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.

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

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/.

Making the World Wide Web Accessible to All Students.

ERIC Educational Resources Information Center

Guthrie, Sally A.

2000-01-01

Examines the accessibility of Web sites belonging to 80 colleges of communications and schools of journalism by examining the hypertext markup language (HTML) used to format the pages. Suggests ways to revise the markup of pages to make them more accessible to students with vision, hearing, and mobility problems. Lists resources of the latest…

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.

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/.

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

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.

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/.

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.

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.

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)

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).

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.

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

"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…

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.

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.

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.

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…

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

Making journals accessible to the visually impaired: the future is near

PubMed Central

GARDNER, John; BULATOV, Vladimir; KELLY, Robert

2010-01-01

The American Physical Society (APS) has been a leader in using markup languages for publishing. ViewPlus has led development of innovative technologies for graphical information accessibility by people with print disabilities. APS, ViewPlus, and other collaborators in the Enhanced Reading Project are working together to develop the necessary technology and infrastructure for APS to publish its journals in the DAISY (Digital Accessible Information SYstem) eXtended Markup Language (XML) format, in which all text, math, and figures would be accessible to people who are blind or have other print disabilities. The first APS DAISY XML publications are targeted for late 2010. PMID:20676358

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.

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

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

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)

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.

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.

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 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

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.

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.

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.

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.

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.

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

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...

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

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…

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.

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…

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.

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.

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

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.

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.

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.

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…

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

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

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.

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.

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…

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)

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.

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.

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;…

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

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)

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.

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.

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.

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…

BioC: a minimalist approach to interoperability for biomedical text processing

PubMed Central

Comeau, Donald C.; Islamaj Doğan, Rezarta; Ciccarese, Paolo; Cohen, Kevin Bretonnel; Krallinger, Martin; Leitner, Florian; Lu, Zhiyong; Peng, Yifan; Rinaldi, Fabio; Torii, Manabu; Valencia, Alfonso; Verspoor, Karin; Wiegers, Thomas C.; Wu, Cathy H.; Wilbur, W. John

2013-01-01

A vast amount of scientific information is encoded in natural language text, and the quantity of such text has become so great that it is no longer economically feasible to have a human as the first step in the search process. Natural language processing and text mining tools have become essential to facilitate the search for and extraction of information from text. This has led to vigorous research efforts to create useful tools and to create humanly labeled text corpora, which can be used to improve such tools. To encourage combining these efforts into larger, more powerful and more capable systems, a common interchange format to represent, store and exchange the data in a simple manner between different language processing systems and text mining tools is highly desirable. Here we propose a simple extensible mark-up language format to share text documents and annotations. The proposed annotation approach allows a large number of different annotations to be represented including sentences, tokens, parts of speech, named entities such as genes or diseases and relationships between named entities. In addition, we provide simple code to hold this data, read it from and write it back to extensible mark-up language files and perform some sample processing. We also describe completed as well as ongoing work to apply the approach in several directions. Code and data are available at http://bioc.sourceforge.net/. Database URL: http://bioc.sourceforge.net/ PMID:24048470

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.

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…

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…

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.

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.

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.

Developing a Markup Language for Encoding Graphic Content in Plan Documents

ERIC Educational Resources Information Center

Li, Jinghuan

2009-01-01

While deliberating and making decisions, participants in urban development processes need easy access to the pertinent content scattered among different plans. A Planning Markup Language (PML) has been proposed to represent the underlying structure of plans in an XML-compliant way. However, PML currently covers only textual information and lacks…

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)

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.…

MXA: a customizable HDF5-based data format for multi-dimensional data sets

NASA Astrophysics Data System (ADS)

Jackson, M.; Simmons, J. P.; De Graef, M.

2010-09-01

A new digital file format is proposed for the long-term archival storage of experimental data sets generated by serial sectioning instruments. The format is known as the multi-dimensional eXtensible Archive (MXA) format and is based on the public domain Hierarchical Data Format (HDF5). The MXA data model, its description by means of an eXtensible Markup Language (XML) file with associated Document Type Definition (DTD) are described in detail. The public domain MXA package is available through a dedicated web site (mxa.web.cmu.edu), along with implementation details and example data 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)

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.

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.…

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…

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.

How to use the WWW to distribute STI

NASA Technical Reports Server (NTRS)

Roper, Donna G.

1994-01-01

This presentation explains how to use the World Wide Web (WWW) to distribute scientific and technical information as hypermedia. WWW clients and servers use the HyperText Transfer Protocol (HTTP) to transfer documents containing links to other text, graphics, video, and sound. The standard language for these documents is the HyperText MarkUp Language (HTML). These are simply text files with formatting codes that contain layout information and hyperlinks. HTML documents can be created with any text editor or with one of the publicly available HTML editors or convertors. HTML can also include links to available image formats. This presentation is available online. The URL is http://sti.larc.nasa. (followed by) gov/demos/workshop/introtext.html.

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…

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.

Application of XML to Journal Table Archiving

NASA Astrophysics Data System (ADS)

Shaya, E. J.; Blackwell, J. H.; Gass, J. E.; Kargatis, V. E.; Schneider, G. L.; Weiland, J. L.; Borne, K. D.; White, R. A.; Cheung, C. Y.

1998-12-01

The Astronomical Data Center (ADC) at the NASA Goddard Space Flight Center is a major archive for machine-readable astronomical data tables. Many ADC tables are derived from published journal articles. Article tables are reformatted to be machine-readable and documentation is crafted to facilitate proper reuse by researchers. The recent switch of journals to web based electronic format has resulted in the generation of large amounts of tabular data that could be captured into machine-readable archive format at fairly low cost. The large data flow of the tables from all major North American astronomical journals (a factor of 100 greater than the present rate at the ADC) necessitates the development of rigorous standards for the exchange of data between researchers, publishers, and the archives. We have selected a suitable markup language that can fully describe the large variety of astronomical information contained in ADC tables. The eXtensible Markup Language XML is a powerful internet-ready documentation format for data. It provides a precise and clear data description language that is both machine- and human-readable. It is rapidly becoming the standard format for business and information transactions on the internet and it is an ideal common metadata exchange format. By labelling, or "marking up", all elements of the information content, documents are created that computers can easily parse. An XML archive can easily and automatically be maintained, ingested into standard databases or custom software, and even totally restructured whenever necessary. Structuring astronomical data into XML format will enable efficient and focused search capabilities via off-the-shelf software. The ADC is investigating XML's expanded hyperlinking power to enhance connectivity within the ADC data/metadata and developing XSL display scripts to enhance display of astronomical data. The ADC XML Definition Type Document can be viewed at http://messier.gsfc.nasa.gov/dtdhtml/DTD-TREE.html

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.

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).

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.

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.

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

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

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.

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

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.

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.

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.

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.

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

Root System Markup Language: Toward a Unified Root Architecture Description Language1[OPEN

PubMed Central

Pound, Michael P.; Pradal, Christophe; Draye, Xavier; Godin, Christophe; Leitner, Daniel; Meunier, Félicien; Pridmore, Tony P.; Schnepf, Andrea

2015-01-01

The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow. PMID:25614065

Root system markup language: toward a unified root architecture description language.

PubMed

Lobet, Guillaume; Pound, Michael P; Diener, Julien; Pradal, Christophe; Draye, Xavier; Godin, Christophe; Javaux, Mathieu; Leitner, Daniel; Meunier, Félicien; Nacry, Philippe; Pridmore, Tony P; Schnepf, Andrea

2015-03-01

The number of image analysis tools supporting the extraction of architectural features of root systems has increased in recent years. These tools offer a handy set of complementary facilities, yet it is widely accepted that none of these software tools is able to extract in an efficient way the growing array of static and dynamic features for different types of images and species. We describe the Root System Markup Language (RSML), which has been designed to overcome two major challenges: (1) to enable portability of root architecture data between different software tools in an easy and interoperable manner, allowing seamless collaborative work; and (2) to provide a standard format upon which to base central repositories that will soon arise following the expanding worldwide root phenotyping effort. RSML follows the XML standard to store two- or three-dimensional image metadata, plant and root properties and geometries, continuous functions along individual root paths, and a suite of annotations at the image, plant, or root scale at one or several time points. Plant ontologies are used to describe botanical entities that are relevant at the scale of root system architecture. An XML schema describes the features and constraints of RSML, and open-source packages have been developed in several languages (R, Excel, Java, Python, and C#) to enable researchers to integrate RSML files into popular research workflow. © 2015 American Society of Plant Biologists. All Rights Reserved.

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)

Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language.

PubMed

Waltemath, Dagmar; Adams, Richard; Bergmann, Frank T; Hucka, Michael; Kolpakov, Fedor; Miller, Andrew K; Moraru, Ion I; Nickerson, David; Sahle, Sven; Snoep, Jacky L; Le Novère, Nicolas

2011-12-15

The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined.

Instrument Remote Control via the Astronomical Instrument Markup Language

NASA Technical Reports Server (NTRS)

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

1998-01-01

The Instrument Remote Control (IRC) project ongoing at NASA's Goddard Space Flight Center's (GSFC) Information Systems Center (ISC) supports NASA's mission by defining an adaptive intranet-based framework that provides robust interactive and distributed control and monitoring of remote instruments. An astronomical IRC architecture that combines the platform-independent processing capabilities of Java with the power of Extensible Markup Language (XML) to express hierarchical data in an equally platform-independent, as well as human readable manner, has been developed. This architecture is implemented using a variety of XML support tools and Application Programming Interfaces (API) written in Java. IRC will enable trusted astronomers from around the world to easily access infrared instruments (e.g., telescopes, cameras, and spectrometers) located in remote, inhospitable environments, such as the South Pole, a high Chilean mountaintop, or an airborne observatory aboard a Boeing 747. Using IRC's frameworks, an astronomer or other scientist can easily define the type of onboard instrument, control the instrument remotely, and return monitoring data all through the intranet. The Astronomical Instrument Markup Language (AIML) is the first implementation of the more general Instrument Markup Language (IML). The key aspects of our approach to instrument description and control applies to many domains, from medical instruments to machine assembly lines. The concepts behind AIML apply equally well to the description and control of instruments in general. IRC enables us to apply our techniques to several instruments, preferably from different observatories.

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.

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…

Design and implementation of CUAHSI WaterML and WaterOneFlow Web Services

NASA Astrophysics Data System (ADS)

Valentine, D. W.; Zaslavsky, I.; Whitenack, T.; Maidment, D.

2007-12-01

WaterOneFlow is a term for a group of web services created by and for the Consortium of Universities for the Advancement of Hydrologic Science, Inc. (CUAHSI) community. CUAHSI web services facilitate the retrieval of hydrologic observations information from online data sources using the SOAP protocol. CUAHSI Water Markup Language (below referred to as WaterML) is an XML schema defining the format of messages returned by the WaterOneFlow web services. \

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.

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.

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.

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.

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

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

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.

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.

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.

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

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.

A program for the conversion of The National Map data from proprietary format to resource description framework (RDF)

USGS Publications Warehouse

Bulen, Andrew; Carter, Jonathan J.; Varanka, Dalia E.

2011-01-01

To expand data functionality and capabilities for users of The National Map of the U.S. Geological Survey, data sets for six watersheds and three urban areas were converted from the Best Practices vector data model formats to Semantic Web data formats. This report describes and documents the conver-sion process. The report begins with an introduction to basic Semantic Web standards and the background of The National Map. Data were converted from a proprietary format to Geog-raphy Markup Language to capture the geometric footprint of topographic data features. Configuration files were designed to eliminate redundancy and make the conversion more efficient. A SPARQL endpoint was established for data validation and queries. The report concludes by describing the results of the conversion.

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

PubMed Central

2011-01-01

Background The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined. PMID:22172142

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.

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.

TME2/342: The Role of the EXtensible Markup Language (XML) for Future Healthcare Application Development

PubMed Central

Noelle, G; Dudeck, J

1999-01-01

Two years, since the World Wide Web Consortium (W3C) has published the first specification of the eXtensible Markup Language (XML) there exist some concrete tools and applications to work with XML-based data. In particular, new generation Web browsers offer great opportunities to develop new kinds of medical, web-based applications. There are several data-exchange formats in medicine, which have been established in the last years: HL-7, DICOM, EDIFACT and, in the case of Germany, xDT. Whereas communication and information exchange becomes increasingly important, the development of appropriate and necessary interfaces causes problems, rising costs and effort. It has been also recognised that it is difficult to define a standardised interchange format, for one of the major future developments in medical telematics: the electronic patient record (EPR) and its availability on the Internet. Whereas XML, especially in an industrial environment, is celebrated as a generic standard and a solution for all problems concerning e-commerce, in a medical context there are only few applications developed. Nevertheless, the medical environment is an appropriate area for building XML applications: as the information and communication management becomes increasingly important in medical businesses, the role of the Internet changes quickly from an information to a communication medium. The first XML based applications in healthcare show us the advantage for a future engagement of the healthcare industry in XML: such applications are open, easy to extend and cost-effective. Additionally, XML is much more than a simple new data interchange format: many proposals for data query (XQL), data presentation (XSL) and other extensions have been proposed to the W3C and partly realised in medical applications.

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)

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.

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

North, Michael J.

SchemaOnRead provides tools for implementing schema-on-read including a single function call (e.g., schemaOnRead("filename")) that reads text (TXT), comma separated value (CSV), raster image (BMP, PNG, GIF, TIFF, and JPG), R data (RDS), HDF5, NetCDF, spreadsheet (XLS, XLSX, ODS, and DIF), Weka Attribute-Relation File Format (ARFF), Epi Info (REC), Pajek network (PAJ), R network (NET), Hypertext Markup Language (HTML), SPSS (SAV), Systat (SYS), and Stata (DTA) files. It also recursively reads folders (e.g., schemaOnRead("folder")), returning a nested list of the contained elements.

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.

Test Generator for MATLAB Simulations

NASA Technical Reports Server (NTRS)

Henry, Joel

2011-01-01

MATLAB Automated Test Tool, version 3.0 (MATT 3.0) is a software package that provides automated tools that reduce the time needed for extensive testing of simulation models that have been constructed in the MATLAB programming language by use of the Simulink and Real-Time Workshop programs. MATT 3.0 runs on top of the MATLAB engine application-program interface to communicate with the Simulink engine. MATT 3.0 automatically generates source code from the models, generates custom input data for testing both the models and the source code, and generates graphs and other presentations that facilitate comparison of the outputs of the models and the source code for the same input data. Context-sensitive and fully searchable help is provided in HyperText Markup Language (HTML) format.

Conversion of Radiology Reporting Templates to the MRRT Standard.

PubMed

Kahn, Charles E; Genereaux, Brad; Langlotz, Curtis P

2015-10-01

In 2013, the Integrating the Healthcare Enterprise (IHE) Radiology workgroup developed the Management of Radiology Report Templates (MRRT) profile, which defines both the format of radiology reporting templates using an extension of Hypertext Markup Language version 5 (HTML5), and the transportation mechanism to query, retrieve, and store these templates. Of 200 English-language report templates published by the Radiological Society of North America (RSNA), initially encoded as text and in an XML schema language, 168 have been converted successfully into MRRT using a combination of automated processes and manual editing; conversion of the remaining 32 templates is in progress. The automated conversion process applied Extensible Stylesheet Language Transformation (XSLT) scripts, an XML parsing engine, and a Java servlet. The templates were validated for proper HTML5 and MRRT syntax using web-based services. The MRRT templates allow radiologists to share best-practice templates across organizations and have been uploaded to the template library to supersede the prior XML-format templates. By using MRRT transactions and MRRT-format templates, radiologists will be able to directly import and apply templates from the RSNA Report Template Library in their own MRRT-compatible vendor systems. The availability of MRRT-format reporting templates will stimulate adoption of the MRRT standard and is expected to advance the sharing and use of templates to improve the quality of radiology reports.

Modeling the Arden Syntax for medical decisions in XML.

PubMed

Kim, Sukil; Haug, Peter J; Rocha, Roberto A; Choi, Inyoung

2008-10-01

A new model expressing Arden Syntax with the eXtensible Markup Language (XML) was developed to increase its portability. Every example was manually parsed and reviewed until the schema and the style sheet were considered to be optimized. When the first schema was finished, several MLMs in Arden Syntax Markup Language (ArdenML) were validated against the schema. They were then transformed to HTML formats with the style sheet, during which they were compared to the original text version of their own MLM. When faults were found in the transformed MLM, the schema and/or style sheet was fixed. This cycle continued until all the examples were encoded into XML documents. The original MLMs were encoded in XML according to the proposed XML schema and reverse-parsed MLMs in ArdenML were checked using a public domain Arden Syntax checker. Two hundred seventy seven examples of MLMs were successfully transformed into XML documents using the model, and the reverse-parse yielded the original text version of MLMs. Two hundred sixty five of the 277 MLMs showed the same error patterns before and after transformation, and all 11 errors related to statement structure were resolved in XML version. The model uses two syntax checking mechanisms, first an XML validation process, and second, a syntax check using an XSL style sheet. Now that we have a schema for ArdenML, we can also begin the development of style sheets for transformation ArdenML into other languages.

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.

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

JSDTImport is a computer program for translating native Shuttle Data Tape (SDT) files from American Standard Code for Information Interchange (ASCII) format into databases in other formats. JSDTImport solves the problem of organizing the SDT content, affording flexibility to enable users to choose how to store the information in a database to better support client and server applications. JSDTImport can be dynamically configured by use of a simple Extensible Markup Language (XML) file. JSDTImport uses this XML file to define how each record and field will be parsed, its layout and definition, and how the resulting database will be structured. JSDTImport also includes a client application programming interface (API) layer that provides abstraction for the data-querying process. The API enables a user to specify the search criteria to apply in gathering all the data relevant to a query. The API can be used to organize the SDT content and translate into a native XML database. The XML format is structured into efficient sections, enabling excellent query performance by use of the XPath query language. Optionally, the content can be translated into a Structured Query Language (SQL) database for fast, reliable SQL queries on standard database server computers.

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)

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.

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'…

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

PubMed Central

Nagasaki, Masao; Saito, Ayumu; Li, Chen; Jeong, Euna; Miyano, Satoru

2008-01-01

Background Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. Results We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. Conclusion By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions. PMID:18570683

Systematic reconstruction of TRANSPATH data into cell system markup language.

PubMed

Nagasaki, Masao; Saito, Ayumu; Li, Chen; Jeong, Euna; Miyano, Satoru

2008-06-23

Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions.

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)

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.

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.

Web portal for dynamic creation and publication of teaching materials in multiple formats from a single source representation

NASA Astrophysics Data System (ADS)

Roganov, E. A.; Roganova, N. A.; Aleksandrov, A. I.; Ukolova, A. V.

2017-01-01

We implement a web portal which dynamically creates documents in more than 30 different formats including html, pdf and docx from a single original material source. It is obtained by using a number of free software such as Markdown (markup language), Pandoc (document converter), MathJax (library to display mathematical notation in web browsers), framework Ruby on Rails. The portal enables the creation of documents with a high quality visualization of mathematical formulas, is compatible with a mobile device and allows one to search documents by text or formula fragments. Moreover, it gives professors the ability to develop the latest technology educational materials, without qualified technicians' assistance, thus improving the quality of the whole educational process.

Electronic Procedures for Medical Operations

NASA Technical Reports Server (NTRS)

2015-01-01

Electronic procedures are replacing text-based documents for recording the steps in performing medical operations aboard the International Space Station. S&K Aerospace, LLC, has developed a content-based electronic system-based on the Extensible Markup Language (XML) standard-that separates text from formatting standards and tags items contained in procedures so they can be recognized by other electronic systems. For example, to change a standard format, electronic procedures are changed in a single batch process, and the entire body of procedures will have the new format. Procedures can be quickly searched to determine which are affected by software and hardware changes. Similarly, procedures are easily shared with other electronic systems. The system also enables real-time data capture and automatic bookmarking of current procedure steps. In Phase II of the project, S&K Aerospace developed a Procedure Representation Language (PRL) and tools to support the creation and maintenance of electronic procedures for medical operations. The goal is to develop these tools in such a way that new advances can be inserted easily, leading to an eventual medical decision support system.

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.

FuGEFlow: data model and markup language for flow cytometry.

PubMed

Qian, Yu; Tchuvatkina, Olga; Spidlen, Josef; Wilkinson, Peter; Gasparetto, Maura; Jones, Andrew R; Manion, Frank J; Scheuermann, Richard H; Sekaly, Rafick-Pierre; Brinkman, Ryan R

2009-06-16

Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata. We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description. The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project. We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development.

ART-ML - a novel XML format for the biological procedures modeling and the representation of blood flow simulation.

PubMed

Karvounis, E C; Tsakanikas, V D; Fotiou, E; Fotiadis, D I

2010-01-01

The paper proposes a novel Extensible Markup Language (XML) based format called ART-ML that aims at supporting the interoperability and the reuse of models of blood flow, mass transport and plaque formation, exported by 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 easy to handle 3D representations. The platform incorporates efficient algorithms which are able to perform blood flow simulation. In addition atherosclerotic plaque development is estimated taking into account morphological, flow and genetic factors. ART-ML provides a XML format that enables the representation and management of embedded models within the ARTool platform and the storage and interchange of well-defined information. This approach influences in the model creation, model exchange, model reuse and result evaluation.

Force-directed visualization for conceptual data models

NASA Astrophysics Data System (ADS)

Battigaglia, Andrew; Sutter, Noah

2017-03-01

Conceptual data models are increasingly stored in an eXtensible Markup Language (XML) format because of its portability between different systems and the ability of databases to use this format for storing data. However, when attempting to capture business or design needs, an organized graphical format is preferred in order to facilitate communication to receive as much input as possible from users and subject-matter experts. Existing methods of achieving this conversion suffer from problems of not being specific enough to capture all of the needs of conceptual data modeling and not being able to handle a large number of relationships between entities. This paper describes an implementation for a modeling solution to clearly illustrate conceptual data models stored in XML formats in well organized and structured diagrams. A force layout with several different parameters is applied to the diagram to create both compact and easily traversable relationships between entities.

