Although many research groups have independently dedicated their efforts to developing software tools for visualizing and analyzing these data, these tools are often not compatible with each other because of different data formats. We developed an open unified format, Biological Dynamics Markup Language (BDML; current version: 0.2), which provides a basic framework for representing quantitative biological dynamics data for objects ranging from molecules to cells to organisms. BDML is based on Extensible Markup Language (XML). Its advantages are machine and human readability and extensibility. BDML will improve the efficiency of development and evaluation of software tools for data visualization and analysis. A specification and a schema file for BDML are freely available online at http://ssbd.qbic.riken.jp/bdml/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Collaborative Planning of Robotic Exploration

NASA Technical Reports Server (NTRS)

Norris, Jeffrey; Backes, Paul; Powell, Mark; Vona, Marsette; Steinke, Robert

2004-01-01

The Science Activity Planner (SAP) software system includes an uplink-planning component, which enables collaborative planning of activities to be undertaken by an exploratory robot on a remote planet or on Earth. Included in the uplink-planning component is the SAP-Uplink Browser, which enables users to load multiple spacecraft activity plans into a single window, compare them, and merge them. The uplink-planning component includes a subcomponent that implements the Rover Markup Language Activity Planning format (RML-AP), based on the Extensible Markup Language (XML) format that enables the representation, within a single document, of planned spacecraft and robotic activities together with the scientific reasons for the activities. Each such document is highly parseable and can be validated easily. Another subcomponent of the uplink-planning component is the Activity Dictionary Markup Language (ADML), which eliminates the need for two mission activity dictionaries - one in a human-readable format and one in a machine-readable format. Style sheets that have been developed along with the ADML format enable users to edit one dictionary in a user-friendly environment without compromising

Technical note: Harmonizing met-ocean model data via standard web services within small research groups

NASA Astrophysics Data System (ADS)

Signell, R. P.; Camossi, E.

2015-11-01

Work over the last decade has resulted in standardized web-services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by: (1) making it simple for providers to enable web service access to existing output files; (2) using technology that is free, and that is easy to deploy and configure; and (3) providing tools to communicate with web services that work in existing research environments. We present a simple, local brokering approach that lets modelers continue producing custom data, but virtually aggregates and standardizes the data using NetCDF Markup Language. The THREDDS Data Server is used for data delivery, pycsw for data search, NCTOOLBOX (Matlab®1) and Iris (Python) for data access, and Ocean Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.1 Mention of trade names or commercial products does not constitute endorsement or recommendation for use by the US Government.

Malaria treatment-seeking behaviour and related factors of Wa ethnic minority in Myanmar: a cross-sectional study

PubMed Central

2012-01-01

Background In Southeast Asia, data on malaria treatment-seeking behaviours and related affecting factors are rare. The population of the Wa ethnic in Myanmar has difficulty in accessing formal health care. To understand malaria treatment-seeking behaviour and household-affecting factors of the Wa people, a cross-sectional study carried out in Shan Special Region II, Myanmar. Methods The two methods, questionnaire-based household surveys to household heads and in-depth interviews to key informants, were carried out independently. The proportion of treatment-seeking patterns was calculated. Logistic regression was used to determine affecting factors of treatment-seeking. Qualitative data were analysed by using Text Analysis Markup System. Results Overall, 87.5% of the febrile population sought treatment, but only 32.0% did so within 24 hours. The proportion accessing the retail sector (79.6%) was statistically significant higher (P<0.0001) than accessing the public sector (10.6%). Multivariable logistic regression analysis identified family income, distances from a health facility, family decision and patient characteristics being independently associated with delayed malaria treatment. Conclusion Malaria treatment-seeking behaviour is not appropriate, and affecting factors include health service systems, social and cultural factors in Wa State of Myanmar. PMID:23237576

PubMed-EX: a web browser extension to enhance PubMed search with text mining features.

PubMed

Tsai, Richard Tzong-Han; Dai, Hong-Jie; Lai, Po-Ting; Huang, Chi-Hsin

2009-11-15

PubMed-EX is a browser extension that marks up PubMed search results with additional text-mining information. PubMed-EX's page mark-up, which includes section categorization and gene/disease and relation mark-up, can help researchers to quickly focus on key terms and provide additional information on them. All text processing is performed server-side, freeing up user resources. PubMed-EX is freely available at http://bws.iis.sinica.edu.tw/PubMed-EX and http://iisr.cse.yzu.edu.tw:8000/PubMed-EX/.

The carbohydrate sequence markup language (CabosML): an XML description of carbohydrate structures.

PubMed

Kikuchi, Norihiro; Kameyama, Akihiko; Nakaya, Shuuichi; Ito, Hiromi; Sato, Takashi; Shikanai, Toshihide; Takahashi, Yoriko; Narimatsu, Hisashi

2005-04-15

Bioinformatics resources for glycomics are very poor as compared with those for genomics and proteomics. The complexity of carbohydrate sequences makes it difficult to define a common language to represent them, and the development of bioinformatics tools for glycomics has not progressed. In this study, we developed a carbohydrate sequence markup language (CabosML), an XML description of carbohydrate structures. The language definition (XML Schema) and an experimental database of carbohydrate structures using an XML database management system are available at http://www.phoenix.hydra.mki.co.jp/CabosDemo.html kikuchi@hydra.mki.co.jp.

cluML: A markup language for clustering and cluster validity assessment of microarray data.

PubMed

Bolshakova, Nadia; Cunningham, Pádraig

2005-01-01

cluML is a new markup language for microarray data clustering and cluster validity assessment. The XML-based format has been designed to address some of the limitations observed in traditional formats, such as inability to store multiple clustering (including biclustering) and validation results within a dataset. cluML is an effective tool to support biomedical knowledge representation in gene expression data analysis. Although cluML was developed for DNA microarray analysis applications, it can be effectively used for the representation of clustering and for the validation of other biomedical and physical data that has no limitations.

Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language.

PubMed

Roehner, Nicholas; Zhang, Zhen; Nguyen, Tramy; Myers, Chris J

2015-08-21

In the context of synthetic biology, model generation is the automated process of constructing biochemical models based on genetic designs. This paper discusses the use cases for model generation in genetic design automation (GDA) software tools and introduces the foundational concepts of standards and model annotation that make this process useful. Finally, this paper presents an implementation of model generation in the GDA software tool iBioSim and provides an example of generating a Systems Biology Markup Language (SBML) model from a design of a 4-input AND sensor written in the Synthetic Biology Open Language (SBOL).

Study on Comparison of Bidding and Pricing Behavior Distinction between Estimate Methods

NASA Astrophysics Data System (ADS)

Morimoto, Emi; Namerikawa, Susumu

The most characteristic trend on bidding and pricing behavior distinction in recent years is the increasing number of bidders just above the criteria for low-price bidding investigations. The contractor's markup is the difference between the bidding price and the execution price. Therefore, the contractor's markup is the difference between criteria for low-price bidding investigations price and the execution price in the public works bid in Japan. Virtually, bidder's strategies and behavior have been controlled by public engineer's budgets. Estimation and bid are inseparably linked in the Japanese public works procurement system. The trial of the unit price-type estimation method begins in 2004. On another front, accumulated estimation method is one of the general methods in public works. So, there are two types of standard estimation methods in Japan. In this study, we did a statistical analysis on the bid information of civil engineering works for the Ministry of Land, Infrastructure, and Transportation in 2008. It presents several issues that bidding and pricing behavior is related to an estimation method (several estimation methods) for public works bid in Japan. The two types of standard estimation methods produce different results that number of bidders (decide on bid-no bid strategy) and distribution of bid price (decide on mark-up strategy).The comparison on the distribution of bid prices showed that the percentage of the bid concentrated on the criteria for low-price bidding investigations have had a tendency to get higher in the large-sized public works by the unit price-type estimation method, comparing with the accumulated estimation method. On one hand, the number of bidders who bids for public works estimated unit-price tends to increase significantly Public works estimated unit-price is likely to have been one of the factors for the construction companies to decide if they participate in the biddings.

Design and study of geosciences data share platform :platform framework, data interoperability, share approach

NASA Astrophysics Data System (ADS)

Lu, H.; Yi, D.

2010-12-01

The Deep Exploration is one of the important approaches to the Geoscience research. Since 1980s we had started it and achieved a lot of data. Researchers usually integrate both data of space exploration and deep exploration to study geological structures and represent the Earth’s subsurface, and analyze and explain on the base of integrated data. Due to the different exploration approach it results the heterogeneity of data, and therefore the data achievement is always of the import issue to make the researchers confused. The problem of data share and interaction has to be solved during the development of the SinoProbe research project. Through the research of domestic and overseas well-known exploration project and geosciences data platform, the subject explores the solution of data share and interaction. Based on SOA we present the deep exploration data share framework which comprises three level: data level is used for the solution of data store and the integration of the heterogeneous data; medial level provides the data service of geophysics, geochemistry, etc. by the means of Web service, and carry out kinds of application combination by the use of GIS middleware and Eclipse RCP; interaction level provides professional and non-professional customer the access to different accuracy data. The framework adopts GeoSciML data interaction approach. GeoSciML is a geosciences information markup language, as an application of the OpenGIS Consortium’s (OGC) Geography Markup Language (GML). It transfers heterogeneous data into one earth frame and implements inter-operation. We dissertate in this article the solution how to integrate the heterogeneous data and share the data in the project of SinoProbe.

A Converter from the Systems Biology Markup Language to the Synthetic Biology Open Language.

PubMed

Nguyen, Tramy; Roehner, Nicholas; Zundel, Zach; Myers, Chris J

2016-06-17

Standards are important to synthetic biology because they enable exchange and reproducibility of genetic designs. This paper describes a procedure for converting between two standards: the Systems Biology Markup Language (SBML) and the Synthetic Biology Open Language (SBOL). SBML is a standard for behavioral models of biological systems at the molecular level. SBOL describes structural and basic qualitative behavioral aspects of a biological design. Converting SBML to SBOL enables a consistent connection between behavioral and structural information for a biological design. The conversion process described in this paper leverages Systems Biology Ontology (SBO) annotations to enable inference of a designs qualitative function.

The Surgical Simulation and Training Markup Language (SSTML): an XML-based language for medical simulation.

PubMed

Bacon, James; Tardella, Neil; Pratt, Janey; Hu, John; English, James

2006-01-01

Under contract with the Telemedicine & Advanced Technology Research Center (TATRC), Energid Technologies is developing a new XML-based language for describing surgical training exercises, the Surgical Simulation and Training Markup Language (SSTML). SSTML must represent everything from organ models (including tissue properties) to surgical procedures. SSTML is an open language (i.e., freely downloadable) that defines surgical training data through an XML schema. This article focuses on the data representation of the surgical procedures and organ modeling, as they highlight the need for a standard language and illustrate the features of SSTML. Integration of SSTML with software is also discussed.

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core.

PubMed

Hucka, Michael; Bergmann, Frank T; Dräger, Andreas; Hoops, Stefan; Keating, Sarah M; Le Novère, Nicolas; Myers, Chris J; Olivier, Brett G; Sahle, Sven; Schaff, James C; Smith, Lucian P; Waltemath, Dagmar; Wilkinson, Darren J

2018-03-09

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML)

PubMed Central

Lechevalier, D.; Ak, R.; Ferguson, M.; Law, K. H.; Lee, Y.-T. T.; Rachuri, S.

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain. PMID:29202125

Gaussian Process Regression (GPR) Representation in Predictive Model Markup Language (PMML).

PubMed

Park, J; Lechevalier, D; Ak, R; Ferguson, M; Law, K H; Lee, Y-T T; Rachuri, S

2017-01-01

This paper describes Gaussian process regression (GPR) models presented in predictive model markup language (PMML). PMML is an extensible-markup-language (XML) -based standard language used to represent data-mining and predictive analytic models, as well as pre- and post-processed data. The previous PMML version, PMML 4.2, did not provide capabilities for representing probabilistic (stochastic) machine-learning algorithms that are widely used for constructing predictive models taking the associated uncertainties into consideration. The newly released PMML version 4.3, which includes the GPR model, provides new features: confidence bounds and distribution for the predictive estimations. Both features are needed to establish the foundation for uncertainty quantification analysis. Among various probabilistic machine-learning algorithms, GPR has been widely used for approximating a target function because of its capability of representing complex input and output relationships without predefining a set of basis functions, and predicting a target output with uncertainty quantification. GPR is being employed to various manufacturing data-analytics applications, which necessitates representing this model in a standardized form for easy and rapid employment. In this paper, we present a GPR model and its representation in PMML. Furthermore, we demonstrate a prototype using a real data set in the manufacturing domain.

Extreme Markup: The Fifty US Hospitals With The Highest Charge-To-Cost Ratios.

PubMed

Bai, Ge; Anderson, Gerard F

2015-06-01

Using Medicare cost reports, we examined the fifty US hospitals with the highest charge-to-cost ratios in 2012. These hospitals have markups (ratios of charges over Medicare-allowable costs) approximately ten times their Medicare-allowable costs compared to a national average of 3.4 and a mode of 2.4. Analysis of the fifty hospitals showed that forty-nine are for profit (98 percent), forty-six are owned by for-profit hospital systems (92 percent), and twenty (40 percent) operate in Florida. One for-profit hospital system owns half of these fifty hospitals. While most public and private health insurers do not use hospital charges to set their payment rates, uninsured patients are commonly asked to pay the full charges, and out-of-network patients and casualty and workers' compensation insurers are often expected to pay a large portion of the full charges. Because it is difficult for patients to compare prices, market forces fail to constrain hospital charges. Federal and state governments may want to consider limitations on the charge-to-cost ratio, some form of all-payer rate setting, or mandated price disclosure to regulate hospital markups. Project HOPE—The People-to-People Health Foundation, Inc.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

PubMed

Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

2015-09-04

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 2.

PubMed

Bergmann, Frank T; Cooper, Jonathan; Le Novère, Nicolas; Nickerson, David; Waltemath, Dagmar

2015-06-01

The number, size and complexity of computational models of biological systems are growing at an ever increasing pace. It is imperative to build on existing studies by reusing and adapting existing models and parts thereof. The description of the structure of models is not sufficient to enable the reproduction of simulation results. One also needs to describe the procedures the models are subjected to, as recommended by the Minimum Information About a Simulation Experiment (MIASE) guidelines. This document presents Level 1 Version 2 of the Simulation Experiment Description Markup Language (SED-ML), a computer-readable format for encoding simulation and analysis experiments to apply to computational models. SED-ML files are encoded in the Extensible Markup Language (XML) and can be used in conjunction with any XML-based model encoding format, such as CellML or SBML. A SED-ML file includes details of which models to use, how to modify them prior to executing a simulation, which simulation and analysis procedures to apply, which results to extract and how to present them. Level 1 Version 2 extends the format by allowing the encoding of repeated and chained procedures.

Pricing and components analysis of some key essential pediatric medicine in Odisha state.

PubMed

Samal, Satyajit; Swain, Trupti Rekha

2017-01-01

Study highlighting prices, i.e., the patients actually pay at ground level is important for interventions such as alternate procurement schemes or to expedite regulatory assessment of essential medicines for children. The present study was undertaken to study pricing and component analysis of few key essential medicines in Odisha state. Six child-specific medicines of different formulations were selected based on use in different disease condition and having widest pricing variation. Data were collected, entered, and analyzed in the price components data collection form of the World Health Organization-Health Action International (WHO-HAI) 2007 Workbook version 5 - Part II provided as part of the WHO/HAI methodology. The analysis includes the cumulative percent markup, total cumulative percent markup, and percent contribution of individual components to the final medicine price in both public and private sector of Odisha state. Add-on costs such as taxes, wholesale, and retail markups contribute substantially to the final price of medicines in private sector, particularly for branded-generic products. The largest contributor to add-on costs is at the level of retailer shop. Policy should be framed to achieve a greater transparency and uniformity of the pricing of medicines at different health sectors of Odisha.

Using XML and Java Technologies for Astronomical Instrument Control

NASA Technical Reports Server (NTRS)

Ames, Troy; Case, Lynne; Powers, Edward I. (Technical Monitor)

2001-01-01

Traditionally, instrument command and control systems have been highly specialized, consisting mostly of custom code that is difficult to develop, maintain, and extend. Such solutions are initially very costly and are inflexible to subsequent engineering change requests, increasing software maintenance costs. Instrument description is too tightly coupled with details of implementation. NASA Goddard Space Flight Center, under the Instrument Remote Control (IRC) project, is developing a general and highly extensible framework that applies to any kind of instrument that can be controlled by a computer. The software architecture combines the platform independent processing capabilities of Java with the power of the Extensible Markup Language (XML), a human readable and machine understandable way to describe structured data. A key aspect of the object-oriented architecture is that the software is driven by an instrument description, written using the Instrument Markup Language (IML), a dialect of XML. IML is used to describe the command sets and command formats of the instrument, communication mechanisms, format of the data coming from the instrument, and characteristics of the graphical user interface to control and monitor the instrument. The IRC framework allows the users to define a data analysis pipeline which converts data coming out of the instrument. The data can be used in visualizations in order for the user to assess the data in real-time, if necessary. The data analysis pipeline algorithms can be supplied by the user in a variety of forms or programming languages. Although the current integration effort is targeted for the High-resolution Airborne Wideband Camera (HAWC) and the Submillimeter and Far Infrared Experiment (SAFIRE), first-light instruments of the Stratospheric Observatory for Infrared Astronomy (SOFIA), the framework is designed to be generic and extensible so that it can be applied to any instrument. Plans are underway to test the framework with other types of instruments, such as remote sensing earth science instruments.

Intended and unintended impacts of price changes for drugs and medical services: Evidence from China.

PubMed

Fu, Hongqiao; Li, Ling; Yip, Winnie

2018-06-18

In 2012, the Chinese government launched a nationwide reform of county-level public hospitals with the goal of controlling the rapid growth of healthcare expenditure. The key components of the reform were the zero markup drug policy (ZMDP), which removed the previously allowed 15% markup for drug sales at public hospitals, and associated increases in fees for medical services. By exploiting the temporal and cross-sectional variations in the policy implementation and using a unique, nationally representative hospital-level dataset in 1880 counties between 2009 and 2014, we find that the policy change led to a reduction in drug expenditures, a rise in expenditures for medical services, and no measurable changes in total health expenditures. However, we also find an increase in expenditures for diagnostic tests/medical consumables at hospitals that had a greater reliance on drug revenues before the reform, which is unintended by policymakers. Further analysis shows that these results were more likely to be driven by the supply side, suggesting that hospitals offset the reductions in drug revenues by increasing the provision of services and products with higher price-cost margins. These findings hold lessons for cost containment policies in both developed and developing countries. Copyright © 2018 Elsevier Ltd. All rights reserved.

Teaching physiology and the World Wide Web: electrochemistry and electrophysiology on the Internet.

PubMed

Dwyer, T M; Fleming, J; Randall, J E; Coleman, T G

1997-12-01

Students seek active learning experiences that can rapidly impart relevant information in the most convenient way possible. Computer-assisted education can now use the resources of the World Wide Web to convey the important characteristics of events as elemental as the physical properties of osmotically active particles in the cell and as complex as the nerve action potential or the integrative behavior of the intact organism. We have designed laboratory exercises that introduce first-year medical students to membrane and action potentials, as well as the more complex example of integrative physiology, using the dynamic properties of computer simulations. Two specific examples are presented. The first presents the physical laws that apply to osmotic, chemical, and electrical gradients, leading to the development of the concept of membrane potentials; this module concludes with the simulation of the ability of the sodium-potassium pump to establish chemical gradients and maintain cell volume. The second module simulates the action potential according to the Hodgkin-Huxley model, illustrating the concepts of threshold, inactivation, refractory period, and accommodation. Students can access these resources during the scheduled laboratories or on their own time via our Web site on the Internet (http./(/)phys-main.umsmed.edu) by using the World Wide Web protocol. Accurate version control is possible because one valid, but easily edited, copy of the labs exists at the Web site. A common graphical interface is possible through the use of the Hypertext mark-up language. Platform independence is possible through the logical and arithmetic calculations inherent to graphical browsers and the Javascript computer language. The initial success of this program indicates that medical education can be very effective both by the use of accurate simulations and by the existence of a universally accessible Internet resource.

Catalogue of HI PArameters (CHIPA)

NASA Astrophysics Data System (ADS)

Saponara, J.; Benaglia, P.; Koribalski, B.; Andruchow, I.

2015-08-01

The catalogue of HI parameters of galaxies HI (CHIPA) is the natural continuation of the compilation by M.C. Martin in 1998. CHIPA provides the most important parameters of nearby galaxies derived from observations of the neutral Hydrogen line. The catalogue contains information of 1400 galaxies across the sky and different morphological types. Parameters like the optical diameter of the galaxy, the blue magnitude, the distance, morphological type, HI extension are listed among others. Maps of the HI distribution, velocity and velocity dispersion can also be display for some cases. The main objective of this catalogue is to facilitate the bibliographic queries, through searching in a database accessible from the internet that will be available in 2015 (the website is under construction). The database was built using the open source `` mysql (SQL, Structured Query Language, management system relational database) '', while the website was built with ''HTML (Hypertext Markup Language)'' and ''PHP (Hypertext Preprocessor)''.

jsNMR: an embedded platform-independent NMR spectrum viewer.

PubMed

Vosegaard, Thomas

2015-04-01

jsNMR is a lightweight NMR spectrum viewer written in JavaScript/HyperText Markup Language (HTML), which provides a cross-platform spectrum visualizer that runs on all computer architectures including mobile devices. Experimental (and simulated) datasets are easily opened in jsNMR by (i) drag and drop on a jsNMR browser window, (ii) by preparing a jsNMR file from the jsNMR web site, or (iii) by mailing the raw data to the jsNMR web portal. jsNMR embeds the original data in the HTML file, so a jsNMR file is a self-transforming dataset that may be exported to various formats, e.g. comma-separated values. The main applications of jsNMR are to provide easy access to NMR data without the need for dedicated software installed and to provide the possibility to visualize NMR spectra on web sites. Copyright © 2015 John Wiley & Sons, Ltd.

Client-side Medical Image Colorization in a Collaborative Environment.

PubMed

Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

2015-01-01

The paper presents an application related to collaborative medicine using a browser based medical visualization system with focus on the medical image colorization process and the underlying open source web development technologies involved. Browser based systems allow physicians to share medical data with their remotely located counterparts or medical students, assisting them during patient diagnosis, treatment monitoring, surgery planning or for educational purposes. This approach brings forth the advantage of ubiquity. The system can be accessed from a any device, in order to process the images, assuring the independence towards having a specific proprietary operating system. The current work starts with processing of DICOM (Digital Imaging and Communications in Medicine) files and ends with the rendering of the resulting bitmap images on a HTML5 (fifth revision of the HyperText Markup Language) canvas element. The application improves the image visualization emphasizing different tissue densities.

GRN2SBML: automated encoding and annotation of inferred gene regulatory networks complying with SBML.

PubMed

Vlaic, Sebastian; Hoffmann, Bianca; Kupfer, Peter; Weber, Michael; Dräger, Andreas

2013-09-01

GRN2SBML automatically encodes gene regulatory networks derived from several inference tools in systems biology markup language. Providing a graphical user interface, the networks can be annotated via the simple object access protocol (SOAP)-based application programming interface of BioMart Central Portal and minimum information required in the annotation of models registry. Additionally, we provide an R-package, which processes the output of supported inference algorithms and automatically passes all required parameters to GRN2SBML. Therefore, GRN2SBML closes a gap in the processing pipeline between the inference of gene regulatory networks and their subsequent analysis, visualization and storage. GRN2SBML is freely available under the GNU Public License version 3 and can be downloaded from http://www.hki-jena.de/index.php/0/2/490. General information on GRN2SBML, examples and tutorials are available at the tool's web page.

mantisGRID: a grid platform for DICOM medical images management in Colombia and Latin America.

PubMed

Garcia Ruiz, Manuel; Garcia Chaves, Alvin; Ruiz Ibañez, Carlos; Gutierrez Mazo, Jorge Mario; Ramirez Giraldo, Juan Carlos; Pelaez Echavarria, Alejandro; Valencia Diaz, Edison; Pelaez Restrepo, Gustavo; Montoya Munera, Edwin Nelson; Garcia Loaiza, Bernardo; Gomez Gonzalez, Sebastian

2011-04-01

This paper presents the mantisGRID project, an interinstitutional initiative from Colombian medical and academic centers aiming to provide medical grid services for Colombia and Latin America. The mantisGRID is a GRID platform, based on open source grid infrastructure that provides the necessary services to access and exchange medical images and associated information following digital imaging and communications in medicine (DICOM) and health level 7 standards. The paper focuses first on the data abstraction architecture, which is achieved via Open Grid Services Architecture Data Access and Integration (OGSA-DAI) services and supported by the Globus Toolkit. The grid currently uses a 30-Mb bandwidth of the Colombian High Technology Academic Network, RENATA, connected to Internet 2. It also includes a discussion on the relational database created to handle the DICOM objects that were represented using Extensible Markup Language Schema documents, as well as other features implemented such as data security, user authentication, and patient confidentiality. Grid performance was tested using the three current operative nodes and the results demonstrated comparable query times between the mantisGRID (OGSA-DAI) and Distributed mySQL databases, especially for a large number of records.

Nuclear data made easily accessible through the Notre Dame Nuclear Database

NASA Astrophysics Data System (ADS)

Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

The Service Environment for Enhanced Knowledge and Research (SEEKR) Framework

NASA Astrophysics Data System (ADS)

King, T. A.; Walker, R. J.; Weigel, R. S.; Narock, T. W.; McGuire, R. E.; Candey, R. M.

2011-12-01

The Service Environment for Enhanced Knowledge and Research (SEEKR) Framework is a configurable service oriented framework to enable the discovery, access and analysis of data shared in a community. The SEEKR framework integrates many existing independent services through the use of web technologies and standard metadata. Services are hosted on systems by using an application server and are callable by using REpresentational State Transfer (REST) protocols. Messages and metadata are transferred with eXtensible Markup Language (XML) encoding which conform to a published XML schema. Space Physics Archive Search and Extract (SPASE) metadata is central to utilizing the services. Resources (data, documents, software, etc.) are described with SPASE and the associated Resource Identifier is used to access and exchange resources. The configurable options for the service can be set by using a web interface. Services are packaged as web application resource (WAR) files for direct deployment on application services such as Tomcat or Jetty. We discuss the composition of the SEEKR framework, how new services can be integrated and the steps necessary to deploying the framework. The SEEKR Framework emerged from NASA's Virtual Magnetospheric Observatory (VMO) and other systems and we present an overview of these systems from a SEEKR Framework perspective.

SBMLmod: a Python-based web application and web service for efficient data integration and model simulation.

PubMed

Schäuble, Sascha; Stavrum, Anne-Kristin; Bockwoldt, Mathias; Puntervoll, Pål; Heiland, Ines

2017-06-24

Systems Biology Markup Language (SBML) is the standard model representation and description language in systems biology. Enriching and analysing systems biology models by integrating the multitude of available data, increases the predictive power of these models. This may be a daunting task, which commonly requires bioinformatic competence and scripting. We present SBMLmod, a Python-based web application and service, that automates integration of high throughput data into SBML models. Subsequent steady state analysis is readily accessible via the web service COPASIWS. We illustrate the utility of SBMLmod by integrating gene expression data from different healthy tissues as well as from a cancer dataset into a previously published model of mammalian tryptophan metabolism. SBMLmod is a user-friendly platform for model modification and simulation. The web application is available at http://sbmlmod.uit.no , whereas the WSDL definition file for the web service is accessible via http://sbmlmod.uit.no/SBMLmod.wsdl . Furthermore, the entire package can be downloaded from https://github.com/MolecularBioinformatics/sbml-mod-ws . We envision that SBMLmod will make automated model modification and simulation available to a broader research community.

Proteome reference map and regulation network of neonatal rat cardiomyocyte

PubMed Central

Li, Zi-jian; Liu, Ning; Han, Qi-de; Zhang, You-yi

2011-01-01

Aim: To study and establish a proteome reference map and regulation network of neonatal rat cardiomyocyte. Methods: Cultured cardiomyocytes of neonatal rats were used. All proteins expressed in the cardiomyocytes were separated and identified by two-dimensional polyacrylamide gel electrophoresis (2-DE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS). Biological networks and pathways of the neonatal rat cardiomyocytes were analyzed using the Ingenuity Pathway Analysis (IPA) program (www.ingenuity.com). A 2-DE database was made accessible on-line by Make2ddb package on a web server. Results: More than 1000 proteins were separated on 2D gels, and 148 proteins were identified. The identified proteins were used for the construction of an extensible markup language-based database. Biological networks and pathways were constructed to analyze the functions associate with cardiomyocyte proteins in the database. The 2-DE database of rat cardiomyocyte proteins can be accessed at http://2d.bjmu.edu.cn. Conclusion: A proteome reference map and regulation network of the neonatal rat cardiomyocytes have been established, which may serve as an international platform for storage, analysis and visualization of cardiomyocyte proteomic data. PMID:21841810

MetNetMaker: a free and open-source tool for the creation of novel metabolic networks in SBML format.

PubMed

Forth, Thomas; McConkey, Glenn A; Westhead, David R

2010-09-15

An application has been developed to help with the creation and editing of Systems Biology Markup Language (SBML) format metabolic networks up to the organism scale. Networks are defined as a collection of Kyoto Encyclopedia of Genes and Genomes (KEGG) LIGAND reactions with an optional associated Enzyme Classification (EC) number for each reaction. Additional custom reactions can be defined by the user. Reactions within the network can be assigned flux constraints and compartmentalization is supported for each reaction in addition to the support for reactions that occur across compartment boundaries. Exported networks are fully SBML L2V4 compatible with an optional L2V1 export for compatibility with old versions of the COBRA toolbox. The software runs in the free Microsoft Access 2007 Runtime (Microsoft Inc.), which is included with the installer and works on Windows XP SP2 or better. Full source code is viewable in the full version of Access 2007 or 2010. Users must have a license to use the KEGG LIGAND database (free academic licensing is available). Please go to www.bioinformatics.leeds.ac.uk/~pytf/metnetmaker for software download, help and tutorials.

The CRUTEM4 land-surface air temperature data set: construction, previous versions and dissemination via Google Earth

NASA Astrophysics Data System (ADS)

Osborn, T. J.; Jones, P. D.