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

PubMed

Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wengler, Katja; Bergmann, Frank T

2015-06-01

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

The Systems Biology Markup Language (SBML) Level 3 Package: Layout, Version 1 Core.

PubMed

Gauges, Ralph; Rost, Ursula; Sahle, Sven; Wengler, Katja; Bergmann, Frank Thomas

2015-09-04

Many software tools provide facilities for depicting reaction network diagrams in a visual form. Two aspects of such a visual diagram can be distinguished: the layout (i.e.: the positioning and connections) of the elements in the diagram, and the graphical form of the elements (for example, the glyphs used for symbols, the properties of the lines connecting them, and so on). For software tools that also read and write models in SBML (Systems Biology Markup Language) format, a common need is to store the network diagram together with the SBML representation of the model. This in turn raises the question of how to encode the layout and the rendering of these diagrams. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding diagrams, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The Layout package for SBML Level 3 adds the necessary features to SBML so that diagram layouts can be encoded in SBML files, and a companion package called SBML Rendering specifies how the graphical rendering of elements can be encoded. The SBML Layout package is based on the principle that reaction network diagrams should be described as representations of entities such as species and reactions (with direct links to the underlying SBML elements), and not as arbitrary drawings or graphs; for this reason, existing languages for the description of vector drawings (such as SVG) or general graphs (such as GraphML) cannot be used.

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)

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)

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.

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.

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/.

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.

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

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.

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…

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…

Archive of Boomer seismic reflection data: collected during USGS Cruise 96CCT01, nearshore south central South Carolina coast, June 26 - July 1, 1996

USGS Publications Warehouse

Calderon, Karynna; Dadisman, Shawn V.; Kindinger, Jack G.; Flocks, James G.; Wiese, Dana S.

2003-01-01

This archive consists of marine seismic reflection profile data collected in four survey areas from southeast of Charleston Harbor to the mouth of the North Edisto River of South Carolina. These data were acquired June 26 - July 1, 1996, aboard the R/V G.K. Gilbert. Included here are data in a variety of formats including binary, American Standard Code for Information Interchange (ASCII), Hyper Text Markup Language (HTML), Portable Document Format (PDF), Rich Text Format (RTF), Graphics Interchange Format (GIF) and Joint Photographic Experts Group (JPEG) images, and shapefiles. Binary data are in Society of Exploration Geophysicists (SEG) SEG-Y format and may be downloaded for further processing or display. Reference maps and GIF images of the profiles may be viewed with a web browser. The Geographic Information Systems (GIS) map documents provided were created with Environmental Systems Research Institute (ESRI) GIS software ArcView 3.2 and 8.1.

Getting Your GIS Data into Google Earth: Data Conversion Tools and Tips

NASA Astrophysics Data System (ADS)

Nurik, R.; Marks, M.

2009-12-01

Google Earth is a powerful platform for displaying your data. You can easily visualize content using the Keyhole Markup Language (KML). But what if you don't have your data in KML format? GIS data comes in a wide variety of formats, including .shp files, CSV, and many others. What can you do? This session will walk you through some of the tools for converting data to KML format. We will explore a variety of tools, including: Google Earth Pro, GDAL/OGR, KML2KML, etc. This session will be paced so that you can follow along on your laptop if you wish. Should you want to follow along, bring a laptop, and install the trial versions of Google Earth Pro and KML2KML. It is also recommended that you download GDAL from gdal.org and install it on your system.

Archive of chirp seismic reflection data collected during USGS cruises 00SCC02 and 00SCC04, Barataria Basin, Louisiana, May 12-31 and June 17-July 2, 2000

USGS Publications Warehouse

Calderon, Karynna; Dadisman, S.V.; Kindinger, J.L.; Flocks, J.G.; Wiese, D.S.; Kulp, Mark; Penland, Shea; Britsch, L.D.; Brooks, G.R.

2003-01-01

This archive consists of two-dimensional marine seismic reflection profile data collected in the Barataria Basin of southern Louisiana. These data were acquired in May, June, and July of 2000 aboard the R/V G.K. Gilbert. Included here are data in a variety of formats including binary, American Standard Code for Information Interchange (ASCII), Hyper-Text Markup Language (HTML), shapefiles, and Graphics Interchange Format (GIF) and Joint Photographic Experts Group (JPEG) images. Binary data are in Society of Exploration Geophysicists (SEG) SEG-Y format and may be downloaded for further processing or display. Reference maps and GIF images of the profiles may be viewed with a web browser. The Geographic Information Systems (GIS) information provided here is compatible with Environmental Systems Research Institute (ESRI) GIS software.

Kinetic Modeling using BioPAX ontology

PubMed Central

Ruebenacker, Oliver; Moraru, Ion. I.; Schaff, James C.; Blinov, Michael L.

2010-01-01

Thousands of biochemical interactions are available for download from curated databases such as Reactome, Pathway Interaction Database and other sources in the Biological Pathways Exchange (BioPAX) format. However, the BioPAX ontology does not encode the necessary information for kinetic modeling and simulation. The current standard for kinetic modeling is the System Biology Markup Language (SBML), but only a small number of models are available in SBML format in public repositories. Additionally, reusing and merging SBML models presents a significant challenge, because often each element has a value only in the context of the given model, and information encoding biological meaning is absent. We describe a software system that enables a variety of operations facilitating the use of BioPAX data to create kinetic models that can be visualized, edited, and simulated using the Virtual Cell (VCell), including improved conversion to SBML (for use with other simulation tools that support this format). PMID:20862270

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)....

FastScript3D - A Companion to Java 3D

NASA Technical Reports Server (NTRS)

Koenig, Patti

2005-01-01

FastScript3D is a computer program, written in the Java 3D(TM) programming language, that establishes an alternative language that helps users who lack expertise in Java 3D to use Java 3D for constructing three-dimensional (3D)-appearing graphics. The FastScript3D language provides a set of simple, intuitive, one-line text-string commands for creating, controlling, and animating 3D models. The first word in a string is the name of a command; the rest of the string contains the data arguments for the command. The commands can also be used as an aid to learning Java 3D. Developers can extend the language by adding custom text-string commands. The commands can define new 3D objects or load representations of 3D objects from files in formats compatible with such other software systems as X3D. The text strings can be easily integrated into other languages. FastScript3D facilitates communication between scripting languages [which enable programming of hyper-text markup language (HTML) documents to interact with users] and Java 3D. The FastScript3D language can be extended and customized on both the scripting side and the Java 3D side.

FuGEFlow: data model and markup language for flow cytometry

PubMed Central

Qian, Yu; Tchuvatkina, Olga; Spidlen, Josef; Wilkinson, Peter; Gasparetto, Maura; Jones, Andrew R; Manion, Frank J; Scheuermann, Richard H; Sekaly, Rafick-Pierre; Brinkman, Ryan R

2009-01-01

Background Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata. Methods We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description. Results The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project. Conclusion We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development. PMID:19531228

The Gel Electrophoresis Markup Language (GelML) from the Proteomics Standards Initiative

PubMed Central

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

2011-01-01

The Human Proteome Organisation’s Proteomics Standards Initiative (HUPO-PSI) has developed the GelML 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 mass spectrometry 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. PMID:20677327

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.

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)

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.

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"…

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…

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.

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

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.

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.

C3I and Modelling and Simulation (M&S) Interoperability

DTIC Science & Technology

2004-03-01

customised Open Source products. The technical implementation is based on the use of the eXtendend Markup Language (XML) and Python . XML is developed...to structure, store and send information. The language is focus on the description of data. Python is a portable, interpreted, object-oriented...programming language. A huge variety of usable Open Source Projects were issued by the Python Community. 3.1 Phase 1: Feasibility Studies Phase 1 was

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.

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.

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

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).

Benefits to the Simulation Training Community of a New ANSI Standard for the Exchange of Aero Simulation Models

NASA Technical Reports Server (NTRS)

Hildreth, Bruce L.; Jackson, E. Bruce

2009-01-01

The American Institute of Aeronautics Astronautics (AIAA) Modeling and Simulation Technical Committee is in final preparation of a new standard for the exchange of flight dynamics models. The standard will become an ANSI standard and is under consideration for submission to ISO for acceptance by the international community. The standard has some a spects that should provide benefits to the simulation training community. Use of the new standard by the training simulation community will reduce development, maintenance and technical refresh investment on each device. Furthermore, it will significantly lower the cost of performing model updates to improve fidelity or expand the envelope of the training device. Higher flight fidelity should result in better transfer of training, a direct benefit to the pilots under instruction. Costs of adopting the standard are minimal and should be paid back within the cost of the first use for that training device. The standard achie ves these advantages by making it easier to update the aerodynamic model. It provides a standard format for the model in a custom eXtensible Markup Language (XML) grammar, the Dynamic Aerospace Vehicle Exchange Markup Language (DAVE-ML). It employs an existing XML grammar, MathML, to describe the aerodynamic model in an input data file, eliminating the requirement for actual software compilation. The major components of the aero model become simply an input data file, and updates are simply new XML input files. It includes naming and axis system conventions to further simplify the exchange of information.

Open Babel: An open chemical toolbox

PubMed Central

2011-01-01

Background A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendor-neutral formats. Results We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license from http://openbabel.org. PMID:21982300

Spectra, chromatograms, Metadata: mzML-the standard data format for mass spectrometer output.

PubMed

Turewicz, Michael; Deutsch, Eric W

2011-01-01

This chapter describes Mass Spectrometry Markup Language (mzML), an XML-based and vendor-neutral standard data format for storage and exchange of mass spectrometer output like raw spectra and peak lists. It is intended to replace its two precursor data formats (mzData and mzXML), which had been developed independently a few years earlier. Hence, with the release of mzML, the problem of having two different formats for the same purposes is solved, and with it the duplicated effort of maintaining and supporting two data formats. The new format has been developed by a broad-based consortium of major instrument vendors, software vendors, and academic researchers under the aegis of the Human Proteome Organisation (HUPO), Proteomics Standards Initiative (PSI), with full participation of the main developers of the precursor formats. This comprehensive approach helped mzML to become a generally accepted standard. Furthermore, the collaborative development insured that mzML has adopted the best features of its precursor formats. In this chapter, we discuss mzML's development history, its design principles and use cases, as well as its main building components. We also present the available documentation, an example file, and validation software for mzML.

MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data.

PubMed

Bunk, Boyke; Kucklick, Martin; Jonas, Rochus; Münch, Richard; Schobert, Max; Jahn, Dieter; Hiller, Karsten

2006-12-01

MetaQuant is a Java-based program for the automatic and accurate quantification of GC/MS-based metabolome data. In contrast to other programs MetaQuant is able to quantify hundreds of substances simultaneously with minimal manual intervention. The integration of a self-acting calibration function allows the parallel and fast calibration for several metabolites simultaneously. Finally, MetaQuant is able to import GC/MS data in the common NetCDF format and to export the results of the quantification into Systems Biology Markup Language (SBML), Comma Separated Values (CSV) or Microsoft Excel (XLS) format. MetaQuant is written in Java and is available under an open source license. Precompiled packages for the installation on Windows or Linux operating systems are freely available for download. The source code as well as the installation packages are available at http://bioinformatics.org/metaquant

MOCCASIN: converting MATLAB ODE models to SBML.

PubMed

Gómez, Harold F; Hucka, Michael; Keating, Sarah M; Nudelman, German; Iber, Dagmar; Sealfon, Stuart C

2016-06-15

MATLAB is popular in biological research for creating and simulating models that use ordinary differential equations (ODEs). However, sharing or using these models outside of MATLAB is often problematic. A community standard such as Systems Biology Markup Language (SBML) can serve as a neutral exchange format, but translating models from MATLAB to SBML can be challenging-especially for legacy models not written with translation in mind. We developed MOCCASIN (Model ODE Converter for Creating Automated SBML INteroperability) to help. MOCCASIN can convert ODE-based MATLAB models of biochemical reaction networks into the SBML format. MOCCASIN is available under the terms of the LGPL 2.1 license (http://www.gnu.org/licenses/lgpl-2.1.html). Source code, binaries and test cases can be freely obtained from https://github.com/sbmlteam/moccasin : mhucka@caltech.edu More information is available at https://github.com/sbmlteam/moccasin. © The Author 2016. Published by Oxford University Press.

Standardization of XML Database Exchanges and the James Webb Space Telescope Experience

NASA Technical Reports Server (NTRS)

Gal-Edd, Jonathan; Detter, Ryan; Jones, Ron; Fatig, Curtis C.

2007-01-01

Personnel from the National Aeronautics and Space Administration (NASA) James Webb Space Telescope (JWST) Project have been working with various standard communities such the Object Management Group (OMG) and the Consultative Committee for Space Data Systems (CCSDS) to assist in the definition of a common extensible Markup Language (XML) for database exchange format. The CCSDS and OMG standards are intended for the exchange of core command and telemetry information, not for all database information needed to exercise a NASA space mission. The mission-specific database, containing all the information needed for a space mission, is translated from/to the standard using a translator. The standard is meant to provide a system that encompasses 90% of the information needed for command and telemetry processing. This paper will discuss standardization of the XML database exchange format, tools used, and the JWST experience, as well as future work with XML standard groups both commercial and government.

SED-ED, a workflow editor for computational biology experiments written in SED-ML.

PubMed

Adams, Richard R

2012-04-15

The simulation experiment description markup language (SED-ML) is a new community data standard to encode computational biology experiments in a computer-readable XML format. Its widespread adoption will require the development of software support to work with SED-ML files. Here, we describe a software tool, SED-ED, to view, edit, validate and annotate SED-ML documents while shielding end-users from the underlying XML representation. SED-ED supports modellers who wish to create, understand and further develop a simulation description provided in SED-ML format. SED-ED is available as a standalone Java application, as an Eclipse plug-in and as an SBSI (www.sbsi.ed.ac.uk) plug-in, all under an MIT open-source license. Source code is at https://sed-ed-sedmleditor.googlecode.com/svn. The application itself is available from https://sourceforge.net/projects/jlibsedml/files/SED-ED/.

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.

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.

QuakeML - An XML Schema for Seismology

NASA Astrophysics Data System (ADS)

Wyss, A.; Schorlemmer, D.; Maraini, S.; Baer, M.; Wiemer, S.

2004-12-01

We propose an extensible format-definition for seismic data (QuakeML). Sharing data and seismic information efficiently is one of the most important issues for research and observational seismology in the future. The eXtensible Markup Language (XML) is playing an increasingly important role in the exchange of a variety of data. Due to its extensible definition capabilities, its wide acceptance and the existing large number of utilities and libraries for XML, a structured representation of various types of seismological data should in our opinion be developed by defining a 'QuakeML' standard. Here we present the QuakeML definitions for parameter databases and further efforts, e.g. a central QuakeML catalog database and a web portal for exchanging codes and stylesheets.

Master Metadata Repository and Metadata-Management System

NASA Technical Reports Server (NTRS)

Armstrong, Edward; Reed, Nate; Zhang, Wen

2007-01-01

A master metadata repository (MMR) software system manages the storage and searching of metadata pertaining to data from national and international satellite sources of the Global Ocean Data Assimilation Experiment (GODAE) High Resolution Sea Surface Temperature Pilot Project [GHRSSTPP]. These sources produce a total of hundreds of data files daily, each file classified as one of more than ten data products representing global sea-surface temperatures. The MMR is a relational database wherein the metadata are divided into granulelevel records [denoted file records (FRs)] for individual satellite files and collection-level records [denoted data set descriptions (DSDs)] that describe metadata common to all the files from a specific data product. FRs and DSDs adhere to the NASA Directory Interchange Format (DIF). The FRs and DSDs are contained in separate subdatabases linked by a common field. The MMR is configured in MySQL database software with custom Practical Extraction and Reporting Language (PERL) programs to validate and ingest the metadata records. The database contents are converted into the Federal Geographic Data Committee (FGDC) standard format by use of the Extensible Markup Language (XML). A Web interface enables users to search for availability of data from all sources.

Google-Earth Based Visualizations for Environmental Flows and Pollutant Dispersion in Urban Areas

PubMed Central

Liu, Daoming; Kenjeres, Sasa

2017-01-01

In the present study, we address the development and application of an efficient tool for conversion of results obtained by an integrated computational fluid dynamics (CFD) and computational reaction dynamics (CRD) approach and their visualization in the Google Earth. We focus on results typical for environmental fluid mechanics studies at a city scale that include characteristic wind flow patterns and dispersion of reactive scalars. This is achieved by developing a code based on the Java language, which converts the typical four-dimensional structure (spatial and temporal dependency) of data results in the Keyhole Markup Language (KML) format. The visualization techniques most often used are revisited and implemented into the conversion tool. The potential of the tool is demonstrated in a case study of smog formation due to an intense traffic emission in Rotterdam (The Netherlands). It is shown that the Google Earth can provide a computationally efficient and user-friendly means of data representation. This feature can be very useful for visualization of pollution at street levels, which is of great importance for the city residents. Various meteorological and traffic emissions can be easily visualized and analyzed, providing a powerful, user-friendly tool for traffic regulations and urban climate adaptations. PMID:28257078

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)

Comparing Emerging XML Based Formats from a Multi-discipline Perspective

NASA Astrophysics Data System (ADS)

Sawyer, D. M.; Reich, L. I.; Nikhinson, S.

2002-12-01

This paper analyzes the similarity and differences among several examples of an emerging generation of Scientific Data Formats that are based on XML technologies. Some of the factors evaluated include the goals of these efforts, the data models, and XML technologies used, and the maturity of currently available software. This paper then investigates the practicality of developing a single set of structural data objects and basic scientific concepts, such as units, that could be used across discipline boundaries and extended by disciplines and missions to create Scientific Data Formats for their communities. This analysis is partly based on an effort sponsored by the ESDIS office at GSFC to compare the Earth Science Markup Language (ESML) and the eXtensible Data Format( XDF), two members of this new generation of XML based Data Description Languages that have been developed by NASA funded efforts in recent years. This paper adds FITSML and potentially CDFML to the list of XML based Scientific Data Formats discussed. This paper draws heavily a Formats Evolution Process Committee (http://ssdoo.gsfc.nasa.gov/nost/fep/) draft white paper primarily developed by Lou Reich, Mike Folk and Don Sawyer to assist the Space Science community in understanding Scientific Data Formats. One of primary conclusions of that paper is that a scientific data format object model should be examined along two basic axes. The first is the complexity of the computer/mathematical data types supported and the second is the level of scientific domain specialization incorporated. This paper also discusses several of the issues that affect the decision on whether to implement a discipline or project specific Scientific Data Format as a formal extension of a general purpose Scientific Data Format or to implement the APIs independently.

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

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.

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

The E-Book: Pipe Dream or Potential Disaster?

ERIC Educational Resources Information Center

Dorman, David

1999-01-01

Discusses the development of electronic books and considers marketing and distribution, rights management, and technical standards. Economic and institutional relationships, copyrights, Extensible Markup Language (XML), access to content, free access versus fees, preservation versus loss of control over long-term storage and access, and trusted…

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,…

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…

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

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.

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

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

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.

Report of Official Foreign Travel to France May 8-27, 1998

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

mason, j d

1998-06-11

The Department of Energy (DOE) has moved ever more rapidly towards electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Among the most widely adopted standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), which DOE has selected as the basis of its electronic management of documents. Besides the official commitment, which has resulted in several specializedmore » projects, DOE makes heavy use of coding derived from SGML, and its use is likely to increase in the future. Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Microsoft, Adobe, and Netscape, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, I have served since 1985 as Convenor of the international committee responsible for SGML and related standards, ISO/IEC JTC1/WG4 (WG4). During this trip I convened the spring 1998 meeting of WG4 in Paris, France. I also attended a major conference on the use of SGML and XML. At the close of the conference, I chaired a workshop of standards developers looking at ways of improving online searching of electronic documents. Note: Since the end of the meetings in France, JTC1 has raised the level of WG4 to a full Subcommittee; its designator is now ISO/IEC JTC1/SC34. WG4 maintains and continues to enhance several standards. In addition to SGML, which is the basis of HTML and XML, WG4 also works on the Document Style Semantics and Specification Language (DSSSL), which is the basis for the W3C's XSL (eXtensible Style Language, to be used with XML) and the Hypermedia/Time-based Document Structuring Language (HyTime), which is a major influence on the W3C's XLink (XML Linking Language). WG4 is also involved in work with the ISO's TC184, Industrial Data, on the linking of STEP (the standard for the interchange of product model data) with SGML. In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there are several SGML-based projects at the Y-12 Plant. My project team in Information Technology Services has developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at Y-12 and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). Supporting standards development allows DOE and Y-12 both input into the process and the opportunity to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML and related topics.« less

The field representation language.

PubMed

Tsafnat, Guy

2008-02-01

The complexity of quantitative biomedical models, and the rate at which they are published, is increasing to a point where managing the information has become all but impossible without automation. International efforts are underway to standardise representation languages for a number of mathematical entities that represent a wide variety of physiological systems. This paper presents the Field Representation Language (FRL), a portable representation of values that change over space and/or time. FRL is an extensible mark-up language (XML) derivative with support for large numeric data sets in Hierarchical Data Format version 5 (HDF5). Components of FRL can be reused through unified resource identifiers (URI) that point to external resources such as custom basis functions, boundary geometries and numerical data. To demonstrate the use of FRL as an interchange we present three models that study hyperthermia cancer treatment: a fractal model of liver tumour microvasculature; a probabilistic model simulating the deposition of magnetic microspheres throughout it; and a finite element model of hyperthermic treatment. The microsphere distribution field was used to compute the heat generation rate field around the tumour. We used FRL to convey results from the microsphere simulation to the treatment model. FRL facilitated the conversion of the coordinate systems and approximated the integral over regions of the microsphere deposition field.

Providing Geographic Datasets as Linked Data in Sdi

NASA Astrophysics Data System (ADS)

Hietanen, E.; Lehto, L.; Latvala, P.

2016-06-01

In this study, a prototype service to provide data from Web Feature Service (WFS) as linked data is implemented. At first, persistent and unique Uniform Resource Identifiers (URI) are created to all spatial objects in the dataset. The objects are available from those URIs in Resource Description Framework (RDF) data format. Next, a Web Ontology Language (OWL) ontology is created to describe the dataset information content using the Open Geospatial Consortium's (OGC) GeoSPARQL vocabulary. The existing data model is modified in order to take into account the linked data principles. The implemented service produces an HTTP response dynamically. The data for the response is first fetched from existing WFS. Then the Geographic Markup Language (GML) format output of the WFS is transformed on-the-fly to the RDF format. Content Negotiation is used to serve the data in different RDF serialization formats. This solution facilitates the use of a dataset in different applications without replicating the whole dataset. In addition, individual spatial objects in the dataset can be referred with URIs. Furthermore, the needed information content of the objects can be easily extracted from the RDF serializations available from those URIs. A solution for linking data objects to the dataset URI is also introduced by using the Vocabulary of Interlinked Datasets (VoID). The dataset is divided to the subsets and each subset is given its persistent and unique URI. This enables the whole dataset to be explored with a web browser and all individual objects to be indexed by search engines.

Managing the computational chemistry big data problem: the ioChem-BD platform.

PubMed

Álvarez-Moreno, M; de Graaf, C; López, N; Maseras, F; Poblet, J M; Bo, C

2015-01-26

We present the ioChem-BD platform ( www.iochem-bd.org ) as a multiheaded tool aimed to manage large volumes of quantum chemistry results from a diverse group of already common simulation packages. The platform has an extensible structure. The key modules managing the main tasks are to (i) upload of output files from common computational chemistry packages, (ii) extract meaningful data from the results, and (iii) generate output summaries in user-friendly formats. A heavy use of the Chemical Mark-up Language (CML) is made in the intermediate files used by ioChem-BD. From them and using XSL techniques, we manipulate and transform such chemical data sets to fulfill researchers' needs in the form of HTML5 reports, supporting information, and other research media.

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

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…

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

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.

ccML, a new mark-up language to improve ISO/EN 13606-based electronic health record extracts practical edition.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Cáceres, Jesús; Somolinos, Roberto; Pascual, Mario; Martínez, Ignacio; Salvador, Carlos H; Monteagudo, José Luis

2013-01-01

The objective of this paper is to introduce a new language called ccML, designed to provide convenient pragmatic information to applications using the ISO/EN13606 reference model (RM), such as electronic health record (EHR) extracts editors. EHR extracts are presently built using the syntactic and semantic information provided in the RM and constrained by archetypes. The ccML extra information enables the automation of the medico-legal context information edition, which is over 70% of the total in an extract, without modifying the RM information. ccML is defined using a W3C XML schema file. Valid ccML files complement the RM with additional pragmatics information. The ccML language grammar is defined using formal language theory as a single-type tree grammar. The new language is tested using an EHR extracts editor application as proof-of-concept system. Seven ccML PVCodes (predefined value codes) are introduced in this grammar to cope with different realistic EHR edition situations. These seven PVCodes have different interpretation strategies, from direct look up in the ccML file itself, to more complex searches in archetypes or system precomputation. The possibility to declare generic types in ccML gives rise to ambiguity during interpretation. The criterion used to overcome ambiguity is that specificity should prevail over generality. The opposite would make the individual specific element declarations useless. A new mark-up language ccML is introduced that opens up the possibility of providing applications using the ISO/EN13606 RM with the necessary pragmatics information to be practical and realistic.

MRML: an extensible communication protocol for interoperability and benchmarking of multimedia information retrieval systems

NASA Astrophysics Data System (ADS)

Mueller, Wolfgang; Mueller, Henning; Marchand-Maillet, Stephane; Pun, Thierry; Squire, David M.; Pecenovic, Zoran; Giess, Christoph; de Vries, Arjen P.

2000-10-01

While in the area of relational databases interoperability is ensured by common communication protocols (e.g. ODBC/JDBC using SQL), Content Based Image Retrieval Systems (CBIRS) and other multimedia retrieval systems are lacking both a common query language and a common communication protocol. Besides its obvious short term convenience, interoperability of systems is crucial for the exchange and analysis of user data. In this paper, we present and describe an extensible XML-based query markup language, called MRML (Multimedia Retrieval markup Language). MRML is primarily designed so as to ensure interoperability between different content-based multimedia retrieval systems. Further, MRML allows researchers to preserve their freedom in extending their system as needed. MRML encapsulates multimedia queries in a way that enable multimedia (MM) query languages, MM content descriptions, MM query engines, and MM user interfaces to grow independently from each other, reaching a maximum of interoperability while ensuring a maximum of freedom for the developer. For benefitting from this, only a few simple design principles have to be respected when extending MRML for one's fprivate needs. The design of extensions withing the MRML framework will be described in detail in the paper. MRML has been implemented and tested for the CBIRS Viper, using the user interface Snake Charmer. Both are part of the GNU project and can be downloaded at our site.

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…

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.…

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…

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…

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)

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.

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…

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

DTIC Science & Technology

2006-08-01

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

Integrating and visualizing primary data from prospective and legacy taxonomic literature

PubMed Central

Agosti, Donat; Penev, Lyubomir; Sautter, Guido; Georgiev, Teodor; Catapano, Terry; Patterson, David; King, David; Pereira, Serrano; Vos, Rutger Aldo; Sierra, Soraya

2015-01-01

Abstract Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions. PMID:26023286

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.…

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…

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…

ccML, a new mark-up language to improve ISO/EN 13606-based electronic health record extracts practical edition

PubMed Central

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Cáceres, Jesús; Somolinos, Roberto; Pascual, Mario; Martínez, Ignacio; Salvador, Carlos H; Monteagudo, José Luis

2013-01-01

Objective The objective of this paper is to introduce a new language called ccML, designed to provide convenient pragmatic information to applications using the ISO/EN13606 reference model (RM), such as electronic health record (EHR) extracts editors. EHR extracts are presently built using the syntactic and semantic information provided in the RM and constrained by archetypes. The ccML extra information enables the automation of the medico-legal context information edition, which is over 70% of the total in an extract, without modifying the RM information. Materials and Methods ccML is defined using a W3C XML schema file. Valid ccML files complement the RM with additional pragmatics information. The ccML language grammar is defined using formal language theory as a single-type tree grammar. The new language is tested using an EHR extracts editor application as proof-of-concept system. Results Seven ccML PVCodes (predefined value codes) are introduced in this grammar to cope with different realistic EHR edition situations. These seven PVCodes have different interpretation strategies, from direct look up in the ccML file itself, to more complex searches in archetypes or system precomputation. Discussion The possibility to declare generic types in ccML gives rise to ambiguity during interpretation. The criterion used to overcome ambiguity is that specificity should prevail over generality. The opposite would make the individual specific element declarations useless. Conclusion A new mark-up language ccML is introduced that opens up the possibility of providing applications using the ISO/EN13606 RM with the necessary pragmatics information to be practical and realistic. PMID:23019241

Collaborative business process support in eHealth: integrating IHE profiles through ebXML business process specification language.

PubMed

Dogac, Asuman; Kabak, Yildiray; Namli, Tuncay; Okcan, Alper

2008-11-01

Integrating healthcare enterprise (IHE) specifies integration profiles describing selected real world use cases to facilitate the interoperability of healthcare information resources. While realizing a complex real-world scenario, IHE profiles are combined by grouping the related IHE actors. Grouping IHE actors implies that the associated business processes (IHE profiles) that the actors are involved must be combined, that is, the choreography of the resulting collaborative business process must be determined by deciding on the execution sequence of transactions coming from different profiles. There are many IHE profiles and each user or vendor may support a different set of IHE profiles that fits to its business need. However, determining the precedence of all the involved transactions manually for each possible combination of the profiles is a very tedious task. In this paper, we describe how to obtain the overall business process automatically when IHE actors are grouped. For this purpose, we represent the IHE profiles through a standard, machine-processable language, namely, Organization for the Advancement of Structured Information Standards (OASIS) ebusiness eXtensible Markup Language (ebXML) Business Process Specification (ebBP) Language. We define the precedence rules among the transactions of the IHE profiles, again, in a machine-processable way. Then, through a graphical tool, we allow users to select the actors to be grouped and automatically produce the overall business process in a machine-processable format.

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

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…

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…

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

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,…

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...

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

Integrated Reconfigurable Intelligent Systems (IRIS) for Complex Naval Systems

DTIC Science & Technology

2009-10-31

water system. This simplified chilled water system includes one chiller -pump plant and two service loads. • X- p«cM*MJ<w*4tf -a ’.•.wVlniX’i • V...and valve7. Pumps and chiller operation states are observable. Valve 7 is STUCKCLOSE at time / = 440sec (me 11th iteration). Valve 11 is STUCKCLOSE...framework is a product from Adobe called Flex. The product is a mixture of the Adobe Action script programming language and a markup language call MXML

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.

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

PubMed

de Jong, Wibe A; Walker, Andrew M; Hanwell, Marcus D

2013-05-24

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 an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. 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 and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple "Google-style" searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature.

Improving Groundwater Data Interoperability: Results of the Second OGC Groundwater Interoperability Experiment

NASA Astrophysics Data System (ADS)

Lucido, J. M.; Booth, N.

2014-12-01

Interoperable sharing of groundwater data across international boarders is essential for the proper management of global water resources. However storage and management of groundwater data is often times distributed across many agencies or organizations. Furthermore these data may be represented in disparate proprietary formats, posing a significant challenge for integration. For this reason standard data models are required to achieve interoperability across geographical and political boundaries. The GroundWater Markup Language 1.0 (GWML1) was developed in 2010 as an extension of the Geography Markup Language (GML) in order to support groundwater data exchange within Spatial Data Infrastructures (SDI). In 2013, development of GWML2 was initiated under the sponsorship of the Open Geospatial Consortium (OGC) for intended adoption by the international community as the authoritative standard for the transfer of groundwater feature data, including data about water wells, aquifers, and related entities. GWML2 harmonizes GWML1 and the EU's INSPIRE models related to geology and hydrogeology. Additionally, an interoperability experiment was initiated to test the model for commercial, technical, scientific, and policy use cases. The scientific use case focuses on the delivery of data required for input into computational flow modeling software used to determine the flow of groundwater within a particular aquifer system. It involves the delivery of properties associated with hydrogeologic units, observations related to those units, and information about the related aquifers. To test this use case web services are being implemented using GWML2 and WaterML2, which is the authoritative standard for water time series observations, in order to serve USGS water well and hydrogeologic data via standard OGC protocols. Furthermore, integration of these data into a computational groundwater flow model will be tested. This submission will present the GWML2 information model and results of an interoperability experiment with a particular emphasis on the scientific use case.

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

PubMed Central

2013-01-01

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 an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization. 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 and molecular orbitals used by the computational chemistry software. Draft dictionary entries and a format for molecular orbitals within CML CompChem were developed. The Avogadro application was extended to read in CML data, and display molecular geometry and electronic structure in the GUI allowing for an end-to-end solution where Avogadro can create input structures, generate input files, NWChem can run the calculation and Avogadro can then read in and analyse the CML output produced. The developments outlined in this paper will be made available in future releases of NWChem, FoX, and Avogadro. Conclusions The production of CML compliant XML files for computational chemistry software such as NWChem can be accomplished relatively easily using the FoX library. The CML data can be read in by a newly developed reader in Avogadro and analysed or visualized in various ways. A community-based effort is needed to further develop the CML CompChem convention and dictionary. This will enable the long-term goal of allowing a researcher to run simple “Google-style” searches of chemistry and physics and have the results of computational calculations returned in a comprehensible form alongside articles from the published literature. PMID:23705910

XML-based data model and architecture for a knowledge-based grid-enabled problem-solving environment for high-throughput biological imaging.

PubMed

Ahmed, Wamiq M; Lenz, Dominik; Liu, Jia; Paul Robinson, J; Ghafoor, Arif

2008-03-01

High-throughput biological imaging uses automated imaging devices to collect a large number of microscopic images for analysis of biological systems and validation of scientific hypotheses. Efficient manipulation of these datasets for knowledge discovery requires high-performance computational resources, efficient storage, and automated tools for extracting and sharing such knowledge among different research sites. Newly emerging grid technologies provide powerful means for exploiting the full potential of these imaging techniques. Efficient utilization of grid resources requires the development of knowledge-based tools and services that combine domain knowledge with analysis algorithms. In this paper, we first investigate how grid infrastructure can facilitate high-throughput biological imaging research, and present an architecture for providing knowledge-based grid services for this field. We identify two levels of knowledge-based services. The first level provides tools for extracting spatiotemporal knowledge from image sets and the second level provides high-level knowledge management and reasoning services. We then present cellular imaging markup language, an extensible markup language-based language for modeling of biological images and representation of spatiotemporal knowledge. This scheme can be used for spatiotemporal event composition, matching, and automated knowledge extraction and representation for large biological imaging datasets. We demonstrate the expressive power of this formalism by means of different examples and extensive experimental results.

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.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis.

PubMed

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. http://www.cemb.edu.pk/sw.html RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language.

Illuminating Northern California’s Active Faults

USGS Publications Warehouse

Prentice, Carol S.; Crosby, Christopher J.; Whitehill, Caroline S.; Arrowsmith, J. Ramon; Furlong, Kevin P.; Philips, David A.

2009-01-01

Newly acquired light detection and ranging (lidar) topographic data provide a powerful community resource for the study of landforms associated with the plate boundary faults of northern California (Figure 1). In the spring of 2007, GeoEarthScope, a component of the EarthScope Facility construction project funded by the U.S. National Science Foundation, acquired approximately 2000 square kilometers of airborne lidar topographic data along major active fault zones of northern California. These data are now freely available in point cloud (x, y, z coordinate data for every laser return), digital elevation model (DEM), and KMZ (zipped Keyhole Markup Language, for use in Google EarthTM and other similar software) formats through the GEON OpenTopography Portal (http://www.OpenTopography.org/data). Importantly, vegetation can be digitally removed from lidar data, producing high-resolution images (0.5- or 1.0-meter DEMs) of the ground surface beneath forested regions that reveal landforms typically obscured by vegetation canopy (Figure 2)

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.

XTCE GOVSAT Tool Suite 1.0

NASA Technical Reports Server (NTRS)

Rice, J. Kevin

2013-01-01

The XTCE GOVSAT software suite contains three tools: validation, search, and reporting. The Extensible Markup Language (XML) Telemetric and Command Exchange (XTCE) GOVSAT Tool Suite is written in Java for manipulating XTCE XML files. XTCE is a Consultative Committee for Space Data Systems (CCSDS) and Object Management Group (OMG) specification for describing the format and information in telemetry and command packet streams. These descriptions are files that are used to configure real-time telemetry and command systems for mission operations. XTCE s purpose is to exchange database information between different systems. XTCE GOVSAT consists of rules for narrowing the use of XTCE for missions. The Validation Tool is used to syntax check GOVSAT XML files. The Search Tool is used to search (i.e. command and telemetry mnemonics) the GOVSAT XML files and view the results. Finally, the Reporting Tool is used to create command and telemetry reports. These reports can be displayed or printed for use by the operations team.

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.

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.

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.

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.

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…

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

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…

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.

Report of Official foreign Travel to Spain April 17-29, 1999. (in English;)

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

Mason, j.d.

The Department of Energy (DOE) has moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards in preference to proprietary designs promoted as "standards" by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardization (ISO)more » and the American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), which DOE has selected as the basis of its electronic management of documents. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML, and its use is likely to increase in the future. Most documents on the WWW are coded in HTML ("Hypertext Markup Language"), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Microsoft, Adobe, and Netscape, is promoting XML ("eXtensible Markup Language"), a class of SGML applications, for the future of the WWW and the basis for EC. W3C has announced its intention of discontinuing future development of HTML and replacing it with XHTML, an application of XML. In support of DOE's use of these standards, I have served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During my April 1999 trip, I convened the spring 1999 meeting of SC34 in Granada, Spain. I also attended a major conference on the use of SGML and XML. SC34 maintains and continues to enhance several standards. In addition to SGML, which is the basis of HTML and XML, SC34 also works on the Document Style Semantics and Specification Language (DSSSL), which is the basis for W3C's XSL ("eXtensible Style Language," to be used with XML) and the Hypermedia/Time-based Document Structuring Language (HyTime), which is a major influence on W3C's XLink ("XML Linking Language"). SC34 is also involved in work with ISO's TC184, Industrial Data, on the linking of STEP (the standard for the interchange of product model data) with SGML. In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there are several SGML-based projects at the Y-12 Plant. My project team in Information Technology Services developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at the Y-12 Plant and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). Supporting standards development allows DOE and the Y-12 plant both input into the process and the opportunity to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML and related topics.« less

A methodology to annotate systems biology markup language models with the synthetic biology open language.

PubMed

Roehner, Nicholas; Myers, Chris J

2014-02-21

Recently, we have begun to witness the potential of synthetic biology, noted here in the form of bacteria and yeast that have been genetically engineered to produce biofuels, manufacture drug precursors, and even invade tumor cells. The success of these projects, however, has often failed in translation and application to new projects, a problem exacerbated by a lack of engineering standards that combine descriptions of the structure and function of DNA. To address this need, this paper describes a methodology to connect the systems biology markup language (SBML) to the synthetic biology open language (SBOL), existing standards that describe biochemical models and DNA components, respectively. Our methodology involves first annotating SBML model elements such as species and reactions with SBOL DNA components. A graph is then constructed from the model, with vertices corresponding to elements within the model and edges corresponding to the cause-and-effect relationships between these elements. Lastly, the graph is traversed to assemble the annotating DNA components into a composite DNA component, which is used to annotate the model itself and can be referenced by other composite models and DNA components. In this way, our methodology can be used to build up a hierarchical library of models annotated with DNA components. Such a library is a useful input to any future genetic technology mapping algorithm that would automate the process of composing DNA components to satisfy a behavioral specification. Our methodology for SBML-to-SBOL annotation is implemented in the latest version of our genetic design automation (GDA) software tool, iBioSim.

Common Data Format: New XML and Conversion Tools

NASA Astrophysics Data System (ADS)

Han, D. B.; Liu, M. H.; McGuire, R. E.

2002-12-01

Common Data Format (CDF) is a self-describing platform-independent data format for storing, accessing, and manipulating scalar and multidimensional scientific data sets. Significant benefit has accrued to specific science communities from their use of standard formats within those communities. Examples include the International Solar Terrestrial Physics (ISTP) community in using CDF for traditional space physics data (fields, particles and plasma, waves, and images), the worldwide astronomical community in using FITS (Flexible Image Transport System) for solar data (primarily spectral images), the NASA Planetary community in using Planetary Data System (PDS) Labels, and the earth science community in using Hierarchical Data Format (HDF). Scientific progress in solar-terrestrial physics continues to be impeded by the multiplicity of available standards for data formats and dearth of general data format translators. As a result, scientists today spend a significant amount of time translating data into the format they are familiar with for their research. To minimize this unnecessary data translation time and to allow more research time, the CDF office located at GSFC National Space Science Data Center (NSSDC) has developed HDF-to-CDF and FITS-to-CDF translators, and employed the eXtensible Markup Language (XML) technology to facilitate and promote data interoperability within the space science community. We will present the current status of the CDF work including the conversion tools that have been recently developed, conversion tools that are planned in the near future, share some of the XML experiences, and use the discussion to gain community feedback to our planned future work.

BIRD: Bio-Image Referral Database. Design and implementation of a new web based and patient multimedia data focused system for effective medical diagnosis and therapy.

PubMed

Pinciroli, Francesco; Masseroli, Marco; Acerbo, Livio A; Bonacina, Stefano; Ferrari, Roberto; Marchente, Mario

2004-01-01

This paper presents a low cost software platform prototype supporting health care personnel in retrieving patient referral multimedia data. These information are centralized in a server machine and structured by using a flexible eXtensible Markup Language (XML) Bio-Image Referral Database (BIRD). Data are distributed on demand to requesting client in an Intranet network and transformed via eXtensible Stylesheet Language (XSL) to be visualized in an uniform way on market browsers. The core server operation software has been developed in PHP Hypertext Preprocessor scripting language, which is very versatile and useful for crafting a dynamic Web environment.

CAD-based Automatic Modeling Method for Geant4 geometry model Through MCAM

NASA Astrophysics Data System (ADS)

Wang, Dong; Nie, Fanzhi; Wang, Guozhong; Long, Pengcheng; LV, Zhongliang; LV, Zhongliang

2014-06-01

Geant4 is a widely used Monte Carlo transport simulation package. Before calculating using Geant4, the calculation model need be established which could be described by using Geometry Description Markup Language (GDML) or C++ language. However, it is time-consuming and error-prone to manually describe the models by GDML. Automatic modeling methods have been developed recently, but there are some problem existed in most of present modeling programs, specially some of them were not accurate or adapted to specifically CAD format. To convert the GDML format models to CAD format accurately, a Geant4 Computer Aided Design (CAD) based modeling method was developed for automatically converting complex CAD geometry model into GDML geometry model. The essence of this method was dealing with CAD model represented with boundary representation (B-REP) and GDML model represented with constructive solid geometry (CSG). At first, CAD model was decomposed to several simple solids which had only one close shell. And then the simple solid was decomposed to convex shell set. Then corresponding GDML convex basic solids were generated by the boundary surfaces getting from the topological characteristic of a convex shell. After the generation of these solids, GDML model was accomplished with series boolean operations. This method was adopted in CAD/Image-based Automatic Modeling Program for Neutronics & Radiation Transport (MCAM), and tested with several models including the examples in Geant4 install package. The results showed that this method could convert standard CAD model accurately, and can be used for Geant4 automatic modeling.