2014-02-01

The CRUTEM4 (Climatic Research Unit Temperature, version 4) land-surface air temperature data set is one of the most widely used records of the climate system. Here we provide an important additional dissemination route for this data set: online access to monthly, seasonal and annual data values and time series graphs via Google Earth. This is achieved via an interface written in Keyhole Markup Language (KML) and also provides access to the underlying weather station data used to construct the CRUTEM4 data set. A mathematical description of the construction of the CRUTEM4 data set (and its predecessor versions) is also provided, together with an archive of some previous versions and a recommendation for identifying the precise version of the data set used in a particular study. The CRUTEM4 data set used here is available from doi:10.5285/EECBA94F-62F9-4B7C-88D3-482F2C93C468.

An integrated healthcare information system for end-to-end standardized exchange and homogeneous management of digital ECG formats.

PubMed

Trigo, Jesús Daniel; Martínez, Ignacio; Alesanco, Alvaro; Kollmann, Alexander; Escayola, Javier; Hayn, Dieter; Schreier, Günter; García, José

2012-07-01

This paper investigates the application of the enterprise information system (EIS) paradigm to standardized cardiovascular condition monitoring. There are many specifications in cardiology, particularly in the ECG standardization arena. The existence of ECG formats, however, does not guarantee the implementation of homogeneous, standardized solutions for ECG management. In fact, hospital management services need to cope with various ECG formats and, moreover, several different visualization applications. This heterogeneity hampers the normalization of integrated, standardized healthcare information systems, hence the need for finding an appropriate combination of ECG formats and a suitable EIS-based software architecture that enables standardized exchange and homogeneous management of ECG formats. Determining such a combination is one objective of this paper. The second aim is to design and develop the integrated healthcare information system that satisfies the requirements posed by the previous determination. The ECG formats selected include ISO/IEEE11073, Standard Communications Protocol for Computer-Assisted Electrocardiography, and an ECG ontology. The EIS-enabling techniques and technologies selected include web services, simple object access protocol, extensible markup language, or business process execution language. Such a selection ensures the standardized exchange of ECGs within, or across, healthcare information systems while providing modularity and accessibility.

The Chandra Source Catalog : Google Earth Interface

NASA Astrophysics Data System (ADS)

Glotfelty, Kenny; McLaughlin, W.; Evans, I.; Evans, J.; Anderson, C. S.; Bonaventura, N. R.; Davis, J. E.; Doe, S. M.; Fabbiano, G.; Galle, E. C.; Gibbs, D. G., II; Grier, J. D.; Hain, R.; Hall, D. M.; Harbo, P. N.; He, H.; Houck, J. C.; Karovska, M.; Kashyap, V. L.; Lauer, J.; McCollough, M. L.; McDowell, J. C.; Miller, J. B.; Mitschang, A. W.; Morgan, D. L.; Mossman, A. E.; Nichols, J. S.; Nowak, M. A.; Plummer, D. A.; Primini, F. A.; Refsdal, B. L.; Rots, A. R.; Siemiginowska, A. L.; Sundheim, B. A.; Tibbetts, M. S.; van Stone, D. W.; Winkelman, S. L.; Zografou, P.

2009-09-01

The Chandra Source Catalog (CSC) contains multi-resolution, exposure corrected, background subtracted, full-field images that are stored as individual FITS files and as three-color JPEG files. In this poster we discuss how we took these data and were able to, with relatively minimal effort, convert them for use with the Google Earth application in its ``Sky'' mode. We will highlight some of the challenges which include converting the data to the required Mercator projection, reworking the 3-color algorithm for pipeline processing, and ways to reduce the data volume through re-binning, using color-maps, and special Keyhole Markup Language (kml) tags to only load images on-demand. The result is a collection of some 11,000 3-color images that are available for all the individual observation in the CSC Release 1. We also have made available all ˜4000 Field-of-View outlines (with per-chip regions), which turns out are trivial to produce starting with a simple dmlist command. In the first week of release, approximately 40% of the images have been accessed at least once through some 50,000 individual web hits which have served over 4Gb of data to roughly 750 users in 60+ countries. We will also highlight some future directions we are exploring, including real-time catalog access to individual source properties and eventual access to file based products such as FITS images, spectra, and light-curves.

Technical Note: Harmonizing met-ocean model data via standard web services within small research groups

USGS Publications Warehouse

Signell, Richard; Camossi, E.

2016-01-01

Work over the last decade has resulted in standardised web services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by (1) making it simple for providers to enable web service access to existing output files; (2) using free technologies that are easy to deploy and configure; and (3) providing standardised, service-based tools that work in existing research environments. We present a simple, local brokering approach that lets modellers continue to use their existing files and tools, while serving virtual data sets that can be used with standardised tools. The goal of this paper is to convince modellers that a standardised framework is not only useful but can be implemented with modest effort using free software components. We use NetCDF Markup language for data aggregation and standardisation, the THREDDS Data Server for data delivery, pycsw for data search, NCTOOLBOX (MATLAB®) and Iris (Python) for data access, and Open Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.

Technical note: Harmonising metocean model data via standard web services within small research groups

NASA Astrophysics Data System (ADS)

Signell, Richard P.; Camossi, Elena

2016-05-01

Work over the last decade has resulted in standardised web services and tools that can significantly improve the efficiency and effectiveness of working with meteorological and ocean model data. While many operational modelling centres have enabled query and access to data via common web services, most small research groups have not. The penetration of this approach into the research community, where IT resources are limited, can be dramatically improved by (1) making it simple for providers to enable web service access to existing output files; (2) using free technologies that are easy to deploy and configure; and (3) providing standardised, service-based tools that work in existing research environments. We present a simple, local brokering approach that lets modellers continue to use their existing files and tools, while serving virtual data sets that can be used with standardised tools. The goal of this paper is to convince modellers that a standardised framework is not only useful but can be implemented with modest effort using free software components. We use NetCDF Markup language for data aggregation and standardisation, the THREDDS Data Server for data delivery, pycsw for data search, NCTOOLBOX (MATLAB®) and Iris (Python) for data access, and Open Geospatial Consortium Web Map Service for data preview. We illustrate the effectiveness of this approach with two use cases involving small research modelling groups at NATO and USGS.

Construction of a nasopharyngeal carcinoma 2D/MS repository with Open Source XML database--Xindice.

PubMed

Li, Feng; Li, Maoyu; Xiao, Zhiqiang; Zhang, Pengfei; Li, Jianling; Chen, Zhuchu

2006-01-11

Many proteomics initiatives require integration of all information with uniformcriteria from collection of samples and data display to publication of experimental results. The integration and exchanging of these data of different formats and structure imposes a great challenge to us. The XML technology presents a promise in handling this task due to its simplicity and flexibility. Nasopharyngeal carcinoma (NPC) is one of the most common cancers in southern China and Southeast Asia, which has marked geographic and racial differences in incidence. Although there are some cancer proteome databases now, there is still no NPC proteome database. The raw NPC proteome experiment data were captured into one XML document with Human Proteome Markup Language (HUP-ML) editor and imported into native XML database Xindice. The 2D/MS repository of NPC proteome was constructed with Apache, PHP and Xindice to provide access to the database via Internet. On our website, two methods, keyword query and click query, were provided at the same time to access the entries of the NPC proteome database. Our 2D/MS repository can be used to share the raw NPC proteomics data that are generated from gel-based proteomics experiments. The database, as well as the PHP source codes for constructing users' own proteome repository, can be accessed at http://www.xyproteomics.org/.

Upcoming hearings in Congress

NASA Astrophysics Data System (ADS)

The following hearings and markups have been tentatively scheduled for the coming weeks by the Senate and House of Representatives. Dates and times should be verified with the committee or subcommittee holding the hearing or markup; all offices on Capitol Hill may be reached by telephoning 202-224-3121. For guidelines on contacting a member of Congress, see AGU's Guide to Legislative Information and Contacts (Eos, August 28, 1984, p. 669).October 8: A joint hearing by the Energy Research & Development Subcommittee of the Senate Energy and Natural Resources Committee and the Nuclear Regulation Subcommittee of the Senate Environment and Public Works Committee on low-level radioactive waste (S. 1517 and S. 1578). Room SD-366, Dirksen Building, 9:30 A.M.

Earth Science Markup Language: Transitioning From Design to Application

NASA Technical Reports Server (NTRS)

Moe, Karen; Graves, Sara; Ramachandran, Rahul

2002-01-01

The primary objective of the proposed Earth Science Markup Language (ESML) research is to transition from design to application. The resulting schema and prototype software will foster community acceptance for the "define once, use anywhere" concept central to ESML. Supporting goals include: 1. Refinement of the ESML schema and software libraries in cooperation with the user community. 2. Application of the ESML schema and software libraries to a variety of Earth science data sets and analysis tools. 3. Development of supporting prototype software for enhanced ease of use. 4. Cooperation with standards bodies in order to assure ESML is aligned with related metadata standards as appropriate. 5. Widespread publication of the ESML approach, schema, and software.

Standardized Semantic Markup for Reference Terminologies, Thesauri and Coding Systems: Benefits for distributed E-Health Applications.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Liu, Raymond; Rudolf, Dirk; Rieger, Joerg; Dudeck, Joachim

2005-01-01

With the introduction of the ICD-10 as the standard for diagnosis, the development of an electronic representation of its complete content, inherent semantics and coding rules is necessary. Our concept refers to current efforts of the CEN/TC 251 to establish a European standard for hierarchical classification systems in healthcare. We have developed an electronic representation of the ICD-10 with the extensible Markup Language (XML) that facilitates the integration in current information systems or coding software taking into account different languages and versions. In this context, XML offers a complete framework of related technologies and standard tools for processing that helps to develop interoperable applications.

Design and Realization of Controllable Ultrasonic Fault Detector Automatic Verification System

NASA Astrophysics Data System (ADS)

Sun, Jing-Feng; Liu, Hui-Ying; Guo, Hui-Juan; Shu, Rong; Wei, Kai-Li

The ultrasonic flaw detection equipment with remote control interface is researched and the automatic verification system is developed. According to use extensible markup language, the building of agreement instruction set and data analysis method database in the system software realizes the controllable designing and solves the diversification of unreleased device interfaces and agreements. By using the signal generator and a fixed attenuator cascading together, a dynamic error compensation method is proposed, completes what the fixed attenuator does in traditional verification and improves the accuracy of verification results. The automatic verification system operating results confirms that the feasibility of the system hardware and software architecture design and the correctness of the analysis method, while changes the status of traditional verification process cumbersome operations, and reduces labor intensity test personnel.

Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3).

PubMed

Bergmann, Frank T; Cooper, Jonathan; König, Matthias; Moraru, Ion; Nickerson, David; Le Novère, Nicolas; Olivier, Brett G; Sahle, Sven; Smith, Lucian; Waltemath, Dagmar

2018-03-19

The creation of computational simulation experiments to inform modern biological research poses challenges to reproduce, annotate, archive, and share such experiments. Efforts such as SBML or CellML standardize the formal representation of computational models in various areas of biology. The Simulation Experiment Description Markup Language (SED-ML) describes what procedures the models are subjected to, and the details of those procedures. These standards, together with further COMBINE standards, describe models sufficiently well for the reproduction of simulation studies among users and software tools. The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format that encodes, for a given simulation experiment, (i) which models to use; (ii) which modifications to apply to models before simulation; (iii) which simulation procedures to run on each model; (iv) how to post-process the data; and (v) how these results should be plotted and reported. SED-ML Level 1 Version 1 (L1V1) implemented support for the encoding of basic time course simulations. SED-ML L1V2 added support for more complex types of simulations, specifically repeated tasks and chained simulation procedures. SED-ML L1V3 extends L1V2 by means to describe which datasets and subsets thereof to use within a simulation experiment.

SBRML: a markup language for associating systems biology data with models.

PubMed

Dada, Joseph O; Spasić, Irena; Paton, Norman W; Mendes, Pedro

2010-04-01

Research in systems biology is carried out through a combination of experiments and models. Several data standards have been adopted for representing models (Systems Biology Markup Language) and various types of relevant experimental data (such as FuGE and those of the Proteomics Standards Initiative). However, until now, there has been no standard way to associate a model and its entities to the corresponding datasets, or vice versa. Such a standard would provide a means to represent computational simulation results as well as to frame experimental data in the context of a particular model. Target applications include model-driven data analysis, parameter estimation, and sharing and archiving model simulations. We propose the Systems Biology Results Markup Language (SBRML), an XML-based language that associates a model with several datasets. Each dataset is represented as a series of values associated with model variables, and their corresponding parameter values. SBRML provides a flexible way of indexing the results to model parameter values, which supports both spreadsheet-like data and multidimensional data cubes. We present and discuss several examples of SBRML usage in applications such as enzyme kinetics, microarray gene expression and various types of simulation results. The XML Schema file for SBRML is available at http://www.comp-sys-bio.org/SBRML under the Academic Free License (AFL) v3.0.

Pricing and components analysis of some key essential pediatric medicine in Odisha state

PubMed Central

Samal, Satyajit; Swain, Trupti Rekha

2017-01-01

Objective: Study highlighting prices, i.e., the patients actually pay at ground level is important for interventions such as alternate procurement schemes or to expedite regulatory assessment of essential medicines for children. The present study was undertaken to study pricing and component analysis of few key essential medicines in Odisha state. Methodology: Six child-specific medicines of different formulations were selected based on use in different disease condition and having widest pricing variation. Data were collected, entered, and analyzed in the price components data collection form of the World Health Organization-Health Action International (WHO-HAI) 2007 Workbook version 5 – Part II provided as part of the WHO/HAI methodology. The analysis includes the cumulative percent markup, total cumulative percent markup, and percent contribution of individual components to the final medicine price in both public and private sector of Odisha state. Results: Add-on costs such as taxes, wholesale, and retail markups contribute substantially to the final price of medicines in private sector, particularly for branded-generic products. The largest contributor to add-on costs is at the level of retailer shop. Conclusion: Policy should be framed to achieve a greater transparency and uniformity of the pricing of medicines at different health sectors of Odisha. PMID:28458429

Retail sector distribution chains for malaria treatment in the developing world: a review of the literature

PubMed Central

2010-01-01

Background In many low-income countries, the retail sector plays an important role in the treatment of malaria and is increasingly being considered as a channel for improving medicine availability. Retailers are the last link in a distribution chain and their supply sources are likely to have an important influence on the availability, quality and price of malaria treatment. This article presents the findings of a systematic literature review on the retail sector distribution chain for malaria treatment in low and middle-income countries. Methods Publication databases were searched using key terms relevant to the distribution chain serving all types of anti-malarial retailers. Organizations involved in malaria treatment and distribution chain related activities were contacted to identify unpublished studies. Results A total of 32 references distributed across 12 developing countries were identified. The distribution chain had a pyramid shape with numerous suppliers at the bottom and fewer at the top. The chain supplying rural and less-formal outlets was made of more levels than that serving urban and more formal outlets. Wholesale markets tended to be relatively concentrated, especially at the top of the chain where few importers accounted for most of the anti-malarial volumes sold. Wholesale price mark-ups varied across chain levels, ranging from 27% to 99% at the top of the chain, 8% at intermediate level (one study only) and 2% to 67% at the level supplying retailers directly. Retail mark-ups tended to be higher, and varied across outlet types, ranging from 3% to 566% in pharmacies, 29% to 669% in drug shops and 100% to 233% in general shops. Information on pricing determinants was very limited. Conclusions Evidence on the distribution chain for retail sector malaria treatment was mainly descriptive and lacked representative data on a national scale. These are important limitations in the advent of the Affordable Medicine Facility for Malaria, which aims to increase consumer access to artemisinin-based combination therapy (ACT), through a subsidy introduced at the top of the distribution chain. This review calls for rigorous distribution chain analysis, notably on the factors that influence ACT availability and prices in order to contribute to efforts towards improved access to effective malaria treatment. PMID:20149246

Risks, prices, and positions: A social network analysis of illegal drug trafficking in the world-economy.

PubMed

Boivin, Rémi

2014-03-01

Illegal drug prices are extremely high, compared to similar goods. There is, however, considerable variation in value depending on place, market level and type of drugs. A prominent framework for the study of illegal drugs is the "risks and prices" model (Reuter & Kleiman, 1986). Enforcement is seen as a "tax" added to the regular price. In this paper, it is argued that such economic models are not sufficient to explain price variations at country-level. Drug markets are analysed as global trade networks in which a country's position has an impact on various features, including illegal drug prices. This paper uses social network analysis (SNA) to explain price markups between pairs of countries involved in the trafficking of illegal drugs between 1998 and 2007. It aims to explore a simple question: why do prices increase between two countries? Using relational data from various international organizations, separate trade networks were built for cocaine, heroin and cannabis. Wholesale price markups are predicted with measures of supply, demand, risks of seizures, geographic distance and global positioning within the networks. Reported prices (in $US) and purchasing power parity-adjusted values are analysed. Drug prices increase more sharply when drugs are headed to countries where law enforcement imposes higher costs on traffickers. The position and role of a country in global drug markets are also closely associated with the value of drugs. Price markups are lower if the destination country is a transit to large potential markets. Furthermore, price markups for cocaine and heroin are more pronounced when drugs are exported to countries that are better positioned in the legitimate world-economy, suggesting that relations in legal and illegal markets are directed in opposite directions. Consistent with the world-system perspective, evidence is found of coherent world drug markets driven by both local realities and international relations. Copyright © 2013 Elsevier B.V. All rights reserved.

Measuring market performance in restructured electricity markets: An empirical analysis of the PJM energy market

NASA Astrophysics Data System (ADS)

Tucker, Russell Jay

2002-09-01

Today the electric industry in the U.S. is transitioning to competitive markets for wholesale electricity. Independent system operators (ISOs) now manage broad regional markets for electrical energy in several areas of the U.S. A recent rulemaking by the Federal Energy Regulatory Commission (FERC) encourages the development of regional transmission organizations (RTOs) and restructured competitive wholesale electricity markets nationwide. To date, the transition to competitive wholesale markets has not been easy. The increased reliance on market forces coupled with unusually high electricity demand for some periods have created conditions amenable to market power abuse in many regions throughout the U.S. In the summer of 1999, hot and humid summer conditions in Pennsylvania, New Jersey, Maryland, Delaware, and the District of Columbia pushed peak demand in the PJM Interconnection to record levels. These demand conditions coincided with the introduction of market-based pricing in the wholesale electricity market. Prices for electricity increased on average by 55 percent, and reached the $1,000/MWh range. This study examines the extent to which generator market power raised prices above competitive levels in the PJM Interconnection during the summer of 1999. It simulates hourly market-clearing prices assuming competitive market behavior and compares these prices with observed market prices in computing price markups over the April 1-August 31, 1999 period. The results of the simulation analysis are supported with an examination of actual generator bid data of incumbent generators. Price markups averaged 14.7 percent above expected marginal cost over the 5-month period for all non-transmission-constrained hours. The evidence presented suggests that the June and July monthly markups were strongly influenced by generator market power as price inelastic peak demand approached the electricity generation capacity constraint of the market. While this analysis of the performance of the PJM market finds evidence of market power, the measured markups are markedly less than estimates from prior analysis of the PJM market.

Impact of Market Behavior, Fleet Composition, and Ancillary Services on Revenue Sufficiency

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

Frew, Bethany; Gallo, Giulia; Brinkman, Gregory

Revenue insufficiency, or the missing money problem, occurs when the revenues that generators earn from the market are not sufficient to cover both fixed and variable costs to remain in the market and/or justify investments in new capacity, which may be needed for reliability. The near-zero marginal cost of variable renewable generators further exacerbates these revenue challenges. Estimating the extent of the missing money problem in current electricity markets is an important, nontrivial task that requires representing both how the power system operates and how market participants behave. This paper explores the missing money problem using a production cost modelmore » that represented a simplified version of the Electric Reliability Council of Texas (ERCOT) energy-only market for the years 2012-2014. We evaluate how various market structures -- including market behavior, ancillary services, and changing fleet compositions -- affect net revenues in this ERCOT-like system. In most production cost modeling exercises, resources are assumed to offer their marginal capabilities at marginal costs. Although this assumption is reasonable for feasibility studies and long-term planning, it does not adequately consider the market behaviors that impact revenue sufficiency. In this work, we simulate a limited set of market participant strategic bidding behaviors by means of different sets of markups; these markups are applied to the true production costs of all gas generators, which are the most prominent generators in ERCOT. Results show that markups can help generators increase their net revenues overall, although net revenues may increase or decrease depending on the technology and the year under study. Results also confirm that conventional, variable-cost-based production cost simulations do not capture prices accurately, and this particular feature calls for proxies for strategic behaviors (e.g., markups) and more accurate representations of how electricity markets work. The analysis also shows that generators face revenue sufficiency challenges in this ERCOT-like energy-only market model; net revenues provided by the market in all base markup cases and sensitivity scenarios (except when a large fraction of the existing coal fleet is retired) are not sufficient to justify investments in new capacity for thermal and nuclear power units. Overall, the work described in this paper points to the need for improved behavioral models of electricity markets to more accurately study current and potential market design issues that could arise in systems with high penetrations of renewable generation.« less

Design and implementation of an internet-based electrical engineering laboratory.

PubMed

He, Zhenlei; Shen, Zhangbiao; Zhu, Shanan

2014-09-01

This paper describes an internet-based electrical engineering laboratory (IEE-Lab) with virtual and physical experiments at Zhejiang University. In order to synthesize the advantages of both experiment styles, the IEE-Lab is come up with Client/Server/Application framework and combines the virtual and physical experiments. The design and workflow of IEE-Lab are introduced. The analog electronic experiment is taken as an example to show Flex plug-in design, data communication based on XML (Extensible Markup Language), experiment simulation modeled by Modelica and control terminals' design. Crown Copyright © 2014. Published by Elsevier Ltd. All rights reserved.

Entry, concentration and market efficiency: A simulation of the PJM energy market

NASA Astrophysics Data System (ADS)

Harvill, Terry

The rapid and substantial expansion of the PJM energy market during 2004 and 2005 provides a unique opportunity to test the theory of market concentration and its effect on market efficiency. With ten years of operational experience, the PJM energy market is uniquely suited to test the theories of market concentration and efficiency in a natural experiment. This research tests the hypothesis that, for a given number of generating units in the industry, system marginal price will be a decreasing function of the number of owners or generators controlling the units (i.e., the industry concentration ratio). Market simulations are utilized to assess price-cost markups in the PJM energy market during three distinct periods of expansion: (1) pre-Commonwealth Edison integration, (2) pre-American Electric Power (AEP), Dayton Power and Light (DPL), Duquesne Light (Duquesne), and Dominion Virginia Power (Dominion) integration, and (3) post-AFT, DPL. Duquesne, and Dominion Integration. The results of the market simulations for the May 1 to August 31 periods for 2003, 2004, and 2005, indicate that the performance of the market improved with the addition of new market participants in 2004 and 2005. The results of the simulation indicate that the load-weighted Lerner index decreased to -3.70 percent in 2005 from 0.92 percent in 2003. Clearly, the addition of Commonwealth Edison in 2004 significantly increased constraints within the PJM energy market and likely impacted the observed prices in PJM during 2004 due to the lack of a significant link to the other PJM market participants. This deficiency was address in 2005 with the addition of American Electric Power. The market simulations also highlight the prevalence of computed negative markups in the simulation results. Many of the off-peak periods in particular are characterized by negative markups where the expected marginal cost exceeds the observed price. Unit commitment constraints are believed to largely account for these results. Overall, the results of the analysis validate the regional transmission organization expansion polices of the Federal Energy Regulatory Commission.

Xeml Lab: a tool that supports the design of experiments at a graphical interface and generates computer-readable metadata files, which capture information about genotypes, growth conditions, environmental perturbations and sampling strategy.

PubMed

Hannemann, Jan; Poorter, Hendrik; Usadel, Björn; Bläsing, Oliver E; Finck, Alex; Tardieu, Francois; Atkin, Owen K; Pons, Thijs; Stitt, Mark; Gibon, Yves

2009-09-01

Data mining depends on the ability to access machine-readable metadata that describe genotypes, environmental conditions, and sampling times and strategy. This article presents Xeml Lab. The Xeml Interactive Designer provides an interactive graphical interface at which complex experiments can be designed, and concomitantly generates machine-readable metadata files. It uses a new eXtensible Mark-up Language (XML)-derived dialect termed XEML. Xeml Lab includes a new ontology for environmental conditions, called Xeml Environment Ontology. However, to provide versatility, it is designed to be generic and also accepts other commonly used ontology formats, including OBO and OWL. A review summarizing important environmental conditions that need to be controlled, monitored and captured as metadata is posted in a Wiki (http://www.codeplex.com/XeO) to promote community discussion. The usefulness of Xeml Lab is illustrated by two meta-analyses of a large set of experiments that were performed with Arabidopsis thaliana during 5 years. The first reveals sources of noise that affect measurements of metabolite levels and enzyme activities. The second shows that Arabidopsis maintains remarkably stable levels of sugars and amino acids across a wide range of photoperiod treatments, and that adjustment of starch turnover and the leaf protein content contribute to this metabolic homeostasis.

The Digital electronic Guideline Library (DeGeL): a hybrid framework for representation and use of clinical guidelines.

PubMed

Shahar, Yuval; Young, Ohad; Shalom, Erez; Mayaffit, Alon; Moskovitch, Robert; Hessing, Alon; Galperin, Maya

2004-01-01

We propose to present a poster (and potentially also a demonstration of the implemented system) summarizing the current state of our work on a hybrid, multiple-format representation of clinical guidelines that facilitates conversion of guidelines from free text to a formal representation. We describe a distributed Web-based architecture (DeGeL) and a set of tools using the hybrid representation. The tools enable performing tasks such as guideline specification, semantic markup, search, retrieval, visualization, eligibility determination, runtime application and retrospective quality assessment. The representation includes four parallel formats: Free text (one or more original sources); semistructured text (labeled by the target guideline-ontology semantic labels); semiformal text (which includes some control specification); and a formal, machine-executable representation. The specification, indexing, search, retrieval, and browsing tools are essentially independent of the ontology chosen for guideline representation, but editing the semi-formal and formal formats requires ontology-specific tools, which we have developed in the case of the Asbru guideline-specification language. The four formats support increasingly sophisticated computational tasks. The hybrid guidelines are stored in a Web-based library. All tools, such as for runtime guideline application or retrospective quality assessment, are designed to operate on all representations. We demonstrate the hybrid framework by providing examples from the semantic markup and search tools.

The place of SGML and HTML in building electronic patient records.

PubMed

Pitty, D; Gordon, C; Reeves, P; Capey, A; Vieyra, P; Rickards, T

1997-01-01

The authors are concerned that, although popular, SGML (Standard Generalized Markup Language) is only one approach to capturing, storing, viewing and exchanging healthcare information and does not provide a suitable paradigm for solving most of the problems associated with paper based patient record systems. Although a discussion of the relative merits of SGML, HTML (HyperText Markup Language) may be interesting, we feel such a discussion is avoiding the real issues associated with the most appropriate way to model, represent, and store electronic patient information in order to solve healthcare problems, and therefore the medical informatics community should firstly concern itself with these issues. The paper substantiates this viewpoint and concludes with some suggestions of how progress can be made.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem.

PubMed

Phadungsukanan, Weerapong; Kraft, Markus; Townsend, Joe A; Murray-Rust, Peter

2012-08-07

: This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

Pathology data integration with eXtensible Markup Language.

PubMed

Berman, Jules J

2005-02-01

It is impossible to overstate the importance of XML (eXtensible Markup Language) as a data organization tool. With XML, pathologists can annotate all of their data (clinical and anatomic) in a format that can transform every pathology report into a database, without compromising narrative structure. The purpose of this manuscript is to provide an overview of XML for pathologists. Examples will demonstrate how pathologists can use XML to annotate individual data elements and to structure reports in a common format that can be merged with other XML files or queried using standard XML tools. This manuscript gives pathologists a glimpse into how XML allows pathology data to be linked to other types of biomedical data and reduces our dependence on centralized proprietary databases.

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

PubMed

Zi, Zhike

2011-04-01

Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors. SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

PubMed Central

2012-01-01

This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications. PMID:22870956

State cigarette minimum price laws - United States, 2009.

PubMed

2010-04-09

Cigarette price increases reduce the demand for cigarettes and thereby reduce smoking prevalence, cigarette consumption, and youth initiation of smoking. Excise tax increases are the most effective government intervention to increase the price of cigarettes, but cigarette manufacturers use trade discounts, coupons, and other promotions to counteract the effects of these tax increases and appeal to price-sensitive smokers. State cigarette minimum price laws, initiated by states in the 1940s and 1950s to protect tobacco retailers from predatory business practices, typically require a minimum percentage markup to be added to the wholesale and/or retail price. If a statute prohibits trade discounts from the minimum price calculation, these laws have the potential to counteract discounting by cigarette manufacturers. To assess the status of cigarette minimum price laws in the United States, CDC surveyed state statutes and identified those states with minimum price laws in effect as of December 31, 2009. This report summarizes the results of that survey, which determined that 25 states had minimum price laws for cigarettes (median wholesale markup: 4.00%; median retail markup: 8.00%), and seven of those states also expressly prohibited the use of trade discounts in the minimum retail price calculation. Minimum price laws can help prevent trade discounting from eroding the positive effects of state excise tax increases and higher cigarette prices on public health.

XML at the ADC: Steps to a Next Generation Data Archive

NASA Astrophysics Data System (ADS)

Shaya, E.; Blackwell, J.; Gass, J.; Oliversen, N.; Schneider, G.; Thomas, B.; Cheung, C.; White, R. A.

1999-05-01

The eXtensible Markup Language (XML) is a document markup language that allows users to specify their own tags, to create hierarchical structures to qualify their data, and to support automatic checking of documents for structural validity. It is being intensively supported by nearly every major corporate software developer. Under the funds of a NASA AISRP proposal, the Astronomical Data Center (ADC, http://adc.gsfc.nasa.gov) is developing an infrastructure for importation, enhancement, and distribution of data and metadata using XML as the document markup language. We discuss the preliminary Document Type Definition (DTD, at http://adc.gsfc.nasa.gov/xml) which specifies the elements and their attributes in our metadata documents. This attempts to define both the metadata of an astronomical catalog and the `header' information of an astronomical table. In addition, we give an overview of the planned flow of data through automated pipelines from authors and journal presses into our XML archive and retrieval through the web via the XML-QL Query Language and eXtensible Style Language (XSL) scripts. When completed, the catalogs and journal tables at the ADC will be tightly hyperlinked to enhance data discovery. In addition one will be able to search on fragmentary information. For instance, one could query for a table by entering that the second author is so-and-so or that the third author is at such-and-such institution.

Issues and solutions for storage, retrieval, and searching of MPEG-7 documents

NASA Astrophysics Data System (ADS)

Chang, Yuan-Chi; Lo, Ming-Ling; Smith, John R.