Report of official foreign travel to France, June 7--20, 2000

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

J.D. Mason

2000-07-11

The Department of Energy (DOE) has moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards over proprietary designs promoted as ``standards'' by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardization (ISO) and themore » American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), to which DOE long ago made a commitment. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML: Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Adobe, IBM, Microsoft, Netscape, Oracle, and Sun, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, the authors has served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During his June 2000 trip, he chaired the spring 2000 meeting of SC34 in Paris, France. He also attended a major conference on the use of SGML and XML and led a meeting of the International SGML/XML Users' Group (ISUG). In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there are several SGML-based projects at the Oak Ridge Y-12 Plant. The local project team developed an SGML-based publications system that has been used for several major reports at the Y-12 Plant and Oak Ridge National Laboratory (ORNL). SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at the Y-12 Plant and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). The Ferret system for automated classification analysis will use XML to structure its knowledge base. Supporting standards development allows DOE and the Y-12 plant the opportunity both to provide input into the process and to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML and related topics.« less

The tissue micro-array data exchange specification: a web based experience browsing imported data

PubMed Central

Nohle, David G; Hackman, Barbara A; Ayers, Leona W

2005-01-01

Background The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11 blocks with 3812 cores from three other institutions were processed with the BrowseTMA tool. Fifty common data elements (CDE) from the TMA DES were used and 42 more created for site-specific data. Researchers can download TMA clinical data in the TMA DES format. Conclusion Virtual TMAs with clinical data can be viewed on the Internet by interested researchers using the BrowseTMA tool. We have organized our approach to producing, sorting, navigating and publishing TMA information to facilitate such review. We have converted Excel TMA data into TMA DES XML, and imported it and TMA DES XML from another institution into BrowseTMA to produce web pages that allow us to browse through the merged data. We proposed enhancements to the TMA DES as a result of this experience. We implemented improvements to the API TMA DES as a result of using exported data from several institutions. A document type definition was written for the API TMA DES (that optionally includes proposed enhancements). Independent validators can be used to check exports against the DTD (with or without the proposed enhancements). Linking tissue core images to readily navigable clinical data greatly improves the value of the TMA. PMID:16086837

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.

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.

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

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.

GeoGML - a Mark-up Language for 4-dimensional geomorphic objects and processes

NASA Astrophysics Data System (ADS)

Löwner, M.-O.

2009-04-01

We developed an use-oriented GML3 based data model that enables researchers to share 4-dimensional information about landforms and their process related interaction. Using the Unified Modelling Language it is implemented as a GML3-based application schema available on the Internet. As the science of the land's surface Geomorphology investigates landforms, their change, and the processes causing this change. The main problem of comparing research results in geomorphology is that the objects under investigation are composed of 3-dimensional geometries that change in time due to processes of material fluxes, e. g. soil erosion or mass movements. They have internal properties, e. g. soil texture or bulk density, that determine the effectiveness of these processes but are under change as well. Worldwide geographical data can be shared over the Internet using Web Feature Services. The precondition is the development of a semantic model or ontology based on international standards like GML3 as an implementation of the ISO 109107 and others. Here we present a GML3-based Mark-up Language or application schema for geomorphic purposes that fulfils the following requirements: First, an object-oriented view of landforms with a true 3-dimensional geometric data format was established. Second, the internal structure and attributes of landforms can be stored. Third, the interaction of processes and landforms is represented. Fourth, the change of all these mentioned attributes over time was considered. The presented application schema is available on the Internet and therefore a first step to enable researchers to share information using an OGC's Web feature service. In this vein comparing modelling results of landscape evolution with results of other scientist's observations is possible. Compared to prevalent data concepts the model presented makes it possible to store information about landforms, their geometry and the characteristics in more detail. It allows to represent the 3D-geometry, the set of material properties and the genesis of a landform by associating processes to a geoobject. Thus, time slices of a geomorphic system can be represented as well as scenarios of landscape modelling. Commercial GI-software is not adapted to the needs of the science of geomorphology. Therefore the development of an application model i. e. a formal description of semantics is imperative to partake in technologies like Web Feature Services supporting interoperable data transfer.

A markup language for electrocardiogram data acquisition and analysis (ecgML)

PubMed Central

Wang, Haiying; Azuaje, Francisco; Jung, Benjamin; Black, Norman

2003-01-01

Background The storage and distribution of electrocardiogram data is based on different formats. There is a need to promote the development of standards for their exchange and analysis. Such models should be platform-/ system- and application-independent, flexible and open to every member of the scientific community. Methods A minimum set of information for the representation and storage of electrocardiogram signals has been synthesised from existing recommendations. This specification is encoded into an XML-vocabulary. The model may aid in a flexible exchange and analysis of electrocardiogram information. Results Based on advantages of XML technologies, ecgML has the ability to present a system-, application- and format-independent solution for representation and exchange of electrocardiogram data. The distinction between the proposal developed by the U.S Food and Drug Administration and ecgML model is given. A series of tools, which aim to facilitate ecgML-based applications, are presented. Conclusions The models proposed here can facilitate the generation of a data format, which opens ways for better and clearer interpretation by both humans and machines. Its structured and transparent organisation will allow researchers to expand and test its capabilities in different application domains. The specification and programs for this protocol are publicly available. PMID:12735790

Tolerance and UQ4SIM: Nimble Uncertainty Documentation and Analysis Software

NASA Technical Reports Server (NTRS)

Kleb, Bil

2008-01-01

Ultimately, scientific numerical models need quantified output uncertainties so that modeling can evolve to better match reality. Documenting model input uncertainties and variabilities is a necessary first step toward that goal. Without known input parameter uncertainties, model sensitivities are all one can determine, and without code verification, output uncertainties are simply not reliable. The basic premise of uncertainty markup is to craft a tolerance and tagging mini-language that offers a natural, unobtrusive presentation and does not depend on parsing each type of input file format. Each file is marked up with tolerances and optionally, associated tags that serve to label the parameters and their uncertainties. The evolution of such a language, often called a Domain Specific Language or DSL, is given in [1], but in final form it parallels tolerances specified on an engineering drawing, e.g., 1 +/- 0.5, 5 +/- 10%, 2 +/- 10 where % signifies percent and o signifies order of magnitude. Tags, necessary for error propagation, can be added by placing a quotation-mark-delimited tag after the tolerance, e.g., 0.7 +/- 20% 'T_effective'. In addition, tolerances might have different underlying distributions, e.g., Uniform, Normal, or Triangular, or the tolerances may merely be intervals due to lack of knowledge (uncertainty). Finally, to address pragmatic considerations such as older models that require specific number-field formats, C-style format specifiers can be appended to the tolerance like so, 1.35 +/- 10U_3.2f. As an example of use, consider figure 1, where a chemical reaction input file is has been marked up to include tolerances and tags per table 1. Not only does the technique provide a natural method of specifying tolerances, but it also servers as in situ documentation of model uncertainties. This tolerance language comes with a utility to strip the tolerances (and tags), to provide a path to the nominal model parameter file. And, as shown in [1], having the ability to quickly mark and identify model parameter uncertainties facilitates error propagation, which in turn yield output uncertainties.

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.

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.

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…

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.

Fingerprinting Reverse Proxies Using Timing Analysis of TCP Flows

DTIC Science & Technology

2013-09-01

bayes classifier,” in Cloud Computing Security , ser. CCSW ’09. New York City, NY: ACM, 2009, pp. 31–42. [30] J. Zhang, R. Perdisci, W. Lee, U. Sarfraz...FSM Finite State Machine HTML Hypertext Markup Language HTTP Hypertext Transfer Protocol HTTPS Hypertext Transfer Protocol Secure ICMP Internet Control...This hidden traffic concept supports network access control, security protection through obfuscation, and performance boosts at the Internet facing

The digital curriculum vitae.

PubMed

Galdino, Greg M; Gotway, Michael

2005-02-01

The curriculum vitae (CV) has been the traditional method for radiologists to illustrate their accomplishments in the field of medicine. Despite its presence in medicine as a standard, widely accepted means to describe one's professional career and its use for decades as an accomplice to most applications and interviews, there is relatively little written in the medical literature regarding the CV. Misrepresentation on medical students', residents', and fellows' applications has been reported. Using digital technology, CVs have the potential to be much more than printed words on paper and offers a solution to misrepresentation. Digital CVs may incorporate full-length articles, graphics, presentations, clinical images, and video. Common formats for digital CVs include CD-ROMs or DVD-ROMs containing articles (in Adobe Portable Document Format) and presentations (in Microsoft PowerPoint format) accompanying printed CVs, word processing documents with hyperlinks to articles and presentations either locally (on CD-ROMs or DVD-ROMs) or remotely (via the Internet), or hypertext markup language documents. Digital CVs afford the ability to provide more information that is readily accessible to those receiving and reviewing them. Articles, presentations, videos, images, and Internet links can be illustrated using standard file formats commonly available to all radiologists. They can be easily updated and distributed on an inexpensive media, such as a CD-ROM or DVD-ROM. With the availability of electronic articles, presentations, and information via the Internet, traditional paper CVs may soon be superseded by their electronic successors.

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.

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.

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.

Visualizing astronomy data using VRML

NASA Astrophysics Data System (ADS)

Beeson, Brett; Lancaster, Michael; Barnes, David G.; Bourke, Paul D.; Rixon, Guy T.

2004-09-01

Visualisation is a powerful tool for understanding the large data sets typical of astronomical surveys and can reveal unsuspected relationships and anomalous regions of parameter space which may be difficult to find programatically. Visualisation is a classic information technology for optimising scientific return. We are developing a number of generic on-line visualisation tools as a component of the Australian Virtual Observatory project. The tools will be deployed within the framework of the International Virtual Observatory Alliance (IVOA), and follow agreed-upon standards to make them accessible by other programs and people. We and our IVOA partners plan to utilise new information technologies (such as grid computing and web services) to advance the scientific return of existing and future instrumentation. Here we present a new tool - VOlume - which visualises point data. Visualisation of astronomical data normally requires the local installation of complex software, the downloading of potentially large datasets, and very often time-consuming and tedious data format conversions. VOlume enables the astronomer to visualise data using just a web browser and plug-in. This is achieved using IVOA standards which allow us to pass data between Web Services, Java Servlet Technology and Common Gateway Interface programs. Data from a catalogue server can be streamed in eXtensible Mark-up Language format to a servlet which produces Virtual Reality Modeling Language output. The user selects elements of the catalogue to map to geometry and then visualises the result in a browser plug-in such as Cortona or FreeWRL. Other than requiring an input VOTable format file, VOlume is very general. While its major use will likely be to display and explore astronomical source catalogues, it can easily render other important parameter fields such as the sky and redshift coverage of proposed surveys or the sampling of the visibility plane by a rotation-synthesis interferometer.

PHYLOGEOrec: A QGIS plugin for spatial phylogeographic reconstruction from phylogenetic tree and geographical information data

NASA Astrophysics Data System (ADS)

Nashrulloh, Maulana Malik; Kurniawan, Nia; Rahardi, Brian

2017-11-01

The increasing availability of genetic sequence data associated with explicit geographic and environment (including biotic and abiotic components) information offers new opportunities to study the processes that shape biodiversity and its patterns. Developing phylogeography reconstruction, by integrating phylogenetic and biogeographic knowledge, provides richer and deeper visualization and information on diversification events than ever before. Geographical information systems such as QGIS provide an environment for spatial modeling, analysis, and dissemination by which phylogenetic models can be explicitly linked with their associated spatial data, and subsequently, they will be integrated with other related georeferenced datasets describing the biotic and abiotic environment. We are introducing PHYLOGEOrec, a QGIS plugin for building spatial phylogeographic reconstructions constructed from phylogenetic tree and geographical information data based on QGIS2threejs. By using PHYLOGEOrec, researchers can integrate existing phylogeny and geographical information data, resulting in three-dimensional geographic visualizations of phylogenetic trees in the Keyhole Markup Language (KML) format. Such formats can be overlaid on a map using QGIS and finally, spatially viewed in QGIS by means of a QGIS2threejs engine for further analysis. KML can also be viewed in reputable geobrowsers with KML-support (i.e., Google Earth).

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.

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.

A tool to convert CAD models for importation into Geant4

NASA Astrophysics Data System (ADS)

Vuosalo, C.; Carlsmith, D.; Dasu, S.; Palladino, K.; LUX-ZEPLIN Collaboration

2017-10-01

The engineering design of a particle detector is usually performed in a Computer Aided Design (CAD) program, and simulation of the detector’s performance can be done with a Geant4-based program. However, transferring the detector design from the CAD program to Geant4 can be laborious and error-prone. SW2GDML is a tool that reads a design in the popular SOLIDWORKS CAD program and outputs Geometry Description Markup Language (GDML), used by Geant4 for importing and exporting detector geometries. Other methods for outputting CAD designs are available, such as the STEP format, and tools exist to convert these formats into GDML. However, these conversion methods produce very large and unwieldy designs composed of tessellated solids that can reduce Geant4 performance. In contrast, SW2GDML produces compact, human-readable GDML that employs standard geometric shapes rather than tessellated solids. This paper will describe the development and current capabilities of SW2GDML and plans for its enhancement. The aim of this tool is to automate importation of detector engineering models into Geant4-based simulation programs to support rapid, iterative cycles of detector design, simulation, and optimization.

Home Page: The Mode of Transport through the Information Superhighway

NASA Technical Reports Server (NTRS)

Lujan, Michelle R.

1995-01-01

The purpose of the project with the Aeroacoustics Branch was to create and submit a home page for the internet about branch information. In order to do this, one must also become familiar with the way that the internet operates. Learning HyperText Markup Language (HTML), and the ability to create a document using this language was the final objective in order to place a home page on the internet (World Wide Web). A manual of instructions regarding maintenance of the home page, and how to keep it up to date was also necessary in order to provide branch members with the opportunity to make any pertinent changes.

Generalized Nuclear Data: A New Structure (with Supporting Infrastructure) for Handling Nuclear Data

NASA Astrophysics Data System (ADS)

Mattoon, C. M.; Beck, B. R.; Patel, N. R.; Summers, N. C.; Hedstrom, G. W.; Brown, D. A.

2012-12-01

The Evaluated Nuclear Data File (ENDF) format was designed in the 1960s to accommodate neutron reaction data to support nuclear engineering applications in power, national security and criticality safety. Over the years, the scope of the format has been extended to handle many other kinds of data including charged particle, decay, atomic, photo-nuclear and thermal neutron scattering. Although ENDF has wide acceptance and support for many data types, its limited support for correlated particle emission, limited numeric precision, and general lack of extensibility mean that the nuclear data community cannot take advantage of many emerging opportunities. More generally, the ENDF format provides an unfriendly environment that makes it difficult for new data evaluators and users to create and access nuclear data. The Cross Section Evaluation Working Group (CSEWG) has begun the design of a new Generalized Nuclear Data (or 'GND') structure, meant to replace older formats with a hierarchy that mirrors the underlying physics, and is aligned with modern coding and database practices. In support of this new structure, Lawrence Livermore National Laboratory (LLNL) has updated its nuclear data/reactions management package Fudge to handle GND structured nuclear data. Fudge provides tools for converting both the latest ENDF format (ENDF-6) and the LLNL Evaluated Nuclear Data Library (ENDL) format to and from GND, as well as for visualizing, modifying and processing (i.e., converting evaluated nuclear data into a form more suitable to transport codes) GND structured nuclear data. GND defines the structure needed for storing nuclear data evaluations and the type of data that needs to be stored. But unlike ENDF and ENDL, GND does not define how the data are to be stored in a file. Currently, Fudge writes the structured GND data to a file using the eXtensible Markup Language (XML), as it is ASCII based and can be viewed with any text editor. XML is a meta-language, meaning that it has a primitive set of definitions for representing hierarchical data/text in a file. Other meta-languages, like HDF5 which stores the data in binary form, can also be used to store GND in a file. In this paper, we will present an overview of the new GND data structures along with associated tools in Fudge.

MaROS Strategic Relay Planning and Coordination Interfaces

NASA Technical Reports Server (NTRS)

Allard, Daniel A.

2010-01-01

The Mars Relay Operations Service (MaROS) is designed to provide planning and analysis tools in support of ongoing Mars Network relay operations. Strategic relay planning requires coordination between lander and orbiter mission ground data system (GDS) teams to schedule and execute relay communications passes. MaROS centralizes this process, correlating all data relevant to relay coordination to provide a cohesive picture of the relay state. Service users interact with the system through thin-layer command line and web user interface client applications. Users provide and utilize data such as lander view periods of orbiters, Deep Space Network (DSN) antenna tracks, and reports of relay pass performance. Users upload and download relevant relay data via formally defined and documented file structures including some described in Extensible Markup Language (XML). Clients interface with the system via an http-based Representational State Transfer (ReST) pattern using Javascript Object Notation (JSON) formats. This paper will provide a general overview of the service architecture and detail the software interfaces and considerations for interface design.

RDNAnalyzer: A tool for DNA secondary structure prediction and sequence analysis

PubMed Central

Afzal, Muhammad; Shahid, Ahmad Ali; Shehzadi, Abida; Nadeem, Shahid; Husnain, Tayyab

2012-01-01

RDNAnalyzer is an innovative computer based tool designed for DNA secondary structure prediction and sequence analysis. It can randomly generate the DNA sequence or user can upload the sequences of their own interest in RAW format. It uses and extends the Nussinov dynamic programming algorithm and has various application for the sequence analysis. It predicts the DNA secondary structure and base pairings. It also provides the tools for routinely performed sequence analysis by the biological scientists such as DNA replication, reverse compliment generation, transcription, translation, sequence specific information as total number of nucleotide bases, ATGC base contents along with their respective percentages and sequence cleaner. RDNAnalyzer is a unique tool developed in Microsoft Visual Studio 2008 using Microsoft Visual C# and Windows Presentation Foundation and provides user friendly environment for sequence analysis. It is freely available. Availability http://www.cemb.edu.pk/sw.html Abbreviations RDNAnalyzer - Random DNA Analyser, GUI - Graphical user interface, XAML - Extensible Application Markup Language. PMID:23055611

Adobe acrobat: an alternative electronic teaching file construction methodology independent of HTML restrictions.

PubMed

Katzman, G L

2001-03-01

The goal of the project was to create a method by which an in-house digital teaching file could be constructed that was simple, inexpensive, independent of hypertext markup language (HTML) restrictions, and appears identical on multiple platforms. To accomplish this, Microsoft PowerPoint and Adobe Acrobat were used in succession to assemble digital teaching files in the Acrobat portable document file format. They were then verified to appear identically on computers running Windows, Macintosh Operating Systems (OS), and the Silicon Graphics Unix-based OS as either a free-standing file using Acrobat Reader software or from within a browser window using the Acrobat browser plug-in. This latter display method yields a file viewed through a browser window, yet remains independent of underlying HTML restrictions, which may confer an advantage over simple HTML teaching file construction. Thus, a hybrid of HTML-distributed Adobe Acrobat generated WWW documents may be a viable alternative for digital teaching file construction and distribution.

[Study of sharing platform of web-based enhanced extracorporeal counterpulsation hemodynamic waveform data].

PubMed

Huang, Mingbo; Hu, Ding; Yu, Donglan; Zheng, Zhensheng; Wang, Kuijian

2011-12-01

Enhanced extracorporeal counterpulsation (EECP) information consists of both text and hemodynamic waveform data. At present EECP text information has been successfully managed through Web browser, while the management and sharing of hemodynamic waveform data through Internet has not been solved yet. In order to manage EECP information completely, based on the in-depth analysis of EECP hemodynamic waveform file of digital imaging and communications in medicine (DICOM) format and its disadvantages in Internet sharing, we proposed the use of the extensible markup language (XML), which is currently the Internet popular data exchange standard, as the storage specification for the sharing of EECP waveform data. Then we designed a web-based sharing system of EECP hemodynamic waveform data via ASP. NET 2.0 platform. Meanwhile, we specifically introduced the four main system function modules and their implement methods, including DICOM to XML conversion module, EECP waveform data management module, retrieval and display of EECP waveform module and the security mechanism of the system.

IDP camp evolvement analysis in Darfur using VHSR optical satellite image time series and scientific visualization on virtual globes

NASA Astrophysics Data System (ADS)

Tiede, Dirk; Lang, Stefan

2010-11-01

In this paper we focus on the application of transferable, object-based image analysis algorithms for dwelling extraction in a camp for internally displaced people (IDP) in Darfur, Sudan along with innovative means for scientific visualisation of the results. Three very high spatial resolution satellite images (QuickBird: 2002, 2004, 2008) were used for: (1) extracting different types of dwellings and (2) calculating and visualizing added-value products such as dwelling density and camp structure. The results were visualized on virtual globes (Google Earth and ArcGIS Explorer) revealing the analysis results (analytical 3D views,) transformed into the third dimension (z-value). Data formats depend on virtual globe software including KML/KMZ (keyhole mark-up language) and ESRI 3D shapefiles streamed as ArcGIS Server-based globe service. In addition, means for improving overall performance of automated dwelling structures using grid computing techniques are discussed using examples from a similar study.

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

PubMed

Olivier, Brett G; Bergmann, Frank T

2015-09-04

Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).

XML, Ontologies, and Their Clinical Applications.

PubMed

Yu, Chunjiang; Shen, Bairong

2016-01-01

The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

The Systems Biology Markup Language (SBML) Level 3 Package: Flux Balance Constraints.

PubMed

Olivier, Brett G; Bergmann, Frank T

2015-06-01

Constraint-based modeling is a well established modelling methodology used to analyze and study biological networks on both a medium and genome scale. Due to their large size, genome scale models are typically analysed using constraint-based optimization techniques. One widely used method is Flux Balance Analysis (FBA) which, for example, requires a modelling description to include: the definition of a stoichiometric matrix, an objective function and bounds on the values that fluxes can obtain at steady state. The Flux Balance Constraints (FBC) Package extends SBML Level 3 and provides a standardized format for the encoding, exchange and annotation of constraint-based models. It includes support for modelling concepts such as objective functions, flux bounds and model component annotation that facilitates reaction balancing. The FBC package establishes a base level for the unambiguous exchange of genome-scale, constraint-based models, that can be built upon by the community to meet future needs (e. g. by extending it to cover dynamic FBC models).

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.

Report of Official Foreign Travel to Germany, May 16-June 1, 2001

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

J. D. Mason

2001-06-18

The Department of Energy (DOE) and associated agencies have moved rapidly toward electronic production, management, and dissemination of scientific and technical information. The World-Wide Web (WWW) has become a primary means of information dissemination. Electronic commerce (EC) is becoming the preferred means of procurement. DOE, like other government agencies, depends on and encourages the use of international standards in data communications. Like most government agencies, DOE has expressed a preference for openly developed standards over proprietary designs promoted as ''standards'' by vendors. In particular, there is a preference for standards developed by organizations such as the International Organization for Standardizationmore » (ISO) and the American National Standards Institute (ANSI) that use open, public processes to develop their standards. Among the most widely adopted international standards is the Standard Generalized Markup Language (SGML, ISO 8879:1986, FIPS 152), to which DOE long ago made a commitment. Besides the official commitment, which has resulted in several specialized projects, DOE makes heavy use of coding derived from SGML: Most documents on the WWW are coded in HTML (Hypertext Markup Language), which is an application of SGML. The World-Wide Web Consortium (W3C), with the backing of major software houses like Adobe, IBM, Microsoft, Netscape, Oracle, and Sun, is promoting XML (eXtensible Markup Language), a class of SGML applications, for the future of the WWW and the basis for EC. In support of DOE's use of these standards, I have served since 1985 as Chairman of the international committee responsible for SGML and related standards, ISO/IEC JTC1/SC34 (SC34) and its predecessor organizations. During my May 2001 trip, I chaired the spring 2001 meeting of SC34 in Berlin, Germany. I also attended XML Europe 2001, a major conference on the use of SGML and XML sponsored by the Graphic Communications Association (GCA), and chaired a meeting of the International SGML/XML Users' Group (ISUG). In addition to the widespread use of the WWW among DOE's plants and facilities in Oak Ridge and among DOE sites across the nation, there have been several past and present SGML- and XML-based projects at the Y-12 National Security Complex (Y-12). Our local project team has done SGML and XML development at Y-12 and Oak Ridge National Laboratory (ORNL) since the late 1980s. SGML is a component of the Weapons Records Archiving and Preservation (WRAP) project at Y-12 and is the format for catalog metadata chosen for weapons records by the Nuclear Weapons Information Group (NWIG). The ''Ferret'' system for automated classification analysis uses XML to structure its knowledge base. The Ferret team also provides XML consulting to OSTI and DOE Headquarters, particularly the National Nuclear Security Administration (NNSA). Supporting standards development allows DOE and Y-12 the opportunity both to provide input into the process and to benefit from contact with some of the leading experts in the subject matter. Oak Ridge has been for some years the location to which other DOE sites turn for expertise in SGML, XML, and related topics.« less

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

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.

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

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.

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

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

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.

Development of a Google-based search engine for data mining radiology reports.

PubMed

Erinjeri, Joseph P; Picus, Daniel; Prior, Fred W; Rubin, David A; Koppel, Paul

2009-08-01

The aim of this study is to develop a secure, Google-based data-mining tool for radiology reports using free and open source technologies and to explore its use within an academic radiology department. A Health Insurance Portability and Accountability Act (HIPAA)-compliant data repository, search engine and user interface were created to facilitate treatment, operations, and reviews preparatory to research. The Institutional Review Board waived review of the project, and informed consent was not required. Comprising 7.9 GB of disk space, 2.9 million text reports were downloaded from our radiology information system to a fileserver. Extensible markup language (XML) representations of the reports were indexed using Google Desktop Enterprise search engine software. A hypertext markup language (HTML) form allowed users to submit queries to Google Desktop, and Google's XML response was interpreted by a practical extraction and report language (PERL) script, presenting ranked results in a web browser window. The query, reason for search, results, and documents visited were logged to maintain HIPAA compliance. Indexing averaged approximately 25,000 reports per hour. Keyword search of a common term like "pneumothorax" yielded the first ten most relevant results of 705,550 total results in 1.36 s. Keyword search of a rare term like "hemangioendothelioma" yielded the first ten most relevant results of 167 total results in 0.23 s; retrieval of all 167 results took 0.26 s. Data mining tools for radiology reports will improve the productivity of academic radiologists in clinical, educational, research, and administrative tasks. By leveraging existing knowledge of Google's interface, radiologists can quickly perform useful searches.

Specifications of insilicoML 1.0: a multilevel biophysical model description language.

PubMed

Asai, Yoshiyuki; Suzuki, Yasuyuki; Kido, Yoshiyuki; Oka, Hideki; Heien, Eric; Nakanishi, Masao; Urai, Takahito; Hagihara, Kenichi; Kurachi, Yoshihisa; Nomura, Taishin

2008-12-01

An extensible markup language format, insilicoML (ISML), version 0.1, describing multi-level biophysical models has been developed and available in the public domain. ISML is fully compatible with CellML 1.0, a model description standard developed by the IUPS Physiome Project, for enhancing knowledge integration and model sharing. This article illustrates the new specifications of ISML 1.0 that largely extend the capability of ISML 0.1. ISML 1.0 can describe various types of mathematical models, including ordinary/partial differential/difference equations representing the dynamics of physiological functions and the geometry of living organisms underlying the functions. ISML 1.0 describes a model using a set of functional elements (modules) each of which can specify mathematical expressions of the functions. Structural and logical relationships between any two modules are specified by edges, which allow modular, hierarchical, and/or network representations of the model. The role of edge-relationships is enriched by key words in order for use in constructing a physiological ontology. The ontology is further improved by the traceability of history of the model's development and by linking between different ISML models stored in the model's database using meta-information. ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery.

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.

Introducing ADES: A New IAU Astrometry Data Exchange Standard

NASA Astrophysics Data System (ADS)

Chesley, Steven R.; Hockney, George M.; Holman, Matthew J.

2017-10-01

For several decades, small body astrometry has been exchanged, distributed and archived in the form of 80-column ASCII records. As a replacement for this obsolescent format, we have worked with a number of members of the community to develop the Astrometric Data Exchange Standard (ADES), which was formally adopted by IAU Commission 20 in August 2015 at the XXIX General Assembly in Honolulu, Hawaii.The purpose of ADES is to ensure that useful and available observational information is submitted, archived, and disseminated as needed. Availability of more complete information will allow orbit computers to process the data more correctly, leading to improved accuracy and reliability of orbital fits. In this way, it will be possible to fully exploit the improving accuracy and increasing number of both optical and radar observations. ADES overcomes several limitations of the previous format by allowing characterization of astrometric and photometric errors, adequate precision in time and angle fields, and flexibility and extensibility.To accommodate a diverse base of users, from automated surveys to hands-on follow-up observers, the ADES protocol allows for two file formats, eXtensible Markup Language (XML) and Pipe-Separated Values (PSV). Each format carries the same information and simple tools allow users to losslessly transform back and forth between XML and PSV.We have further developed and refined ADES since it was first announced in July 2015 [1]. The proposal at that time [2] has undergone several modest revisions to aid validation and avoid overloaded fields. We now have validation schema and file transformation utilities. Suitable example files, test suites, and input/output libraries in a number of modern programming languages are now available. Acknowledgements: Useful feedback during the development of ADES has been received from numerous colleagues in the community of observers and orbit specialists working on asteroids comets and planetary satellites. References: [1] Chesley, S.R. (2015) M.P.E.C. 2015-O06. [2] http://minorplanetcenter.net/iau/ info/IAU2015_ADES.pdf

National Authentication Framework Implementation Study

DTIC Science & Technology

2009-12-01

Identifiers RA Registration Authority SAML Security Assertion Markup Language SFA Single-factor Authentication SMS Short Messaging System SOA ...written on  paper  disclosed;  passwords stored in electronic file  copied. 1,2,3,4 Eaves‐  dropping The token secret or authenticator is  revealed to...Internet 2.0 and the growing interest in systems developed based upon the Service- Oriented Architecture ( SOA ). While core specifications upon which

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

XML Schema Guide for Secondary 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 1.1 XML schema for the Joint Submission Form. Please note that the order of the elements must match the schema.

Internet Economics IV

DTIC Science & Technology

2004-08-01

components, and B2B /B2C aspects of those in a technical and economic snapshot. Talk number six discusses the trade-off between quality and cost, which...web services have been defined. The fifth talk summarizes key aspects of XML (Extended Markup Language), Web Services and their components, and B2B ...Internet is Run: A Worldwide Perspective 69 Christoph Pauls 5 XML, Web Services and B2C/ B2B : A Technical and Economical Snap- shot 87 Matthias Pitt 6

Operational Monitoring of Volcanoes Using Keyhole Markup Language

NASA Astrophysics Data System (ADS)

Dehn, J.; Bailey, J. E.; Webley, P.

2007-12-01

Volcanoes are some of the most geologically powerful, dynamic, visually appealing structures on the Earth's landscape. Volcanic eruptions are hard to predict, difficult to quantify and impossible to prevent, making effective monitoring a difficult proposition. In Alaska, volcanoes are an intrinsic part of the culture, with over 100 volcanoes and volcanic fields that have been active in historic time monitored by the Alaska Volcano Observatory (AVO). Observations and research are performed using a suite of methods and tools in the fields of remote sensing, seismology, geodesy and geology, producing large volumes of geospatial data. Keyhole Markup Language (KML) offers a context in which these different, and in the past disparate, data can be displayed simultaneously. Dynamic links keep these data current, allowing it to be used in an operational capacity. KML is used to display information from the aviation color codes and activity alert levels for volcanoes to locations of thermal anomalies, earthquake locations and ash plume modeling. The dynamic refresh and time primitive are used to display volcano webcam and satellite image overlays in near real-time. In addition a virtual globe browser using KML, such as Google Earth, provides an interface to further information using the hyperlink, rich- text and flash-embedding abilities supported within object description balloons. By merging these data sets in an easy to use interface, a virtual globe browser provides a better tool for scientists and emergency managers alike to mitigate volcanic crises.

CytometryML: a markup language for analytical cytology

NASA Astrophysics Data System (ADS)

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

2003-06-01

Cytometry Markup Language, CytometryML, is a proposed new analytical cytology data standard. CytometryML is a set of XML schemas for encoding both flow cytometry and digital microscopy text based data types. CytometryML schemas reference both DICOM (Digital Imaging and Communications in Medicine) codes and FCS keywords. These schemas provide representations for the keywords in FCS 3.0 and will soon include DICOM microscopic image data. Flow Cytometry Standard (FCS) list-mode has been mapped to the DICOM Waveform Information Object. A preliminary version of a list mode binary data type, which does not presently exist in DICOM, has been designed. This binary type is required to enhance the storage and transmission of flow cytometry and digital microscopy data. Index files based on Waveform indices will be used to rapidly locate the cells present in individual subsets. DICOM has the advantage of employing standard file types, TIF and JPEG, for Digital Microscopy. Using an XML schema based representation means that standard commercial software packages such as Excel and MathCad can be used to analyze, display, and store analytical cytometry data. Furthermore, by providing one standard for both DICOM data and analytical cytology data, it eliminates the need to create and maintain special purpose interfaces for analytical cytology data thereby integrating the data into the larger DICOM and other clinical communities. A draft version of CytometryML is available at www.newportinstruments.com.

Education Office Application Design and Development

NASA Technical Reports Server (NTRS)

Johnson, Jamie E.

2013-01-01

The content of this project focuses on designing and implementing a new prototype website for the Kennedy Intern Tracking System (KITS). The goal of the new website is to allow the user to search for interns based on several different categories and fields. In hence, making it easier to find a count of interns matching a set of criteria. The KSC office of education is the primary users of KITS, their job is to recruit interns year-round. As a secondary goal, each user will be able to generate a report of their searches onto a portable document format (PDF) me. The results of each search will be set to a limited amount per page. This site will be used for Kennedy Space Center internal purposes only. After the implementations are done, a visual walk through using screen shots will be used to guide the users through all of the different scenarios that are likely to occur when the users are navigating through the site. In addition, a demo of the site will be presented to the KSC Office of Education. JavaScript and JQuery are the languages that will focus on the functionality of the implementation. Hyper Text Markup Language will be used to form the foundation for the body structure of the website. Ruby will be the programming language used to elevate the prototype to a dynamic website and enable the programmer to finish with in an efficient time frame. Cascading Style Sheet will be the language used for the design and styling purposes. Rails is the framework that the new website will be built upon. By default, the database will be managed by Sequel Lite (SQLite). All users will need to be granted special privileges in order to use the site.

Balancing medicine prices and business sustainability: analyses of pharmacy costs, revenues and profit shed light on retail medicine mark-ups in rural Kyrgyzstan

PubMed Central

2010-01-01

Background Numerous not-for-profit pharmacies have been created to improve access to medicines for the poor, but many have failed due to insufficient financial planning and management. These pharmacies are not well described in health services literature despite strong demand from policy makers, implementers, and researchers. Surveys reporting unaffordable medicine prices and high mark-ups have spurred efforts to reduce medicine prices, but price reduction goals are arbitrary in the absence of information on pharmacy costs, revenues, and profit structures. Health services research is needed to develop sustainable and "reasonable" medicine price goals and strategic initiatives to reach them. Methods We utilized cost accounting methods on inventory and financial information obtained from a not-for-profit rural pharmacy network in mountainous Kyrgyzstan to quantify costs, revenues, profits and medicine mark-ups during establishment and maintenance periods (October 2004-December 2007). Results Twelve pharmacies and one warehouse were established in remote Kyrgyzstan with < US $25,000 due to governmental resource-sharing. The network operated at break-even profit, leaving little room to lower medicine prices and mark-ups. Medicine mark-ups needed for sustainability were greater than originally envisioned by network administration. In 2005, 55%, 35%, and 10% of the network's top 50 products revealed mark-ups of < 50%, 50-99% and > 100%, respectively. Annual mark-ups increased dramatically each year to cover increasing recurrent costs, and by 2007, only 19% and 46% of products revealed mark-ups of < 50% and 50-99%, respectively; while 35% of products revealed mark-ups > 100%. 2007 medicine mark-ups varied substantially across these products, ranging from 32% to 244%. Mark-ups needed to sustain private pharmacies would be even higher in the absence of government subsidies. Conclusion Pharmacy networks can be established in hard-to-reach regions with little funding using public-private partnership, resource-sharing models. Medicine prices and mark-ups must be interpreted with consideration for regional costs of business. Mark-ups vary dramatically across medicines. Some mark-ups appear "excessive" but are likely necessary for pharmacy viability. Pharmacy financial data is available in remote settings and can be used towards determination of "reasonable" medicine price goals. Health systems researchers must document the positive and negative financial experiences of pharmacy initiatives to inform future projects and advance access to medicines goals. PMID:20626904

Balancing medicine prices and business sustainability: analyses of pharmacy costs, revenues and profit shed light on retail medicine mark-ups in rural Kyrgyzstan.

PubMed

Waning, Brenda; Maddix, Jason; Soucy, Lyne

2010-07-13

Numerous not-for-profit pharmacies have been created to improve access to medicines for the poor, but many have failed due to insufficient financial planning and management. These pharmacies are not well described in health services literature despite strong demand from policy makers, implementers, and researchers. Surveys reporting unaffordable medicine prices and high mark-ups have spurred efforts to reduce medicine prices, but price reduction goals are arbitrary in the absence of information on pharmacy costs, revenues, and profit structures. Health services research is needed to develop sustainable and "reasonable" medicine price goals and strategic initiatives to reach them. We utilized cost accounting methods on inventory and financial information obtained from a not-for-profit rural pharmacy network in mountainous Kyrgyzstan to quantify costs, revenues, profits and medicine mark-ups during establishment and maintenance periods (October 2004-December 2007). Twelve pharmacies and one warehouse were established in remote Kyrgyzstan with < US $25,000 due to governmental resource-sharing. The network operated at break-even profit, leaving little room to lower medicine prices and mark-ups. Medicine mark-ups needed for sustainability were greater than originally envisioned by network administration. In 2005, 55%, 35%, and 10% of the network's top 50 products revealed mark-ups of < 50%, 50-99% and > 100%, respectively. Annual mark-ups increased dramatically each year to cover increasing recurrent costs, and by 2007, only 19% and 46% of products revealed mark-ups of < 50% and 50-99%, respectively; while 35% of products revealed mark-ups > 100%. 2007 medicine mark-ups varied substantially across these products, ranging from 32% to 244%. Mark-ups needed to sustain private pharmacies would be even higher in the absence of government subsidies. Pharmacy networks can be established in hard-to-reach regions with little funding using public-private partnership, resource-sharing models. Medicine prices and mark-ups must be interpreted with consideration for regional costs of business. Mark-ups vary dramatically across medicines. Some mark-ups appear "excessive" but are likely necessary for pharmacy viability. Pharmacy financial data is available in remote settings and can be used towards determination of "reasonable" medicine price goals. Health systems researchers must document the positive and negative financial experiences of pharmacy initiatives to inform future projects and advance access to medicines goals.

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.

Defense Advanced Research Projects Agency (DARPA) Agent Markup Language Computer Aided Knowledge Acquisition

DTIC Science & Technology

2005-06-01

34> <rdfs:subClassOf rdf:resource="#Condition"/> <rdfs:label>Economic Self -Sufficiency Class</rdfs:label> <cnd:categoryCode>C</cnd:categoryCode...cnd:index>3.3.4.1</cnd:index> <cnd:title>Economic Self -Sufficiency</cnd:title> <cnd:definition>The ability of a nation to...34#International_Economic_Position"/> <cnd:subCategory rdf:resource="# Self -Sufficiency_In_Food"/> <cnd:subCategory rdf:resource="# Self

The Air Force Records Management Program: A Paradigm Shift from Compliance to Guiding Principles in an Ever-Changing Information Environment

DTIC Science & Technology

2014-06-22

GIG Global Information Grid GOTS Government Off-the-Shelf HTML Hyper Text Markup Language ICT Information and Communication Technology IEC...maintenance, retrieval, and preservation of vital information created in public and private organizations in all sectors of the economy . It is also the...constructed in the 1940’s, as part of a government-effort to provide employment 120 during the Depression, and boost the economy . This road is set in

Engineering Analysis Using a Web-based Protocol

NASA Technical Reports Server (NTRS)

Schoeffler, James D.; Claus, Russell W.

2002-01-01

This paper reviews the development of a web-based framework for engineering analysis. A one-dimensional, high-speed analysis code called LAPIN was used in this study, but the approach can be generalized to any engineering analysis tool. The web-based framework enables users to store, retrieve, and execute an engineering analysis from a standard web-browser. We review the encapsulation of the engineering data into the eXtensible Markup Language (XML) and various design considerations in the storage and retrieval of application data.

Semantically Enriched Data Access Policies in eHealth.

PubMed

Drozdowicz, Michał; Ganzha, Maria; Paprzycki, Marcin

2016-11-01

Internet of Things (IoT) requires novel solutions to facilitate autonomous, though controlled, resource access. Access policies have to facilitate interactions between heterogeneous entities (devices and humans). Here, we focus our attention on access control in eHealth. We propose an approach based on enriching policies, based on well-known and widely-used eXtensible Access Control Markup Language, with semantics. In the paper we describe an implementation of a Policy Information Point integrated with the HL7 Security and Privacy Ontology.

An interactive HTML ocean nowcast GUI based on Perl and JavaScript

NASA Astrophysics Data System (ADS)

Sakalaukus, Peter J.; Fox, Daniel N.; Louise Perkins, A.; Smedstad, Lucy F.

1999-02-01

We describe the use of Hyper Text Markup Language (HTML), JavaScript code, and Perl I/O to create and validate forms in an Internet-based graphical user interface (GUI) for the Naval Research Laboratory (NRL) Ocean models and Assimilation Demonstration System (NOMADS). The resulting nowcast system can be operated from any compatible browser across the Internet, for although the GUI was prepared in a Netscape browser, it used no Netscape extensions. Code available at: http://www.iamg.org/CGEditor/index.htm

Development of Semantic Web - Markup Languages, Web Services, Rules, Explanation, Querying, Proof and Reasoning

DTIC Science & Technology

2008-07-01

Study. WWW2006 Workshop on the Models of Trust for the Web (MTW󈧊), Edinburgh, Scotland, May 22, 2006. • Daniel J. Weitzner, Hal Abelson, Tim Berners ...McGuinness gave an invited talk on ontologies in Intel’s Semantic web day. Other invited speakers were Hendler and Berners - Lee . February 4, 2002...Burke (DARPA) concerning ontology tools. July 19-20, 2000. McGuinness met with W3C representatives ( Berners - Lee , Connolly, Lassila) and other

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.

Mobile terrestrial light detection and ranging (T-LiDAR) survey of areas on Dauphin Island, Alabama, in the aftermath of Hurricane Isaac, 2012

USGS Publications Warehouse

Kimbrow, Dustin R.

2014-01-01

Topographic survey data of areas on Dauphin Island on the Alabama coast were collected using a truck-mounted mobile terrestrial light detection and ranging system. This system is composed of a high frequency laser scanner in conjunction with an inertial measurement unit and a position and orientation computer to produce highly accurate topographic datasets. A global positioning system base station was set up on a nearby benchmark and logged vertical and horizontal position information during the survey for post-processing. Survey control points were also collected throughout the study area to determine residual errors. Data were collected 5 days after Hurricane Isaac made landfall in early September 2012 to document sediment deposits prior to clean-up efforts. Three data files in ASCII text format with the extension .xyz are included in this report, and each file is named according to both the acquisition date and the relative geographic location on Dauphin Island (for example, 20120903_Central.xyz). Metadata are also included for each of the files in both Extensible Markup Language with the extension .xml and ASCII text formats. These topographic data can be used to analyze the effects of storm surge on barrier island environments and also serve as a baseline dataset for future change detection analyses.