2000-10-01

The ongoing MPEG-7 standardization activity aims at creating a standard for describing multimedia content in order to facilitate the interpretation of the associated information content. Attempting to address a broad range of applications, MPEG-7 has defined a flexible framework consisting of Descriptors, Description Schemes, and Description Definition Language. Descriptors and Description Schemes describe features, structure and semantics of multimedia objects. They are written in the Description Definition Language (DDL). In the most recent revision, DDL applies XML (Extensible Markup Language) Schema with MPEG-7 extensions. DDL has constructs that support inclusion, inheritance, reference, enumeration, choice, sequence, and abstract type of Description Schemes and Descriptors. In order to enable multimedia systems to use MPEG-7, a number of important problems in storing, retrieving and searching MPEG-7 documents need to be solved. This paper reports on initial finding on issues and solutions of storing and accessing MPEG-7 documents. In particular, we discuss the benefits of using a virtual document management framework based on XML Access Server (XAS) in order to bridge the MPEG-7 multimedia applications and database systems. The need arises partly because MPEG-7 descriptions need customized storage schema, indexing and search engines. We also discuss issues arising in managing dependence and cross-description scheme search.

Light at Night Markup Language (LANML): XML Technology for Light at Night Monitoring Data

NASA Astrophysics Data System (ADS)

Craine, B. L.; Craine, E. R.; Craine, E. M.; Crawford, D. L.

2013-05-01

Light at Night Markup Language (LANML) is a standard, based upon XML, useful in acquiring, validating, transporting, archiving and analyzing multi-dimensional light at night (LAN) datasets of any size. The LANML standard can accommodate a variety of measurement scenarios including single spot measures, static time-series, web based monitoring networks, mobile measurements, and airborne measurements. LANML is human-readable, machine-readable, and does not require a dedicated parser. In addition LANML is flexible; ensuring future extensions of the format will remain backward compatible with analysis software. The XML technology is at the heart of communicating over the internet and can be equally useful at the desktop level, making this standard particularly attractive for web based applications, educational outreach and efficient collaboration between research groups.

Dealing with Diversity in Computational Cancer Modeling

PubMed Central

Johnson, David; McKeever, Steve; Stamatakos, Georgios; Dionysiou, Dimitra; Graf, Norbert; Sakkalis, Vangelis; Marias, Konstantinos; Wang, Zhihui; Deisboeck, Thomas S.

2013-01-01

This paper discusses the need for interconnecting computational cancer models from different sources and scales within clinically relevant scenarios to increase the accuracy of the models and speed up their clinical adaptation, validation, and eventual translation. We briefly review current interoperability efforts drawing upon our experiences with the development of in silico models for predictive oncology within a number of European Commission Virtual Physiological Human initiative projects on cancer. A clinically relevant scenario, addressing brain tumor modeling that illustrates the need for coupling models from different sources and levels of complexity, is described. General approaches to enabling interoperability using XML-based markup languages for biological modeling are reviewed, concluding with a discussion on efforts towards developing cancer-specific XML markup to couple multiple component models for predictive in silico oncology. PMID:23700360

Medicare program; revisions to payment policies under the Physician Fee Schedule, and other part B payment policies for CY 2008; delay of the date of applicability of the revised anti-markup provisions for certain services furnished in certain locations (Sec. 414.50). Final rule.

PubMed

2008-01-03

This final rule delays until January 1, 2009 the applicability of the anti-markup provisions in Sec. 414.50, as revised at 72 FR 66222, except with respect to the technical component of a purchased diagnostic test and with respect to any anatomic pathology diagnostic testing services furnished in space that: Is utilized by a physician group practice as a "centralized building" (as defined at Sec. 411.351 of this chapter) for purposes of complying with the physician self-referral rules; and does not qualify as a "same building" under Sec. 411.355(b)(2)(i) of this chapter.

Improving the Interoperability of Disaster Models: a Case Study of Proposing Fireml for Forest Fire Model

NASA Astrophysics Data System (ADS)

Jiang, W.; Wang, F.; Meng, Q.; Li, Z.; Liu, B.; Zheng, X.

2018-04-01

This paper presents a new standardized data format named Fire Markup Language (FireML), extended by the Geography Markup Language (GML) of OGC, to elaborate upon the fire hazard model. The proposed FireML is able to standardize the input and output documents of a fire model for effectively communicating with different disaster management systems to ensure a good interoperability. To demonstrate the usage of FireML and testify its feasibility, an adopted forest fire spread model being compatible with FireML is described. And a 3DGIS disaster management system is developed to simulate the dynamic procedure of forest fire spread with the defined FireML documents. The proposed approach will enlighten ones who work on other disaster models' standardization work.

The use of geospatial web services for exchanging utilities data

NASA Astrophysics Data System (ADS)

Kuczyńska, Joanna

2013-04-01

Geographic information technologies and related geo-information systems currently play an important role in the management of public administration in Poland. One of these tasks is to maintain and update Geodetic Evidence of Public Utilities (GESUT), part of the National Geodetic and Cartographic Resource, which contains an important for many institutions information of technical infrastructure. It requires an active exchange of data between the Geodesy and Cartography Documentation Centers and institutions, which administrate transmission lines. The administrator of public utilities, is legally obliged to provide information about utilities to GESUT. The aim of the research work was to develop a universal data exchange methodology, which can be implemented on a variety of hardware and software platforms. This methodology use Unified Modeling Language (UML), eXtensible Markup Language (XML), and Geography Markup Language (GML). The proposed methodology is based on the two different strategies: Model Driven Architecture (MDA) and Service Oriented Architecture (SOA). Used solutions are consistent with the INSPIRE Directive and ISO 19100 series standards for geographic information. On the basis of analysis of the input data structures, conceptual models were built for both databases. Models were written in the universal modeling language: UML. Combined model that defines a common data structure was also built. This model was transformed into developed for the exchange of geographic information GML standard. The structure of the document describing the data that may be exchanged is defined in the .xsd file. Network services were selected and implemented in the system designed for data exchange based on open source tools. Methodology was implemented and tested. Data in the agreed data structure and metadata were set up on the server. Data access was provided by geospatial network services: data searching possibilities by Catalog Service for the Web (CSW), data collection by Web Feature Service (WFS). WFS provides also operation for modification data, for example to update them by utility administrator. The proposed solution significantly increases the efficiency of data exchange and facilitates maintenance the National Geodetic and Cartographic Resource.

Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database.

PubMed

Yoshida, Yutaka; Miyazaki, Kenji; Kamiie, Junichi; Sato, Masao; Okuizumi, Seiji; Kenmochi, Akihisa; Kamijo, Ken'ichi; Nabetani, Takuji; Tsugita, Akira; Xu, Bo; Zhang, Ying; Yaoita, Eishin; Osawa, Tetsuo; Yamamoto, Tadashi

2005-03-01

To contribute to physiology and pathophysiology of the glomerulus of human kidney, we have launched a proteomic study of human glomerulus, and compiled a profile of proteins expressed in the glomerulus of normal human kidney by two-dimensional gel electrophoresis (2-DE) and identification with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS). Kidney cortices with normal appearance were obtained from patients under surgical nephrectomy due to renal tumor, and glomeruli were highly purified by a standard sieving method followed by picking-up under a phase-contrast microscope. The glomerular proteins were separated by 2-DE with 24 cm immobilized pH gradient strips in the 3-10 range in the first dimension and 26 x 20 cm sodium dodecyl sulfate polyacrylamide electrophoresis gels of 12.5% in the second dimension. Gels were silver-stained, and valid spots were processed for identification through an integrated robotic system that consisted of a spot picker, an in-gel digester, and a MALDI-TOF MS and / or a LC-MS/MS. From 2-DE gel images of glomeruli of four subjects with no apparent pathologic manifestations, a synthetic gel image of normal glomerular proteins was created. The synthetic gel image contained 1713 valid spots, of which 1559 spots were commonly observed in the respective 2-DE gels. Among the 1559 spots, 347 protein spots, representing 212 proteins, have so far been identified, and used for the construction of an extensible markup language (XML)-based database. The database is deposited on a web site (http://www.sw.nec.co.jp/bio/rd/hgldb/index.html) in a form accessible to researchers to contribute to proteomic studies of human glomerulus in health and disease.

A web application to support telemedicine services in Brazil.

PubMed

Barbosa, Ana Karina P; de A Novaes, Magdala; de Vasconcelos, Alexandre M L

2003-01-01

This paper describes a system that has been developed to support Telemedicine activities in Brazil, a country that has serious problems in the delivery of health services. The system is a part of the broader Tele-health Project that has been developed to make health services more accessible to the low-income population in the northeast region. The HealthNet system is based upon a pilot area that uses fetal and pediatric cardiology. This article describes both the system's conceptual model, including the tele-diagnosis and second medical opinion services, as well as its architecture and development stages. The system model describes both collaborating tools used asynchronously, such as discussion forums, and synchronous tools, such as videoconference services. Web and free-of-charge tools are utilized for implementation, such as Java and MySQL database. Furthermore, an interface with Electronic Patient Record (EPR) systems using Extended Markup Language (XML) technology is also proposed. Finally, considerations concerning the development and implementation process are presented.

Resource Discovery for Extreme Scale Collaboration (RDESC) Final Report - RPI/TWC - Year 3

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

Fox, Peter

The amount of data produced in the practice of science is growing rapidly. Despite the accumulation and demand for scientific data, relatively little is actually made available for the broader scientific community. We surmise that the root of the problem is the perceived difficulty to electronically publish scientific data and associated metadata in a way that makes it discoverable. We propose to exploit Semantic Web technologies and practices to make (meta)data discoverable and easy to publish. We share our experiences in curating metadata to illustrate both the flexibility of our approach and the pain of discovering data in the currentmore » research environment. We also make recommendations by concrete example of how data publishers can provide their (meta)data by adding some limited, additional markup to HTML pages on the Web. With little additional effort from data publishers, the difficulty of data discovery/access/sharing can be greatly reduced and the impact of research data greatly enhanced.« less

A Java viewer to publish Digital Imaging and Communications in Medicine (DICOM) radiologic images on the World Wide Web.

PubMed

Setti, E; Musumeci, R

2001-06-01

The world wide web is an exciting service that allows one to publish electronic documents made of text and images on the internet. Client software called a web browser can access these documents, and display and print them. The most popular browsers are currently Microsoft Internet Explorer (Microsoft, Redmond, WA) and Netscape Communicator (Netscape Communications, Mountain View, CA). These browsers can display text in hypertext markup language (HTML) format and images in Joint Photographic Expert Group (JPEG) and Graphic Interchange Format (GIF). Currently, neither browser can display radiologic images in native Digital Imaging and Communications in Medicine (DICOM) format. With the aim to publish radiologic images on the internet, we wrote a dedicated Java applet. Our software can display radiologic and histologic images in DICOM, JPEG, and GIF formats, and provides a a number of functions like windowing and magnification lens. The applet is compatible with some web browsers, even the older versions. The software is free and available from the author.

Google Earth and Geo Applications: A Toolset for Viewing Earth's Geospatial Information

NASA Astrophysics Data System (ADS)

Tuxen-Bettman, K.

2016-12-01

Earth scientists measure and derive fundamental data that can be of broad general interest to the public and policy makers. Yet, one of the challenges that has always faced the Earth science community is how to present their data and findings in an easy-to-use and compelling manner. Google's Geo Tools offer an efficient and dynamic way for scientists, educators, journalists and others to both access data and view or tell stories in a dynamic three-dimensional geospatial context. Google Earth in particular provides a dense canvas of satellite imagery on which can be viewed rich vector and raster datasets using the medium of Keyhole Markup Language (KML). Through KML, Google Earth can combine the analytical capabilities of Earth Engine, collaborative mapping of My Maps, and storytelling of Tour Builder and more to make Google's Geo Applications a coherent suite of tools for exploring our planet.https://earth.google.com/https://earthengine.google.com/https://mymaps.google.com/https://tourbuilder.withgoogle.com/https://www.google.com/streetview/

The role of markup for enabling interoperability in health informatics.

PubMed

McKeever, Steve; Johnson, David

2015-01-01

Interoperability is the faculty of making information systems work together. In this paper we will distinguish a number of different forms that interoperability can take and show how they are realized on a variety of physiological and health care use cases. The last 15 years has seen the rise of very cheap digital storage both on and off site. With the advent of the Internet of Things people's expectations are for greater interconnectivity and seamless interoperability. The potential impact these technologies have on healthcare are dramatic: from improved diagnoses through immediate access to a patient's electronic health record, to in silico modeling of organs and early stage drug trials, to predictive medicine based on top-down modeling of disease progression and treatment. We will begin by looking at the underlying technology, classify the various kinds of interoperability that exist in the field, and discuss how they are realized. We conclude with a discussion on future possibilities that big data and further standardizations will enable.

Atmosphere-based image classification through luminance and hue

NASA Astrophysics Data System (ADS)

Xu, Feng; Zhang, Yujin

2005-07-01

In this paper a novel image classification system is proposed. Atmosphere serves an important role in generating the scene"s topic or in conveying the message behind the scene"s story, which belongs to abstract attribute level in semantic levels. At first, five atmosphere semantic categories are defined according to rules of photo and film grammar, followed by global luminance and hue features. Then the hierarchical SVM classifiers are applied. In each classification stage, corresponding features are extracted and the trained linear SVM is implemented, resulting in two classes. After three stages of classification, five atmosphere categories are obtained. At last, the text annotation of the atmosphere semantics and the corresponding features by Extensible Markup Language (XML) in MPEG-7 is defined, which can be integrated into more multimedia applications (such as searching, indexing and accessing of multimedia content). The experiment is performed on Corel images and film frames. The classification results prove the effectiveness of the definition of atmosphere semantic classes and the corresponding features.

Seabird databases and the new paradigm for scientific publication and attribution

USGS Publications Warehouse

Hatch, Scott A.

2010-01-01

For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

Enhancing the Impact of Science Data: Toward Data Discovery and Reuse

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

Chappell, Alan R.; Weaver, Jesse R.; Purohit, Sumit

The amount of data produced in support of scientific research continues to grow rapidly. Despite the accumulation and demand for scientific data, relatively little data are actually made available for the broader scientific community. We surmise that one root of this problem is the perceived difficulty of electronically publishing scientific data and associated metadata in a way that makes it discoverable. We propose exploiting Semantic Web technologies and best practices to make metadata both discoverable and easy to publish. We share experiences in curating metadata to illustrate the cumbersome nature of data reuse in the current research environment. We alsomore » make recommendations with a real-world example of how data publishers can provide their metadata by adding limited additional markup to HTML pages on the Web. With little additional effort from data publishers, the difficulty of data discovery, access, and sharing can be greatly reduced and the impact of research data greatly enhanced.« less

Genomic Sequence Variation Markup Language (GSVML).

PubMed

Nakaya, Jun; Kimura, Michio; Hiroi, Kaei; Ido, Keisuke; Yang, Woosung; Tanaka, Hiroshi

2010-02-01

With the aim of making good use of internationally accumulated genomic sequence variation data, which is increasing rapidly due to the explosive amount of genomic research at present, the development of an interoperable data exchange format and its international standardization are necessary. Genomic Sequence Variation Markup Language (GSVML) will focus on genomic sequence variation data and human health applications, such as gene based medicine or pharmacogenomics. We developed GSVML through eight steps, based on case analysis and domain investigations. By focusing on the design scope to human health applications and genomic sequence variation, we attempted to eliminate ambiguity and to ensure practicability. We intended to satisfy the requirements derived from the use case analysis of human-based clinical genomic applications. Based on database investigations, we attempted to minimize the redundancy of the data format, while maximizing the data covering range. We also attempted to ensure communication and interface ability with other Markup Languages, for exchange of omics data among various omics researchers or facilities. The interface ability with developing clinical standards, such as the Health Level Seven Genotype Information model, was analyzed. We developed the human health-oriented GSVML comprising variation data, direct annotation, and indirect annotation categories; the variation data category is required, while the direct and indirect annotation categories are optional. The annotation categories contain omics and clinical information, and have internal relationships. For designing, we examined 6 cases for three criteria as human health application and 15 data elements for three criteria as data formats for genomic sequence variation data exchange. The data format of five international SNP databases and six Markup Languages and the interface ability to the Health Level Seven Genotype Model in terms of 317 items were investigated. GSVML was developed as a potential data exchanging format for genomic sequence variation data exchange focusing on human health applications. The international standardization of GSVML is necessary, and is currently underway. GSVML can be applied to enhance the utilization of genomic sequence variation data worldwide by providing a communicable platform between clinical and research applications. Copyright 2009 Elsevier Ireland Ltd. All rights reserved.

GASP- General Aviation Synthesis Program. Volume 7: Economics

NASA Technical Reports Server (NTRS)

1978-01-01

The economic analysis includes: manufacturing costs; labor costs; parts costs; operating costs; markups and consumer price. A user's manual for a computer program to calculate the final consumer price is included.

Introducing Today's SGML.

ERIC Educational Resources Information Center

Gilmore, Elizabeth

1993-01-01

Describes the fundamental concepts and potential of Standard General Markup Language (SGML), a system that allows computer users to exchange, reuse, and reformat information without constraint. Illustrates the concepts of SGML through a simple example. (SR)

XML DTD and Schemas for HDF-EOS

NASA Technical Reports Server (NTRS)

Ullman, Richard; Yang, Jingli

2008-01-01

An Extensible Markup Language (XML) document type definition (DTD) standard for the structure and contents of HDF-EOS files and their contents, and an equivalent standard in the form of schemas, have been developed.

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping.

PubMed

Boulos, Maged N Kamel; Warren, Jeffrey; Gong, Jianya; Yue, Peng

2010-03-03

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities.

Running MONET and SALT with Remote Telescope Markup Language 3.0

NASA Astrophysics Data System (ADS)

Hessman, F. V.; Romero, E.

2003-05-01

Complex robotic and service observations in heterogenous networks of telescopes require a common telescopic lingua franca for the description and transport of observing requests and results. Building upon the experience gained within the Hands-On Universe (HOU) and advanced amateur communities with Remote Telescope Markup Language (RTML) Version 2.1 (http://sunra.lbl.gov/rtml), we have implemented a revised RTML syntax (Version 3.0) which is fully capable of - running the two 1.2m MONET robotic telescopes for a very inhomogeneous clientel from 3 research institutions and high school classes all over the world; - connecting MONET to the HOU telescope network; - connecting MONET as a trigger to the 11m SALT telescope; - providing all the objects needed to perform and document internet-based user support, ranging all the way from proposal submission and time-allocation to observation reports.

The Schema.org Datasets Schema: Experiences at the National Snow and Ice Data Center

NASA Astrophysics Data System (ADS)

Duerr, R.; Billingsley, B. W.; Harper, D.; Kovarik, J.

2014-12-01

Data discovery, is still a major challenge for many users. Relevant data may be located anywhere. There are currently no existing universal data registries. Often users start with a simple query through their web browser. But how do you get your data to actually show up near the top of the results? One relatively new way to accomplish this is to use schema.org dataset markup in your data pages. Theoretically this provides web crawlers the additional information needed so that a query for data will preferentially return those pages that were marked up accordingly. The National Snow and Ice Data Center recently implemented an initial set of markup in the data set pages returned by its catalog. The Datasets data model, our process, challenges encountered and results will be described.

The development of MML (Medical Markup Language) version 3.0 as a medical document exchange format for HL7 messages.

PubMed

Guo, Jinqiu; Takada, Akira; Tanaka, Koji; Sato, Junzo; Suzuki, Muneou; Suzuki, Toshiaki; Nakashima, Yusei; Araki, Kenji; Yoshihara, Hiroyuki

2004-12-01

Medical Markup Language (MML), as a set of standards, has been developed over the last 8 years to allow the exchange of medical data between different medical information providers. MML Version 2.21 used XML as a metalanguage and was announced in 1999. In 2001, MML was updated to Version 2.3, which contained 12 modules. The latest version--Version 3.0--is based on the HL7 Clinical Document Architecture (CDA). During the development of this new version, the structure of MML Version 2.3 was analyzed, subdivided into several categories, and redefined so the information defined in MML could be described in HL7 CDA Level One. As a result of this development, it has become possible to exchange MML Version 3.0 medical documents via HL7 messages.

HGML: a hypertext guideline markup language.

PubMed Central

Hagerty, C. G.; Pickens, D.; Kulikowski, C.; Sonnenberg, F.

2000-01-01

Existing text-based clinical practice guidelines can be difficult to put into practice. While a growing number of such documents have gained acceptance in the medical community and contain a wealth of valuable information, the time required to digest them is substantial. Yet the expressive power, subtlety and flexibility of natural language pose challenges when designing computer tools that will help in their application. At the same time, formal computer languages typically lack such expressiveness and the effort required to translate existing documents into these languages may be costly. We propose a method based on the mark-up concept for converting text-based clinical guidelines into a machine-operable form. This allows existing guidelines to be manipulated by machine, and viewed in different formats at various levels of detail according to the needs of the practitioner, while preserving their originally published form. PMID:11079898

Geospatial Visualization of Scientific Data Through Keyhole Markup Language

NASA Astrophysics Data System (ADS)

Wernecke, J.; Bailey, J. E.

2008-12-01

The development of virtual globes has provided a fun and innovative tool for exploring the surface of the Earth. However, it has been the paralleling maturation of Keyhole Markup Language (KML) that has created a new medium and perspective through which to visualize scientific datasets. Originally created by Keyhole Inc., and then acquired by Google in 2004, in 2007 KML was given over to the Open Geospatial Consortium (OGC). It became an OGC international standard on 14 April 2008, and has subsequently been adopted by all major geobrowser developers (e.g., Google, Microsoft, ESRI, NASA) and many smaller ones (e.g., Earthbrowser). By making KML a standard at a relatively young stage in its evolution, developers of the language are seeking to avoid the issues that plagued the early World Wide Web and development of Hypertext Markup Language (HTML). The popularity and utility of Google Earth, in particular, has been enhanced by KML features such as the Smithsonian volcano layer and the dynamic weather layers. Through KML, users can view real-time earthquake locations (USGS), view animations of polar sea-ice coverage (NSIDC), or read about the daily activities of chimpanzees (Jane Goodall Institute). Perhaps even more powerful is the fact that any users can create, edit, and share their own KML, with no or relatively little knowledge of manipulating computer code. We present an overview of the best current scientific uses of KML and a guide to how scientists can learn to use KML themselves.

Transparent ICD and DRG coding using information technology: linking and associating information sources with the eXtensible Markup Language.

PubMed

Hoelzer, Simon; Schweiger, Ralf K; Dudeck, Joachim

2003-01-01

With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or "semantically associated" parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach.

Transparent ICD and DRG Coding Using Information Technology: Linking and Associating Information Sources with the eXtensible Markup Language

PubMed Central

Hoelzer, Simon; Schweiger, Ralf K.; Dudeck, Joachim

2003-01-01

With the introduction of ICD-10 as the standard for diagnostics, it becomes necessary to develop an electronic representation of its complete content, inherent semantics, and coding rules. The authors' design relates to the current efforts by the CEN/TC 251 to establish a European standard for hierarchical classification systems in health care. The authors have developed an electronic representation of ICD-10 with the eXtensible Markup Language (XML) that facilitates integration into current information systems and coding software, taking different languages and versions into account. In this context, XML provides a complete processing framework of related technologies and standard tools that helps develop interoperable applications. XML provides semantic markup. It allows domain-specific definition of tags and hierarchical document structure. The idea of linking and thus combining information from different sources is a valuable feature of XML. In addition, XML topic maps are used to describe relationships between different sources, or “semantically associated” parts of these sources. The issue of achieving a standardized medical vocabulary becomes more and more important with the stepwise implementation of diagnostically related groups, for example. The aim of the authors' work is to provide a transparent and open infrastructure that can be used to support clinical coding and to develop further software applications. The authors are assuming that a comprehensive representation of the content, structure, inherent semantics, and layout of medical classification systems can be achieved through a document-oriented approach. PMID:12807813

Using XML Configuration-Driven Development to Create a Customizable Ground Data System

NASA Technical Reports Server (NTRS)

Nash, Brent; DeMore, Martha

2009-01-01

The Mission data Processing and Control Subsystem (MPCS) is being developed as a multi-mission Ground Data System with the Mars Science Laboratory (MSL) as the first fully supported mission. MPCS is a fully featured, Java-based Ground Data System (GDS) for telecommand and telemetry processing based on Configuration-Driven Development (CDD). The eXtensible Markup Language (XML) is the ideal language for CDD because it is easily readable and editable by all levels of users and is also backed by a World Wide Web Consortium (W3C) standard and numerous powerful processing tools that make it uniquely flexible. The CDD approach adopted by MPCS minimizes changes to compiled code by using XML to create a series of configuration files that provide both coarse and fine grained control over all aspects of GDS operation.

Flight Simulation Model Exchange. Volume 1

NASA Technical Reports Server (NTRS)

Murri, Daniel G.; Jackson, E. Bruce

2011-01-01

The NASA Engineering and Safety Center Review Board sponsored an assessment of the draft Standard, Flight Dynamics Model Exchange Standard, BSR/ANSI-S-119-201x (S-119) that was conducted by simulation and guidance, navigation, and control engineers from several NASA Centers. The assessment team reviewed the conventions and formats spelled out in the draft Standard and the actual implementation of two example aerodynamic models (a subsonic F-16 and the HL-20 lifting body) encoded in the Extensible Markup Language grammar. During the implementation, the team kept records of lessons learned and provided feedback to the American Institute of Aeronautics and Astronautics Modeling and Simulation Technical Committee representative. This document contains the results of the assessment.

User's Manual for the Object User Interface (OUI): An Environmental Resource Modeling Framework

USGS Publications Warehouse

Markstrom, Steven L.; Koczot, Kathryn M.

2008-01-01

The Object User Interface is a computer application that provides a framework for coupling environmental-resource models and for managing associated temporal and spatial data. The Object User Interface is designed to be easily extensible to incorporate models and data interfaces defined by the user. Additionally, the Object User Interface is highly configurable through the use of a user-modifiable, text-based control file that is written in the eXtensible Markup Language. The Object User Interface user's manual provides (1) installation instructions, (2) an overview of the graphical user interface, (3) a description of the software tools, (4) a project example, and (5) specifications for user configuration and extension.

Flight Simulation Model Exchange. Volume 2; Appendices

NASA Technical Reports Server (NTRS)

Murri, Daniel G.; Jackson, E. Bruce

2011-01-01

The NASA Engineering and Safety Center Review Board sponsored an assessment of the draft Standard, Flight Dynamics Model Exchange Standard, BSR/ANSI-S-119-201x (S-119) that was conducted by simulation and guidance, navigation, and control engineers from several NASA Centers. The assessment team reviewed the conventions and formats spelled out in the draft Standard and the actual implementation of two example aerodynamic models (a subsonic F-16 and the HL-20 lifting body) encoded in the Extensible Markup Language grammar. During the implementation, the team kept records of lessons learned and provided feedback to the American Institute of Aeronautics and Astronautics Modeling and Simulation Technical Committee representative. This document contains the appendices to the main report.

Web Browser Trends and Technologies.

ERIC Educational Resources Information Center

Goodwin-Jones, Bob

2000-01-01

Discusses Web browsers and how their capabilities have been expanded, support for Web browsing on different devices (cell phones, palmtop computers, TV sets), and browser support for the next-generation Web authoring language, XML ("extensible markup language"). (Author/VWL)

CLAIM (CLinical Accounting InforMation)--an XML-based data exchange standard for connecting electronic medical record systems to patient accounting systems.

PubMed

Guo, Jinqiu; Takada, Akira; Tanaka, Koji; Sato, Junzo; Suzuki, Muneou; Takahashi, Kiwamu; Daimon, Hiroyuki; Suzuki, Toshiaki; Nakashima, Yusei; Araki, Kenji; Yoshihara, Hiroyuki

2005-08-01

With the evolving and diverse electronic medical record (EMR) systems, there appears to be an ever greater need to link EMR systems and patient accounting systems with a standardized data exchange format. To this end, the CLinical Accounting InforMation (CLAIM) data exchange standard was developed. CLAIM is subordinate to the Medical Markup Language (MML) standard, which allows the exchange of medical data among different medical institutions. CLAIM uses eXtensible Markup Language (XML) as a meta-language. The current version, 2.1, inherited the basic structure of MML 2.x and contains two modules including information related to registration, appointment, procedure and charging. CLAIM 2.1 was implemented successfully in Japan in 2001. Consequently, it was confirmed that CLAIM could be used as an effective data exchange format between EMR systems and patient accounting systems.

Restructuring an EHR system and the Medical Markup Language (MML) standard to improve interoperability by archetype technology.

PubMed

Kobayashi, Shinji; Kume, Naoto; Yoshihara, Hiroyuki

2015-01-01

In 2001, we developed an EHR system for regional healthcare information inter-exchange and to provide individual patient data to patients. This system was adopted in three regions in Japan. We also developed a Medical Markup Language (MML) standard for inter- and intra-hospital communications. The system was built on a legacy platform, however, and had not been appropriately maintained or updated to meet clinical requirements. To improve future maintenance costs, we reconstructed the EHR system using archetype technology on the Ruby on Rails platform, and generated MML equivalent forms from archetypes. The system was deployed as a cloud-based system for preliminary use as a regional EHR. The system now has the capability to catch up with new requirements, maintaining semantic interoperability with archetype technology. It is also more flexible than the legacy EHR system.

Combinational pixel-by-pixel and object-level classifying, segmenting, and agglomerating in performing quantitative image analysis that distinguishes between healthy non-cancerous and cancerous cell nuclei and delineates nuclear, cytoplasm, and stromal material objects from stained biological tissue materials

DOEpatents

Boucheron, Laura E

2013-07-16

Quantitative object and spatial arrangement-level analysis of tissue are detailed using expert (pathologist) input to guide the classification process. A two-step method is disclosed for imaging tissue, by classifying one or more biological materials, e.g. nuclei, cytoplasm, and stroma, in the tissue into one or more identified classes on a pixel-by-pixel basis, and segmenting the identified classes to agglomerate one or more sets of identified pixels into segmented regions. Typically, the one or more biological materials comprises nuclear material, cytoplasm material, and stromal material. The method further allows a user to markup the image subsequent to the classification to re-classify said materials. The markup is performed via a graphic user interface to edit designated regions in the image.

ADASS Web Database XML Project

NASA Astrophysics Data System (ADS)

Barg, M. I.; Stobie, E. B.; Ferro, A. J.; O'Neil, E. J.

In the spring of 2000, at the request of the ADASS Program Organizing Committee (POC), we began organizing information from previous ADASS conferences in an effort to create a centralized database. The beginnings of this database originated from data (invited speakers, participants, papers, etc.) extracted from HyperText Markup Language (HTML) documents from past ADASS host sites. Unfortunately, not all HTML documents are well formed and parsing them proved to be an iterative process. It was evident at the beginning that if these Web documents were organized in a standardized way, such as XML (Extensible Markup Language), the processing of this information across the Web could be automated, more efficient, and less error prone. This paper will briefly review the many programming tools available for processing XML, including Java, Perl and Python, and will explore the mapping of relational data from our MySQL database to XML.

XML Based Scientific Data Management Facility

NASA Technical Reports Server (NTRS)

Mehrotra, Piyush; Zubair, M.; Ziebartt, John (Technical Monitor)

2001-01-01

The World Wide Web consortium has developed an Extensible Markup Language (XML) to support the building of better information management infrastructures. The scientific computing community realizing the benefits of HTML has designed markup languages for scientific data. In this paper, we propose a XML based scientific data management facility, XDMF. The project is motivated by the fact that even though a lot of scientific data is being generated, it is not being shared because of lack of standards and infrastructure support for discovering and transforming the data. The proposed data management facility can be used to discover the scientific data itself, the transformation functions, and also for applying the required transformations. We have built a prototype system of the proposed data management facility that can work on different platforms. We have implemented the system using Java, and Apache XSLT engine Xalan. To support remote data and transformation functions, we had to extend the XSLT specification and the Xalan package.

XML Based Scientific Data Management Facility

NASA Technical Reports Server (NTRS)

Mehrotra, P.; Zubair, M.; Bushnell, Dennis M. (Technical Monitor)

2002-01-01

The World Wide Web consortium has developed an Extensible Markup Language (XML) to support the building of better information management infrastructures. The scientific computing community realizing the benefits of XML has designed markup languages for scientific data. In this paper, we propose a XML based scientific data management ,facility, XDMF. The project is motivated by the fact that even though a lot of scientific data is being generated, it is not being shared because of lack of standards and infrastructure support for discovering and transforming the data. The proposed data management facility can be used to discover the scientific data itself, the transformation functions, and also for applying the required transformations. We have built a prototype system of the proposed data management facility that can work on different platforms. We have implemented the system using Java, and Apache XSLT engine Xalan. To support remote data and transformation functions, we had to extend the XSLT specification and the Xalan package.

Web GIS in practice VIII: HTML5 and the canvas element for interactive online mapping

PubMed Central

2010-01-01

HTML5 is being developed as the next major revision of HTML (Hypertext Markup Language), the core markup language of the World Wide Web. It aims at reducing the need for proprietary, plug-in-based rich Internet application (RIA) technologies such as Adobe Flash. The canvas element is part of HTML5 and is used to draw graphics using scripting (e.g., JavaScript). This paper introduces Cartagen, an open-source, vector-based, client-side framework for rendering plug-in-free, offline-capable, interactive maps in native HTML5 on a wide range of Web browsers and mobile phones. Cartagen was developed at MIT Media Lab's Design Ecology group. Potential applications of the technology as an enabler for participatory online mapping include mapping real-time air pollution, citizen reporting, and disaster response, among many other possibilities. PMID:20199681

Standard Generalized Markup Language for self-defining structured reports.

PubMed

Kahn, C E

1999-01-01

Structured reporting is the process of using standardized data elements and predetermined data-entry formats to record observations. The Standard Generalized Markup Language (SGML; International Standards Organization (ISO) 8879:1986)--an open, internationally accepted standard for document interchange was used to encode medical observations acquired in an Internet-based structured reporting system. The resulting report is self-documenting: it includes a definition of its allowable data fields and values encoded as a report-specific SGML document type definition (DTD). The data-entry forms, DTD, and report document instances are based on report specifications written in a simple, SGML-based language designed for that purpose. Reporting concepts can be linked with those of external vocabularies such as the Unified Medical Language System (UMLS) Metathesaurus. The use of open standards such as SGML is an important step in the creation of open, universally comprehensible structured reports.

GEM at 10: a decade's experience with the Guideline Elements Model.

PubMed

Hajizadeh, Negin; Kashyap, Nitu; Michel, George; Shiffman, Richard N

2011-01-01

The Guideline Elements Model (GEM) was developed in 2000 to organize the information contained in clinical practice guidelines using XML and to represent guideline content in a form that can be understood by human readers and processed by computers. In this work, we systematically reviewed the literature to better understand how GEM was being used, potential barriers to its use, and suggestions for improvement. Fifty external and twelve internally produced publications were identified and analyzed. GEM was used most commonly for modeling and ontology creation. Other investigators applied GEM for knowledge extraction and data mining, for clinical decision support for guideline generation. The GEM Cutter software-used to markup guidelines for translation into XML- has been downloaded 563 times since 2000. Although many investigators found GEM to be valuable, others critiqued its failure to clarify guideline semantics, difficulties in markup, and the fact that GEM files are not usually executable.

SBML-PET: a Systems Biology Markup Language-based parameter estimation tool.

PubMed

Zi, Zhike; Klipp, Edda

2006-11-01

The estimation of model parameters from experimental data remains a bottleneck for a major breakthrough in systems biology. We present a Systems Biology Markup Language (SBML) based Parameter Estimation Tool (SBML-PET). The tool is designed to enable parameter estimation for biological models including signaling pathways, gene regulation networks and metabolic pathways. SBML-PET supports import and export of the models in the SBML format. It can estimate the parameters by fitting a variety of experimental data from different experimental conditions. SBML-PET has a unique feature of supporting event definition in the SMBL model. SBML models can also be simulated in SBML-PET. Stochastic Ranking Evolution Strategy (SRES) is incorporated in SBML-PET for parameter estimation jobs. A classic ODE Solver called ODEPACK is used to solve the Ordinary Differential Equation (ODE) system. http://sysbio.molgen.mpg.de/SBML-PET/. The website also contains detailed documentation for SBML-PET.

A standard MIGS/MIMS compliant XML Schema: toward the development of the Genomic Contextual Data Markup Language (GCDML).

PubMed

Kottmann, Renzo; Gray, Tanya; Murphy, Sean; Kagan, Leonid; Kravitz, Saul; Lombardot, Thierry; Field, Dawn; Glöckner, Frank Oliver

2008-06-01

The Genomic Contextual Data Markup Language (GCDML) is a core project of the Genomic Standards Consortium (GSC) that implements the "Minimum Information about a Genome Sequence" (MIGS) specification and its extension, the "Minimum Information about a Metagenome Sequence" (MIMS). GCDML is an XML Schema for generating MIGS/MIMS compliant reports for data entry, exchange, and storage. When mature, this sample-centric, strongly-typed schema will provide a diverse set of descriptors for describing the exact origin and processing of a biological sample, from sampling to sequencing, and subsequent analysis. Here we describe the need for such a project, outline design principles required to support the project, and make an open call for participation in defining the future content of GCDML. GCDML is freely available, and can be downloaded, along with documentation, from the GSC Web site (http://gensc.org).

Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project.

PubMed

Hucka, M; Finney, A; Bornstein, B J; Keating, S M; Shapiro, B E; Matthews, J; Kovitz, B L; Schilstra, M J; Funahashi, A; Doyle, J C; Kitano, H

2004-06-01

Biologists are increasingly recognising that computational modelling is crucial for making sense of the vast quantities of complex experimental data that are now being collected. The systems biology field needs agreed-upon information standards if models are to be shared, evaluated and developed cooperatively. Over the last four years, our team has been developing the Systems Biology Markup Language (SBML) in collaboration with an international community of modellers and software developers. SBML has become a de facto standard format for representing formal, quantitative and qualitative models at the level of biochemical reactions and regulatory networks. In this article, we summarise the current and upcoming versions of SBML and our efforts at developing software infrastructure for supporting and broadening its use. We also provide a brief overview of the many SBML-compatible software tools available today.

Intended and unintended consequences of China's zero markup drug policy.

PubMed

Yi, Hongmei; Miller, Grant; Zhang, Linxiu; Li, Shaoping; Rozelle, Scott

2015-08-01

Since economic liberalization in the late 1970s, China's health care providers have grown heavily reliant on revenue from drugs, which they both prescribe and sell. To curb abuse and to promote the availability, safety, and appropriate use of essential drugs, China introduced its national essential drug list in 2009 and implemented a zero markup policy designed to decouple provider compensation from drug prescription and sales. We collected and analyzed representative data from China's township health centers and their catchment-area populations both before and after the reform. We found large reductions in drug revenue, as intended by policy makers. However, we also found a doubling of inpatient care that appeared to be driven by supply, instead of demand. Thus, the reform had an important unintended consequence: China's health care providers have sought new, potentially inappropriate, forms of revenue. Project HOPE—The People-to-People Health Foundation, Inc.

Web-Based Customizable Viewer for Mars Network Overflight Opportunities

NASA Technical Reports Server (NTRS)

Gladden, Roy E.; Wallick, Michael N.; Allard, Daniel A.

2012-01-01

This software displays a full summary of information regarding the overflight opportunities between any set of lander and orbiter pairs that the user has access to view. The information display can be customized, allowing the user to choose which fields to view/hide and filter. The software works from a Web browser on any modern operating system. A full summary of information pertaining to an overflight is available, including the proposed, tentative, requested, planned, and implemented. This gives the user a chance to quickly check for inconsistencies and fix any problems. Overflights from multiple lander/ orbiter pairs can be compared instantly, and information can be filtered through the query and shown/hidden, giving the user a customizable view of the data. The information can be exported to a CSV (comma separated value) or XML (extensible markup language) file. The software only grants access to users who are authorized to view the information. This application is an addition to the MaROS Web suite. Prior to this addition, information pertaining to overflight opportunities would have a limited amount of data (displayed graphically) and could only be shown in strict temporal ordering. This new display shows more information, allows direct comparisons between overflights, and allows the data to be manipulated in ways that it was unable to be done in the past. The current software solution is to use CSV files to view the overflight opportunities.

Semantics of data and service registration to advance interdisciplinary information and data access.

NASA Astrophysics Data System (ADS)

Fox, P. P.; McGuinness, D. L.; Raskin, R.; Sinha, A. K.

2008-12-01

In developing an application of semantic web methods and technologies to address the integration of heterogeneous and interdisciplinary earth-science datasets, we have developed methodologies for creating rich semantic descriptions (ontologies) of the application domains. We have leveraged and extended where possible existing ontology frameworks such as SWEET. As a result of this semantic approach, we have also utilized ontologic descriptions of key enabling elements of the application, such as the registration of datasets with ontologies at several levels of granularity. This has enabled the location and usage of the data across disciplines. We are also realizing the need to develop similar semantic registration of web service data holdings as well as those provided with community and/or standard markup languages (e.g. GeoSciML). This level of semantic enablement extending beyond domain terms and relations significantly enhances our ability to provide a coherent semantic data framework for data and information systems. Much of this work is on the frontier of technology development and we will present the current and near-future capabilities we are developing. This work arises from the Semantically-Enabled Science Data Integration (SESDI) project, which is an NASA/ESTO/ACCESS-funded project involving the High Altitude Observatory at the National Center for Atmospheric Research (NCAR), McGuinness Associates Consulting, NASA/JPL and Virginia Polytechnic University.

[The development and operation of a package inserts service system for electronic medical records].

PubMed

Yamada, Hidetoshi; Nishimura, Sachiho; Shimamori, Yoshimitsu; Sato, Seiji; Hayase, Yukitoshi

2003-03-01

To promote the appropriate use of pharmaceuticals and to prevent side effects, physicians need package inserts on medicinal drugs as soon as possible. A medicinal drug information service system was established for electronic medical records to speed up and increase the efficiency of package insert communications within a medical institution. Development of this system facilitates access to package inserts by, for example, physicians. The time required to maintain files of package inserts was shortened, and the efficiency of the drug information service increased. As a source of package inserts for this system, package inserts using a standard generalized markup language (SGML) form were used, which are accessible to the public on the homepage of the Organization for Pharmaceutical Safety and Research (OPSR). This study found that a delay occurred in communicating revised package inserts from pharmaceutical companies to the OPSR. Therefore a pharmaceutical department page was set up as part of the homepage of the medical institution for electronic medical records to shorten the delay in the revision of package inserts posted on the medicinal drug information service homepage of the OPSR. The usefulness of this package insert service system for electronic medical records is clear. For more effective use of this system based on the OPSR homepage pharmaceutical companies have been requested to provide quicker updating of package inserts.

Effects of Inaccurate Identification of Interictal Epileptiform Discharges in Concurrent EEG-fMRI

NASA Astrophysics Data System (ADS)

Gkiatis, K.; Bromis, K.; Kakkos, I.; Karanasiou, I. S.; Matsopoulos, G. K.; Garganis, K.

2017-11-01

Concurrent continuous EEG-fMRI is a novel multimodal technique that is finding its way into clinical practice in epilepsy. EEG timeseries are used to identify the timing of interictal epileptiform discharges (IEDs) which is then included in a GLM analysis in fMRI to localize the epileptic onset zone. Nevertheless, there are still some concerns about its reliability concerning BOLD changes correlated with IEDs. Even though IEDs are identified by an experienced neurologist-epiliptologist, the reliability and concordance of the mark-ups is depending on many factors including the level of fatigue, the amount of time that he spent or, in some cases, even the screen that is being used for the display of timeseries. This investigation is aiming to unravel the effect of misidentification or inaccuracy in the mark-ups of IEDs in the fMRI statistical parametric maps. Concurrent EEG-fMRI was conducted in six subjects with various types of epilepsy. IEDs were identified by an experienced neurologist-epiliptologist. Analysis of EEG was performed with EEGLAB and analysis of fMRI was conducted in FSL. Preliminary results revealed lower statistical significance for missing events or larger period of IEDs than the actual ones and the introduction of false positives and false negatives in statistical parametric maps when random events were included in the GLM on top of the IEDs. Our results suggest that mark-ups in EEG for simultaneous EEG-fMRI should be done with caution from an experienced and restful neurologist as it affects the fMRI results in various and unpredicted ways.

User-Friendly Interface Developed for a Web-Based Service for SpaceCAL Emulations

NASA Technical Reports Server (NTRS)

Liszka, Kathy J.; Holtz, Allen P.

2004-01-01

A team at the NASA Glenn Research Center is developing a Space Communications Architecture Laboratory (SpaceCAL) for protocol development activities for coordinated satellite missions. SpaceCAL will provide a multiuser, distributed system to emulate space-based Internet architectures, backbone networks, formation clusters, and constellations. As part of a new effort in 2003, building blocks are being defined for an open distributed system to make the satellite emulation test bed accessible through an Internet connection. The first step in creating a Web-based service to control the emulation remotely is providing a user-friendly interface for encoding the data into a well-formed and complete Extensible Markup Language (XML) document. XML provides coding that allows data to be transferred between dissimilar systems. Scenario specifications include control parameters, network routes, interface bandwidths, delay, and bit error rate. Specifications for all satellite, instruments, and ground stations in a given scenario are also included in the XML document. For the SpaceCAL emulation, the XML document can be created using XForms, a Webbased forms language for data collection. Contrary to older forms technology, the interactive user interface makes the science prevalent, not the data representation. Required versus optional input fields, default values, automatic calculations, data validation, and reuse will help researchers quickly and accurately define missions. XForms can apply any XML schema defined for the test mission to validate data before forwarding it to the emulation facility. New instrument definitions, facilities, and mission types can be added to the existing schema. The first prototype user interface incorporates components for interactive input and form processing. Internet address, data rate, and the location of the facility are implemented with basic form controls with default values provided for convenience and efficiency using basic XForms operations. Because different emulation scenarios will vary widely in their component structure, more complex operations are used to add and delete facilities.

The XML approach to implementing space link extension service management

NASA Technical Reports Server (NTRS)

Tai, W.; Welz, G. A.; Theis, G.; Yamada, T.

2001-01-01

A feasibility study has been conducted at JPL, ESOC, and ISAS to assess the possible applications of the eXtensible Mark-up Language (XML) capabilities to the implementation of the CCSDS Space Link Extension (SLE) Service Management function.

Designing for the Next Web.

ERIC Educational Resources Information Center

Bremser, Wayne

1998-01-01

Discusses how to choose from the available interactive graphic-design possibilities for the World Wide Web. Compatibility and appropriateness are discussed; and DHTML (Dynamic Hypertext Markup Language), Java, CSS (Cascading Style Sheets), plug-ins, ActiveX, and Push and channel technologies are described. (LRW)

Dictionary as Database.

ERIC Educational Resources Information Center

Painter, Derrick

1996-01-01

Discussion of dictionaries as databases focuses on the digitizing of The Oxford English dictionary (OED) and the use of Standard Generalized Mark-Up Language (SGML). Topics include the creation of a consortium to digitize the OED, document structure, relational databases, text forms, sequence, and discourse. (LRW)

Integration, warehousing, and analysis strategies of Omics data.

PubMed

Gedela, Srinubabu

2011-01-01

"-Omics" is a current suffix for numerous types of large-scale biological data generation procedures, which naturally demand the development of novel algorithms for data storage and analysis. With next generation genome sequencing burgeoning, it is pivotal to decipher a coding site on the genome, a gene's function, and information on transcripts next to the pure availability of sequence information. To explore a genome and downstream molecular processes, we need umpteen results at the various levels of cellular organization by utilizing different experimental designs, data analysis strategies and methodologies. Here comes the need for controlled vocabularies and data integration to annotate, store, and update the flow of experimental data. This chapter explores key methodologies to merge Omics data by semantic data carriers, discusses controlled vocabularies as eXtensible Markup Languages (XML), and provides practical guidance, databases, and software links supporting the integration of Omics data.

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena

PubMed Central

Tohsato, Yukako; Ho, Kenneth H. L.; Kyoda, Koji; Onami, Shuichi

2016-01-01

Motivation: Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis. Results: We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus. The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. Availability and Implementation: SSBD is accessible at http://ssbd.qbic.riken.jp. Contact: sonami@riken.jp PMID:27412095

XML and its impact on content and structure in electronic health care documents.

PubMed Central

Sokolowski, R.; Dudeck, J.

1999-01-01

Worldwide information networks have the requirement that electronic documents must be easily accessible, portable, flexible and system-independent. With the development of XML (eXtensible Markup Language), the future of electronic documents, health care informatics and the Web itself are about to change. The intent of the recently formed ASTM E31.25 subcommittee, "XML DTDs for Health Care", is to develop standard electronic document representations of paper-based health care documents and forms. A goal of the subcommittee is to work together to enhance existing levels of interoperability among the various XML/SGML standardization efforts, products and systems in health care. The ASTM E31.25 subcommittee uses common practices and software standards to develop the implementation recommendations for XML documents in health care. The implementation recommendations are being developed to standardize the many different structures of documents. These recommendations are in the form of a set of standard DTDs, or document type definitions that match the electronic document requirements in the health care industry. This paper discusses recent efforts of the ASTM E31.25 subcommittee. PMID:10566338

seismo-live: Training in Seismology using Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Igel, Heiner; Krischer, Lion; van Driel, Martin; Tape, Carl

2017-04-01

Practical training in computational methodologies is still underrepresented in Earth science curriculae despite the increasing use of sometimes highly sophisticated simulation and data processing technologies in research projects. At the same time well-engineered community codes make it easy to return results yet with the danger that the inherent traps of black-box solutions are not well understood. For this purpose we have initiated a community platform (www.seismo-live.org) where Python-based Jupyter notebooks can be accessed and run without necessary downloads or local software installations. The increasingly popular Jupyter notebooks allow combining markup language, graphics, equations, with interactive, executable python codes. The platform already includes general Python training, introduction to the ObsPy library for seismology as well as seismic data processing, noise analysis, and a variety of forward solvers for seismic wave propagation. In addition, an example is shown how Jupyter notebooks can be used to increase reproducibility of published results. Submission of Jupyter notebooks for general seismology are encouraged. The platform can be used for complementary teaching in Earth Science courses on compute-intensive research areas. We present recent developments and new features.

Word add-in for ontology recognition: semantic enrichment of scientific literature.

PubMed

Fink, J Lynn; Fernicola, Pablo; Chandran, Rahul; Parastatidis, Savas; Wade, Alex; Naim, Oscar; Quinn, Gregory B; Bourne, Philip E

2010-02-24

In the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely necessary and new media are allowing information and knowledge to be more interactive and immediate. One approach to making knowledge more accessible is the addition of machine-readable semantic data to scholarly articles. The Word add-in presented here will assist authors in this effort by automatically recognizing and highlighting words or phrases that are likely information-rich, allowing authors to associate semantic data with those words or phrases, and to embed that data in the document as XML. The add-in and source code are publicly available at http://www.codeplex.com/UCSDBioLit. The Word add-in for ontology term recognition makes it possible for an author to add semantic data to a document as it is being written and it encodes these data using XML tags that are effectively a standard in life sciences literature. Allowing authors to mark-up their own work will help increase the amount and quality of machine-readable literature metadata.

SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena.

PubMed

Tohsato, Yukako; Ho, Kenneth H L; Kyoda, Koji; Onami, Shuichi

2016-11-15

Rapid advances in live-cell imaging analysis and mathematical modeling have produced a large amount of quantitative data on spatiotemporal dynamics of biological objects ranging from molecules to organisms. There is now a crucial need to bring these large amounts of quantitative biological dynamics data together centrally in a coherent and systematic manner. This will facilitate the reuse of this data for further analysis. We have developed the Systems Science of Biological Dynamics database (SSBD) to store and share quantitative biological dynamics data. SSBD currently provides 311 sets of quantitative data for single molecules, nuclei and whole organisms in a wide variety of model organisms from Escherichia coli to Mus musculus The data are provided in Biological Dynamics Markup Language format and also through a REST API. In addition, SSBD provides 188 sets of time-lapse microscopy images from which the quantitative data were obtained and software tools for data visualization and analysis. SSBD is accessible at http://ssbd.qbic.riken.jp CONTACT: sonami@riken.jp. © The Author 2016. Published by Oxford University Press.

An XML-based interchange format for genotype-phenotype data.

PubMed

Whirl-Carrillo, M; Woon, M; Thorn, C F; Klein, T E; Altman, R B

2008-02-01

Recent advances in high-throughput genotyping and phenotyping have accelerated the creation of pharmacogenomic data. Consequently, the community requires standard formats to exchange large amounts of diverse information. To facilitate the transfer of pharmacogenomics data between databases and analysis packages, we have created a standard XML (eXtensible Markup Language) schema that describes both genotype and phenotype data as well as associated metadata. The schema accommodates information regarding genes, drugs, diseases, experimental methods, genomic/RNA/protein sequences, subjects, subject groups, and literature. The Pharmacogenetics and Pharmacogenomics Knowledge Base (PharmGKB; www.pharmgkb.org) has used this XML schema for more than 5 years to accept and process submissions containing more than 1,814,139 SNPs on 20,797 subjects using 8,975 assays. Although developed in the context of pharmacogenomics, the schema is of general utility for exchange of genotype and phenotype data. We have written syntactic and semantic validators to check documents using this format. The schema and code for validation is available to the community at http://www.pharmgkb.org/schema/index.html (last accessed: 8 October 2007). (c) 2007 Wiley-Liss, Inc.

iPad: Semantic annotation and markup of radiological images.

PubMed

Rubin, Daniel L; Rodriguez, Cesar; Shah, Priyanka; Beaulieu, Chris

2008-11-06

Radiological images contain a wealth of information,such as anatomy and pathology, which is often not explicit and computationally accessible. Information schemes are being developed to describe the semantic content of images, but such schemes can be unwieldy to operationalize because there are few tools to enable users to capture structured information easily as part of the routine research workflow. We have created iPad, an open source tool enabling researchers and clinicians to create semantic annotations on radiological images. iPad hides the complexity of the underlying image annotation information model from users, permitting them to describe images and image regions using a graphical interface that maps their descriptions to structured ontologies semi-automatically. Image annotations are saved in a variety of formats,enabling interoperability among medical records systems, image archives in hospitals, and the Semantic Web. Tools such as iPad can help reduce the burden of collecting structured information from images, and it could ultimately enable researchers and physicians to exploit images on a very large scale and glean the biological and physiological significance of image content.

Rock.XML - Towards a library of rock physics models

NASA Astrophysics Data System (ADS)

Jensen, Erling Hugo; Hauge, Ragnar; Ulvmoen, Marit; Johansen, Tor Arne; Drottning, Åsmund

2016-08-01

Rock physics modelling provides tools for correlating physical properties of rocks and their constituents to the geophysical observations we measure on a larger scale. Many different theoretical and empirical models exist, to cover the range of different types of rocks. However, upon reviewing these, we see that they are all built around a few main concepts. Based on this observation, we propose a format for digitally storing the specifications for rock physics models which we have named Rock.XML. It does not only contain data about the various constituents, but also the theories and how they are used to combine these building blocks to make a representative model for a particular rock. The format is based on the Extensible Markup Language XML, making it flexible enough to handle complex models as well as scalable towards extending it with new theories and models. This technology has great advantages as far as documenting and exchanging models in an unambiguous way between people and between software. Rock.XML can become a platform for creating a library of rock physics models; making them more accessible to everyone.

A BPMN solution for chaining OGC services to quality assure location-based crowdsourced data

NASA Astrophysics Data System (ADS)

Meek, Sam; Jackson, Mike; Leibovici, Didier G.

2016-02-01

The Open Geospatial Consortium (OGC) Web Processing Service (WPS) standard enables access to a centralized repository of processes and services from compliant clients. A crucial part of the standard includes the provision to chain disparate processes and services to form a reusable workflow. To date this has been realized by methods such as embedding XML requests, using Business Process Execution Language (BPEL) engines and other external orchestration engines. Although these allow the user to define tasks and data artifacts as web services, they are often considered inflexible and complicated, often due to vendor specific solutions and inaccessible documentation. This paper introduces a new method of flexible service chaining using the standard Business Process Markup Notation (BPMN). A prototype system has been developed upon an existing open source BPMN suite to illustrate the advantages of the approach. The motivation for the software design is qualification of crowdsourced data for use in policy-making. The software is tested as part of a project that seeks to qualify, assure, and add value to crowdsourced data in a biological monitoring use case.

Teaching Critical Thinking in the Business Mathematics Course.

ERIC Educational Resources Information Center

Rosenbaum, Roberta

1986-01-01

Appropriate strategies for teaching students to interpret and understand quantitative data in marketing, management, accounting, and data processing are described. Accompanying figures illustrate samples of percentage markups, trade discounts, gross earning, gross commissions, accounting entries, balance sheet entries, and percentage problems. (CT)

"The Wonder Years" of XML.

ERIC Educational Resources Information Center

Gazan, Rich

2000-01-01

Surveys the current state of Extensible Markup Language (XML), a metalanguage for creating structured documents that describe their own content, and its implications for information professionals. Predicts that XML will become the common language underlying Web, word processing, and database formats. Also discusses Extensible Stylesheet Language…

Descriptive Analysis on the Impacts of Universal Zero-Markup Drug Policy on a Chinese Urban Tertiary Hospital

PubMed Central

Yang, Dong

2016-01-01

Background Universal Zero-Markup Drug Policy (UZMDP) mandates no price mark-ups on any drug dispensed by a healthcare institution, and covers the medicines not included in the China’s National Essential Medicine System. Five tertiary hospitals in Beijing, China implemented UZMDP in 2012. Its impacts on these hospitals are unknown. We described the effects of UZMDP on a participating hospital, Jishuitan Hospital, Beijing, China (JST). Methods This retrospective longitudinal study examined the hospital-level data of JST and city-level data of tertiary hospitals of Beijing, China (BJT) 2009–2015. Rank-sum tests and join-point regression analyses were used to assess absolute changes and differences in trends, respectively. Results In absolute terms, after the UZDMP implementation, there were increased annual patient-visits and decreased ratios of medicine-to-healthcare-charges (RMOH) in JST outpatient and inpatient services; however, in outpatient service, physician work-days decreased and physician-workload and inflation-adjusted per-visit healthcare charges increased, while the inpatient physician work-days increased and inpatient mortality-rate reduced. Interestingly, the decreasing trend in inpatient mortality-rate was neutralized after UZDMP implementation. Compared with BJT and under influence of UZDMP, JST outpatient and inpatient services both had increasing trends in annual patient-visits (annual percentage changes[APC] = 8.1% and 6.5%, respectively) and decreasing trends in RMOH (APC = -4.3% and -5.4%, respectively), while JST outpatient services had increasing trend in inflation-adjusted per-visit healthcare charges (APC = 3.4%) and JST inpatient service had decreasing trend in inflation-adjusted per-visit medicine-charges (APC = -5.2%). Conclusion Implementation of UZMDP seems to increase annual patient-visits, reduce RMOH and have different impacts on outpatient and inpatient services in a Chinese urban tertiary hospital. PMID:27627811

Medicine prices, availability, and affordability in 36 developing and middle-income countries: a secondary analysis.

PubMed

Cameron, A; Ewen, M; Ross-Degnan, D; Ball, D; Laing, R

2009-01-17

WHO and Health Action International (HAI) have developed a standardised method for surveying medicine prices, availability, affordability, and price components in low-income and middle-income countries. Here, we present a secondary analysis of medicine availability in 45 national and subnational surveys done using the WHO/HAI methodology. Data from 45 WHO/HAI surveys in 36 countries were adjusted for inflation or deflation and purchasing power parity. International reference prices from open international procurements for generic products were used as comparators. Results are presented for 15 medicines included in at least 80% of surveys and four individual medicines. Average public sector availability of generic medicines ranged from 29.4% to 54.4% across WHO regions. Median government procurement prices for 15 generic medicines were 1.11 times corresponding international reference prices, although purchasing efficiency ranged from 0.09 to 5.37 times international reference prices. Low procurement prices did not always translate into low patient prices. Private sector patients paid 9-25 times international reference prices for lowest-priced generic products and over 20 times international reference prices for originator products across WHO regions. Treatments for acute and chronic illness were largely unaffordable in many countries. In the private sector, wholesale mark-ups ranged from 2% to 380%, whereas retail mark-ups ranged from 10% to 552%. In countries where value added tax was applied to medicines, the amount charged varied from 4% to 15%. Overall, public and private sector prices for originator and generic medicines were substantially higher than would be expected if purchasing and distribution were efficient and mark-ups were reasonable. Policy options such as promoting generic medicines and alternative financing mechanisms are needed to increase availability, reduce prices, and improve affordability.

Descriptive Analysis on the Impacts of Universal Zero-Markup Drug Policy on a Chinese Urban Tertiary Hospital.