A mobile information management system used in textile enterprises

NASA Astrophysics Data System (ADS)

Huang, C.-R.; Yu, W.-D.

2008-02-01

The mobile information management system (MIMS) for textile enterprises is based on Microsoft Visual Studios. NET2003 Server, Microsoft SQL Server 2000, C++ language and wireless application protocol (WAP) and wireless markup language (WML) technology. The portable MIMS is composed of three-layer structures, i.e. showing layer; operating layer; and data visiting layer corresponding to the port-link module; processing module; and database module. By using the MIMS, not only the information exchanges become more convenient and easier, but also the compatible between the giant information capacity and a micro-cell phone and functional expansion nature in operating and designing can be realized by means of build-in units. The development of MIMS is suitable for the utilization in textile enterprises.

XML technology planning database : lessons learned

NASA Technical Reports Server (NTRS)

Some, Raphael R.; Neff, Jon M.

2005-01-01

A hierarchical Extensible Markup Language(XML) database called XCALIBR (XML Analysis LIBRary) has been developed by Millennium Program to assist in technology investment (ROI) analysis and technology Language Capability the New return on portfolio optimization. The database contains mission requirements and technology capabilities, which are related by use of an XML dictionary. The XML dictionary codifies a standardized taxonomy for space missions, systems, subsystems and technologies. In addition to being used for ROI analysis, the database is being examined for use in project planning, tracking and documentation. During the past year, the database has moved from development into alpha testing. This paper describes the lessons learned during construction and testing of the prototype database and the motivation for moving from an XML taxonomy to a standard XML-based ontology.

Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

2006-12-01

Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

Enriching public descriptions of marine phages using the Genomic Standards Consortium MIGS standard

PubMed Central

Duhaime, Melissa Beth; Kottmann, Renzo; Field, Dawn; Glöckner, Frank Oliver

2011-01-01

In any sequencing project, the possible depth of comparative analysis is determined largely by the amount and quality of the accompanying contextual data. The structure, content, and storage of this contextual data should be standardized to ensure consistent coverage of all sequenced entities and facilitate comparisons. The Genomic Standards Consortium (GSC) has developed the “Minimum Information about Genome/Metagenome Sequences (MIGS/MIMS)” checklist for the description of genomes and here we annotate all 30 publicly available marine bacteriophage sequences to the MIGS standard. These annotations build on existing International Nucleotide Sequence Database Collaboration (INSDC) records, and confirm, as expected that current submissions lack most MIGS fields. MIGS fields were manually curated from the literature and placed in XML format as specified by the Genomic Contextual Data Markup Language (GCDML). These “machine-readable” reports were then analyzed to highlight patterns describing this collection of genomes. Completed reports are provided in GCDML. This work represents one step towards the annotation of our complete collection of genome sequences and shows the utility of capturing richer metadata along with raw sequences. PMID:21677864

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

Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0

PubMed Central

Schellenberger, Jan; Que, Richard; Fleming, Ronan M. T.; Thiele, Ines; Orth, Jeffrey D.; Feist, Adam M.; Zielinski, Daniel C.; Bordbar, Aarash; Lewis, Nathan E.; Rahmanian, Sorena; Kang, Joseph; Hyduke, Daniel R.; Palsson, Bernhard Ø.

2012-01-01

Over the past decade, a growing community of researchers has emerged around the use of COnstraint-Based Reconstruction and Analysis (COBRA) methods to simulate, analyze and predict a variety of metabolic phenotypes using genome-scale models. The COBRA Toolbox, a MATLAB package for implementing COBRA methods, was presented earlier. Here we present a significant update of this in silico ToolBox. Version 2.0 of the COBRA Toolbox expands the scope of computations by including in silico analysis methods developed since its original release. New functions include: (1) network gap filling, (2) 13C analysis, (3) metabolic engineering, (4) omics-guided analysis, and (5) visualization. As with the first version, the COBRA Toolbox reads and writes Systems Biology Markup Language formatted models. In version 2.0, we improved performance, usability, and the level of documentation. A suite of test scripts can now be used to learn the core functionality of the Toolbox and validate results. This Toolbox lowers the barrier of entry to use powerful COBRA methods. PMID:21886097

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

HDF-EOS 5 Validator

NASA Technical Reports Server (NTRS)

Ullman, Richard; Bane, Bob; Yang, Jingli

2008-01-01

A computer program partly automates the task of determining whether an HDF-EOS 5 file is valid in that it conforms to specifications for such characteristics as attribute names, dimensionality of data products, and ranges of legal data values. ["HDF-EOS" and variants thereof are defined in "Converting EOS Data From HDF-EOS to netCDF" (GSC-15007-1), which is the first of several preceding articles in this issue of NASA Tech Briefs.] Previously, validity of a file was determined in a tedious and error-prone process in which a person examined human-readable dumps of data-file-format information. The present software helps a user to encode the specifications for an HDFEOS 5 file, and then inspects the file for conformity with the specifications: First, the user writes the specifications in Extensible Markup Language (XML) by use of a document type definition (DTD) that is part of the program. Next, the portion of the program (denoted the validator) that performs the inspection is executed, using, as inputs, the specifications in XML and the HDF-EOS 5 file to be validated. Finally, the user examines the output of the validator.

FNV: light-weight flash-based network and pathway viewer.

PubMed

Dannenfelser, Ruth; Lachmann, Alexander; Szenk, Mariola; Ma'ayan, Avi

2011-04-15

Network diagrams are commonly used to visualize biochemical pathways by displaying the relationships between genes, proteins, mRNAs, microRNAs, metabolites, regulatory DNA elements, diseases, viruses and drugs. While there are several currently available web-based pathway viewers, there is still room for improvement. To this end, we have developed a flash-based network viewer (FNV) for the visualization of small to moderately sized biological networks and pathways. Written in Adobe ActionScript 3.0, the viewer accepts simple Extensible Markup Language (XML) formatted input files to display pathways in vector graphics on any web-page providing flexible layout options, interactivity with the user through tool tips, hyperlinks and the ability to rearrange nodes on the screen. FNV was utilized as a component in several web-based systems, namely Genes2Networks, Lists2Networks, KEA, ChEA and PathwayGenerator. In addition, FVN can be used to embed pathways inside pdf files for the communication of pathways in soft publication materials. FNV is available for use and download along with the supporting documentation and sample networks at http://www.maayanlab.net/FNV. avi.maayan@mssm.edu.

Automation Hooks Architecture Trade Study for Flexible Test Orchestration

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin A.; Maclean, John R.; Graffagnino, Frank J.; McCartney, Patrick A.

2010-01-01

We describe the conclusions of a technology and communities survey supported by concurrent and follow-on proof-of-concept prototyping to evaluate feasibility of defining a durable, versatile, reliable, visible software interface to support strategic modularization of test software development. The objective is that test sets and support software with diverse origins, ages, and abilities can be reliably integrated into test configurations that assemble and tear down and reassemble with scalable complexity in order to conduct both parametric tests and monitored trial runs. The resulting approach is based on integration of three recognized technologies that are currently gaining acceptance within the test industry and when combined provide a simple, open and scalable test orchestration architecture that addresses the objectives of the Automation Hooks task. The technologies are automated discovery using multicast DNS Zero Configuration Networking (zeroconf), commanding and data retrieval using resource-oriented Restful Web Services, and XML data transfer formats based on Automatic Test Markup Language (ATML). This open-source standards-based approach provides direct integration with existing commercial off-the-shelf (COTS) analysis software tools.

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.

Organizing Community-Based Data Standards: Lessons from Developing a Successful Open Standard in Systems Biology

NASA Astrophysics Data System (ADS)

Hucka, M.

2015-09-01

In common with many fields, including astronomy, a vast number of software tools for computational modeling and simulation are available today in systems biology. This wealth of resources is a boon to researchers, but it also presents interoperability problems. Despite working with different software tools, researchers want to disseminate their work widely as well as reuse and extend the models of other researchers. This situation led in the year 2000 to an effort to create a tool-independent, machine-readable file format for representing models: SBML, the Systems Biology Markup Language. SBML has since become the de facto standard for its purpose. Its success and general approach has inspired and influenced other community-oriented standardization efforts in systems biology. Open standards are essential for the progress of science in all fields, but it is often difficult for academic researchers to organize successful community-based standards. I draw on personal experiences from the development of SBML and summarize some of the lessons learned, in the hope that this may be useful to other groups seeking to develop open standards in a community-oriented fashion.

Implications of the Java language on computer-based patient records.

PubMed

Pollard, D; Kucharz, E; Hammond, W E

1996-01-01

The growth of the utilization of the World Wide Web (WWW) as a medium for the delivery of computer-based patient records (CBPR) has created a new paradigm in which clinical information may be delivered. Until recently the authoring tools and environment for application development on the WWW have been limited to Hyper Text Markup Language (HTML) utilizing common gateway interface scripts. While, at times, this provides an effective medium for the delivery of CBPR, it is a less than optimal solution. The server-centric dynamics and low levels of interactivity do not provide for a robust application which is required in a clinical environment. The emergence of Sun Microsystems' Java language is a solution to the problem. In this paper we examine the Java language and its implications to the CBPR. A quantitative and qualitative assessment was performed. The Java environment is compared to HTML and Telnet CBPR environments. Qualitative comparisons include level of interactivity, server load, client load, ease of use, and application capabilities. Quantitative comparisons include data transfer time delays. The Java language has demonstrated promise for delivering CBPRs.

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.

Transformation of Arden Syntax's medical logic modules into ArdenML for a business rules management system.

PubMed

Jung, Chai Young; Choi, Jong-Ye; Jeong, Seong Jik; Cho, Kyunghee; Koo, Yong Duk; Bae, Jin Hee; Kim, Sukil

2016-05-16

Arden Syntax is a Health Level Seven International (HL7) standard language that is used for representing medical knowledge as logic statements. Arden Syntax Markup Language (ArdenML) is a new representation of Arden Syntax based on XML. Compilers are required to execute medical logic modules (MLMs) in the hospital environment. However, ArdenML may also replace the compiler. The purpose of this study is to demonstrate that MLMs, encoded in ArdenML, can be transformed into a commercial rule engine format through an XSLT stylesheet and made executable in a target system. The target rule engine selected was Blaze Advisor. We developed an XSLT stylesheet to transform MLMs in ArdenML into Structured Rules Language (SRL) in Blaze Advisor, through a comparison of syntax between the two languages. The stylesheet was then refined recursively, by building and applying rules collected from the billing and coding guidelines of the Korean health insurance service. Two nurse coders collected and verified the rules and two information technology (IT) specialists encoded the MLMs and built the XSLT stylesheet. Finally, the stylesheet was validated by importing the MLMs into Blaze Advisor and applying them to claims data. The language comparison revealed that Blaze Advisor requires the declaration of variables with explicit types. We used both integer and real numbers for numeric types in ArdenML. "IF∼THEN" statements and assignment statements in ArdenML become rules in Blaze Advisor. We designed an XSLT stylesheet to solve this issue. In addition, we maintained the order of rule execution in the transformed rules, and added two small programs to support variable declarations and action statements. A total of 1489 rules were reviewed during this study, of which 324 rules were collected. We removed duplicate rules and encoded 241 unique MLMs in ArdenML, which were successfully transformed into SRL and imported to Blaze Advisor via the XSLT stylesheet. When applied to 73,841 outpatients' insurance claims data, the review result was the same as that of the legacy system. We have demonstrated that ArdenML can replace a compiler for transforming MLMs into commercial rule engine format. While the proposed XSLT stylesheet requires refinement for general use, we anticipate that the development of further XSLT stylesheets will support various rule engines. Copyright © 2016 Elsevier B.V. All rights reserved.

RPPAML/RIMS: A metadata format and an information management system for reverse phase protein arrays

PubMed Central

Stanislaus, Romesh; Carey, Mark; Deus, Helena F; Coombes, Kevin; Hennessy, Bryan T; Mills, Gordon B; Almeida, Jonas S

2008-01-01

Background Reverse Phase Protein Arrays (RPPA) are convenient assay platforms to investigate the presence of biomarkers in tissue lysates. As with other high-throughput technologies, substantial amounts of analytical data are generated. Over 1000 samples may be printed on a single nitrocellulose slide. Up to 100 different proteins may be assessed using immunoperoxidase or immunoflorescence techniques in order to determine relative amounts of protein expression in the samples of interest. Results In this report an RPPA Information Management System (RIMS) is described and made available with open source software. In order to implement the proposed system, we propose a metadata format known as reverse phase protein array markup language (RPPAML). RPPAML would enable researchers to describe, document and disseminate RPPA data. The complexity of the data structure needed to describe the results and the graphic tools necessary to visualize them require a software deployment distributed between a client and a server application. This was achieved without sacrificing interoperability between individual deployments through the use of an open source semantic database, S3DB. This data service backbone is available to multiple client side applications that can also access other server side deployments. The RIMS platform was designed to interoperate with other data analysis and data visualization tools such as Cytoscape. Conclusion The proposed RPPAML data format hopes to standardize RPPA data. Standardization of data would result in diverse client applications being able to operate on the same set of data. Additionally, having data in a standard format would enable data dissemination and data analysis. PMID:19102773

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.

Baseline coastal oblique aerial photographs collected from Owls Head, Maine, to the Virginia/North Carolina border, May 19-22, 2009

USGS Publications Warehouse

Morgan, Karen L.M.; Hapke, Cheryl J.; Himmelstoss, Emily A.

2015-01-01

Table 1 provides detailed information about the GPS location, name, date, and time for each of the 12,726 photographs taken along with links to each photograph. In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided and can be used 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

Amelie: A Recombinant Computing Framework for Ambient Awareness

NASA Astrophysics Data System (ADS)

Metaxas, Georgios; Markopoulos, Panos; Aarts, Emile

This paper presents Amelie, a service oriented framework that supports the implementation of awareness systems. Amelie adopts the tenets of Recombinant computing to address an important non-functional requirement for Ambient Intelligence software, namely the heterogeneous combination of services and components. Amelie is founded upon FN-AAR an abstract model of Awareness Systems which enables the immediate expression and implementation of socially salient requirements, such as symmetry and social translucence. We discuss the framework and show how system behaviours can be specified using the Awareness Mark-up Language AML.

The semantic architecture of the World-Wide Molecular Matrix (WWMM)

PubMed Central

2011-01-01

The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption. PMID:21999475

The semantic architecture of the World-Wide Molecular Matrix (WWMM).

PubMed

Murray-Rust, Peter; Adams, Sam E; Downing, Jim; Townsend, Joe A; Zhang, Yong

2011-10-14

The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption.

The semantics of Chemical Markup Language (CML): dictionaries and conventions.

PubMed

Murray-Rust, Peter; Townsend, Joe A; Adams, Sam E; Phadungsukanan, Weerapong; Thomas, Jens

2011-10-14

The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs.

CMLLite: a design philosophy for CML

PubMed Central

2011-01-01

CMLLite is a collection of definitions and processes which provide strong and flexible validation for a document in Chemical Markup Language (CML). It consists of an updated CML schema (schema3), conventions specifying rules in both human and machine-understandable forms and a validator available both online and offline to check conformance. This article explores the rationale behind the changes which have been made to the schema, explains how conventions interact and how they are designed, formulated, implemented and tested, and gives an overview of the validation service. PMID:21999395

The semantics of Chemical Markup Language (CML): dictionaries and conventions

PubMed Central

2011-01-01

The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs. PMID:21999509

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…

Semantic e-Science: From Microformats to Models

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Freemantle, J. R.; Aldridge, K. D.

2009-05-01

A platform has been developed to transform semi-structured ASCII data into a representation based on the eXtensible Markup Language (XML). A subsequent transformation allows the XML-based representation to be rendered in the Resource Description Format (RDF). Editorial metadata, expressed as external annotations (via XML Pointer Language), also survives this transformation process (e.g., Lumb et al., http://dx.doi.org/10.1016/j.cageo.2008.03.009). Because the XML-to-RDF transformation uses XSLT (eXtensible Stylesheet Language Transformations), semantic microformats ultimately encode the scientific data (Lumb & Aldridge, http://dx.doi.org/10.1109/HPCS.2006.26). In building the relationship-centric representation in RDF, a Semantic Model of the scientific data is extracted. The systematic enhancement in the expressivity and richness of the scientific data results in representations of knowledge that are readily understood and manipulated by intelligent software agents. Thus scientists are able to draw upon various resources within and beyond their discipline to use in their scientific applications. Since the resulting Semantic Models are independent conceptualizations of the science itself, the representation of scientific knowledge and interaction with the same can stimulate insight from different perspectives. Using the Global Geodynamics Project (GGP) for the purpose of illustration, the introduction of GGP microformats enable a Semantic Model for the GGP that can be semantically queried (e.g., via SPARQL, http://www.w3.org/TR/rdf-sparql-query). Although the present implementation uses the Open Source Redland RDF Libraries (http://librdf.org/), the approach is generalizable to other platforms and to projects other than the GGP (e.g., Baker et al., Informatics and the 2007-2008 Electronic Geophysical Year, Eos Trans. Am. Geophys. Un., 89(48), 485-486, 2008).

Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.

PubMed

Huang, Yang; Lowe, Henry J; Klein, Dan; Cucina, Russell J

2005-01-01

The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain.

OpenCOR: a modular and interoperable approach to computational biology

PubMed Central

Garny, Alan; Hunter, Peter J.

2015-01-01

Computational biologists have been developing standards and formats for nearly two decades, with the aim of easing the description and exchange of experimental data, mathematical models, simulation experiments, etc. One of those efforts is CellML (cellml.org), an XML-based markup language for the encoding of mathematical models. Early CellML-based environments include COR and OpenCell. However, both of those tools have limitations and were eventually replaced with OpenCOR (opencor.ws). OpenCOR is an open source modeling environment that is supported on Windows, Linux and OS X. It relies on a modular approach, which means that all of its features come in the form of plugins. Those plugins can be used to organize, edit, simulate and analyze models encoded in the CellML format. We start with an introduction to CellML and two of its early adopters, which limitations eventually led to the development of OpenCOR. We then go onto describing the general philosophy behind OpenCOR, as well as describing its openness and its development process. Next, we illustrate various aspects of OpenCOR, such as its user interface and some of the plugins that come bundled with it (e.g., its editing and simulation plugins). Finally, we discuss some of the advantages and limitations of OpenCOR before drawing some concluding remarks. PMID:25705192

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.

An introduction to the Semantic Web for health sciences librarians.

PubMed

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-04-01

The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects.

A program code generator for multiphysics biological simulation using markup languages.

PubMed

Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi

2012-01-01

To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.

[Research on tumor information grid framework].

PubMed

Zhang, Haowei; Qin, Zhu; Liu, Ying; Tan, Jianghao; Cao, Haitao; Chen, Youping; Zhang, Ke; Ding, Yuqing

2013-10-01

In order to realize tumor disease information sharing and unified management, we utilized grid technology to make the data and software resources which distributed in various medical institutions for effective integration so that we could make the heterogeneous resources consistent and interoperable in both semantics and syntax aspects. This article describes the tumor grid framework, the type of the service being packaged in Web Service Description Language (WSDL) and extensible markup language schemas definition (XSD), the client use the serialized document to operate the distributed resources. The service objects could be built by Unified Modeling Language (UML) as middle ware to create application programming interface. All of the grid resources are registered in the index and released in the form of Web Services based on Web Services Resource Framework (WSRF). Using the system we can build a multi-center, large sample and networking tumor disease resource sharing framework to improve the level of development in medical scientific research institutions and the patient's quality of life.

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.

Representing nested semantic information in a linear string of text using XML.

PubMed

Krauthammer, Michael; Johnson, Stephen B; Hripcsak, George; Campbell, David A; Friedman, Carol

2002-01-01

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a Natural Language Processor. Traditional approaches to this problem separate the structured information from the actual text mark up. This paper introduces an alternative solution, which tightly integrates the semantic structure with the text. The resulting XML markup preserves the linearity of the medical texts and can therefore be easily expanded with additional types of information.

Representing nested semantic information in a linear string of text using XML.

PubMed Central

Krauthammer, Michael; Johnson, Stephen B.; Hripcsak, George; Campbell, David A.; Friedman, Carol

2002-01-01

XML has been widely adopted as an important data interchange language. The structure of XML enables sharing of data elements with variable degrees of nesting as long as the elements are grouped in a strict tree-like fashion. This requirement potentially restricts the usefulness of XML for marking up written text, which often includes features that do not properly nest within other features. We encountered this problem while marking up medical text with structured semantic information from a Natural Language Processor. Traditional approaches to this problem separate the structured information from the actual text mark up. This paper introduces an alternative solution, which tightly integrates the semantic structure with the text. The resulting XML markup preserves the linearity of the medical texts and can therefore be easily expanded with additional types of information. PMID:12463856

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.

imzML: Imaging Mass Spectrometry Markup Language: A common data format for mass spectrometry imaging.

PubMed

Römpp, Andreas; Schramm, Thorsten; Hester, Alfons; Klinkert, Ivo; Both, Jean-Pierre; Heeren, Ron M A; Stöckli, Markus; Spengler, Bernhard

2011-01-01

Imaging mass spectrometry is the method of scanning a sample of interest and generating an "image" of the intensity distribution of a specific analyte. The data sets consist of a large number of mass spectra which are usually acquired with identical settings. Existing data formats are not sufficient to describe an MS imaging experiment completely. The data format imzML was developed to allow the flexible and efficient exchange of MS imaging data between different instruments and data analysis software.For this purpose, the MS imaging data is divided in two separate files. The mass spectral data is stored in a binary file to ensure efficient storage. All metadata (e.g., instrumental parameters, sample details) are stored in an XML file which is based on the standard data format mzML developed by HUPO-PSI. The original mzML controlled vocabulary was extended to include specific parameters of imaging mass spectrometry (such as x/y position and spatial resolution). The two files (XML and binary) are connected by offset values in the XML file and are unambiguously linked by a universally unique identifier. The resulting datasets are comparable in size to the raw data and the separate metadata file allows flexible handling of large datasets.Several imaging MS software tools already support imzML. This allows choosing from a (growing) number of processing tools. One is no longer limited to proprietary software, but is able to use the processing software which is best suited for a specific question or application. On the other hand, measurements from different instruments can be compared within one software application using identical settings for data processing. All necessary information for evaluating and implementing imzML can be found at http://www.imzML.org .