PubMed

Tian, Wei; Yuan, Jiangfan; Yang, Dong; Zhang, Lanjing

2016-01-01

Universal Zero-Markup Drug Policy (UZMDP) mandates no price mark-ups on any drug dispensed by a healthcare institution, and covers the medicines not included in the China's National Essential Medicine System. Five tertiary hospitals in Beijing, China implemented UZMDP in 2012. Its impacts on these hospitals are unknown. We described the effects of UZMDP on a participating hospital, Jishuitan Hospital, Beijing, China (JST). This retrospective longitudinal study examined the hospital-level data of JST and city-level data of tertiary hospitals of Beijing, China (BJT) 2009-2015. Rank-sum tests and join-point regression analyses were used to assess absolute changes and differences in trends, respectively. In absolute terms, after the UZDMP implementation, there were increased annual patient-visits and decreased ratios of medicine-to-healthcare-charges (RMOH) in JST outpatient and inpatient services; however, in outpatient service, physician work-days decreased and physician-workload and inflation-adjusted per-visit healthcare charges increased, while the inpatient physician work-days increased and inpatient mortality-rate reduced. Interestingly, the decreasing trend in inpatient mortality-rate was neutralized after UZDMP implementation. Compared with BJT and under influence of UZDMP, JST outpatient and inpatient services both had increasing trends in annual patient-visits (annual percentage changes[APC] = 8.1% and 6.5%, respectively) and decreasing trends in RMOH (APC = -4.3% and -5.4%, respectively), while JST outpatient services had increasing trend in inflation-adjusted per-visit healthcare charges (APC = 3.4%) and JST inpatient service had decreasing trend in inflation-adjusted per-visit medicine-charges (APC = -5.2%). Implementation of UZMDP seems to increase annual patient-visits, reduce RMOH and have different impacts on outpatient and inpatient services in a Chinese urban tertiary hospital.

CytometryML, an XML format based on DICOM and FCS for analytical cytology data.

PubMed

Leif, Robert C; Leif, Suzanne B; Leif, Stephanie H

2003-07-01

Flow Cytometry Standard (FCS) was initially created to standardize the software researchers use to analyze, transmit, and store data produced by flow cytometers and sorters. Because of the clinical utility of flow cytometry, it is necessary to have a standard consistent with the requirements of medical regulatory agencies. We extended the existing mapping of FCS to the Digital Imaging and Communications in Medicine (DICOM) standard to include list-mode data produced by flow cytometry, laser scanning cytometry, and microscopic image cytometry. FCS list-mode was mapped to the DICOM Waveform Information Object. We created a collection of Extensible Markup Language (XML) schemas to express the DICOM analytical cytologic text-based data types except for large binary objects. We also developed a cytometry markup language, CytometryML, in an open environment subject to continuous peer review. The feasibility of expressing the data contained in FCS, including list-mode in DICOM, was demonstrated; and a preliminary mapping for list-mode data in the form of XML schemas and documents was completed. DICOM permitted the creation of indices that can be used to rapidly locate in a list-mode file the cells that are members of a subset. DICOM and its coding schemes for other medical standards can be represented by XML schemas, which can be combined with other relevant XML applications, such as Mathematical Markup Language (MathML). The use of XML format based on DICOM for analytical cytology met most of the previously specified requirements and appears capable of meeting the others; therefore, the present FCS should be retired and replaced by an open, XML-based, standard CytometryML. Copyright 2003 Wiley-Liss, Inc.

Does the leading pharmaceutical reform in China really solve the issue of overly expensive healthcare services? Evidence from an empirical study

PubMed Central

He, Yunzhen; Dou, Guanshen; Huang, Qiaoyun; Zhang, Xinyu; Ye, Yingfeng; Qian, Mengcen

2018-01-01

Background Healthcare system reform of Sanming city has become a leading healthcare reform model in China. It has developed a rigorous pharmaceutical reform consisted of the Zero Mark-up Drug Policy and the Centralized Procurement of Medicine Policy to bring down drug expenses and total health expenditures. However, despite the credit and much attention have been given to Sanming’s pharmaceutical reform, its impact still remains unclear. Therefore, the purpose of this study was to explore the impact of the pharmaceutical reform of Sanming on both drug and total health expenditures. Methods Interrupted time series analysis with three segments divided by two intervention points was employed to evaluate the impact of the pharmaceutical reform. Segment 1 was the pre-reform period which captured the baseline information. Segment 2 occurred after the first intervention point when the Zero Mark-up Drug Policy was implemented, whereas Segment 3 was after the implementation of the Centralized Procurement of Medicine Policy. Primary outcomes are outpatient drug expenditure, outpatient total health expenditure, inpatient drug expenditure, and inpatient total health expenditure. Data spanning from May 2012 to May 2014 are included. Results Both drug and total health expenditures exhibited rising trends before any policy was carried out. The launch of Zero Mark-up Drug Policy led to significant instant reductions in levels of outpatient drug expenditure (coefficient = -6,602.99, p<0.01), outpatient total health expenditure (coefficient = -9,958.58, p<0.05), inpatient drug expenditure (coefficient = -7,520.90, p<0.01), and inpatient total health expenditure (coefficient = -16,737, p<0.01). Moreover, the previous upward trends were changed into downward trends for inpatient drug expenditure (coefficient = -2,747.02, p = 0.00) and total health expenditure (coefficient = -3,069.29, p = 0.12). However, after the implementation of Centralized Procurement of Medicine Policy, we observed no significant instant level changes and also, the inpatient drug expenditure (coefficient = 372.95, p = 0.01) and total health expenditure (coefficient = 788.76, p = 0.06) resumed upward trends again. Conclusions Although the pharmaceutical reform could control or reduced drug expenditure and total health expenditure in short term, expenditures gradually resumed growing again and reached or even exceeded their baseline levels of pre-reform period, indicating the effect became weakened or even faded out in long term. In all, the pharmaceutical reform as a whole failed to meet its goal of combating sharp growth of drug and total health expenditure. PMID:29338038

Essays on Commodity Prices and Macroeconomic Performance of Developing and Resources Rich Economies: Evidence from Kazakhstan

NASA Astrophysics Data System (ADS)

Bilgin, Ferhat I.

My dissertation consists of three essays in empirical macroeconomics. The objective of this research is to use rigorous time-series econometric analysis to investigate the impact of commodity prices on macroeconomic performance of a small, developing and resource-rich country, which is in the process of transition from a purely command and control economy to a market oriented one. Essay 1 studies the relationship between Kazakhstan's GDP, total government expenditure, real effective exchange rate and the world oil price. Specifically, I use the cointegrated vector autoregression (CVAR) and error correction modeling (ECM) approach to identify the long and short-run relations that may exist among these macroeconomic variables. I found a long-run relationship for Kazakhstan's GDP, which depends on government spending and the oil price positively, and on the real effective exchange rate negatively. In the short run, the growth rate of GDP depends on the growth rates of the oil price, investment and the magnitude of the deviation from the long-run equilibrium. Essay 2 studies the inflation process in Kazakhstan based on the analysis of price formation in the following sectors: monetary, external, labor and goods and services. The modeling is conducted from two different perspectives: the first is the monetary model of inflation framework and the second is the mark-up modeling framework. Encompassing test results show that the mark-up model performs better than the monetary model in explaining inflation in Kazakhstan. According to the mark-up inflation model, in the long run, the price level is positively related to unit labor costs, import prices and government administered prices as well the world oil prices. In the short run, the inflation is positively influenced by the previous quarter's inflation, the contemporaneous changes in the government administered prices, oil prices and by the changes of contemporaneous and lagged unit labor costs, and negatively affected by the previous quarter's mark-up. Essay 3 empirically examines the determinants of the trade balance for a small oil exporting country within the context of Kazakhstan. The dominant theory by Harberger-Lauren-Metzler (HML) predicts that positive terms of trade shocks will improve the trade balance in the short run, but will fade away in the long run. I estimate cointegrated vector autoregression (CVAR) and vector error correction model (VECM) to study the long-run and short-run impacts on the trade balance. The results suggest that, in the long run, an increase in the terms of trade has a positive effect on the trade balance, an increase in GDP and appreciation of the real effective exchange rate have negative effect on the trade balance. In the short run, the terms of trade has a direct positive impact on the trade balance, real income and real exchange rate. On the other hand, appreciation of the currency has a negative impact on the trade balance. The error correction term, which represents the deviation from the long- run equilibrium between the trade balance, real income, terms of trade and real exchange rate, has a negative effect on the growth rate of the trade balance. These results provide further evidence to the idea that, in the long run, the HML effect not only depends on the duration of the shock, but also depends on the structure of the economy.

Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase.

PubMed

Patil, Sonali; Pincas, Hanna; Seto, Jeremy; Nudelman, German; Nudelman, Irina; Sealfon, Stuart C

2010-10-07

Dendritic cells are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems. Much research has focused on the signaling pathways triggered upon infection of dendritic cells by various pathogens. The high level of activity in the field makes it desirable to have a pathway-based resource to access the information in the literature. Current pathway diagrams lack either comprehensiveness, or an open-access editorial interface. Hence, there is a need for a dependable, expertly curated knowledgebase that integrates this information into a map of signaling networks. We have built a detailed diagram of the dendritic cell signaling network, with the goal of providing researchers with a valuable resource and a facile method for community input. Network construction has relied on comprehensive review of the literature and regular updates. The diagram includes detailed depictions of pathways activated downstream of different pathogen recognition receptors such as Toll-like receptors, retinoic acid-inducible gene-I-like receptors, C-type lectin receptors and nucleotide-binding oligomerization domain-like receptors. Initially assembled using CellDesigner software, it provides an annotated graphical representation of interactions stored in Systems Biology Mark-up Language. The network, which comprises 249 nodes and 213 edges, has been web-published through the Biological Pathway Publisher software suite. Nodes are annotated with PubMed references and gene-related information, and linked to a public wiki, providing a discussion forum for updates and corrections. To gain more insight into regulatory patterns of dendritic cell signaling, we analyzed the network using graph-theory methods: bifan, feedforward and multi-input convergence motifs were enriched. This emphasis on activating control mechanisms is consonant with a network that subserves persistent and coordinated responses to pathogen detection. This map represents a navigable aid for presenting a consensus view of the current knowledge on dendritic cell signaling that can be continuously improved through contributions of research community experts. Because the map is available in a machine readable format, it can be edited and may assist researchers in data analysis. Furthermore, the availability of a comprehensive knowledgebase might help further research in this area such as vaccine development. The dendritic cell signaling knowledgebase is accessible at http://tsb.mssm.edu/pathwayPublisher/DC_pathway/DC_pathway_index.html.

Chroni - an Android Application for Geochronologists to Access Archived Sample Analyses from the NSF-Funded Geochron.Org Data Repository.

NASA Astrophysics Data System (ADS)

Nettles, J. J.; Bowring, J. F.

2014-12-01

NSF requires data management plans as part of funding proposals and geochronologists, among other scientists, are archiving their data and results to the public cloud archives managed by the NSF-funded Integrated Earth Data Applications, or IEDA. GeoChron is a database for geochronology housed within IEDA. The software application U-Pb_Redux developed at the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES.org) at the College of Charleston provides seamless connectivity to GeoChron for uranium-lead (U-Pb) geochronologists to automatically upload and retrieve their data and results. U-Pb_Redux also manages publication-quality documents including report tables and graphs. CHRONI is a lightweight mobile application for Android devices that provides easy access to these archived data and results. With CHRONI, U-Pb geochronologists can view archived data and analyses downloaded from the Geochron database, or any other location, in a customizable format. CHRONI uses the same extensible markup language (XML) schema and documents used by U-Pb_Redux and GeoChron. Report Settings are special XML files that can be customized in U-Pb_Redux, stored in the cloud, and then accessed and used in CHRONI to create the same customized data display on the mobile device. In addition to providing geologists effortless and mobile access to archived data and analyses, CHRONI allows users to manage their GeoChron credentials, quickly download private and public files via a specified IEDA International Geo Sample Number (IGSN) or URL, and view specialized graphics associated with particular IGSNs. Future versions of CHRONI will be developed to support iOS compatible devices. CHRONI is an open source project under the Apache 2 license and is hosted at https://github.com/CIRDLES/CHRONI. We encourage community participation in its continued development.

Citation and Recognition of contributions using Semantic Provenance Knowledge Captured in the OPeNDAP Software Framework

NASA Astrophysics Data System (ADS)

West, P.; Michaelis, J.; Lebot, T.; McGuinness, D. L.; Fox, P. A.

2014-12-01

Providing proper citation and attribution for published data, derived data products, and the software tools used to generate them, has always been an important aspect of scientific research. However, It is often the case that this type of detailed citation and attribution is lacking. This is in part because it often requires manual markup since dynamic generation of this type of provenance information is not typically done by the tools used to access, manipulate, transform, and visualize data. In addition, the tools themselves lack the information needed to be properly cited themselves. The OPeNDAP Hyrax Software Framework is a tool that provides access to and the ability to constrain, manipulate, and transform, different types of data from different data formats, into a common format, the DAP (Data Access Protocol), in order to derive new data products. A user, or another software client, specifies an HTTP URL in order to access a particular piece of data, and appropriately transform it to suit a specific purpose of use. The resulting data products, however, do not contain any information about what data was used to create it, or the software process used to generate it, let alone information that would allow the proper citing and attribution to down stream researchers and tool developers. We will present our approach to provenance capture in Hyrax including a mechanism that can be used to report back to the hosting site any derived products, such as publications and reports, using the W3C PROV recommendation pingback service. We will demonstrate our utilization of Semantic Web and Web standards, the development of an information model that extends the PROV model for provenance capture, and the development of the pingback service. We will present our findings, as well as our practices for providing provenance information, visualization of the provenance information, and the development of pingback services, to better enable scientists and tool developers to be recognized and properly cited for their contributions.

Developing Intranets: Practical Issues for Implementation and Design.

ERIC Educational Resources Information Center

Trowbridge, Dave

1996-01-01

An intranet is a system which has "domesticated" the technologies of the Internet for specific organizational settings and goals. Although the adaptability of Hypertext Markup Language to intranets is sometimes limited, implementing various protocols and technologies enable organizations to share files among heterogeneous computers,…

XML under the Hood.

ERIC Educational Resources Information Center

Scharf, David

2002-01-01

Discusses XML (extensible markup language), particularly as it relates to libraries. Topics include organizing information; cataloging; metadata; similarities to HTML; organizations dealing with XML; making XML useful; a history of XML; the semantic Web; related technologies; XML at the Library of Congress; and its role in improving the…

From data to analysis: linking NWChem and Avogadro with the syntax and semantics of Chemical Markup Language

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

De Jong, Wibe A.; Walker, Andrew M.; Hanwell, Marcus D.

Background Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper the generation of semantically rich data from the NWChem computational chemistry software is discussed within the Chemical Markup Language (CML) framework. Results The NWChem computational chemistry software has been modified and coupled to the FoX library to write CML compliant XML data files. The FoX library was expanded to represent the lexical input files used by the computational chemistry software. Conclusions The production of CML compliant XMLmore » files for the computational chemistry software NWChem can be relatively easily accomplished using the FoX library. A unified computational chemistry or CompChem convention and dictionary needs to be developed through a community-based effort. The long-term goal is to enable a researcher to do Google-style chemistry and physics searches.« less

Adding Hierarchical Objects to Relational Database General-Purpose XML-Based Information Managements

NASA Technical Reports Server (NTRS)

Lin, Shu-Chun; Knight, Chris; La, Tracy; Maluf, David; Bell, David; Tran, Khai Peter; Gawdiak, Yuri

2006-01-01

NETMARK is a flexible, high-throughput software system for managing, storing, and rapid searching of unstructured and semi-structured documents. NETMARK transforms such documents from their original highly complex, constantly changing, heterogeneous data formats into well-structured, common data formats in using Hypertext Markup Language (HTML) and/or Extensible Markup Language (XML). The software implements an object-relational database system that combines the best practices of the relational model utilizing Structured Query Language (SQL) with those of the object-oriented, semantic database model for creating complex data. In particular, NETMARK takes advantage of the Oracle 8i object-relational database model using physical-address data types for very efficient keyword searches of records across both context and content. NETMARK also supports multiple international standards such as WEBDAV for drag-and-drop file management and SOAP for integrated information management using Web services. The document-organization and -searching capabilities afforded by NETMARK are likely to make this software attractive for use in disciplines as diverse as science, auditing, and law enforcement.

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways.

PubMed

Beltrame, Luca; Calura, Enrica; Popovici, Razvan R; Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-08-01

Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and 'wet lab' scientists. The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X.

Converting CSV Files to RKSML Files

NASA Technical Reports Server (NTRS)

Trebi-Ollennu, Ashitey; Liebersbach, Robert

2009-01-01

A computer program converts, into a format suitable for processing on Earth, files of downlinked telemetric data pertaining to the operation of the Instrument Deployment Device (IDD), which is a robot arm on either of the Mars Explorer Rovers (MERs). The raw downlinked data files are in comma-separated- value (CSV) format. The present program converts the files into Rover Kinematics State Markup Language (RKSML), which is an Extensible Markup Language (XML) format that facilitates representation of operations of the IDD and enables analysis of the operations by means of the Rover Sequencing Validation Program (RSVP), which is used to build sequences of commanded operations for the MERs. After conversion by means of the present program, the downlinked data can be processed by RSVP, enabling the MER downlink operations team to play back the actual IDD activity represented by the telemetric data against the planned IDD activity. Thus, the present program enhances the diagnosis of anomalies that manifest themselves as differences between actual and planned IDD activities.

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool

PubMed Central

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-01-01

Background It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. Results This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. Conclusion SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes. PMID:18706080

AllerML: markup language for allergens.

PubMed

Ivanciuc, Ovidiu; Gendel, Steven M; Power, Trevor D; Schein, Catherine H; Braun, Werner

2011-06-01

Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis. Copyright © 2011 Elsevier Inc. All rights reserved.

SBML-SAT: a systems biology markup language (SBML) based sensitivity analysis tool.

PubMed

Zi, Zhike; Zheng, Yanan; Rundell, Ann E; Klipp, Edda

2008-08-15

It has long been recognized that sensitivity analysis plays a key role in modeling and analyzing cellular and biochemical processes. Systems biology markup language (SBML) has become a well-known platform for coding and sharing mathematical models of such processes. However, current SBML compatible software tools are limited in their ability to perform global sensitivity analyses of these models. This work introduces a freely downloadable, software package, SBML-SAT, which implements algorithms for simulation, steady state analysis, robustness analysis and local and global sensitivity analysis for SBML models. This software tool extends current capabilities through its execution of global sensitivity analyses using multi-parametric sensitivity analysis, partial rank correlation coefficient, SOBOL's method, and weighted average of local sensitivity analyses in addition to its ability to handle systems with discontinuous events and intuitive graphical user interface. SBML-SAT provides the community of systems biologists a new tool for the analysis of their SBML models of biochemical and cellular processes.

The gel electrophoresis markup language (GelML) from the Proteomics Standards Initiative.

PubMed

Gibson, Frank; Hoogland, Christine; Martinez-Bartolomé, Salvador; Medina-Aunon, J Alberto; Albar, Juan Pablo; Babnigg, Gyorgy; Wipat, Anil; Hermjakob, Henning; Almeida, Jonas S; Stanislaus, Romesh; Paton, Norman W; Jones, Andrew R

2010-09-01

The Human Proteome Organisation's Proteomics Standards Initiative has developed the GelML (gel electrophoresis markup language) data exchange format for representing gel electrophoresis experiments performed in proteomics investigations. The format closely follows the reporting guidelines for gel electrophoresis, which are part of the Minimum Information About a Proteomics Experiment (MIAPE) set of modules. GelML supports the capture of metadata (such as experimental protocols) and data (such as gel images) resulting from gel electrophoresis so that laboratories can be compliant with the MIAPE Gel Electrophoresis guidelines, while allowing such data sets to be exchanged or downloaded from public repositories. The format is sufficiently flexible to capture data from a broad range of experimental processes, and complements other PSI formats for MS data and the results of protein and peptide identifications to capture entire gel-based proteome workflows. GelML has resulted from the open standardisation process of PSI consisting of both public consultation and anonymous review of the specifications.

AllerML: Markup Language for Allergens

PubMed Central

Ivanciuc, Ovidiu; Gendel, Steven M.; Power, Trevor D.; Schein, Catherine H.; Braun, Werner

2011-01-01

Many concerns have been raised about the potential allergenicity of novel, recombinant proteins into food crops. Guidelines, proposed by WHO/FAO and EFSA, include the use of bioinformatics screening to assess the risk of potential allergenicity or cross-reactivities of all proteins introduced, for example, to improve nutritional value or promote crop resistance. However, there are no universally accepted standards that can be used to encode data on the biology of allergens to facilitate using data from multiple databases in this screening. Therefore, we developed AllerML a markup language for allergens to assist in the automated exchange of information between databases and in the integration of the bioinformatics tools that are used to investigate allergenicity and cross-reactivity. As proof of concept, AllerML was implemented using the Structural Database of Allergenic Proteins (SDAP; http://fermi.utmb.edu/SDAP/) database. General implementation of AllerML will promote automatic flow of validated data that will aid in allergy research and regulatory analysis. PMID:21420460

Short-term differences in drug prices after implementation of the national essential medicines system: A case study in rural Jiangxi Province, China.

PubMed

Wang, Junyong; Liu, Xia; Wang, Suzhen; Chen, Heli; Wang, Xun; Zhou, Wei; Wang, Li; Zhu, Yanchen; Zheng, Xianping; Hao, Mo

2015-01-01

China's 2009 national essential medicine system (NEMS) was designed to reduce prices through a zero-markup policy and a centralized bidding system. To analyze NEMS's short-term impact on drug prices, we estimated the retail and wholesale prices before and after the reform at health institutions in rural Jiangxi Province. We undertook two cross-sectional surveys of prices of 39 medicines in November 2008 and May 2010, calculated inflation adjusted prices, and used the Wilcoxon signed-rank and rank-sum tests to examine price changes at different health institutions. Retail prices at pilot (P < 0.01) and nonpilot (P < 0.01) township health centers decreased significantly, whereas the declines at retail pharmacies (P = 0.57) and village clinics (P = 0.29) were insignificant. The decline at pilot township health centers was the largest, compared with other kinds of health institutions (P < 0.01). Retail prices of essential and non-essential medicines declined significantly at pilot facilities (P < 0.05); price drops for non-essential medicines occurred only at pilot facilities (P < 0.05). No significant decline of wholesale prices were found at pilot (P = 0.86) and nonpilot units (P = 0.18), retail pharmacies (P = 0.18), and village clinics (P = 0.20). The wholesale prices changes at pilot units before and after the reform were higher than at nonpilot public units (P < 0.05), retail pharmacies (P < 0.05), and village clinics (P < 0.05). While the NEMS zero-markup policy significantly reduced retail prices at pilot health institutions, the centralized bidding system was insufficient to lower wholesale prices. A drug price management system should be constructed to control medicine prices and a long-term price information system is needed to monitor price changes.

A service protocol for post-processing of medical images on the mobile device

NASA Astrophysics Data System (ADS)

He, Longjun; Ming, Xing; Xu, Lang; Liu, Qian

2014-03-01

With computing capability and display size growing, the mobile device has been used as a tool to help clinicians view patient information and medical images anywhere and anytime. It is uneasy and time-consuming for transferring medical images with large data size from picture archiving and communication system to mobile client, since the wireless network is unstable and limited by bandwidth. Besides, limited by computing capability, memory and power endurance, it is hard to provide a satisfactory quality of experience for radiologists to handle some complex post-processing of medical images on the mobile device, such as real-time direct interactive three-dimensional visualization. In this work, remote rendering technology is employed to implement the post-processing of medical images instead of local rendering, and a service protocol is developed to standardize the communication between the render server and mobile client. In order to make mobile devices with different platforms be able to access post-processing of medical images, the Extensible Markup Language is taken to describe this protocol, which contains four main parts: user authentication, medical image query/ retrieval, 2D post-processing (e.g. window leveling, pixel values obtained) and 3D post-processing (e.g. maximum intensity projection, multi-planar reconstruction, curved planar reformation and direct volume rendering). And then an instance is implemented to verify the protocol. This instance can support the mobile device access post-processing of medical image services on the render server via a client application or on the web page.

Low Income Life-Styles and the Consumption of Durable Goods: Implications for Consumer Educators

ERIC Educational Resources Information Center

Jolly, Desmond A.

1978-01-01

Low-income consumers badly need special purchasing skills, due to merchandising practices and greater markups for durable goods in low-income communities. The author discusses some of the ways in which these people are victimized, with implications for consumer education. (MF)

XBRL: Beyond Basic XML

ERIC Educational Resources Information Center

VanLengen, Craig Alan

2010-01-01

The Securities and Exchange Commission (SEC) has recently announced a proposal that will require all public companies to report their financial data in Extensible Business Reporting Language (XBRL). XBRL is an extension of Extensible Markup Language (XML). Moving to a standard reporting format makes it easier for organizations to report the…

Computer Literacy and Non-IS Majors

ERIC Educational Resources Information Center

Thomas, Jennifer D. E.; Blackwood, Martina

2010-01-01

This paper presents an investigation of non-Information Systems (IS) major's perceptions and performance when enrolled in a required introductory Computer Information Systems course. Students of various academic backgrounds were taught Excel, Hypertext Markup Language (HTML), JavaScript and computer literacy in a 14-week introductory course, in…

UCD IIRG at TREC 2012 Medical Track

DTIC Science & Technology

2012-11-01

documents. For ex- ample, the query “shakespeare.author” would en- sure that documents matching shakespeare in the au- thor field are returned. On the...corpus side, field extents are identified using XMLlike markup, e.g. <author> shakespeare </author>. 3 System Background & Motivation This section outlines

Global Situational Awareness with Free Tools

DTIC Science & Technology

2015-01-15

Client Technical Solutions • Software Engineering Measurement and Analysis • Architecture Practices • Product Line Practice • Team Software Process...multiple data sources • Snort (Snorby on Security Onion ) • Nagios • SharePoint RSS • Flow • Others • Leverage standard data formats • Keyhole Markup Language

XML in Libraries.

ERIC Educational Resources Information Center

Tennant, Roy, Ed.

This book presents examples of how libraries are using XML (eXtensible Markup Language) to solve problems, expand services, and improve systems. Part I contains papers on using XML in library catalog records: "Updating MARC Records with XMLMARC" (Kevin S. Clarke, Stanford University) and "Searching and Retrieving XML Records via the…

Applying Data Mining Principles to Library Data Collection.

ERIC Educational Resources Information Center

Guenther, Kim

2000-01-01

Explains how libraries can use data mining techniques for more effective data collection. Highlights include three phases: data selection and acquisition; data preparation and processing, including a discussion of the use of XML (extensible markup language); and data interpretation and integration, including database management systems. (LRW)

How Does XML Help Libraries?

ERIC Educational Resources Information Center

Banerjee, Kyle

2002-01-01

Discusses XML, how it has transformed the way information is managed and delivered, and its impact on libraries. Topics include how XML differs from other markup languages; the document object model (DOM); style sheets; practical applications for archival materials, interlibrary loans, digital collections, and MARC data; and future possibilities.…

Cornerstone: Foundational Models and Services for Integrated Battle Planning

DTIC Science & Technology

2012-06-01

We close with a summary of future planned research. 3 Cross-Domain Knowledge Representation One of the primary reasons behind the...mission data using Google Earth to display the results of a Keyhole Markup Language (KML) mission data translator. Finally, we successfully ran Thread 1

How to Assess Data Availability, Accessibility and Format for Risk Analysis?

PubMed

Humblet, M-F; Vandeputte, S; Mignot, C; Bellet, C; De Koeijer, A; Swanenburg, M; Afonso, A; Sanaa, M; Saegerman, C

2016-12-01

Risk assessments are mostly carried out based on available data, which do not reflect all data theoretically required by experts to answer them. This study aimed at developing a methodology to assess data availability, accessibility and format, based on a scoring system and focusing on two diseases: Venezuelan equine encephalomyelitis (VEE), still exotic to Europe, and alveolar echinococcosis, caused by Echinococcus multilocularis (EM), endemic in several Member States (MSs). After reviewing 36 opinions of the EFSA-AHAW Panel on risk assessment of animal health questions, a generic list of needed data was elaborated. The methodology consisted, first, in implementing a direct and an indirect survey to collect the data needed for both case studies: the direct survey consisted in a questionnaire sent to contact points of three European MSs (Belgium, France and the Netherlands), and the organization of a workshop gathering experts on both diseases. The indirect survey, focusing on the three MSs involved in the direct survey plus Spain, relied on web searches. Secondly, a scoring system with reference to data availability, accessibility and format was elaborated, to, finally, compare both diseases and data between MSs. The accessibility of data was generally related to their availability. Web searches resulted in more data available for VEE compared to EM, despite its current exotic status in the European Union. Hypertext markup language and portable document files were the main formats of available data. Data availability, accessibility and format should be improved for research scientists/assessors. The format of data plays a key role in the feasibility and rapidness of data management and analysis, through a prompt compilation, combination and aggregation in working databases. Harmonization of data collection process is encouraged, according to standardized procedures, to provide useful and reliable data, both at the national and the international levels for both animal and human health; it would allow assessing data gaps through comparative studies. The present methodology is a good way of assessing the relevance of data for risk assessment, as it allows integrating the uncertainty linked to the quality of data used. Such an approach could be described as transparent and traceable and should be performed systematically. © 2015 Blackwell Verlag GmbH.

Provenance through Time

NASA Astrophysics Data System (ADS)

Chandler, C. L.; Groman, R. C.; Shepherd, A.; Allison, M. D.; Kinkade, D.; Rauch, S.; Wiebe, P. H.; Glover, D. M.

2014-12-01

The ability to reproduce scientific results is a cornerstone of the scientific method, and access to the data upon which the results are based is essential to reproducibility. Access to the data alone is not enough though, and research communities have recognized the importance of metadata (data documentation) to enable discovery and data access, and facilitate interpretation and accurate reuse. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) was first funded in late 2006 by the National Science Foundation (NSF) Division of Ocean Sciences (OCE) Biology and Chemistry Sections to help ensure that data generated during NSF OCE funded research would be preserved and available for future use. The BCO-DMO was formed by combining the formerly independent data management offices of two marine research programs: the United States Joint Global Ocean Flux Study (US JGOFS) and the US GLOBal Ocean ECosystems Dynamics (US GLOBEC) program. Since the US JGOFS and US GLOBEC programs were both active (1990s) there have been significant changes in all aspects of the research data life cycle, and the staff at BCO-DMO has modified the way in which we manage data contributed to the office. The supporting documentation that describes each dataset was originally displayed as a human-readable text file retrievable via a Web browser. BCO-DMO still offers that form because our primary audience is marine researchers using Web browser clients; however we are seeing an increased demand to support machine client access. Metadata records from the BCO-DMO data system are now extracted and published out in a variety of formats. The system supports ISO 19115, FGDC, GCMD DIF, schema.org Dataset extension, formal publication with a DOI, and RDF with semantic markup including PROV-O, FOAF and more. In the 1990s, data documentation helped researchers locate data of interest and understand the provenance sufficiently to determine fitness for purpose. Today, providing data documentation in a machine interpretable form enables researchers to make more effective use of machine clients to discover and access data. This presentation will describe the challenges associated with and benefits realized from layering modern Semantic Web technologies on top of a legacy data system. http://bco-dmo.org/

Home Page, Sweet Home Page: Creating a Web Presence.

ERIC Educational Resources Information Center

Falcigno, Kathleen; Green, Tim

1995-01-01

Focuses primarily on design issues and practical concerns involved in creating World Wide Web documents for use within an organization. Concerns for those developing Web home pages are: learning HyperText Markup Language (HTML); defining customer group; allocating staff resources for maintenance of documents; providing feedback mechanism for…

42 CFR 405.515 - Reimbursement for clinical laboratory services billed by physicians.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 42 Public Health 2 2010-10-01 2010-10-01 false Reimbursement for clinical laboratory services... Criteria for Determining Reasonable Charges § 405.515 Reimbursement for clinical laboratory services billed... limitation on reimbursement for markups on clinical laboratory services billed by physicians. If a physician...

Using the Structured Product Labeling format to index versatile chemical data (ACS Spring meeting)

EPA Science Inventory

Structured Product Labeling (SPL) is a document markup standard approved by the Health Level Seven (HL7) standards organization and adopted by the FDA as a mechanism for exchanging product and facility information. Product information provided by companies in SPL format may be ac...

A Google Earth Grand Tour of the Terrestrial Planets

ERIC Educational Resources Information Center

De Paor, Declan; Coba, Filis; Burgin, Stephen

2016-01-01

Google Earth is a powerful instructional resource for geoscience education. We have extended the virtual globe to include all terrestrial planets. Downloadable Keyhole Markup Language (KML) files (Google Earth's scripting language) associated with this paper include lessons about Mercury, Venus, the Moon, and Mars. We created "grand…

Ontario Hydro and SGML.

ERIC Educational Resources Information Center

Rockley, Ann

1993-01-01

Describes how an analysis of Ontario Hydro's conversion of 20,000 pages of paper manuals to online documentation established the scope of the project, provided a set of design criteria, and recommended the use of Standard Generalized Markup Language to create the new documentation and the purchase of the "Dinatext" program to produce it.…

Teaching XBRL to Graduate Business Students: A Hands-On Approach

ERIC Educational Resources Information Center

Pinsker, Robert

2004-01-01

EXtensible Business Reporting Language (XBRL) is a non-proprietary, computer language that has many uses. Known primarily as the Extensible Markup Language (XML) for business reporting, XBRL allows entities to report their business information (i.e., financial statements, announcements, etc.) on the Internet and communicate with other entities'…

The Essen Learning Model--A Step towards a Representation of Learning Objectives.

ERIC Educational Resources Information Center

Bick, Markus; Pawlowski, Jan M.; Veith, Patrick

The importance of the Extensible Markup Language (XML) technology family in the field of Computer Assisted Learning (CAL) can not be denied. The Instructional Management Systems Project (IMS), for example, provides a learning resource XML binding specification. Considering this specification and other implementations using XML to represent…

78 FR 39023 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-28

... confirmations than larger firms because they effect fewer transactions. The Commission staff estimates the costs... regarding their securities transactions. This information includes: the date and time of the transaction... as well as mark-up and mark-down information. For transactions in debt securities, Rule 10b-10...

Assessing Place Location Knowledge Using a Virtual Globe

ERIC Educational Resources Information Center

Zhu, Liangfeng; Pan, Xin; Gao, Gongcheng

2016-01-01

Advances in the Google Earth virtual globe and the concomitant Keyhole Markup Language (KML) are providing educators with a convenient platform to cultivate and assess one's place location knowledge (PLK). This article presents a general framework and associated implementation methods for the online testing of PLK using Google Earth. The proposed…

The World-Wide Web and Mosaic: An Overview for Librarians.

ERIC Educational Resources Information Center

Morgan, Eric Lease

1994-01-01

Provides an overview of the Internet's World-Wide Web (Web), a hypertext system. Highlights include the client/server model; Uniform Resource Locator; examples of software; Web servers versus Gopher servers; HyperText Markup Language (HTML); converting files; Common Gateway Interface; organizing Web information; and the role of librarians in…

Searchers Net Treasure in Monterey.

ERIC Educational Resources Information Center

McDermott, Irene E.

1999-01-01

Reports on Web keyword searching, metadata, Dublin Core, Extensible Markup Language (XML), metasearch engines (metasearch engines search several Web indexes and/or directories and/or Usenet and/or specific Web sites), and the Year 2000 (Y2K) dilemma, all topics discussed at the second annual Internet Librarian Conference sponsored by Information…

Making Technology Work for Scholarship: Investing in the Data.

ERIC Educational Resources Information Center

Hockey, Susan

This paper examines issues related to how providers and consumers can make the best use of electronic information, focusing on the humanities. Topics include: new technology or old; electronic text and data formats; Standard Generalized Markup Language (SGML); text encoding initiative; encoded archival description (EAD); other applications of…

The Implications of Well-Formedness on Web-Based Educational Resources.

ERIC Educational Resources Information Center

Mohler, James L.

Within all institutions, Web developers are beginning to utilize technologies that make sites more than static information resources. Databases such as XML (Extensible Markup Language) and XSL (Extensible Stylesheet Language) are key technologies that promise to extend the Web beyond the "information storehouse" paradigm and provide…

Semantic-Aware Components and Services of ActiveMath

ERIC Educational Resources Information Center

Melis, Erica; Goguadze, Giorgi; Homik, Martin; Libbrecht, Paul; Ullrich, Carsten; Winterstein, Stefan

2006-01-01

ActiveMath is a complex web-based adaptive learning environment with a number of components and interactive learning tools. The basis for handling semantics of learning content is provided by its semantic (mathematics) content markup, which is additionally annotated with educational metadata. Several components, tools and external services can…

XML Schema Languages: Beyond DTD.

ERIC Educational Resources Information Center

Ioannides, Demetrios

2000-01-01

Discussion of XML (extensible markup language) and the traditional DTD (document type definition) format focuses on efforts of the World Wide Web Consortium's XML schema working group to develop a schema language to replace DTD that will be capable of defining the set of constraints of any possible data resource. (Contains 14 references.) (LRW)

Converting from XML to HDF-EOS

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A computer program recreates an HDF-EOS file from an Extensible Markup Language (XML) representation of the contents of that file. This program is one of two programs written to enable testing of the schemas described in the immediately preceding article to determine whether the schemas capture all details of HDF-EOS files.

17 CFR 1.33 - Monthly and confirmation statements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... customer— (i) The open contracts with prices at which acquired; (ii) The net unrealized profits or losses... transactions received from or disbursed to such customer, premiums charged and received, and realized profits... of the premium, as well as each mark-up thereon, if applicable, and all other commissions, costs...

Silicon Graphics' IRIS InSight: An SGML Success Story.

ERIC Educational Resources Information Center

Glushko, Robert J.; Kershner, Ken

1993-01-01

Offers a case history of the development of the Silicon Graphics "IRIS InSight" system, a system for viewing on-line documentation using Standard Generalized Markup Language. Notes that SGML's explicit encoding of structure and separation of structure and presentation make possible structure-based search, alternative structural views of…

A data model and database for high-resolution pathology analytical image informatics.

PubMed

Wang, Fusheng; Kong, Jun; Cooper, Lee; Pan, Tony; Kurc, Tahsin; Chen, Wenjin; Sharma, Ashish; Niedermayr, Cristobal; Oh, Tae W; Brat, Daniel; Farris, Alton B; Foran, David J; Saltz, Joel

2011-01-01

The systematic analysis of imaged pathology specimens often results in a vast amount of morphological information at both the cellular and sub-cellular scales. While microscopy scanners and computerized analysis are capable of capturing and analyzing data rapidly, microscopy image data remain underutilized in research and clinical settings. One major obstacle which tends to reduce wider adoption of these new technologies throughout the clinical and scientific communities is the challenge of managing, querying, and integrating the vast amounts of data resulting from the analysis of large digital pathology datasets. This paper presents a data model, which addresses these challenges, and demonstrates its implementation in a relational database system. This paper describes a data model, referred to as Pathology Analytic Imaging Standards (PAIS), and a database implementation, which are designed to support the data management and query requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines on whole-slide images and tissue microarrays (TMAs). (1) Development of a data model capable of efficiently representing and storing virtual slide related image, annotation, markup, and feature information. (2) Development of a database, based on the data model, capable of supporting queries for data retrieval based on analysis and image metadata, queries for comparison of results from different analyses, and spatial queries on segmented regions, features, and classified objects. The work described in this paper is motivated by the challenges associated with characterization of micro-scale features for comparative and correlative analyses involving whole-slides tissue images and TMAs. Technologies for digitizing tissues have advanced significantly in the past decade. Slide scanners are capable of producing high-magnification, high-resolution images from whole slides and TMAs within several minutes. Hence, it is becoming increasingly feasible for basic, clinical, and translational research studies to produce thousands of whole-slide images. Systematic analysis of these large datasets requires efficient data management support for representing and indexing results from hundreds of interrelated analyses generating very large volumes of quantifications such as shape and texture and of classifications of the quantified features. We have designed a data model and a database to address the data management requirements of detailed characterization of micro-anatomic morphology through many interrelated analysis pipelines. The data model represents virtual slide related image, annotation, markup and feature information. The database supports a wide range of metadata and spatial queries on images, annotations, markups, and features. We currently have three databases running on a Dell PowerEdge T410 server with CentOS 5.5 Linux operating system. The database server is IBM DB2 Enterprise Edition 9.7.2. The set of databases consists of 1) a TMA database containing image analysis results from 4740 cases of breast cancer, with 641 MB storage size; 2) an algorithm validation database, which stores markups and annotations from two segmentation algorithms and two parameter sets on 18 selected slides, with 66 GB storage size; and 3) an in silico brain tumor study database comprising results from 307 TCGA slides, with 365 GB storage size. The latter two databases also contain human-generated annotations and markups for regions and nuclei. Modeling and managing pathology image analysis results in a database provide immediate benefits on the value and usability of data in a research study. The database provides powerful query capabilities, which are otherwise difficult or cumbersome to support by other approaches such as programming languages. Standardized, semantic annotated data representation and interfaces also make it possible to more efficiently share image data and analysis results.

Semantic message oriented middleware for publish/subscribe networks

NASA Astrophysics Data System (ADS)

Li, Han; Jiang, Guofei

2004-09-01

The publish/subscribe paradigm of Message Oriented Middleware provides a loosely coupled communication model between distributed applications. Traditional publish/subscribe middleware uses keywords to match advertisements and subscriptions and does not support deep semantic matching. To this end, we designed and implemented a Semantic Message Oriented Middleware system to provide such capabilities for semantic description and matching. We adopted the DARPA Agent Markup Language and Ontology Inference Layer, a formal knowledge representation language for expressing sophisticated classifications and enabling automated inference, as the topic description language in our middleware system. A simple description logic inference system was implemented to handle the matching process between the subscriptions of subscribers and the advertisements of publishers. Moreover our middleware system also has a security architecture to support secure communication and user privilege control.

Real-time WebRTC-based design for a telepresence wheelchair.

PubMed

Van Kha Ly Ha; Rifai Chai; Nguyen, Hung T

2017-07-01

This paper presents a novel approach to the telepresence wheelchair system which is capable of real-time video communication and remote interaction. The investigation of this emerging technology aims at providing a low-cost and efficient way for assisted-living of people with disabilities. The proposed system has been designed and developed by deploying the JavaScript with Hyper Text Markup Language 5 (HTML5) and Web Real-time Communication (WebRTC) in which the adaptive rate control algorithm for video transmission is invoked. We conducted experiments in real-world environments, and the wheelchair was controlled from a distance using the Internet browser to compare with existing methods. The results show that the adaptively encoded video streaming rate matches the available bandwidth. The video streaming is high-quality with approximately 30 frames per second (fps) and round trip time less than 20 milliseconds (ms). These performance results confirm that the WebRTC approach is a potential method for developing a telepresence wheelchair system.

The New Frontier: Conquering the World Wide Web by Mule.

ERIC Educational Resources Information Center

Gresham, Morgan

1999-01-01

Examines effects of teaching hypertext markup language on students' perceptions of class goals in a networked composition classroom. Suggests sending documents via file transfer protocol by command line and viewing the Web with a textual browser shifted emphasis from writing to coding. Argues that helping students identify a balance between…

Internet Resources: Using Web Pages in Social Studies.

ERIC Educational Resources Information Center

Dale, Jack

1999-01-01

Contends that students in social studies classes can utilize Hypertext Markup Language (HTML) as a presentation and collaborative tool by developing websites. Presents two activities where students submitted webpages for country case studies and created a timeline for the French Revolution. Describes how to use HTML by discussing the various tags.…

Development and Evaluation of a Thai Learning System on the Web Using Natural Language Processing.

ERIC Educational Resources Information Center

Dansuwan, Suyada; Nishina, Kikuko; Akahori, Kanji; Shimizu, Yasutaka

2001-01-01

Describes the Thai Learning System, which is designed to help learners acquire the Thai word order system. The system facilitates the lessons on the Web using HyperText Markup Language and Perl programming, which interfaces with natural language processing by means of Prolog. (Author/VWL)

36 CFR 1235.50 - What specifications and standards for transfer apply to electronic records?

Code of Federal Regulations, 2012 CFR

2012-07-01

... electronic records in a format that is independent of specific hardware or software. Except as specified in... a request from NARA to provide the software to decompress the records. (3) Agencies interested in... organization. Acceptable transfer formats include the Geography Markup Language (GML) as defined by the Open...

Federated Process Framework in a Virtual Enterprise Using an Object-Oriented Database and Extensible Markup Language.

ERIC Educational Resources Information Center

Bae, Kyoung-Il; Kim, Jung-Hyun; Huh, Soon-Young

2003-01-01

Discusses process information sharing among participating organizations in a virtual enterprise and proposes a federated process framework and system architecture that provide a conceptual design for effective implementation of process information sharing supporting the autonomy and agility of the organizations. Develops the framework using an…

71 FR 66315 - Notice of Availability of Invention for Licensing; Government-Owned Invention

Federal Register 2010, 2011, 2012, 2013, 2014

2006-11-14

... Coating and Method of Formulator.//Navy Case No. 97,486: Processing Semantic Markups in Web Ontology... Rotating Clip.//Navy Case No. 97,886: Adding Semantic Support to Existing UDDI Infrastructure.//Navy Case..., Binding, and Integration of Non-Registered Geospatial Web Services.//Navy Case No. 98,094: Novel, Single...

Computer-Aided Assessment in Mechanics: Question Design and Test Evaluation

ERIC Educational Resources Information Center

Gill, M.; Greenhow, M.

2007-01-01

This article describes pedagogic issues in setting objective tests in mechanics using Question Mark Perception, coupled with MathML mathematics mark-up and the Scalable Vector Graphics (SVG) syntax for producing diagrams. The content of the questions (for a range of question types such as multi-choice, numerical input and variants such as…

Setting the Standard: XML on Campus.

ERIC Educational Resources Information Center

Rawlins, Mike

2001-01-01

Explains what XML (Extensible Markup Language) is; where to find it in a few years (everywhere from Web pages, to database management systems, to common campus applications); issues that will make XML somewhat of an experimental strategy in the near term; and the importance of decision-makers being abreast of XML trends in standards, tools…

Extensions to the Dynamic Aerospace Vehicle Exchange Markup Language

NASA Technical Reports Server (NTRS)

Brian, Geoffrey J.; Jackson, E. Bruce

2011-01-01

The Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML) is a syntactical language for exchanging flight vehicle dynamic model data. It provides a framework for encoding entire flight vehicle dynamic model data packages for exchange and/or long-term archiving. Version 2.0.1 of DAVE-ML provides much of the functionality envisioned for exchanging aerospace vehicle data; however, it is limited in only supporting scalar time-independent data. Additional functionality is required to support vector and matrix data, abstracting sub-system models, detailing dynamics system models (both discrete and continuous), and defining a dynamic data format (such as time sequenced data) for validation of dynamics system models and vehicle simulation packages. Extensions to DAVE-ML have been proposed to manage data as vectors and n-dimensional matrices, and record dynamic data in a compatible form. These capabilities will improve the clarity of data being exchanged, simplify the naming of parameters, and permit static and dynamic data to be stored using a common syntax within a single file; thereby enhancing the framework provided by DAVE-ML for exchanging entire flight vehicle dynamic simulation models.

A two-way interface between limited Systems Biology Markup Language and R.

PubMed

Radivoyevitch, Tomas

2004-12-07

Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures. The open source statistical programming environment R is widely used by biostatisticians involved in microarray analyses. An interface between SBML and R does not exist, though one might be useful to R users interested in SBML, and SBML users interested in R. A model structure that parallels SBML to a limited degree is defined in R. An interface between this structure and SBML is provided through two function definitions: write.SBML() which maps this R model structure to SBML level 2, and read.SBML() which maps a limited range of SBML level 2 files back to R. A published model of purine metabolism is provided in this SBML-like format and used to test the interface. The model reproduces published time course responses before and after its mapping through SBML. List infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted.

A two-way interface between limited Systems Biology Markup Language and R

PubMed Central

Radivoyevitch, Tomas

2004-01-01

Background Systems Biology Markup Language (SBML) is gaining broad usage as a standard for representing dynamical systems as data structures. The open source statistical programming environment R is widely used by biostatisticians involved in microarray analyses. An interface between SBML and R does not exist, though one might be useful to R users interested in SBML, and SBML users interested in R. Results A model structure that parallels SBML to a limited degree is defined in R. An interface between this structure and SBML is provided through two function definitions: write.SBML() which maps this R model structure to SBML level 2, and read.SBML() which maps a limited range of SBML level 2 files back to R. A published model of purine metabolism is provided in this SBML-like format and used to test the interface. The model reproduces published time course responses before and after its mapping through SBML. Conclusions List infrastructure preexisting in R makes it well-suited for manipulating SBML models. Further developments of this SBML-R interface seem to be warranted. PMID:15585059

Enhancement of CLAIM (clinical accounting information) for a localized Chinese version.

PubMed

Guo, Jinqiu; Takada, Akira; Niu, Tie; He, Miao; Tanaka, Koji; Sato, Junzo; Suzuki, Muneou; Takahashi, Kiwamu; Daimon, Hiroyuki; Suzuki, Toshiaki; Nakashima, Yusei; Araki, Kenji; Yoshihara, Hiroyuki

2005-10-01

CLinical Accounting InforMation (CLAIM) is a standard for the exchange of data between patient accounting systems and electronic medical record (EMR) systems. It uses eXtensible Markup Language (XML) as a meta-language and was developed in Japan. CLAIM is subordinate to the Medical Markup Language (MML) standard, which allows the exchange of medical data between different medical institutions. It has inherited the basic structure of MML 2.x and the current version, version 2.1, contains two modules and nine data definition tables. In China, no data exchange standard yet exists that links EMR systems to accounting systems. Taking advantage of CLAIM's flexibility, we created a localized Chinese version based on CLAIM 2.1. Since Chinese receipt systems differ from those of Japan, some information such as prescription formats, etc. are also different from those in Japan. Two CLAIM modules were re-engineered and six data definition tables were either added or redefined. The Chinese version of CLAIM takes local needs into account, and consequently it is now possible to transfer data between the patient accounting systems and EMR systems of Chinese medical institutions effectively.

Assessing the impact of privatizing public hospitals in three American states: implications for universal health coverage.

PubMed

Villa, Stefano; Kane, Nancy

2013-01-01

Many countries with universal health systems have relied primarily on publicly-owned hospitals to provide acute care services to covered populations; however, many policymakers have experimented with expansion of the private sector for what they hope will yield more cost-effective care. The study provides new insight into the effects of hospital privatization in three American states (California, Florida, and Massachusetts) in the period 1994 to 2003, focusing on three aspects: 1) profitability; 2) productivity and efficiency; and 3) benefits to the community (particularly, scope of services offered, price level, and impact on charity care). For each variable analyzed, we compared the 3-year mean values pre- and postconversion. Pre- and postconversion changes in hospitals' performance were then compared with a nonequivalent comparison group of American public hospitals. The results of our study indicate that following privatization, hospitals increased operating margins, reduced their length of stay, and enjoyed higher occupancy, but at some possible cost to access to care for their communities in terms of higher price markups and loss of beneficial but unprofitable services. Copyright © 2013 International Society for Pharmacoeconomics and Outcomes Research (ISPOR). Published by Elsevier Inc. All rights reserved.

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks.

PubMed

Balaur, Irina; Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J; Auffray, Charles

2017-04-01

The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/ . The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework . ibalaur@eisbm.org. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

PubMed Central

Mazein, Alexander; Saqi, Mansoor; Lysenko, Artem; Rawlings, Christopher J.; Auffray, Charles

2017-01-01

Abstract Summary: The goal of this work is to offer a computational framework for exploring data from the Recon2 human metabolic reconstruction model. Advanced user access features have been developed using the Neo4j graph database technology and this paper describes key features such as efficient management of the network data, examples of the network querying for addressing particular tasks, and how query results are converted back to the Systems Biology Markup Language (SBML) standard format. The Neo4j-based metabolic framework facilitates exploration of highly connected and comprehensive human metabolic data and identification of metabolic subnetworks of interest. A Java-based parser component has been developed to convert query results (available in the JSON format) into SBML and SIF formats in order to facilitate further results exploration, enhancement or network sharing. Availability and Implementation: The Neo4j-based metabolic framework is freely available from: https://diseaseknowledgebase.etriks.org/metabolic/browser/. The java code files developed for this work are available from the following url: https://github.com/ibalaur/MetabolicFramework. Contact: ibalaur@eisbm.org Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27993779

An enhanced security solution for electronic medical records based on AES hybrid technique with SOAP/XML and SHA-1.

PubMed

Kiah, M L Mat; Nabi, Mohamed S; Zaidan, B B; Zaidan, A A

2013-10-01

This study aims to provide security solutions for implementing electronic medical records (EMRs). E-Health organizations could utilize the proposed method and implement recommended solutions in medical/health systems. Majority of the required security features of EMRs were noted. The methods used were tested against each of these security features. In implementing the system, the combination that satisfied all of the security features of EMRs was selected. Secure implementation and management of EMRs facilitate the safeguarding of the confidentiality, integrity, and availability of e-health organization systems. Health practitioners, patients, and visitors can use the information system facilities safely and with confidence anytime and anywhere. After critically reviewing security and data transmission methods, a new hybrid method was proposed to be implemented on EMR systems. This method will enhance the robustness, security, and integration of EMR systems. The hybrid of simple object access protocol/extensible markup language (XML) with advanced encryption standard and secure hash algorithm version 1 has achieved the security requirements of an EMR system with the capability of integrating with other systems through the design of XML messages.

The future application of GML database in GIS

NASA Astrophysics Data System (ADS)

Deng, Yuejin; Cheng, Yushu; Jing, Lianwen

2006-10-01

In 2004, the Geography Markup Language (GML) Implementation Specification (version 3.1.1) was published by Open Geospatial Consortium, Inc. Now more and more applications in geospatial data sharing and interoperability depend on GML. The primary purpose of designing GML is for exchange and transportation of geo-information by standard modeling and encoding of geography phenomena. However, the problems of how to organize and access lots of GML data effectively arise in applications. The research on GML database focuses on these problems. The effective storage of GML data is a hot topic in GIS communities today. GML Database Management System (GDBMS) mainly deals with the problem of storage and management of GML data. Now two types of XML database, namely Native XML Database, and XML-Enabled Database are classified. Since GML is an application of the XML standard to geographic data, the XML database system can also be used for the management of GML. In this paper, we review the status of the art of XML database, including storage, index and query languages, management systems and so on, then move on to the GML database. At the end, the future prospect of GML database in GIS application is presented.

Geospatial Multi-Agency Coordination (GeoMAC) wildland fire perimeters, 2008

USGS Publications Warehouse

Walters, Sandra P.; Schneider, Norma J.; Guthrie, John D.

2011-01-01

The Geospatial Multi-Agency Coordination (GeoMAC) has been collecting and storing data on wildland fire perimeters since August 2000. The dataset presented via this U.S. Geological Survey Data Series product contains the GeoMAC wildland fire perimeter data for the calendar year 2008, which are based upon input from incident intelligence sources, Global Positioning System (GPS) data, and infrared (IR) imagery. Wildland fire perimeter data are obtained from the incidents, evaluated for completeness and accuracy, and processed to reflect consistent field names and attributes. After a quality check, the perimeters are loaded to GeoMAC databases, which support the GeoMAC Web application for access by wildland fire managers and the public. The wildland fire perimeters are viewed through the Web application. The data are subsequently archived according to year and state and are made available for downloading through the Internet in shapefile and Keyhole Markup Language (KML) format. These wildland fire perimeter data are also retained for historical, planning, and research purposes. The datasets that pertain to this report can be found on the Rocky Mountain Geographic Science Center HTTP site at http://rmgsc.cr.usgs.gov/outgoing/GeoMAC/historic_fire_data/. The links are also provided on the sidebar.

Word add-in for ontology recognition: semantic enrichment of scientific literature

PubMed Central

2010-01-01

Background In the current era of scientific research, efficient communication of information is paramount. As such, the nature of scholarly and scientific communication is changing; cyberinfrastructure is now absolutely necessary and new media are allowing information and knowledge to be more interactive and immediate. One approach to making knowledge more accessible is the addition of machine-readable semantic data to scholarly articles. Results The Word add-in presented here will assist authors in this effort by automatically recognizing and highlighting words or phrases that are likely information-rich, allowing authors to associate semantic data with those words or phrases, and to embed that data in the document as XML. The add-in and source code are publicly available at http://www.codeplex.com/UCSDBioLit. Conclusions The Word add-in for ontology term recognition makes it possible for an author to add semantic data to a document as it is being written and it encodes these data using XML tags that are effectively a standard in life sciences literature. Allowing authors to mark-up their own work will help increase the amount and quality of machine-readable literature metadata. PMID:20181245

Essays in market power mitigation and supply function equilibrium

NASA Astrophysics Data System (ADS)

Subramainam, Thiagarajah Natchie

Market power mitigation has been an integral part of wholesale electricity markets since deregulation. In wholesale electricity markets, different regions in the US take different approaches to regulating market power. While the exercise of market power has received considerable attention in the literature, the issue of market power mitigation has attracted scant attention. In the first chapter, I examine the market power mitigation rules used in New York ISO (Independent System Operator) and California ISO (CAISO) with respect to day-ahead and real-time energy markets. I test whether markups associated with New York in-city generators would be lower with an alternative approach to mitigation, the CAISO approach. Results indicate the difference in markups between these two mitigation rules is driven by the shape of residual demand curves for suppliers. Analysis of residual demand curves faced by New York in-city suppliers show similar markups under both mitigation rules when no one supplier is necessary to meet the demand (i.e., when no supplier is pivotal). However, when some supplier is crucial for the market to clear, the mitigation rule adopted by the NYISO consistently leads to higher markups than would the CAISO rule. This result suggest that market power episodes in New York is confined to periods where some supplier is pivotal. As a result, I find that applying the CAISOs' mitigation rules to the New York market could lower wholesale electricity prices by 18%. The second chapter of my dissertation focuses on supply function equilibrium. In power markets, suppliers submit offer curves in auctions, indicating their willingness to supply at different price levels. Although firms are allowed to submit different offer curves for different time periods, surprisingly many firms stick to a single offer curve for the entire day. This essentially means that firms are submitting a single offer curve for multiple demand realizations. A suitable framework to analyze such oligopolistic competition between power market suppliers is supply function equilibrium models. Using detailed bidding data, I develop equilibrium in supply functions by restricting supplier offers to a class of supply functions. By collating equilibrium supply functions corresponding to different realizations of demand, I obtain a single optimal supply function for the entire day. Then I compare the resulting supply function with actual day-ahead offers in New York. In addition to supply function equilibrium, I also develop a conservative bidding approach in which each firm assumes that rivals bid at marginal costs. Results show that the supply functions derived from equilibrium bidding model in this paper is not consistent with actual bidding in New York. This result is mainly driven by the class of supply functions used in this study to generate the equilibrium. Further, actual offers do not resemble offers generated by the conservative bidding algorithm.

ElVisML: an open data format for the exchange and storage of electrophysiological data in ophthalmology.

PubMed

Strasser, Torsten; Peters, Tobias; Jägle, Herbert; Zrenner, Eberhart

2018-02-01

The ISCEV standards and recommendations for electrophysiological recordings in ophthalmology define a set of protocols with stimulus parameters, acquisition settings, and recording conditions, to unify the data and enable comparability of results across centers. Up to now, however, there are no standards to define the storage and exchange of such electrophysiological recordings. The aim of this study was to develop an open standard data format for the exchange and storage of visual electrophysiological data (ElVisML). We first surveyed existing data formats for biomedical signals and examined their suitability for electrophysiological data in ophthalmology. We then compared the suitability of text-based and binary formats, as well as encoding in Extensible Markup Language (XML) and character/comma-separated values. The results of the methodological consideration led to the development of ElVisML with an XML-encoded text-based format. This allows referential integrity, extensibility, the storing of accompanying units, as well as ensuring confidentiality and integrity of the data. A visualization of ElVisML documents (ElVisWeb) has additionally been developed, which facilitates the exchange of recordings on mailing lists and allows open access to data along with published articles. The open data format ElVisML ensures the quality, validity, and integrity of electrophysiological data transmission and storage as well as providing manufacturer-independent access and long-term archiving in a future-proof format. Standardization of the format of such neurophysiology data would promote the development of new techniques and open software for the use of neurophysiological data in both clinic and research.

OnEarth: An Open Source Solution for Efficiently Serving High-Resolution Mapped Image Products

NASA Astrophysics Data System (ADS)

Thompson, C. K.; Plesea, L.; Hall, J. R.; Roberts, J. T.; Cechini, M. F.; Schmaltz, J. E.; Alarcon, C.; Huang, T.; McGann, J. M.; Chang, G.; Boller, R. A.; Ilavajhala, S.; Murphy, K. J.; Bingham, A. W.