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.

Automation Hooks Architecture for Flexible Test Orchestration - Concept Development and Validation

NASA Technical Reports Server (NTRS)

Lansdowne, C. A.; Maclean, John R.; Winton, Chris; McCartney, Pat

2011-01-01

The Automation Hooks Architecture Trade Study for Flexible Test Orchestration sought a standardized data-driven alternative to conventional automated test programming interfaces. The study recommended composing the interface using multicast DNS (mDNS/SD) service discovery, Representational State Transfer (Restful) Web Services, and Automatic Test Markup Language (ATML). We describe additional efforts to rapidly mature the Automation Hooks Architecture candidate interface definition by validating it in a broad spectrum of applications. These activities have allowed us to further refine our concepts and provide observations directed toward objectives of economy, scalability, versatility, performance, severability, maintainability, scriptability and others.

A Platform-Independent Plugin for Navigating Online Radiology Cases.

PubMed

Balkman, Jason D; Awan, Omer A

2016-06-01

Software methods that enable navigation of radiology cases on various digital platforms differ between handheld devices and desktop computers. This has resulted in poor compatibility of online radiology teaching files across mobile smartphones, tablets, and desktop computers. A standardized, platform-independent, or "agnostic" approach for presenting online radiology content was produced in this work by leveraging modern hypertext markup language (HTML) and JavaScript web software technology. We describe the design and evaluation of this software, demonstrate its use across multiple viewing platforms, and make it publicly available as a model for future development efforts.

Visualization and dissemination of global crustal models on virtual globes

NASA Astrophysics Data System (ADS)

Zhu, Liang-feng; Pan, Xin; Sun, Jian-zhong

2016-05-01

Global crustal models, such as CRUST 5.1 and its descendants, are very useful in a broad range of geoscience applications. The current method for representing the existing global crustal models relies heavily on dedicated computer programs to read and work with those models. Therefore, it is not suited to visualize and disseminate global crustal information to non-geological users. This shortcoming is becoming obvious as more and more people from both academic and non-academic institutions are interested in understanding the structure and composition of the crust. There is a pressing need to provide a modern, universal and user-friendly method to represent and visualize the existing global crustal models. In this paper, we present a systematic framework to easily visualize and disseminate the global crustal structure on virtual globes. Based on crustal information exported from the existing global crustal models, we first create a variety of KML-formatted crustal models with different levels of detail (LODs). And then the KML-formatted models can be loaded into a virtual globe for 3D visualization and model dissemination. A Keyhole Markup Language (KML) generator (Crust2KML) is developed to automatically convert crustal information obtained from the CRUST 1.0 model into KML-formatted global crustal models, and a web application (VisualCrust) is designed to disseminate and visualize those models over the Internet. The presented framework and associated implementations can be conveniently exported to other applications to support visualizing and analyzing the Earth's internal structure on both regional and global scales in a 3D virtual-globe environment.

ShinyKGode: an interactive application for ODE parameter inference using gradient matching.

PubMed

Wandy, Joe; Niu, Mu; Giurghita, Diana; Daly, Rónán; Rogers, Simon; Husmeier, Dirk

2018-07-01

Mathematical modelling based on ordinary differential equations (ODEs) is widely used to describe the dynamics of biological systems, particularly in systems and pathway biology. Often the kinetic parameters of these ODE systems are unknown and have to be inferred from the data. Approximate parameter inference methods based on gradient matching (which do not require performing computationally expensive numerical integration of the ODEs) have been getting popular in recent years, but many implementations are difficult to run without expert knowledge. Here, we introduce ShinyKGode, an interactive web application to perform fast parameter inference on ODEs using gradient matching. ShinyKGode can be used to infer ODE parameters on simulated and observed data using gradient matching. Users can easily load their own models in Systems Biology Markup Language format, and a set of pre-defined ODE benchmark models are provided in the application. Inferred parameters are visualized alongside diagnostic plots to assess convergence. The R package for ShinyKGode can be installed through the Comprehensive R Archive Network (CRAN). Installation instructions, as well as tutorial videos and source code are available at https://joewandy.github.io/shinyKGode. Supplementary data are available at Bioinformatics online.

[The compression and storage of enhanced external counterpulsation waveform based on DICOM standard].

PubMed

Hu, Ding; Xie, Shuqun; Yu, Donglan; Zheng, Zhensheng; Wang, Kuijian

2010-04-01

The development of external counterpulsation (ECP) local area network system and extensible markup language (XML)-based remote ECP medical information system conformable to digital imaging and communications in medicine (DICOM) standard has been improving the digital interchangeablity and sharability of ECP data. However, the therapy process of ECP is a continuous and longtime supervision which builds a mass of waveform data. In order to reduce the storage space and improve the transmission efficiency, the waveform data with the normative format of ECP data files have to be compressed. In this article, we introduced the compression arithmetic of template matching and improved quick fitting of linear approximation distance thresholding (LADT) in combimation with the characters of enhanced external counterpulsation (EECP) waveform signal. The DICOM standard is used as the storage and transmission standard to make our system compatible with hospital information system. According to the rules of transfer syntaxes, we defined private transfer syntax for one-dimensional compressed waveform data and stored EECP data into a DICOM file. Testing result indicates that the compressed and normative data can be correctly transmitted and displayed between EECP workstations in our EECP laboratory.

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

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.

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.

NIST Gas Hydrate Research Database and Web Dissemination Channel.

PubMed

Kroenlein, K; Muzny, C D; Kazakov, A; Diky, V V; Chirico, R D; Frenkel, M; Sloan, E D

2010-01-01

To facilitate advances in application of technologies pertaining to gas hydrates, a freely available data resource containing experimentally derived information about those materials was developed. This work was performed by the Thermodynamic Research Center (TRC) paralleling a highly successful database of thermodynamic and transport properties of molecular pure compounds and their mixtures. Population of the gas-hydrates database required development of guided data capture (GDC) software designed to convert experimental data and metadata into a well organized electronic format, as well as a relational database schema to accommodate all types of numerical and metadata within the scope of the project. To guarantee utility for the broad gas hydrate research community, TRC worked closely with the Committee on Data for Science and Technology (CODATA) task group for Data on Natural Gas Hydrates, an international data sharing effort, in developing a gas hydrate markup language (GHML). The fruits of these efforts are disseminated through the NIST Sandard Reference Data Program [1] as the Clathrate Hydrate Physical Property Database (SRD #156). A web-based interface for this database, as well as scientific results from the Mallik 2002 Gas Hydrate Production Research Well Program [2], is deployed at http://gashydrates.nist.gov.

XML Flight/Ground Data Dictionary Management

NASA Technical Reports Server (NTRS)

Wright, Jesse; Wiklow, Colette

2007-01-01

A computer program generates Extensible Markup Language (XML) files that effect coupling between the command- and telemetry-handling software running aboard a spacecraft and the corresponding software running in ground support systems. The XML files are produced by use of information from the flight software and from flight-system engineering. The XML files are converted to legacy ground-system data formats for command and telemetry, transformed into Web-based and printed documentation, and used in developing new ground-system data-handling software. Previously, the information about telemetry and command was scattered in various paper documents that were not synchronized. The process of searching and reading the documents was time-consuming and introduced errors. In contrast, the XML files contain all of the information in one place. XML structures can evolve in such a manner as to enable the addition, to the XML files, of the metadata necessary to track the changes and the associated documentation. The use of this software has reduced the extent of manual operations in developing a ground data system, thereby saving considerable time and removing errors that previously arose in the translation and transcription of software information from the flight to the ground system.

[The aspects of pricing policy in Azerbaijan pharmaceutical sector].

PubMed

Dzhalilova, K I; Alieva, K Ia

2012-01-01

The effect of macro-, middle- and microeconomic factors on price formation in Azerbaijan pharmaceutical market has been studied. Worldwide pharmaceutical leaders have the goals to become leader on the pharmaceutical market of Azerbaijan and maximize their market share. Non-leaders pharmaceutical companies use different strategies of price formation: prime cost plus markup, or price formation on the base of current prices. It was revealed that domestic pharmaceutical market has high demand elasticity. Future market development is related to stimulation of product development, and hard penetration to the market through realization of price formation strategy. Non-state pharmaceutical organizations to achieve the purpose of survive in conditions of high competition should take in to account the factor perceptions of assortment by customers.

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

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.

The need for the use of XACML access control policy in a distributed EHR and some performance considerations.

PubMed

Sucurovic, Snezana; Milutinovic, Veljko

2008-01-01

The Internet based distributed large scale information systems implements attribute based access control (ABAC) rather than Role Based Access Control (RBAC). The reason is that the Internet is identity less and that ABAC scales better. EXtensible Access Control Markup Language is standardized language for writing access control policies, access control requests and access control responses in ABAC. XACML can provide decentralized administration and credentials distribution. In year 2002 version of CEN ENV 13 606 attributes have been attached to EHCR components and in such a system ABAC and XACML have been easy to implement. This paper presents writing XACML policies in the case when attributes are in hierarchical structure. It is presented two possible solutions to write XACML policy in that case and that the solution when set functions are used is more compact and provides 10% better performances.

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)''.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

A Journey in Standard Development: The Core Manufacturing Simulation Data (CMSD) Information Model.

PubMed

Lee, Yung-Tsun Tina

2015-01-01

This report documents a journey "from research to an approved standard" of a NIST-led standard development activity. That standard, Core Manufacturing Simulation Data (CMSD) information model, provides neutral structures for the efficient exchange of manufacturing data in a simulation environment. The model was standardized under the auspices of the international Simulation Interoperability Standards Organization (SISO). NIST started the research in 2001 and initiated the standardization effort in 2004. The CMSD standard was published in two SISO Products. In the first Product, the information model was defined in the Unified Modeling Language (UML) and published in 2010 as SISO-STD-008-2010. In the second Product, the information model was defined in Extensible Markup Language (XML) and published in 2013 as SISO-STD-008-01-2012. Both SISO-STD-008-2010 and SISO-STD-008-01-2012 are intended to be used together.

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

An introduction to the Semantic Web for health sciences librarians*

PubMed Central

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-01-01

Objectives: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. Methodology: The paper is structured into two main parts. “Semantic Web Technology” provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. “Semantic Web Applications and Research Projects in the Biomedical Field” is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Discussion and Conclusions: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects. PMID:16636713

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.

An Implementation-Focused Bio/Algorithmic Workflow for Synthetic Biology.

PubMed

Goñi-Moreno, Angel; Carcajona, Marta; Kim, Juhyun; Martínez-García, Esteban; Amos, Martyn; de Lorenzo, Víctor

2016-10-21

As synthetic biology moves away from trial and error and embraces more formal processes, workflows have emerged that cover the roadmap from conceptualization of a genetic device to its construction and measurement. This latter aspect (i.e., characterization and measurement of synthetic genetic constructs) has received relatively little attention to date, but it is crucial for their outcome. An end-to-end use case for engineering a simple synthetic device is presented, which is supported by information standards and computational methods and focuses on such characterization/measurement. This workflow captures the main stages of genetic device design and description and offers standardized tools for both population-based measurement and single-cell analysis. To this end, three separate aspects are addressed. First, the specific vector features are discussed. Although device/circuit design has been successfully automated, important structural information is usually overlooked, as in the case of plasmid vectors. The use of the Standard European Vector Architecture (SEVA) is advocated for selecting the optimal carrier of a design and its thorough description in order to unequivocally correlate digital definitions and molecular devices. A digital version of this plasmid format was developed with the Synthetic Biology Open Language (SBOL) along with a software tool that allows users to embed genetic parts in vector cargoes. This enables annotation of a mathematical model of the device's kinetic reactions formatted with the Systems Biology Markup Language (SBML). From that point onward, the experimental results and their in silico counterparts proceed alongside, with constant feedback to preserve consistency between them. A second aspect involves a framework for the calibration of fluorescence-based measurements. One of the most challenging endeavors in standardization, metrology, is tackled by reinterpreting the experimental output in light of simulation results, allowing us to turn arbitrary fluorescence units into relative measurements. Finally, integration of single-cell methods into a framework for multicellular simulation and measurement is addressed, allowing standardized inspection of the interplay between the carrier chassis and the culture conditions.

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.

The inclusion of an online journal in PubMed central - a difficult path.

PubMed

Grech, Victor

2016-01-01

The indexing of a journal in a prominent database (such as PubMed) is an important imprimatur. Journals accepted for inclusion in PubMed Central (PMC) are automatically indexed in PubMed but must provide the entire contents of their publications as XML-tagged (Extensible Markup Language) data files compliant with PubMed's document type definition (DTD). This paper describes the various attempts that the journal Images in Paediatric Cardiology made in its efforts to convert the journal contents (including all of the extant backlog) to PMC-compliant XML for archiving and indexing in PubMed after the journal was accepted for inclusion by the database.

Post-Hurricane Ivan coastal oblique aerial photographs collected from Crawfordville, Florida, to Petit Bois Island, Mississippi, September 17, 2004

USGS Publications Warehouse

Morgan, Karen L.M.; Krohn, M. Dennis; Peterson, Russell D.; Thompson, Philip R.; Subino, Janice A.

2015-01-01

Table 1 provides detailed information about the GPS location, image name, date, and time for each of the 3,381 photographs taken, along with links to each photograph. The photographs are organized into segments, also referred to as contact sheets, and represent approximately 5 minutes of flight time. In addition to the photographs, a Google Earth Keyhole Markup Language (KML) file is provided, which 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.

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.

Creation of an Open Framework for Point-of-Care Computer-Assisted Reporting and Decision Support Tools for Radiologists.

PubMed

Alkasab, Tarik K; Bizzo, Bernardo C; Berland, Lincoln L; Nair, Sujith; Pandharipande, Pari V; Harvey, H Benjamin

2017-09-01

Decreasing unnecessary variation in radiology reporting and producing guideline-concordant reports is fundamental to radiology's success in value-based payment models and good for patient care. In this article, we present an open authoring system for point-of-care clinical decision support tools integrated into the radiologist reporting environment referred to as the computer-assisted reporting and decision support (CAR/DS) framework. The CAR/DS authoring system, described herein, includes: (1) a definition format for representing radiology clinical guidelines as structured, machine-readable Extensible Markup Language documents and (2) a user-friendly reference implementation to test the fidelity of the created definition files with the clinical guideline. The proposed definition format and reference implementation will enable content creators to develop CAR/DS tools that voice recognition software (VRS) vendors can use to extend the commercial tools currently in use. In making the definition format and reference implementation software freely available, we hope to empower individual radiologists, expert groups such as the ACR, and VRS vendors to develop a robust ecosystem of CAR/DS tools that can further improve the quality and efficiency of the patient care that our field provides. We hope that this initial effort can serve as the basis for a community-owned open standard for guideline definition that the imaging informatics and VRS vendor communities will embrace and strengthen. To this end, the ACR Assist™ initiative is intended to make the College's clinical content, including the Incidental Findings Committee White Papers, available for decision support tool creation based upon the herein described CAR/DS framework. Copyright © 2017 American College of Radiology. Published by Elsevier Inc. All rights reserved.

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...

DTD Creation for the Software Technology for Adaptable, Reliable Systems (STARS) Program

DTIC Science & Technology

1990-06-23

developed to store documents in a format peculiar to the program’s design . Editing the document became easy since word processors adjust all spacing and...descriptive markup may be output to a 3 CDRL 1810 January 26, 1990 variety of devices ranging from high quality typography printers through laser printers...provision for non-SGML material, such as graphics , to be inserted in a document. For these reasons the Computer-Aided Acquisition and Logistics Support

Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon

PubMed Central

Huang, Yang; Lowe, Henry J.; Klein, Dan; Cucina, Russell J.

2005-01-01

Objective: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS® Specialist Lexicon to improve noun phrase identification within clinical radiology documents. Design: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)® Clinical Document Architecture (CDA)–compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. Results: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. Conclusion: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain. PMID:15684131

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

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.

Informatics in radiology (infoRAD): HTML and Web site design for the radiologist: a primer.

PubMed

Ryan, Anthony G; Louis, Luck J; Yee, William C

2005-01-01

A Web site has enormous potential as a medium for the radiologist to store, present, and share information in the form of text, images, and video clips. With a modest amount of tutoring and effort, designing a site can be as painless as preparing a Microsoft PowerPoint presentation. The site can then be used as a hub for the development of further offshoots (eg, Web-based tutorials, storage for a teaching library, publication of information about one's practice, and information gathering from a wide variety of sources). By learning the basics of hypertext markup language (HTML), the reader will be able to produce a simple and effective Web page that permits display of text, images, and multimedia files. The process of constructing a Web page can be divided into five steps: (a) creating a basic template with formatted text, (b) adding color, (c) importing images and multimedia files, (d) creating hyperlinks, and (e) uploading one's page to the Internet. This Web page may be used as the basis for a Web-based tutorial comprising text documents and image files already in one's possession. Finally, there are many commercially available packages for Web page design that require no knowledge of HTML.

VIOLIN: vaccine investigation and online information network.

PubMed

Xiang, Zuoshuang; Todd, Thomas; Ku, Kim P; Kovacic, Bethany L; Larson, Charles B; Chen, Fang; Hodges, Andrew P; Tian, Yuying; Olenzek, Elizabeth A; Zhao, Boyang; Colby, Lesley A; Rush, Howard G; Gilsdorf, Janet R; Jourdian, George W; He, Yongqun

2008-01-01

Vaccines are among the most efficacious and cost-effective tools for reducing morbidity and mortality caused by infectious diseases. The vaccine investigation and online information network (VIOLIN) is a web-based central resource, allowing easy curation, comparison and analysis of vaccine-related research data across various human pathogens (e.g. Haemophilus influenzae, human immunodeficiency virus (HIV) and Plasmodium falciparum) of medical importance and across humans, other natural hosts and laboratory animals. Vaccine-related peer-reviewed literature data have been downloaded into the database from PubMed and are searchable through various literature search programs. Vaccine data are also annotated, edited and submitted to the database through a web-based interactive system that integrates efficient computational literature mining and accurate manual curation. Curated information includes general microbial pathogenesis and host protective immunity, vaccine preparation and characteristics, stimulated host responses after vaccination and protection efficacy after challenge. Vaccine-related pathogen and host genes are also annotated and available for searching through customized BLAST programs. All VIOLIN data are available for download in an eXtensible Markup Language (XML)-based data exchange format. VIOLIN is expected to become a centralized source of vaccine information and to provide investigators in basic and clinical sciences with curated data and bioinformatics tools for vaccine research and development. VIOLIN is publicly available at http://www.violinet.org.

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.

The Essential Component in DNA-Based Information Storage System: Robust Error-Tolerating Module

PubMed Central

Yim, Aldrin Kay-Yuen; Yu, Allen Chi-Shing; Li, Jing-Woei; Wong, Ada In-Chun; Loo, Jacky F. C.; Chan, King Ming; Kong, S. K.; Yip, Kevin Y.; Chan, Ting-Fung

2014-01-01

The size of digital data is ever increasing and is expected to grow to 40,000 EB by 2020, yet the estimated global information storage capacity in 2011 is <300 EB, indicating that most of the data are transient. DNA, as a very stable nano-molecule, is an ideal massive storage device for long-term data archive. The two most notable illustrations are from Church et al. and Goldman et al., whose approaches are well-optimized for most sequencing platforms – short synthesized DNA fragments without homopolymer. Here, we suggested improvements on error handling methodology that could enable the integration of DNA-based computational process, e.g., algorithms based on self-assembly of DNA. As a proof of concept, a picture of size 438 bytes was encoded to DNA with low-density parity-check error-correction code. We salvaged a significant portion of sequencing reads with mutations generated during DNA synthesis and sequencing and successfully reconstructed the entire picture. A modular-based programing framework – DNAcodec with an eXtensible Markup Language-based data format was also introduced. Our experiments demonstrated the practicability of long DNA message recovery with high error tolerance, which opens the field to biocomputing and synthetic biology. PMID:25414846

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.

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

Modeling languages for biochemical network simulation: reaction vs equation based approaches.

PubMed

Wiechert, Wolfgang; Noack, Stephan; Elsheikh, Atya

2010-01-01

Biochemical network modeling and simulation is an essential task in any systems biology project. The systems biology markup language (SBML) was established as a standardized model exchange language for mechanistic models. A specific strength of SBML is that numerous tools for formulating, processing, simulation and analysis of models are freely available. Interestingly, in the field of multidisciplinary simulation, the problem of model exchange between different simulation tools occurred much earlier. Several general modeling languages like Modelica have been developed in the 1990s. Modelica enables an equation based modular specification of arbitrary hierarchical differential algebraic equation models. Moreover, libraries for special application domains can be rapidly developed. This contribution compares the reaction based approach of SBML with the equation based approach of Modelica and explains the specific strengths of both tools. Several biological examples illustrating essential SBML and Modelica concepts are given. The chosen criteria for tool comparison are flexibility for constraint specification, different modeling flavors, hierarchical, modular and multidisciplinary modeling. Additionally, support for spatially distributed systems, event handling and network analysis features is discussed. As a major result it is shown that the choice of the modeling tool has a strong impact on the expressivity of the specified models but also strongly depends on the requirements of the application context.