2013-12-01

This presentation introduces OnEarth, a server side software package originally developed at the Jet Propulsion Laboratory (JPL), that facilitates network-based, minimum-latency geolocated image access independent of image size or spatial resolution. The key component in this package is the Meta Raster Format (MRF), a specialized raster file extension to the Geospatial Data Abstraction Library (GDAL) consisting of an internal indexed pyramid of image tiles. Imagery to be served is converted to the MRF format and made accessible online via an expandable set of server modules handling requests in several common protocols, including the Open Geospatial Consortium (OGC) compliant Web Map Tile Service (WMTS) as well as Tiled WMS and Keyhole Markup Language (KML). OnEarth has recently transitioned to open source status and is maintained and actively developed as part of GIBS (Global Imagery Browse Services), a collaborative project between JPL and Goddard Space Flight Center (GSFC). The primary function of GIBS is to enhance and streamline the data discovery process and to support near real-time (NRT) applications via the expeditious ingestion and serving of full-resolution imagery representing science products from across the NASA Earth Science spectrum. Open source software solutions are leveraged where possible in order to utilize existing available technologies, reduce development time, and enlist wider community participation. We will discuss some of the factors and decision points in transitioning OnEarth to a suitable open source paradigm, including repository and licensing agreement decision points, institutional hurdles, and perceived benefits. We will also provide examples illustrating how OnEarth is integrated within GIBS and other applications.

A Courseware to Script Animated Pedagogical Agents in Instructional Material for Elementary Students in English Education

ERIC Educational Resources Information Center

Hong, Zeng-Wei; Chen, Yen-Lin; Lan, Chien-Ho

2014-01-01

Animated agents are virtual characters who demonstrate facial expressions, gestures, movements, and speech to facilitate students' engagement in the learning environment. Our research developed a courseware that supports a XML-based markup language and an authoring tool for teachers to script animated pedagogical agents in teaching materials. The…

Today's Authoring Tools for Tomorrow's Semantic Web.

ERIC Educational Resources Information Center

Dingley, Andy; Shabajee, Paul

This paper reports on the development of a prototype authoring tool developed as part of on-going research around the needs of the ARKive project. The project holds text, rich-media and descriptions of factual statements about bio-diversity and conservation information. A key user community is that of school age children, requiring the mark-up of…

Utilization of Forward Error Correction (FEC) Techniques With Extensible Markup Language (XML) Schema-Based Binary Compression (XSBC) Technology

DTIC Science & Technology

2004-12-01

NY 7. Erik Chaum NUWC Newport, RI 8. David Bellino NPRI Newport, RI 9. Dick Nadolink NUWC Newport, RI 10. VADM Roger Bacon (Ret...Science Advisor Pearl Harbor, HI 16. LT Andrew Hurvitz, USN FNMOC Monterey, CA 17. ENS Darin Keeter, USN FNMOC Monterey, CA 18. CAPT David

Adding XML to the MIS Curriculum: Lessons from the Classroom

ERIC Educational Resources Information Center

Wagner, William P.; Pant, Vik; Hilken, Ralph

2008-01-01

eXtensible Markup Language (XML) is a new technology that is currently being extolled by many industry experts and software vendors. Potentially it represents a platform independent language for sharing information over networks in a way that is much more seamless than with previous technologies. It is extensible in that XML serves as a "meta"…

Web-Writing in One Minute--and Beyond.

ERIC Educational Resources Information Center

Hughes, Kenneth

This paper describes how librarians can teach patrons the basics of hypertext markup language (HTML) so that patrons can publish their own homepages on the World Wide Web. With proper use of handouts and practice time afterwards, the three basics of HTML can be conveyed in only 60 seconds. The three basics are: the basic template of Web tags, used…

Online Survey, Enrollment, and Examination: Special Internet Applications in Teacher Education.

ERIC Educational Resources Information Center

Tu, Jho-Ju; Babione, Carolyn; Chen, Hsin-Chu

The Teachers College at Emporia State University in Kansas is now utilizing World Wide Web technology for automating the application procedure for student teaching. The general concepts and some of the key terms that are important for understanding the process involved in this project include: a client-server model, HyperText Markup Language,…

Nassi-Schneiderman Diagram in HTML Based on AML

ERIC Educational Resources Information Center

Menyhárt, László

2013-01-01

In an earlier work I defined an extension of XML called Algorithm Markup Language (AML) for easy and understandable coding in an IDE which supports XML editing (e.g. NetBeans). The AML extension contains annotations and native language (English or Hungarian) tag names used when coding our algorithm. This paper presents a drawing tool with which…

The Ontological Perspectives of the Semantic Web and the Metadata Harvesting Protocol: Applications of Metadata for Improving Web Search.

ERIC Educational Resources Information Center

Fast, Karl V.; Campbell, D. Grant

2001-01-01

Compares the implied ontological frameworks of the Open Archives Initiative Protocol for Metadata Harvesting and the World Wide Web Consortium's Semantic Web. Discusses current search engine technology, semantic markup, indexing principles of special libraries and online databases, and componentization and the distinction between data and…

Gear Up Your Research Guides with the Emerging OPML Codes

ERIC Educational Resources Information Center

Wilcox, Kimberley

2006-01-01

Outline Processor Markup Language (OPML) is an emerging format that allows for the creation of customized research packages to push to patrons. It is a way to gather collections of Web resources (links, RSS feeds, multimedia files), organize them as outlines, and publish them in a format that others can share and even subscribe to. In this…

Contextual Markup and Mining in Digital Games for Science Learning: Connecting Player Behaviors to Learning Goals

ERIC Educational Resources Information Center

Kinnebrew John S.; Killingsworth, Stephen S.; Clark, Douglas B.; Biswas, Gautam; Sengupta, Pratim; Minstrell, James; Martinez-Garza, Mario; Krinks, Kara

2017-01-01

Digital games can make unique and powerful contributions to K-12 science education, but much of that potential remains unrealized. Research evaluating games for learning still relies primarily on pre- and post-test data, which limits possible insights into more complex interactions between game design features, gameplay, and formal assessment.…

Archive of Boomer and Chirp Seismic Reflection Data Collected During USGS Cruise 01RCE02, Southern Louisiana, April and May 2001

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Flocks, James G.; Wiese, Dana S.

2003-01-01

In April and May of 2001, the U.S. Geological Survey conducted a geophysical study of the Mississippi River Delta, Atchafalaya River Delta, and Shell Island Pass in southern Louisiana. This study was part of a larger USGS River Contaminant Evaluation (RCE) Project. This disc serves as an archive of unprocessed digital seismic reflection data, trackline navigation files, shotpoint navigation maps, observers' logbooks, GIS information, and formal Federal Geographic Data Committee (FGDC) metadata. In addition, a filtered and gained digital GIF-formatted image of each seismic profile is provided. For your convenience, a list of acronyms and abbreviations frequently used in this report has also been provided. This DVD (Digital Versatile Disc) document is readable on any computing platform that has standard DVD driver software installed. Documentation on this DVD was produced using Hyper Text Markup Language (HTML) utilized by the World Wide Web (WWW) and allows the user to access the information by using a web browser (i.e. Netscape or Internet Explorer). To access the information contained on this disc, open the file 'index.htm' located at the top level of the disc using your web browser. This report also contains WWW links to USGS collaborators and other agencies. These links are only accessible if access to the internet is available while viewing the DVD. The archived boomer and chirp seismic reflection data are in standard Society of Exploration Geophysicists (SEG) SEG-Y format (Barry et al., 1975) and may be downloaded for processing with public domain software such as Seismic Unix (SU), currently located at http://www.cwp.mines.edu/cwpcodes. Examples of SU processing scripts are provided in the boom.tar and chirp.tar files located in the SU subfolder of the SOFTWARE folder located at the top level of this DVD. In-house (USGS) DOS and Microsoft Windows compatible software for viewing SEG-Y headers - DUMPSEGY.EXE (Zilhman, 1992) - is provided in the USGS subfolder of the SOFTWARE folder. Processed profile images, shotpoint navigation maps, logbooks, and formal metadata may be viewed with your web browser.

An editor for pathway drawing and data visualization in the Biopathways Workbench.

PubMed

Byrnes, Robert W; Cotter, Dawn; Maer, Andreia; Li, Joshua; Nadeau, David; Subramaniam, Shankar

2009-10-02

Pathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface. The Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server http://www.lipidmaps.org. Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system. Inclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

Teaching and Learning Communities through Online Annotation

NASA Astrophysics Data System (ADS)

van der Pluijm, B.

2016-12-01

What do colleagues do with your assigned textbook? What they say or think about the material? Want students to be more engaged in their learning experience? If so, online materials that complement standard lecture format provide new opportunity through managed, online group annotation that leverages the ubiquity of internet access, while personalizing learning. The concept is illustrated with the new online textbook "Processes in Structural Geology and Tectonics", by Ben van der Pluijm and Stephen Marshak, which offers a platform for sharing of experiences, supplementary materials and approaches, including readings, mathematical applications, exercises, challenge questions, quizzes, alternative explanations, and more. The annotation framework used is Hypothes.is, which offers a free, open platform markup environment for annotation of websites and PDF postings. The annotations can be public, grouped or individualized, as desired, including export access and download of annotations. A teacher group, hosted by a moderator/owner, limits access to members of a user group of teachers, so that its members can use, copy or transcribe annotations for their own lesson material. Likewise, an instructor can host a student group that encourages sharing of observations, questions and answers among students and instructor. Also, the instructor can create one or more closed groups that offers study help and hints to students. Options galore, all of which aim to engage students and to promote greater responsibility for their learning experience. Beyond new capacity, the ability to analyze student annotation supports individual learners and their needs. For example, student notes can be analyzed for key phrases and concepts, and identify misunderstandings, omissions and problems. Also, example annotations can be shared to enhance notetaking skills and to help with studying. Lastly, online annotation allows active application to lecture posted slides, supporting real-time notetaking during lecture presentation. Sharing of experiences and practices of annotation could benefit teachers and learners alike, and does not require complicated software, coding skills or special hardware environments.

Next Generation Landsat Products Delivered Using Virtual Globes and OGC Standard Services

NASA Astrophysics Data System (ADS)

Neiers, M.; Dwyer, J.; Neiers, S.

2008-12-01

The Landsat Data Continuity Mission (LDCM) is the next in the series of Landsat satellite missions and is tasked with the objective of delivering data acquired by the Operational Land Imager (OLI). The OLI instrument will provide data continuity to over 30 years of global multispectral data collected by the Landsat series of satellites. The U.S. Geological Survey Earth Resources Observation and Science (USGS EROS) Center has responsibility for the development and operation of the LDCM ground system. One of the mission objectives of the LDCM is to distribute OLI data products electronically over the Internet to the general public on a nondiscriminatory basis and at no cost. To ensure the user community and general public can easily access LDCM data from multiple clients, the User Portal Element (UPE) of the LDCM ground system will use OGC standards and services such as Keyhole Markup Language (KML), Web Map Service (WMS), Web Coverage Service (WCS), and Geographic encoding of Really Simple Syndication (GeoRSS) feeds for both access to and delivery of LDCM products. The USGS has developed and tested the capabilities of several successful UPE prototypes for delivery of Landsat metadata, full resolution browse, and orthorectified (L1T) products from clients such as Google Earth, Google Maps, ESRI ArcGIS Explorer, and Microsoft's Virtual Earth. Prototyping efforts included the following services: using virtual globes to search the historical Landsat archive by dynamic generation of KML; notification of and access to new Landsat acquisitions and L1T downloads from GeoRSS feeds; Google indexing of KML files containing links to full resolution browse and data downloads; WMS delivery of reduced resolution browse, full resolution browse, and cloud mask overlays; and custom data downloads using WCS clients. These various prototypes will be demonstrated and LDCM service implementation plans will be discussed during this session.

Phased development of a web-based PACS viewer

NASA Astrophysics Data System (ADS)

Gidron, Yoad; Shani, Uri; Shifrin, Mark

2000-05-01

The Web browser is an excellent environment for the rapid development of an effective and inexpensive PACS viewer. In this paper we will share our experience in developing a browser-based viewer, from the inception and prototype stages to its current state of maturity. There are many operational advantages to a browser-based viewer, even when native viewers already exist in the system (with multiple and/or high resolution screens): (1) It can be used on existing personal workstations throughout the hospital. (2) It is easy to make the service available from physician's homes. (3) The viewer is extremely portable and platform independent. There is a wide variety of means available for implementing the browser- based viewer. Each file sent to the client by the server can perform some end-user or client/server interaction. These means range from HTML (for HyperText Markup Language) files, through Java Script, to Java applets. Some data types may also invoke plug-in code in the client, although this would reduce the portability of the viewer, it would provide the needed efficiency in critical places. On the server side the range of means is also very rich: (1) A set of files: html, Java Script, Java applets, etc. (2) Extensions of the server via cgi-bin programs, (3) Extensions of the server via servlets, (4) Any other helper application residing and working with the server to access the DICOM archive. The viewer architecture consists of two basic parts: The first part performs query and navigation through the DICOM archive image folders. The second part does the image access and display. While the first part deals with low data traffic, it involves many database transactions. The second part is simple as far as access transactions are concerned, but requires much more data traffic and display functions. Our web-based viewer has gone through three development stages characterized by the complexity of the means and tools employed on both client and server sides.

Post-Nor'Ida coastal oblique aerial photographs collected from Ocean City, Maryland, to Hatteras, North Carolina, December 4, 2009

USGS Publications Warehouse

Morgan, Karen L. M.; Krohn, M. Dennis; Guy, Kristy K.

2015-01-01

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files.

Baseline Coastal Oblique Aerial Photographs Collected from Navarre Beach, Florida, to Breton Island, Louisiana, September 1, 2014

USGS Publications Warehouse

Morgan, Karen L. M.

2015-08-31

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files.

Evaluating the Informative Quality of Documents in SGML Format from Judgements by Means of Fuzzy Linguistic Techniques Based on Computing with Words.

ERIC Educational Resources Information Center

Herrera-Viedma, Enrique; Peis, Eduardo

2003-01-01

Presents a fuzzy evaluation method of SGML documents based on computing with words. Topics include filtering the amount of information available on the Web to assist users in their search processes; document type definitions; linguistic modeling; user-system interaction; and use with XML and other markup languages. (Author/LRW)

Benefits and Pitfalls of Using HTML as a CD-ROM Development Tool.

ERIC Educational Resources Information Center

Misanchuk, Earl R.; Schwier, Richard A.

The hypertext markup language (HTML) used to develop pages for the world wide web also has potential for use in creating some types of multimedia instruction destined for CD-ROMs. After providing a brief overview of HTML, this document presents pros and cons relevant to CD-ROM production. HTML can offer compatibility to both Windows and Macintosh…

75 FR 71479 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-23

... Series (Order Audit Trail System); NASD Rule 2320 (Best Execution and Interpositioning); NASD Rule 2400 Series (Commissions, Mark-Ups and Charges); NASD IM-2110-2 (Trading Ahead of Customer Limit Order); and... prepared to purchase or sell at that price and under the conditions stated at the time of the offer to buy...

75 FR 52562 - Self-Regulatory Organizations; Financial Industry Regulatory Authority, Inc.; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-26

... NMS (National Market System), 17 CFR 242.600-242.612; FINRA Rule 7400 Series (Order Audit Trail System... 08-80 (December 2008)]; NASD Rule 2400 Series (Commissions, Mark-Ups and Charges); NASD IM-2110-2... as are stated at the time of such offer to buy or sell. Moreover, the use of fictitious transactions...

Gopher Is No Longer Just a Rodent: Using Gopher and World Wide Web in Composition Studies.

ERIC Educational Resources Information Center

Krause, Steve

Gopher and World Wide Web (WWW) are two useful Internet technologies for the composition and rhetoric classroom. Gopher software makes available a wide variety of text-based information in the Internet. A Gopher at Bowling Green State University offers many types of information. The World Wide Web, using a fairly simple markup language, is also…

Using XML to Separate Content from the Presentation Software in eLearning Applications

ERIC Educational Resources Information Center

Merrill, Paul F.

2005-01-01

This paper has shown how XML (extensible Markup Language) can be used to mark up content. Since XML documents, with meaningful tags, can be interpreted easily by humans as well as computers, they are ideal for the interchange of information. Because XML tags can be defined by an individual or organization, XML documents have proven useful in a…

The Biological Connection Markup Language: a SBGN-compliant format for visualization, filtering and analysis of biological pathways

PubMed Central

Rizzetto, Lisa; Guedez, Damariz Rivero; Donato, Michele; Romualdi, Chiara; Draghici, Sorin; Cavalieri, Duccio

2011-01-01

Motivation: Many models and analysis of signaling pathways have been proposed. However, neither of them takes into account that a biological pathway is not a fixed system, but instead it depends on the organism, tissue and cell type as well as on physiological, pathological and experimental conditions. Results: The Biological Connection Markup Language (BCML) is a format to describe, annotate and visualize pathways. BCML is able to store multiple information, permitting a selective view of the pathway as it exists and/or behave in specific organisms, tissues and cells. Furthermore, BCML can be automatically converted into data formats suitable for analysis and into a fully SBGN-compliant graphical representation, making it an important tool that can be used by both computational biologists and ‘wet lab’ scientists. Availability and implementation: The XML schema and the BCML software suite are freely available under the LGPL for download at http://bcml.dc-atlas.net. They are implemented in Java and supported on MS Windows, Linux and OS X. Contact: duccio.cavalieri@unifi.it; sorin@wayne.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21653523

High medicine prices and poor affordability.

PubMed

Suh, Guk-Hee

2011-07-01

In developing countries, most people who need medicines have to pay for them out of their own pockets. This review focuses on publications to explore the affordability gap of medicines and ways to close it. Cardiovascular medicines were unaffordable in low-income to middle-income countries, whereas dementia medicines were only affordable in regions of wealth. In urban Mozambique, local mark-ups are up to two-thirds of final price in private pharmacies, whereas some governments consistently paid higher prices above the international reference prices to procure a number of medicines. Generics competition from India made an originator brand manufacturer of a AIDS drug willing to supply the drug at a cheaper rate to poorer countries, whereas a Brazilian national program to produce nonprofit generics against protected patent of originator brand products to provide free AIDS drugs had cut the number of people dying by half and hospitalization by 80%, which saved about half a billion US dollars, making the program almost fund itself. Although lowering the manufacturer's price has a greater effect on the cost, policies to eliminate duties and taxes on medicines and regulate mark-ups are practical strategies to avoid excessive add-on costs.

Telescope networking and user support via Remote Telescope Markup Language

NASA Astrophysics Data System (ADS)

Hessman, Frederic V.; Pennypacker, Carlton R.; Romero-Colmenero, Encarni; Tuparev, Georg

2004-09-01

Remote Telescope Markup Language (RTML) is an XML-based interface/document format designed to facilitate the exchange of astronomical observing requests and results between investigators and observatories as well as within networks of observatories. While originally created to support simple imaging telescope requests (Versions 1.0-2.1), RTML Version 3.0 now supports a wide range of applications, from request preparation, exposure calculation, spectroscopy, and observation reports to remote telescope scheduling, target-of-opportunity observations and telescope network administration. The elegance of RTML is that all of this is made possible using a public XML Schema which provides a general-purpose, easily parsed, and syntax-checked medium for the exchange of astronomical and user information while not restricting or otherwise constraining the use of the information at either end. Thus, RTML can be used to connect heterogeneous systems and their users without requiring major changes in existing local resources and procedures. Projects as very different as a number of advanced amateur observatories, the global Hands-On Universe project, the MONET network (robotic imaging), the STELLA consortium (robotic spectroscopy), and the 11-m Southern African Large Telescope are now using or intending to use RTML in various forms and for various purposes.

Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

PubMed

Watanabe, Leandro; Myers, Chris J

2016-08-19

The Systems Biology Markup Language (SBML) has been widely used for modeling biological systems. Although SBML has been successful in representing a wide variety of biochemical models, the core standard lacks the structure for representing large complex regular systems in a standard way, such as whole-cell and cellular population models. These models require a large number of variables to represent certain aspects of these types of models, such as the chromosome in the whole-cell model and the many identical cell models in a cellular population. While SBML core is not designed to handle these types of models efficiently, the proposed SBML arrays package can represent such regular structures more easily. However, in order to take full advantage of the package, analysis needs to be aware of the arrays structure. When expanding the array constructs within a model, some of the advantages of using arrays are lost. This paper describes a more efficient way to simulate arrayed models. To illustrate the proposed method, this paper uses a population of repressilator and genetic toggle switch circuits as examples. Results show that there are memory benefits using this approach with a modest cost in runtime.

Using SpaceClaimTD Direct for Modeling Components with Complex Geometries for the Thermal Desktop-Based Advanced Stirling Radioisotope Generator Model

NASA Technical Reports Server (NTRS)

Fabanich, William A., Jr.

2014-01-01

SpaceClaim/TD Direct has been used extensively in the development of the Advanced Stirling Radioisotope Generator (ASRG) thermal model. This paper outlines the workflow for that aspect of the task and includes proposed best practices and lessons learned. The ASRG thermal model was developed to predict component temperatures and power output and to provide insight into the prime contractor's thermal modeling efforts. The insulation blocks, heat collectors, and cold side adapter flanges (CSAFs) were modeled with this approach. The model was constructed using mostly TD finite difference (FD) surfaces/solids. However, some complex geometry could not be reproduced with TD primitives while maintaining the desired degree of geometric fidelity. Using SpaceClaim permitted the import of original CAD files and enabled the defeaturing/repair of those geometries. TD Direct (a SpaceClaim add-on from CRTech) adds features that allowed the "mark-up" of that geometry. These so-called "mark-ups" control how finite element (FE) meshes are to be generated through the "tagging" of features (e.g. edges, solids, surfaces). These tags represent parameters that include: submodels, material properties, material orienters, optical properties, and radiation analysis groups. TD aliases were used for most tags to allow analysis to be performed with a variety of parameter values. "Domain-tags" were also attached to individual and groups of surfaces and solids to allow them to be used later within TD to populate objects like, for example, heaters and contactors. These tools allow the user to make changes to the geometry in SpaceClaim and then easily synchronize the mesh in TD without having to redefine the objects each time as one would if using TDMesher. The use of SpaceClaim/TD Direct helps simplify the process for importing existing geometries and in the creation of high fidelity FE meshes to represent complex parts. It also saves time and effort in the subsequent analysis.

Using SpaceClaim/TD Direct for Modeling Components with Complex Geometries for the Thermal Desktop-Based Advanced Stirling Radioisotope Generator Model

NASA Technical Reports Server (NTRS)

Fabanich, William

2014-01-01

SpaceClaim/TD Direct has been used extensively in the development of the Advanced Stirling Radioisotope Generator (ASRG) thermal model. This paper outlines the workflow for that aspect of the task and includes proposed best practices and lessons learned. The ASRG thermal model was developed to predict component temperatures and power output and to provide insight into the prime contractors thermal modeling efforts. The insulation blocks, heat collectors, and cold side adapter flanges (CSAFs) were modeled with this approach. The model was constructed using mostly TD finite difference (FD) surfaces solids. However, some complex geometry could not be reproduced with TD primitives while maintaining the desired degree of geometric fidelity. Using SpaceClaim permitted the import of original CAD files and enabled the defeaturing repair of those geometries. TD Direct (a SpaceClaim add-on from CRTech) adds features that allowed the mark-up of that geometry. These so-called mark-ups control how finite element (FE) meshes were generated and allowed the tagging of features (e.g. edges, solids, surfaces). These tags represent parameters that include: submodels, material properties, material orienters, optical properties, and radiation analysis groups. TD aliases were used for most tags to allow analysis to be performed with a variety of parameter values. Domain-tags were also attached to individual and groups of surfaces and solids to allow them to be used later within TD to populate objects like, for example, heaters and contactors. These tools allow the user to make changes to the geometry in SpaceClaim and then easily synchronize the mesh in TD without having to redefine these objects each time as one would if using TD Mesher.The use of SpaceClaim/TD Direct has helped simplify the process for importing existing geometries and in the creation of high fidelity FE meshes to represent complex parts. It has also saved time and effort in the subsequent analysis.

Virtual Sensor Web Architecture

NASA Astrophysics Data System (ADS)

Bose, P.; Zimdars, A.; Hurlburt, N.; Doug, S.

2006-12-01

NASA envisions the development of smart sensor webs, intelligent and integrated observation network that harness distributed sensing assets, their associated continuous and complex data sets, and predictive observation processing mechanisms for timely, collaborative hazard mitigation and enhanced science productivity and reliability. This paper presents Virtual Sensor Web Infrastructure for Collaborative Science (VSICS) Architecture for sustained coordination of (numerical and distributed) model-based processing, closed-loop resource allocation, and observation planning. VSICS's key ideas include i) rich descriptions of sensors as services based on semantic markup languages like OWL and SensorML; ii) service-oriented workflow composition and repair for simple and ensemble models; event-driven workflow execution based on event-based and distributed workflow management mechanisms; and iii) development of autonomous model interaction management capabilities providing closed-loop control of collection resources driven by competing targeted observation needs. We present results from initial work on collaborative science processing involving distributed services (COSEC framework) that is being extended to create VSICS.

Future perspectives - proposal for Oxford Physiome Project.

PubMed

Oku, Yoshitaka

2010-01-01

The Physiome Project is an effort to understand living creatures using "analysis by synthesis" strategy, i.e., by reproducing their behaviors. In order to achieve its goal, sharing developed models between different computer languages and application programs to incorporate into integrated models is critical. To date, several XML-based markup languages has been developed for this purpose. However, source codes written with XML-based languages are very difficult to read and edit using text editors. An alternative way is to use an object-oriented meta-language, which can be translated to different computer languages and transplanted to different application programs. Object-oriented languages are suitable for describing structural organization by hierarchical classes and taking advantage of statistical properties to reduce the number of parameter while keeping the complexity of behaviors. Using object-oriented languages to describe each element and posting it to a public domain should be the next step to build up integrated models of the respiratory control system.

Interactive Visualization of Infrared Spectral Data: Synergy of Computation, Visualization, and Experiment for Learning Spectroscopy

NASA Astrophysics Data System (ADS)

Lahti, Paul M.; Motyka, Eric J.; Lancashire, Robert J.

2000-05-01

A straightforward procedure is described to combine computation of molecular vibrational modes using commonly available molecular modeling programs with visualization of the modes using advanced features of the MDL Information Systems Inc. Chime World Wide Web browser plug-in. Minor editing of experimental spectra that are stored in the JCAMP-DX format allows linkage of IR spectral frequency ranges to Chime molecular display windows. The spectra and animation files can be combined by Hypertext Markup Language programming to allow interactive linkage between experimental spectra and computationally generated vibrational displays. Both the spectra and the molecular displays can be interactively manipulated to allow the user maximum control of the objects being viewed. This procedure should be very valuable not only for aiding students through visual linkage of spectra and various vibrational animations, but also by assisting them in learning the advantages and limitations of computational chemistry by comparison to experiment.

Techniques for integrating ‐omics data

PubMed Central

Akula, Siva Prasad; Miriyala, Raghava Naidu; Thota, Hanuman; Rao, Allam Appa; Gedela, Srinubabu

2009-01-01

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present ‐omics community, because ‐omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data. PMID:19255651

Techniques for integrating -omics data.

PubMed

Akula, Siva Prasad; Miriyala, Raghava Naidu; Thota, Hanuman; Rao, Allam Appa; Gedela, Srinubabu

2009-01-01

The challenge for -omics research is to tackle the problem of fragmentation of knowledge by integrating several sources of heterogeneous information into a coherent entity. It is widely recognized that successful data integration is one of the keys to improve productivity for stored data. Through proper data integration tools and algorithms, researchers may correlate relationships that enable them to make better and faster decisions. The need for data integration is essential for present -omics community, because -omics data is currently spread world wide in wide variety of formats. These formats can be integrated and migrated across platforms through different techniques and one of the important techniques often used is XML. XML is used to provide a document markup language that is easier to learn, retrieve, store and transmit. It is semantically richer than HTML. Here, we describe bio warehousing, database federation, controlled vocabularies and highlighting the XML application to store, migrate and validate -omics data.

[Development of quality assurance/quality control web system in radiotherapy].

PubMed

Okamoto, Hiroyuki; Mochizuki, Toshihiko; Yokoyama, Kazutoshi; Wakita, Akihisa; Nakamura, Satoshi; Ueki, Heihachi; Shiozawa, Keiko; Sasaki, Koji; Fuse, Masashi; Abe, Yoshihisa; Itami, Jun

2013-12-01

Our purpose is to develop a QA/QC (quality assurance/quality control) web system using a server-side script language such as HTML (HyperText Markup Language) and PHP (Hypertext Preprocessor), which can be useful as a tool to share information about QA/QC in radiotherapy. The system proposed in this study can be easily built in one's own institute, because HTML can be easily handled. There are two desired functions in a QA/QC web system: (i) To review the results of QA/QC for a radiotherapy machine, manuals, and reports necessary for routinely performing radiotherapy through this system. By disclosing the results, transparency can be maintained, (ii) To reveal a protocol for QA/QC in one's own institute using pictures and movies relating to QA/QC for simplicity's sake, which can also be used as an educational tool for junior radiation technologists and medical physicists. By using this system, not only administrators, but also all staff involved in radiotherapy, can obtain information about the conditions and accuracy of treatment machines through the QA/QC web system.

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C

2006-01-01

Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

Geolokit: An interactive tool for visualising and exploring geoscientific data in Google Earth

NASA Astrophysics Data System (ADS)

Triantafyllou, Antoine; Watlet, Arnaud; Bastin, Christophe

2017-10-01

Virtual globes have been developed to showcase different types of data combining a digital elevation model and basemaps of high resolution satellite imagery. Hence, they became a standard to share spatial data and information, although they suffer from a lack of toolboxes dedicated to the formatting of large geoscientific dataset. From this perspective, we developed Geolokit: a free and lightweight software that allows geoscientists - and every scientist working with spatial data - to import their data (e.g., sample collections, structural geology, cross-sections, field pictures, georeferenced maps), to handle and to transcribe them to Keyhole Markup Language (KML) files. KML files are then automatically opened in the Google Earth virtual globe and the spatial data accessed and shared. Geolokit comes with a large number of dedicated tools that can process and display: (i) multi-points data, (ii) scattered data interpolations, (iii) structural geology features in 2D and 3D, (iv) rose diagrams, stereonets and dip-plunge polar histograms, (v) cross-sections and oriented rasters, (vi) georeferenced field pictures, (vii) georeferenced maps and projected gridding. Therefore, together with Geolokit, Google Earth becomes not only a powerful georeferenced data viewer but also a stand-alone work platform. The toolbox (available online at http://www.geolokit.org) is written in Python, a high-level, cross-platform programming language and is accessible through a graphical user interface, designed to run in parallel with Google Earth, through a workflow that requires no additional third party software. Geolokit features are demonstrated in this paper using typical datasets gathered from two case studies illustrating its applicability at multiple scales of investigation: a petro-structural investigation of the Ile d'Yeu orthogneissic unit (Western France) and data collection of the Mariana oceanic subduction zone (Western Pacific).

Parameter Balancing in Kinetic Models of Cell Metabolism†

PubMed Central

2010-01-01

Kinetic modeling of metabolic pathways has become a major field of systems biology. It combines structural information about metabolic pathways with quantitative enzymatic rate laws. Some of the kinetic constants needed for a model could be collected from ever-growing literature and public web resources, but they are often incomplete, incompatible, or simply not available. We address this lack of information by parameter balancing, a method to complete given sets of kinetic constants. Based on Bayesian parameter estimation, it exploits the thermodynamic dependencies among different biochemical quantities to guess realistic model parameters from available kinetic data. Our algorithm accounts for varying measurement conditions in the input data (pH value and temperature). It can process kinetic constants and state-dependent quantities such as metabolite concentrations or chemical potentials, and uses prior distributions and data augmentation to keep the estimated quantities within plausible ranges. An online service and free software for parameter balancing with models provided in SBML format (Systems Biology Markup Language) is accessible at www.semanticsbml.org. We demonstrate its practical use with a small model of the phosphofructokinase reaction and discuss its possible applications and limitations. In the future, parameter balancing could become an important routine step in the kinetic modeling of large metabolic networks. PMID:21038890

seismo-live: Training in Computational Seismology using Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Igel, H.; Krischer, L.; van Driel, M.; Tape, C.

2016-12-01

Practical training in computational methodologies is still underrepresented in Earth science curriculae despite the increasing use of sometimes highly sophisticated simulation technologies in research projects. At the same time well-engineered community codes make it easy to return simulation-based results yet with the danger that the inherent traps of numerical solutions are not well understood. It is our belief that training with highly simplified numerical solutions (here to the equations describing elastic wave propagation) with carefully chosen elementary ingredients of simulation technologies (e.g., finite-differencing, function interpolation, spectral derivatives, numerical integration) could substantially improve this situation. For this purpose we have initiated a community platform (www.seismo-live.org) where Python-based Jupyter notebooks can be accessed and run without and necessary downloads or local software installations. The increasingly popular Jupyter notebooks allow combining markup language, graphics, equations with interactive, executable python codes. We demonstrate the potential with training notebooks for the finite-difference method, pseudospectral methods, finite/spectral element methods, the finite-volume and the discontinuous Galerkin method. The platform already includes general Python training, introduction to the ObsPy library for seismology as well as seismic data processing and noise analysis. Submission of Jupyter notebooks for general seismology are encouraged. The platform can be used for complementary teaching in Earth Science courses on compute-intensive research areas.

Tracking the polio virus down the Congo River: a case study on the use of Google Earth™ in public health planning and mapping

PubMed Central

Kamadjeu, Raoul

2009-01-01

Background The use of GIS in public health is growing, a consequence of a rapidly evolving technology and increasing accessibility to a wider audience. Google Earth™ (GE) is becoming an important mapping infrastructure for public health. However, generating traditional public health maps for GE is still beyond the reach of most public health professionals. In this paper, we explain, through the example of polio eradication activities in the Democratic Republic of Congo, how we used GE Earth as a planning tool and we share the methods used to generate public health maps. Results The use of GE improved field operations and resulted in better dispatch of vaccination teams and allocation of resources. It also allowed the creation of maps of high quality for advocacy, training and to help understand the spatiotemporal relationship between all the entities involved in the polio outbreak and response. Conclusion GE has the potential of making mapping available to a new set of public health users in developing countries. High quality and free satellite imagery, rich features including Keyhole Markup Language or image overlay provide a flexible but yet powerful platform that set it apart from traditional GIS tools and this power is still to be fully harnessed by public health professionals. PMID:19161606

Distribution of immunodeficiency fact files with XML--from Web to WAP.

PubMed

Väliaho, Jouni; Riikonen, Pentti; Vihinen, Mauno

2005-06-26

Although biomedical information is growing rapidly, it is difficult to find and retrieve validated data especially for rare hereditary diseases. There is an increased need for services capable of integrating and validating information as well as proving it in a logically organized structure. A XML-based language enables creation of open source databases for storage, maintenance and delivery for different platforms. Here we present a new data model called fact file and an XML-based specification Inherited Disease Markup Language (IDML), that were developed to facilitate disease information integration, storage and exchange. The data model was applied to primary immunodeficiencies, but it can be used for any hereditary disease. Fact files integrate biomedical, genetic and clinical information related to hereditary diseases. IDML and fact files were used to build a comprehensive Web and WAP accessible knowledge base ImmunoDeficiency Resource (IDR) available at http://bioinf.uta.fi/idr/. A fact file is a user oriented user interface, which serves as a starting point to explore information on hereditary diseases. The IDML enables the seamless integration and presentation of genetic and disease information resources in the Internet. IDML can be used to build information services for all kinds of inherited diseases. The open source specification and related programs are available at http://bioinf.uta.fi/idml/.

Web-based visualization of gridded dataset usings OceanBrowser

NASA Astrophysics Data System (ADS)

Barth, Alexander; Watelet, Sylvain; Troupin, Charles; Beckers, Jean-Marie

2015-04-01

OceanBrowser is a web-based visualization tool for gridded oceanographic data sets. Those data sets are typically four-dimensional (longitude, latitude, depth and time). OceanBrowser allows one to visualize horizontal sections at a given depth and time to examine the horizontal distribution of a given variable. It also offers the possibility to display the results on an arbitrary vertical section. To study the evolution of the variable in time, the horizontal and vertical sections can also be animated. Vertical section can be generated by using a fixed distance from coast or fixed ocean depth. The user can customize the plot by changing the color-map, the range of the color-bar, the type of the plot (linearly interpolated color, simple contours, filled contours) and download the current view as a simple image or as Keyhole Markup Language (KML) file for visualization in applications such as Google Earth. The data products can also be accessed as NetCDF files and through OPeNDAP. Third-party layers from a web map service can also be integrated. OceanBrowser is used in the frame of the SeaDataNet project (http://gher-diva.phys.ulg.ac.be/web-vis/) and EMODNET Chemistry (http://oceanbrowser.net/emodnet/) to distribute gridded data sets interpolated from in situ observation using DIVA (Data-Interpolating Variational Analysis).

Intelligent retrieval of medical images from the Internet

NASA Astrophysics Data System (ADS)

Tang, Yau-Kuo; Chiang, Ted T.

1996-05-01

The object of this study is using Internet resources to provide a cost-effective, user-friendly method to access the medical image archive system and to provide an easy method for the user to identify the images required. This paper describes the prototype system architecture, the implementation, and results. In the study, we prototype the Intelligent Medical Image Retrieval (IMIR) system as a Hypertext Transport Prototype server and provide Hypertext Markup Language forms for user, as an Internet client, using browser to enter image retrieval criteria for review. We are developing the intelligent retrieval engine, with the capability to map the free text search criteria to the standard terminology used for medical image identification. We evaluate retrieved records based on the number of the free text entries matched and their relevance level to the standard terminology. We are in the integration and testing phase. We have collected only a few different types of images for testing and have trained a few phrases to map the free text to the standard medical terminology. Nevertheless, we are able to demonstrate the IMIR's ability to search, retrieve, and review medical images from the archives using general Internet browser. The prototype also uncovered potential problems in performance, security, and accuracy. Additional studies and enhancements will make the system clinically operational.

Development and evaluation of a dynamic web-based application.

PubMed

Hsieh, Yichuan; Brennan, Patricia Flatley

2007-10-11

Traditional consumer health informatics (CHI) applications that were developed for lay public on the Web were commonly written in a Hypertext Markup Language (HTML). As genetics knowledge rapidly advances and requires updating information in a timely fashion, a different content structure is therefore needed to facilitate information delivery. This poster will present the process of developing a dynamic database-driven Web CHI application.

Baseline coastal oblique aerial photographs collected from the Virginia/North Carolina border to Montauk Point, New York, October 5-6, 2014

USGS Publications Warehouse

Morgan, Karen L. M.

2015-10-02

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files.

[Radiology information system using HTML, JavaScript, and Web server].

PubMed

Sone, M; Sasaki, M; Oikawa, H; Yoshioka, K; Ehara, S; Tamakawa, Y

1997-12-01

We have developed a radiology information system using intranet techniques, including hypertext markup language, JavaScript, and Web server. JavaScript made it possible to develop an easy-to-use application, as well as to reduce network traffic and load on the server. The system we have developed is inexpensive and flexible, and its development and maintenance are much easier than with the previous system.

Defense Financial and Investment Review

DTIC Science & Technology

1985-06-01

productivity -enhancing improvements. Other methods are required. Other SubJects o Shipbuilding contract pricing , financing and markup policies nced re...34 . . . current tax and profit policies appear to discourage capital investment in new facilities and equipment that would increase productivity and...borrowing and profits may not be productive . o The liquidity model postulates new capital expenditures as a function of rofits or cash flow. There are two

PORIDGE: Postmodern Rhizomatics in Digitally Generated Environments--Do We Need a Metatheory for W3?

ERIC Educational Resources Information Center

Wallmannsberger, Josef

1994-01-01

Discusses the World Wide Web (W3) and its relevance to a philosophy of science. Topics include PORIDGE, an electronically mediated encyclopedia of postmodern knowledge; hypertext mark-up language; W3 as a medium for information ecologies; the relationship between W3 and the user; social manufacture of knowledge; and W3 as a model. (29 references)…

SSO - Single-Sign-On Profile: Authentication Mechanisms Version 2.0

NASA Astrophysics Data System (ADS)

Taffoni, Giuliano; Schaaf, André; Rixon, Guy; Major, Brian; Taffoni, Giuliano

2017-05-01

Approved client-server authentication mechanisms are described for the IVOA single-sign-on profile: No Authentication; HTTP Basic Authentication; TLS with passwords; TLS with client certificates; Cookies; Open Authentication; Security Assertion Markup Language; OpenID. Normative rules are given for the implementation of these mechanisms, mainly by reference to pre-existing standards. The Authorization mechanisms are out of the scope of this document.

Defining Linkages between the GSC and NSF's LTER Program: How the Ecological Metadata Language (EML) Relates to GCDML and Other Outcomes

Treesearch

Inigo San Gil; Wade Sheldon; Tom Schmidt; Mark Servilla; Raul Aguilar; Corinna Gries; Tanya Gray; Dawn Field; James Cole; Jerry Yun Pan; Giri Palanisamy; Donald Henshaw; Margaret O' Brien; Linda Kinkel; Kathrine McMahon; Renzo Kottmann; Linda Amaral-Zettler; John Hobbie; Philip Goldstein; Robert P. Guralnick; James Brunt; William K. Michener

2008-01-01

The Genomic Standards Consortium (GSC) invited a representative of the Long-Term Ecological Research (LTER) to its fifth workshop to present the Ecological Metadata Language (EML) metadata standard and its relationship to the Minimum Information about a Genome/Metagenome Sequence (MIGS/MIMS) and its implementation, the Genomic Contextual Data Markup Language (GCDML)....

Schema for Spacecraft-Command Dictionary

NASA Technical Reports Server (NTRS)

Laubach, Sharon; Garcia, Celina; Maxwell, Scott; Wright, Jesse

2008-01-01

An Extensible Markup Language (XML) schema was developed as a means of defining and describing a structure for capturing spacecraft command- definition and tracking information in a single location in a form readable by both engineers and software used to generate software for flight and ground systems. A structure defined within this schema is then used as the basis for creating an XML file that contains command definitions.

Consolidated Environmental Resource Database Information Process (CERDIP)

DTIC Science & Technology

2015-11-19

Secretary of the Army for Installations, Energy and Environment [OASA(IE&E)] ESOH 5850 21st Street, Bldg 211, Second Floor Fort Belvoir, VA 22060-5938...Elizabeth J. Keysar 7. PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES) National Defense Center for Energy and Environment Operated by Concurrent...Markup Language NDCEE National Defense Center for Energy and Environment NFDD National Geospatial–Intelligence Agency Feature Data Dictionary

Empowering radiologic education on the Internet: a new virtual website technology for hosting interactive educational content on the World Wide Web.

PubMed

Frank, M S; Dreyer, K

2001-06-01

We describe a virtual web site hosting technology that enables educators in radiology to emblazon and make available for delivery on the world wide web their own interactive educational content, free from dependencies on in-house resources and policies. This suite of technologies includes a graphically oriented software application, designed for the computer novice, to facilitate the input, storage, and management of domain expertise within a database system. The database stores this expertise as choreographed and interlinked multimedia entities including text, imagery, interactive questions, and audio. Case-based presentations or thematic lectures can be authored locally, previewed locally within a web browser, then uploaded at will as packaged knowledge objects to an educator's (or department's) personal web site housed within a virtual server architecture. This architecture can host an unlimited number of unique educational web sites for individuals or departments in need of such service. Each virtual site's content is stored within that site's protected back-end database connected to Internet Information Server (Microsoft Corp, Redmond WA) using a suite of Active Server Page (ASP) modules that incorporate Microsoft's Active Data Objects (ADO) technology. Each person's or department's electronic teaching material appears as an independent web site with different levels of access--controlled by a username-password strategy--for teachers and students. There is essentially no static hypertext markup language (HTML). Rather, all pages displayed for a given site are rendered dynamically from case-based or thematic content that is fetched from that virtual site's database. The dynamically rendered HTML is displayed within a web browser in a Socratic fashion that can assess the recipient's current fund of knowledge while providing instantaneous user-specific feedback. Each site is emblazoned with the logo and identification of the participating institution. Individuals with teacher-level access can use a web browser to upload new content as well as manage content already stored on their virtual site. Each virtual site stores, collates, and scores participants' responses to the interactive questions posed on line. This virtual web site strategy empowers the educator with an end-to-end solution for creating interactive educational content and hosting that content within the educator's personalized and protected educational site on the world wide web, thus providing a valuable outlet that can magnify the impact of his or her talents and contributions.

Harmonised information exchange between decentralised food composition database systems.

PubMed

Pakkala, H; Christensen, T; de Victoria, I Martínez; Presser, K; Kadvan, A

2010-11-01

The main aim of the European Food Information Resource (EuroFIR) project is to develop and disseminate a comprehensive, coherent and validated data bank for the distribution of food composition data (FCD). This can only be accomplished by harmonising food description and data documentation and by the use of standardised thesauri. The data bank is implemented through a network of local FCD storages (usually national) under the control and responsibility of the local (national) EuroFIR partner. The implementation of the system based on the EuroFIR specifications is under development. The data interchange happens through the EuroFIR Web Services interface, allowing the partners to implement their system using methods and software suitable for the local computer environment. The implementation uses common international standards, such as Simple Object Access Protocol, Web Service Description Language and Extensible Markup Language (XML). A specifically constructed EuroFIR search facility (eSearch) was designed for end users. The EuroFIR eSearch facility compiles queries using a specifically designed Food Data Query Language and sends a request to those network nodes linked to the EuroFIR Web Services that will most likely have the requested information. The retrieved FCD are compiled into a specifically designed data interchange format (the EuroFIR Food Data Transport Package) in XML, which is sent back to the EuroFIR eSearch facility as the query response. The same request-response operation happens in all the nodes that have been selected in the EuroFIR eSearch facility for a certain task. Finally, the FCD are combined by the EuroFIR eSearch facility and delivered to the food compiler. The implementation of FCD interchange using decentralised computer systems instead of traditional data-centre models has several advantages. First of all, the local partners have more control over their FCD, which will increase commitment and improve quality. Second, a multicentred solution is more economically viable than the creation of a centralised data bank, because of the lack of national political support for multinational systems.

Taming Log Files from Game/Simulation-Based Assessments: Data Models and Data Analysis Tools. Research Report. ETS RR-16-10

ERIC Educational Resources Information Center

Hao, Jiangang; Smith, Lawrence; Mislevy, Robert; von Davier, Alina; Bauer, Malcolm

2016-01-01

Extracting information efficiently from game/simulation-based assessment (G/SBA) logs requires two things: a well-structured log file and a set of analysis methods. In this report, we propose a generic data model specified as an extensible markup language (XML) schema for the log files of G/SBAs. We also propose a set of analysis methods for…

Advanced Video Technology for Safe and Efficient Surgical Operating Rooms

DTIC Science & Technology

2005-03-01

should be easy to integrate into the system by non-technical personnel. " Disruptive Technologies - Such technologies can have both positive and negative...integrate new, emerging, and otherwise " disruptive technologies ." " Medical Manufacturer Markups - In some cases, potential vendor pricing of...POSITIVE disruptive technologies as they would, in some cases, eliminate the need for monitor screens. NETWORK BANDWIDTH j% J a The System must be able to

The Air Force Aviation Investment Challenge

DTIC Science & Technology

2015-12-11

Report R42136, U.S. Unmanned Aerial Systems. 6 Procurement percentage excludes modification funding. 7 IOC from Department of Defense, Annual Aviation...different picture. Spending for the LRS-B, following its recent contract award and entering its engineering and manufacturing development phase, is...Budget As part of its markup of the Navy’s proposed FY2015 budget, Congress created the National Sea- Based Deterrence Fund (NSBDF), a fund in the DOD

The Air Force Aviation Investment Challenge

DTIC Science & Technology

2015-12-17

7 Procurement percentage excludes modification funding. 8 IOC from Department of Defense, Annual Aviation Inventory and Funding Plan, Fiscal Years...its engineering and manufacturing development phase, is projected to triple over the course of the FYDP. 9 The newer programs begin with relatively...Through a Non-Air Force Budget As part of its markup of the Navy’s proposed FY2015 budget, Congress created the National Sea- Based Deterrence Fund

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

DTIC Science & Technology

2006-06-01

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

Baseline coastal oblique aerial photographs collected from Navarre Beach, Florida, to Breton Island, Louisiana, September 18–19, 2015

USGS Publications Warehouse

Morgan, Karen L. M.

2016-08-01

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then the thumbnail or the link below the thumbnail. The KML file was created using the photographic navigation files. This KML file can be found in the kml folder.

Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions.

PubMed

Holliday, Gemma L; Murray-Rust, Peter; Rzepa, Henry S

2006-01-01

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally defined as XMLSchema components, and their semantics are developed. New syntax and semantics in CML are reported and illustrated with 10 examples.

Extending Phrase-Based Decoding with a Dependency-Based Reordering Model

DTIC Science & Technology

2009-11-01

strictly within the confines of phrase-based translation. The hope was to introduce an approach that could take advantage of monolingual syntactic...tuple represents one element of the XML markup, where element is the name of this element, attributes is a dictionary (mapping strings to strings...representing the range of possible compressions, in the form of a dictionary mapping the latter to the former. To represent multiple dependency

CellML and associated tools and techniques.

PubMed

Garny, Alan; Nickerson, David P; Cooper, Jonathan; Weber dos Santos, Rodrigo; Miller, Andrew K; McKeever, Steve; Nielsen, Poul M F; Hunter, Peter J

2008-09-13

We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results. The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001. Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.

Informatics in radiology: automated structured reporting of imaging findings using the AIM standard and XML.

PubMed

Zimmerman, Stefan L; Kim, Woojin; Boonn, William W

2011-01-01

Quantitative and descriptive imaging data are a vital component of the radiology report and are frequently of paramount importance to the ordering physician. Unfortunately, current methods of recording these data in the report are both inefficient and error prone. In addition, the free-text, unstructured format of a radiology report makes aggregate analysis of data from multiple reports difficult or even impossible without manual intervention. A structured reporting work flow has been developed that allows quantitative data created at an advanced imaging workstation to be seamlessly integrated into the radiology report with minimal radiologist intervention. As an intermediary step between the workstation and the reporting software, quantitative and descriptive data are converted into an extensible markup language (XML) file in a standardized format specified by the Annotation and Image Markup (AIM) project of the National Institutes of Health Cancer Biomedical Informatics Grid. The AIM standard was created to allow image annotation data to be stored in a uniform machine-readable format. These XML files containing imaging data can also be stored on a local database for data mining and analysis. This structured work flow solution has the potential to improve radiologist efficiency, reduce errors, and facilitate storage of quantitative and descriptive imaging data for research. Copyright © RSNA, 2011.

Developing and integrating an adverse drug reaction reporting system with the hospital information system.

PubMed

Kataoka, Satoshi; Ohe, Kazuhiko; Mochizuki, Mayumi; Ueda, Shiro

2002-01-01

We have developed an adverse drug reaction (ADR) reporting system integrating it with Hospital Information System (HIS) of the University of Tokyo Hospital. Since this system is designed with JAVA, it is portable without re-compiling to any operating systems on which JAVA virtual machines work. In this system, we implemented an automatic data filling function using XML-based (extended Markup Language) files generated by HIS. This new specification would decrease the time needed for physicians and pharmacists to fill the spontaneous ADR reports. By clicking a button, the report is sent to the text database through Simple Mail Transfer Protocol (SMTP) electronic mails. The destination of the report mail can be changed arbitrarily by administrators, which adds this system more flexibility for practical operation. Although we tried our best to use the SGML-based (Standard Generalized Markup Language) ICH M2 guideline to follow the global standard of the case report, we eventually adopted XML as the output report format. This is because we found some problems in handling two bytes characters with ICH guideline and XML has a lot of useful features. According to our pilot survey conducted at the University of Tokyo Hospital, many physicians answered that our idea, integrating ADR reporting system to HIS, would increase the ADR reporting numbers.

Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping.

PubMed

Milius, Robert P; Heuer, Michael; Valiga, Daniel; Doroschak, Kathryn J; Kennedy, Caleb J; Bolon, Yung-Tsi; Schneider, Joel; Pollack, Jane; Kim, Hwa Ran; Cereb, Nezih; Hollenbach, Jill A; Mack, Steven J; Maiers, Martin

2015-12-01

We present an electronic format for exchanging data for HLA and KIR genotyping with extensions for next-generation sequencing (NGS). This format addresses NGS data exchange by refining the Histoimmunogenetics Markup Language (HML) to conform to the proposed Minimum Information for Reporting Immunogenomic NGS Genotyping (MIRING) reporting guidelines (miring.immunogenomics.org). Our refinements of HML include two major additions. First, NGS is supported by new XML structures to capture additional NGS data and metadata required to produce a genotyping result, including analysis-dependent (dynamic) and method-dependent (static) components. A full genotype, consensus sequence, and the surrounding metadata are included directly, while the raw sequence reads and platform documentation are externally referenced. Second, genotype ambiguity is fully represented by integrating Genotype List Strings, which use a hierarchical set of delimiters to represent allele and genotype ambiguity in a complete and accurate fashion. HML also continues to enable the transmission of legacy methods (e.g. site-specific oligonucleotide, sequence-specific priming, and Sequence Based Typing (SBT)), adding features such as allowing multiple group-specific sequencing primers, and fully leveraging techniques that combine multiple methods to obtain a single result, such as SBT integrated with NGS. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Enhancing Access to Drought Information Using the CUAHSI Hydrologic Information System

NASA Astrophysics Data System (ADS)

Schreuders, K. A.; Tarboton, D. G.; Horsburgh, J. S.; Sen Gupta, A.; Reeder, S.

2011-12-01

The National Drought Information System (NIDIS) Upper Colorado River Basin pilot study is investigating and establishing capabilities for better dissemination of drought information for early warning and management. As part of this study we are using and extending functionality from the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) Hydrologic Information System (HIS) to provide better access to drought-related data in the Upper Colorado River Basin. The CUAHSI HIS is a federated system for sharing hydrologic data. It is comprised of multiple data servers, referred to as HydroServers, that publish data in a standard XML format called Water Markup Language (WaterML), using web services referred to as WaterOneFlow web services. HydroServers can also publish geospatial data using Open Geospatial Consortium (OGC) web map, feature and coverage services and are capable of hosting web and map applications that combine geospatial datasets with observational data served via web services. HIS also includes a centralized metadata catalog that indexes data from registered HydroServers and a data access client referred to as HydroDesktop. For NIDIS, we have established a HydroServer to publish drought index values as well as the input data used in drought index calculations. Primary input data required for drought index calculation include streamflow, precipitation, reservoir storages, snow water equivalent, and soil moisture. We have developed procedures to redistribute the input data to the time and space scales chosen for drought index calculation, namely half monthly time intervals for HUC 10 subwatersheds. The spatial redistribution approaches used for each input parameter are dependent on the spatial linkages for that parameter, i.e., the redistribution procedure for streamflow is dependent on the upstream/downstream connectivity of the stream network, and the precipitation redistribution procedure is dependent on elevation to account for orographic effects. A set of drought indices are then calculated from the redistributed data. We have created automated data and metadata harvesters that periodically scan and harvest new data from each of the input databases, and calculates extensions to the resulting derived data sets, ensuring that the data available on the drought server is kept up to date. This paper will describe this system, showing how it facilitates the integration of data from multiple sources to inform the planning and management of water resources during drought. The system may be accessed at http://drought.usu.edu.

Do Interactive Globes and Games Help Students Learn Planetary Science?

NASA Astrophysics Data System (ADS)

Coba, Filis; Burgin, Stephen; De Paor, Declan; Georgen, Jennifer

2016-01-01

The popularity of animations and interactive visualizations in undergraduate science education might lead one to assume that these teaching aids enhance student learning. We tested this assumption for the case of the Google Earth virtual globe with a comparison of control and treatment student groups in a general education class of over 370 students at a large public university. Earth and Planetary Science course content was developed in two formats: using Keyhole Markup Language (KML) to create interactive tours in Google Earth (the treatment group) and Portable Document Format (PDF) for on-screen reading (the control group). The PDF documents contained identical text and images to the placemark balloons or "tour stops" in the Google Earth version. Some significant differences were noted between the two groups based on the immediate post-questionnaire with the KML students out-performing the PDF students, but not on the delayed measure. In a separate but related project, we undertake preliminary investigations into methods of teaching basic concepts in planetary mantle convection using numerical simulations. The goal of this project is to develop an interface with a two-dimensional finite element model that will allow students to vary parameters such as the temperatures assigned to the boundaries of the model domain, to help them actively explore important variables that control convection.

Applications of the pipeline environment for visual informatics and genomics computations

PubMed Central

2011-01-01

Background Contemporary informatics and genomics research require efficient, flexible and robust management of large heterogeneous data, advanced computational tools, powerful visualization, reliable hardware infrastructure, interoperability of computational resources, and detailed data and analysis-protocol provenance. The Pipeline is a client-server distributed computational environment that facilitates the visual graphical construction, execution, monitoring, validation and dissemination of advanced data analysis protocols. Results This paper reports on the applications of the LONI Pipeline environment to address two informatics challenges - graphical management of diverse genomics tools, and the interoperability of informatics software. Specifically, this manuscript presents the concrete details of deploying general informatics suites and individual software tools to new hardware infrastructures, the design, validation and execution of new visual analysis protocols via the Pipeline graphical interface, and integration of diverse informatics tools via the Pipeline eXtensible Markup Language syntax. We demonstrate each of these processes using several established informatics packages (e.g., miBLAST, EMBOSS, mrFAST, GWASS, MAQ, SAMtools, Bowtie) for basic local sequence alignment and search, molecular biology data analysis, and genome-wide association studies. These examples demonstrate the power of the Pipeline graphical workflow environment to enable integration of bioinformatics resources which provide a well-defined syntax for dynamic specification of the input/output parameters and the run-time execution controls. Conclusions The LONI Pipeline environment http://pipeline.loni.ucla.edu provides a flexible graphical infrastructure for efficient biomedical computing and distributed informatics research. The interactive Pipeline resource manager enables the utilization and interoperability of diverse types of informatics resources. The Pipeline client-server model provides computational power to a broad spectrum of informatics investigators - experienced developers and novice users, user with or without access to advanced computational-resources (e.g., Grid, data), as well as basic and translational scientists. The open development, validation and dissemination of computational networks (pipeline workflows) facilitates the sharing of knowledge, tools, protocols and best practices, and enables the unbiased validation and replication of scientific findings by the entire community. PMID:21791102

IBM techexplorer and MathML: Interactive Multimodal Scientific Documents

NASA Astrophysics Data System (ADS)

Diaz, Angel

2001-06-01

The World Wide Web provides a standard publishing platform for disseminating scientific and technical articles, books, journals, courseware, or even homework on the internet; however, the transition from paper to web-based interactive content has brought new opportunities for creating interactive content. Students, scientists, and engineers are now faced with the task of rendering the 2D presentational structure of mathematics, harnessing the wealth of scientific and technical software, and creating truly accessible scientific portals across international boundaries and markets. The recent emergence of World Wide Web Consortium (W3C) standards such as the Mathematical Markup Language (MathML), Language (XSL), and Aural CSS (ACSS) provide a foundation whereby mathematics can be displayed, enlivened, computed, and audio formatted. With interoperability ensured by standards, software applications can be easily brought together to create extensible and interactive scientific content. In this presentation we will provide an overview of the IBM techexplorer Hypermedia Browser, a web browser plug-in and ActiveX control aimed at bringing interactive mathematics to the masses across platforms and applications. We will demonstrate "live" mathematics where documents that contain MathML expressions can be edited and computed right inside your favorite web browser. This demonstration will be generalized as we show how MathML can be used to enliven even PowerPoint presentations. Finally, we will close the loop by demonstrating a novel approach to spoken mathematics based on MathML, DOM, XSL, ACSS, techexplorer, and IBM ViaVoice. By making use of techexplorer as the glue that binds the rendered content to the web browser, the back-end computation software, the Java applets that augment the exposition, and voice-rendering systems such as ViaVoice, authors can indeed create truly extensible and interactive scientific content. For more information see: [http://www.software.ibm.com/techexplorer] [http://www.alphaworks.ibm.com] [http://www.w3.org

Baseline coastal oblique aerial photographs collected from Key Largo, Florida, to the Florida/Georgia border, September 5-6, 2014

USGS Publications Warehouse

Morgan, Karen L. M.

2015-09-14

In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used to view the images by clicking on the marker and then clicking on either the thumbnail or the link above the thumbnail. The KML files were created using the photographic navigation files. These KML files can be found in the kml folder.

XML Schema Guide for Primary CDR Submissions

EPA Pesticide Factsheets

This document presents the extensible markup language (XML) schema guide for the Office of Pollution Prevention and Toxics’ (OPPT) e-CDRweb tool. E-CDRweb is the electronic, web-based tool provided by Environmental Protection Agency (EPA) for the submission of Chemical Data Reporting (CDR) information. This document provides the user with tips and guidance on correctly using the version 1.7 XML schema. Please note that the order of the elements must match the schema.

Expanding the Toolkit and Resource Environment to Assist Translation (TREAT) and Its User Base

DTIC Science & Technology

2011-06-01

3 Figure 2. Screenshot of TREAT (translation of Arabic source into English target) and two corresponding markup tool windows on Arabic source...initial framework in place, we decided to expand TREAT to provide support to two new groups of users: students learning to be Arabic -language...translators and teachers training them. The students and the teachers are native English speakers, so the training includes learning how to read Arabic