Web-Based Collaborative Publications System: R&Tserve

NASA Technical Reports Server (NTRS)

Abrams, Steve

1997-01-01

R&Tserve is a publications system based on 'commercial, off-the-shelf' (COTS) software that provides a persistent, collaborative workspace for authors and editors to support the entire publication development process from initial submission, through iterative editing in a hierarchical approval structure, and on to 'publication' on the WWW. It requires no specific knowledge of the WWW (beyond basic use) or HyperText Markup Language (HTML). Graphics and URLs are automatically supported. The system includes a transaction archive, a comments utility, help functionality, automated graphics conversion, automated table generation, and an email-based notification system. It may be configured and administered via the WWW and can support publications ranging from single page documents to multiple-volume 'tomes'.

Guide to the Internet. The world wide web.

PubMed Central

Pallen, M.

1995-01-01

The world wide web provides a uniform, user friendly interface to the Internet. Web pages can contain text and pictures and are interconnected by hypertext links. The addresses of web pages are recorded as uniform resource locators (URLs), transmitted by hypertext transfer protocol (HTTP), and written in hypertext markup language (HTML). Programs that allow you to use the web are available for most operating systems. Powerful on line search engines make it relatively easy to find information on the web. Browsing through the web--"net surfing"--is both easy and enjoyable. Contributing to the web is not difficult, and the web opens up new possibilities for electronic publishing and electronic journals. Images p1554-a Fig 5 PMID:8520402

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.

Framework and prototype for a secure XML-based electronic health records system.

PubMed

Steele, Robert; Gardner, William; Chandra, Darius; Dillon, Tharam S

2007-01-01

Security of personal medical information has always been a challenge for the advancement of Electronic Health Records (EHRs) initiatives. eXtensible Markup Language (XML), is rapidly becoming the key standard for data representation and transportation. The widespread use of XML and the prospect of its use in the Electronic Health (e-health) domain highlights the need for flexible access control models for XML data and documents. This paper presents a declarative access control model for XML data repositories that utilises an expressive XML role control model. The operational semantics of this model are illustrated by Xplorer, a user interface generation engine which supports search-browse-navigate activities on XML repositories.

Post-Hurricane Irene coastal oblique aerial photographs collected from Ocracoke Inlet, North Carolina, to Virginia Beach, Virginia, August 30-31, 2011

USGS Publications Warehouse

Morgan, Karen L. M.; Krohn, M. Dennis

2016-02-17

Table 1 provides detailed information about the GPS location, image name, date, and time for each of the 2,688 photographs that were taken along with links to each photograph.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 also shows the track of Hurricane Irene. The KML files were created using the photographic navigation files. These KML file(s) can be found in the kml folder.

WITH: a system to write clinical trials using XML and RDBMS.

PubMed Central

Fazi, Paola; Luzi, Daniela; Manco, Mariarosaria; Ricci, Fabrizio L.; Toffoli, Giovanni; Vignetti, Marco

2002-01-01

The paper illustrates the system WITH (Write on Internet clinical Trials in Haematology) which supports the writing of a clinical trial (CT) document. The requirements of this system have been defined analysing the writing process of a CT and then modelling the content of its sections together with their logical and temporal relationships. The system WITH allows: a) editing the document text; b) re-using the text; and c) facilitating the cooperation and the collaborative writing. It is based on XML mark-up language, and on a RDBMS. This choice guarantees: a) process standardisation; b) process management; c) efficient delivery of information-based tasks; and d) explicit focus on process design. PMID:12463823

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

Trajectory Specification for High-Capacity Air Traffic Control

NASA Technical Reports Server (NTRS)

Paielli, Russell A.

2004-01-01

In the current air traffic management system, the fundamental limitation on airspace capacity is the cognitive ability of human air traffic controllers to maintain safe separation with high reliability. The doubling or tripling of airspace capacity that will be needed over the next couple of decades will require that tactical separation be at least partially automated. Standardized conflict-free four-dimensional trajectory assignment will be needed to accomplish that objective. A trajectory specification format based on the Extensible Markup Language is proposed for that purpose. This format can be used to downlink a trajectory request, which can then be checked on the ground for conflicts and approved or modified, if necessary, then uplinked as the assigned trajectory. The horizontal path is specified as a series of geodetic waypoints connected by great circles, and the great-circle segments are connected by turns of specified radius. Vertical profiles for climb and descent are specified as low-order polynomial functions of along-track position, which is itself specified as a function of time. Flight technical error tolerances in the along-track, cross-track, and vertical axes define a bounding space around the reference trajectory, and conformance will guarantee the required separation for a period of time known as the conflict time horizon. An important safety benefit of this regimen is that the traffic will be able to fly free of conflicts for at least several minutes even if all ground systems and the entire communication infrastructure fail. Periodic updates in the along-track axis will adjust for errors in the predicted along-track winds.

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.

[The therapeutic drug monitoring network server of tacrolimus for Chinese renal transplant patients].

PubMed

Deng, Chen-Hui; Zhang, Guan-Min; Bi, Shan-Shan; Zhou, Tian-Yan; Lu, Wei

2011-07-01

This study is to develop a therapeutic drug monitoring (TDM) network server of tacrolimus for Chinese renal transplant patients, which can facilitate doctor to manage patients' information and provide three levels of predictions. Database management system MySQL was employed to build and manage the database of patients and doctors' information, and hypertext mark-up language (HTML) and Java server pages (JSP) technology were employed to construct network server for database management. Based on the population pharmacokinetic model of tacrolimus for Chinese renal transplant patients, above program languages were used to construct the population prediction and subpopulation prediction modules. Based on Bayesian principle and maximization of the posterior probability function, an objective function was established, and minimized by an optimization algorithm to estimate patient's individual pharmacokinetic parameters. It is proved that the network server has the basic functions for database management and three levels of prediction to aid doctor to optimize the regimen of tacrolimus for Chinese renal transplant patients.

Mercury Shopping Cart Interface

NASA Technical Reports Server (NTRS)

Pfister, Robin; McMahon, Joe

2006-01-01

Mercury Shopping Cart Interface (MSCI) is a reusable component of the Power User Interface 5.0 (PUI) program described in another article. MSCI is a means of encapsulating the logic and information needed to describe an orderable item consistent with Mercury Shopping Cart service protocol. Designed to be used with Web-browser software, MSCI generates Hypertext Markup Language (HTML) pages on which ordering information can be entered. MSCI comprises two types of Practical Extraction and Report Language (PERL) modules: template modules and shopping-cart logic modules. Template modules generate HTML pages for entering the required ordering details and enable submission of the order via a Hypertext Transfer Protocol (HTTP) post. Shopping cart modules encapsulate the logic and data needed to describe an individual orderable item to the Mercury Shopping Cart service. These modules evaluate information entered by the user to determine whether it is sufficient for the Shopping Cart service to process the order. Once an order has been passed from MSCI to a deployed Mercury Shopping Cart server, there is no further interaction with the user.

A standard-enabled workflow for synthetic biology.

PubMed

Myers, Chris J; Beal, Jacob; Gorochowski, Thomas E; Kuwahara, Hiroyuki; Madsen, Curtis; McLaughlin, James Alastair; Mısırlı, Göksel; Nguyen, Tramy; Oberortner, Ernst; Samineni, Meher; Wipat, Anil; Zhang, Michael; Zundel, Zach

2017-06-15

A synthetic biology workflow is composed of data repositories that provide information about genetic parts, sequence-level design tools to compose these parts into circuits, visualization tools to depict these designs, genetic design tools to select parts to create systems, and modeling and simulation tools to evaluate alternative design choices. Data standards enable the ready exchange of information within such a workflow, allowing repositories and tools to be connected from a diversity of sources. The present paper describes one such workflow that utilizes, among others, the Synthetic Biology Open Language (SBOL) to describe genetic designs, the Systems Biology Markup Language to model these designs, and SBOL Visual to visualize these designs. We describe how a standard-enabled workflow can be used to produce types of design information, including multiple repositories and software tools exchanging information using a variety of data standards. Recently, the ACS Synthetic Biology journal has recommended the use of SBOL in their publications. © 2017 The Author(s); published by Portland Press Limited on behalf of the Biochemical Society.

The medical simulation markup language - simplifying the biomechanical modeling workflow.

PubMed

Suwelack, Stefan; Stoll, Markus; Schalck, Sebastian; Schoch, Nicolai; Dillmann, Rüdiger; Bendl, Rolf; Heuveline, Vincent; Speidel, Stefanie

2014-01-01

Modeling and simulation of the human body by means of continuum mechanics has become an important tool in diagnostics, computer-assisted interventions and training. This modeling approach seeks to construct patient-specific biomechanical models from tomographic data. Usually many different tools such as segmentation and meshing algorithms are involved in this workflow. In this paper we present a generalized and flexible description for biomechanical models. The unique feature of the new modeling language is that it not only describes the final biomechanical simulation, but also the workflow how the biomechanical model is constructed from tomographic data. In this way, the MSML can act as a middleware between all tools used in the modeling pipeline. The MSML thus greatly facilitates the prototyping of medical simulation workflows for clinical and research purposes. In this paper, we not only detail the XML-based modeling scheme, but also present a concrete implementation. Different examples highlight the flexibility, robustness and ease-of-use of the approach.

Towards health care process description framework: an XML DTD design.

PubMed Central

Staccini, P.; Joubert, M.; Quaranta, J. F.; Aymard, S.; Fieschi, D.; Fieschi, M.

2001-01-01

The development of health care and hospital information systems has to meet users needs as well as requirements such as the tracking of all care activities and the support of quality improvement. The use of process-oriented analysis is of-value to provide analysts with: (i) a systematic description of activities; (ii) the elicitation of the useful data to perform and record care tasks; (iii) the selection of relevant decision-making support. But paper-based tools are not a very suitable way to manage and share the documentation produced during this step. The purpose of this work is to propose a method to implement the results of process analysis according to XML techniques (eXtensible Markup Language). It is based on the IDEF0 activity modeling language (Integration DEfinition for Function modeling). A hierarchical description of a process and its components has been defined through a flat XML file with a grammar of proper metadata tags. Perspectives of this method are discussed. PMID:11825265

Automating Data Submission to a National Archive

NASA Astrophysics Data System (ADS)

Work, T. T.; Chandler, C. L.; Groman, R. C.; Allison, M. D.; Gegg, S. R.; Biological; Chemical Oceanography Data Management Office

2010-12-01

In late 2006, the U.S. National Science Foundation (NSF) funded the Biological and Chemical Oceanographic Data Management Office (BCO-DMO) at Woods Hole Oceanographic Institution (WHOI) to work closely with investigators to manage oceanographic data generated from their research projects. One of the final data management tasks is to ensure that the data are permanently archived at the U.S. National Oceanographic Data Center (NODC) or other appropriate national archiving facility. In the past, BCO-DMO submitted data to NODC as an email with attachments including a PDF file (a manually completed metadata record) and one or more data files. This method is no longer feasible given the rate at which data sets are contributed to BCO-DMO. Working with collaborators at NODC, a more streamlined and automated workflow was developed to keep up with the increased volume of data that must be archived at NODC. We will describe our new workflow; a semi-automated approach for contributing data to NODC that includes a Federal Geographic Data Committee (FGDC) compliant Extensible Markup Language (XML) metadata file accompanied by comma-delimited data files. The FGDC XML file is populated from information stored in a MySQL database. A crosswalk described by an Extensible Stylesheet Language Transformation (XSLT) is used to transform the XML formatted MySQL result set to a FGDC compliant XML metadata file. To ensure data integrity, the MD5 algorithm is used to generate a checksum and manifest of the files submitted to NODC for permanent archive. The revised system supports preparation of detailed, standards-compliant metadata that facilitate data sharing and enable accurate reuse of multidisciplinary information. The approach is generic enough to be adapted for use by other data management groups.

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).

DICOM router: an open source toolbox for communication and correction of DICOM objects.

PubMed

Hackländer, Thomas; Kleber, Klaus; Martin, Jens; Mertens, Heinrich

2005-03-01

Today, the exchange of medical images and clinical information is well defined by the digital imaging and communications in medicine (DICOM) and Health Level Seven (ie, HL7) standards. The interoperability among information systems is specified by the integration profiles of IHE (Integrating the Healthcare Enterprise). However, older imaging modalities frequently do not correctly support these interfaces and integration profiles, and some use cases are not yet specified by IHE. Therefore, corrections of DICOM objects are necessary to establish conformity. The aim of this project was to develop a toolbox that can automatically perform these recurrent corrections of the DICOM objects. The toolbox is composed of three main components: 1) a receiver to receive DICOM objects, 2) a processing pipeline to correct each object, and 3) one or more senders to forward each corrected object to predefined addressees. The toolbox is implemented under Java as an open source project. The processing pipeline is realized by means of plug ins. One of the plug ins can be programmed by the user via an external eXtensible Stylesheet Language (ie, XSL) file. Using this plug in, DICOM objects can also be converted into eXtensible Markup Language (ie, XML) documents or other data formats. DICOM storage services, DICOM CD-ROMs, and the local file system are defined as input and output channel. The toolbox is used clinically for different application areas. These are the automatic correction of DICOM objects from non-IHE-conforming modalities, the import of DICOM CD-ROMs into the picture archiving and communication system and the pseudo naming of DICOM images. The toolbox has been accepted by users in a clinical setting. Because of the open programming interfaces, the functionality can easily be adapted to future applications.

Improving Collaboration by Standardization Efforts in Systems Biology

PubMed Central

Dräger, Andreas; Palsson, Bernhard Ø.

2014-01-01

Collaborative genome-scale reconstruction endeavors of metabolic networks would not be possible without a common, standardized formal representation of these systems. The ability to precisely define biological building blocks together with their dynamic behavior has even been considered a prerequisite for upcoming synthetic biology approaches. Driven by the requirements of such ambitious research goals, standardization itself has become an active field of research on nearly all levels of granularity in biology. In addition to the originally envisaged exchange of computational models and tool interoperability, new standards have been suggested for an unambiguous graphical display of biological phenomena, to annotate, archive, as well as to rank models, and to describe execution and the outcomes of simulation experiments. The spectrum now even covers the interaction of entire neurons in the brain, three-dimensional motions, and the description of pharmacometric studies. Thereby, the mathematical description of systems and approaches for their (repeated) simulation are clearly separated from each other and also from their graphical representation. Minimum information definitions constitute guidelines and common operation protocols in order to ensure reproducibility of findings and a unified knowledge representation. Central database infrastructures have been established that provide the scientific community with persistent links from model annotations to online resources. A rich variety of open-source software tools thrives for all data formats, often supporting a multitude of programing languages. Regular meetings and workshops of developers and users lead to continuous improvement and ongoing development of these standardization efforts. This article gives a brief overview about the current state of the growing number of operation protocols, mark-up languages, graphical descriptions, and fundamental software support with relevance to systems biology. PMID:25538939

Model annotation for synthetic biology: automating model to nucleotide sequence conversion

PubMed Central

Misirli, Goksel; Hallinan, Jennifer S.; Yu, Tommy; Lawson, James R.; Wimalaratne, Sarala M.; Cooling, Michael T.; Wipat, Anil

2011-01-01

Motivation: The need for the automated computational design of genetic circuits is becoming increasingly apparent with the advent of ever more complex and ambitious synthetic biology projects. Currently, most circuits are designed through the assembly of models of individual parts such as promoters, ribosome binding sites and coding sequences. These low level models are combined to produce a dynamic model of a larger device that exhibits a desired behaviour. The larger model then acts as a blueprint for physical implementation at the DNA level. However, the conversion of models of complex genetic circuits into DNA sequences is a non-trivial undertaking due to the complexity of mapping the model parts to their physical manifestation. Automating this process is further hampered by the lack of computationally tractable information in most models. Results: We describe a method for automatically generating DNA sequences from dynamic models implemented in CellML and Systems Biology Markup Language (SBML). We also identify the metadata needed to annotate models to facilitate automated conversion, and propose and demonstrate a method for the markup of these models using RDF. Our algorithm has been implemented in a software tool called MoSeC. Availability: The software is available from the authors' web site http://research.ncl.ac.uk/synthetic_biology/downloads.html. Contact: anil.wipat@ncl.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21296753

Software for Better Documentation of Other Software

NASA Technical Reports Server (NTRS)

Pinedo, John

2003-01-01

The Literate Programming Extraction Engine is a Practical Extraction and Reporting Language- (PERL-)based computer program that facilitates and simplifies the implementation of a concept of self-documented literate programming in a fashion tailored to the typical needs of scientists. The advantage for the programmer is that documentation and source code are written side-by-side in the same file, reducing the likelihood that the documentation will be inconsistent with the code and improving the verification that the code performs its intended functions. The advantage for the user is the knowledge that the documentation matches the software because they come from the same file. This program unifies the documentation process for a variety of programming languages, including C, C++, and several versions of FORTRAN. This program can process the documentation in any markup language, and incorporates the LaTeX typesetting software. The program includes sample Makefile scripts for automating both the code-compilation (when appropriate) and documentation-generation processes into a single command-line statement. Also included are macro instructions for the Emacs display-editor software, making it easy for a programmer to toggle between editing in a code or a documentation mode.

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.

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.

76 FR 70187 - Self-Regulatory Organizations; NASDAQ OMX PHLX LLC; Notice of Filing and Immediate Effectiveness...

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...

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.

76 FR 8791 - Self-Regulatory Organizations; The NASDAQ Stock Market LLC; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

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...

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...

Informatics in radiology: An open-source and open-access cancer biomedical informatics grid annotation and image markup template builder.

PubMed

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

2012-01-01

In a routine clinical environment or clinical trial, a case report form or structured reporting template can be used to quickly generate uniform and consistent reports. Annotation and image markup (AIM), a project supported by the National Cancer Institute's cancer biomedical informatics grid, can be used to collect information for a case report form or structured reporting template. AIM is designed to store, in a single information source, (a) the description of pixel data with use of markups or graphical drawings placed on the image, (b) calculation results (which may or may not be directly related to the markups), and (c) supplemental information. To facilitate the creation of AIM annotations with data entry templates, an AIM template schema and an open-source template creation application were developed to assist clinicians, image researchers, and designers of clinical trials to quickly create a set of data collection items, thereby ultimately making image information more readily accessible.

Informatics in Radiology: An Open-Source and Open-Access Cancer Biomedical Informatics Grid Annotation and Image Markup Template Builder

PubMed Central

Channin, David S.; Rubin, Vladimir Kleper Daniel L.

2012-01-01

In a routine clinical environment or clinical trial, a case report form or structured reporting template can be used to quickly generate uniform and consistent reports. Annotation and Image Markup (AIM), a project supported by the National Cancer Institute’s cancer Biomedical Informatics Grid, can be used to collect information for a case report form or structured reporting template. AIM is designed to store, in a single information source, (a) the description of pixel data with use of markups or graphical drawings placed on the image, (b) calculation results (which may or may not be directly related to the markups), and (c) supplemental information. To facilitate the creation of AIM annotations with data entry templates, an AIM template schema and an open-source template creation application were developed to assist clinicians, image researchers, and designers of clinical trials to quickly create a set of data collection items, thereby ultimately making image information more readily accessible. © RSNA, 2012 PMID:22556315

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.

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.

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

Carnes, E.T.; Truett, D.F.; Truett, L.F.

In the handful of years since the World Wide Web (WWW or Web) came into being, Web sites have developed at an astonishing rate. With the influx of Web pages comes a disparity of site types, including personal homepages, commercial sales sites, and educational data. The variety of sites and the deluge of information contained on the Web exemplify the individual nature of the WWW. Whereas some people argue that it is this eclecticism which gives the Web its charm, we propose that sites which are repositories of technical data would benefit from standardization. This paper proffers a methodology formore » publishing ecological research on the Web. The template we describe uses capabilities of HTML (the HyperText Markup Language) to enhance the value of the traditional scientific paper.« less

Aligning Greek-English parallel texts

NASA Astrophysics Data System (ADS)

Galiotou, Eleni; Koronakis, George; Lazari, Vassiliki

2015-02-01

In this paper, we discuss issues concerning the alignment of parallel texts written in languages with different alphabets based on an experiment of aligning texts from the proceedings of the European Parliament in Greek and English. First, we describe our implementation of the k-vec algorithm and its application to the bilingual corpus. Then the output of the algorithm is used as a starting point for an alignment procedure at a sentence level which also takes into account mark-ups of meta-information. The results of the implementation are compared to those of the application of the Church and Gale alignment algorithm on the Europarl corpus. The conclusions of this comparison can give useful insights as for the efficiency of alignment algorithms when applied to the particular bilingual corpus.

Bioinformatics data distribution and integration via Web Services and XML.

PubMed

Li, Xiao; Zhang, Yizheng

2003-11-01

It is widely recognized that exchange, distribution, and integration of biological data are the keys to improve bioinformatics and genome biology in post-genomic era. However, the problem of exchanging and integrating biology data is not solved satisfactorily. The eXtensible Markup Language (XML) is rapidly spreading as an emerging standard for structuring documents to exchange and integrate data on the World Wide Web (WWW). Web service is the next generation of WWW and is founded upon the open standards of W3C (World Wide Web Consortium) and IETF (Internet Engineering Task Force). This paper presents XML and Web Services technologies and their use for an appropriate solution to the problem of bioinformatics data exchange and integration.

Generating and Describing Affective Eye Behaviors

NASA Astrophysics Data System (ADS)

Mao, Xia; Li, Zheng

The manner of a person's eye movement conveys much about nonverbal information and emotional intent beyond speech. This paper describes work on expressing emotion through eye behaviors in virtual agents based on the parameters selected from the AU-Coded facial expression database and real-time eye movement data (pupil size, blink rate and saccade). A rule-based approach to generate primary (joyful, sad, angry, afraid, disgusted and surprise) and intermediate emotions (emotions that can be represented as the mixture of two primary emotions) utilized the MPEG4 FAPs (facial animation parameters) is introduced. Meanwhile, based on our research, a scripting tool, named EEMML (Emotional Eye Movement Markup Language) that enables authors to describe and generate emotional eye movement of virtual agents, is proposed.