QUESTION ANSWERING SYSTEM BERBASIS ARTIFICIAL INTELLIGENCE MARKUP LANGUAGE SEBAGAI MEDIA INFORMASI

Directory of Open Access Journals (Sweden)

Fajrin Azwary

2016-04-01

Full Text Available Artificial intelligence technology nowadays, can be processed with a variety of forms, such as chatbot, and the various methods, one of them using Artificial Intelligence Markup Language (AIML. AIML using template matching, by comparing the specific patterns in the database. AIML template design process begins with determining the necessary information, then formed into questions, these questions adapted to AIML pattern. From the results of the study, can be known that the Question-Answering System in the chatbot using Artificial Intelligence Markup Language are able to communicate and deliver information. Keywords: Artificial Intelligence, Template Matching, Artificial Intelligence Markup Language, AIML Teknologi kecerdasan buatan saat ini dapat diolah dengan berbagai macam bentuk, seperti ChatBot, dan berbagai macam metode, salah satunya menggunakan Artificial Intelligence Markup Language (AIML. AIML menggunakan metode template matching yaitu dengan membandingkan pola-pola tertentu pada database. Proses perancangan template AIML diawali dengan menentukan informasi yang diperlukan, kemudian dibentuk menjadi pertanyaan, pertanyaan tersebut disesuaikan dengan bentuk pattern AIML. Hasil penelitian dapat diperoleh bahwa Question-Answering System dalam bentuk ChatBot menggunakan Artificial Intelligence Markup Language dapat berkomunikasi dan menyampaikan informasi. Kata kunci : Kecerdasan Buatan, Pencocokan Pola, Artificial Intelligence Markup Language, AIML

Improving Interoperability by Incorporating UnitsML Into Markup Languages.

Science.gov (United States)

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.

An object-oriented approach for harmonization of multimedia markup languages

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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.

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

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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.

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

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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.

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

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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.

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

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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.

STMML. A markup language for scientific, technical and medical publishing

Directory of Open Access Journals (Sweden)

Peter Murray-Rust

2006-01-01

Full Text Available STMML is an XML-based markup language covering many generic aspects of scientific information. It has been developed as a re-usable core for more specific markup languages. It supports data structures, data types, metadata, scientific units and some basic components of scientific narrative. The central means of adding semantic information is through dictionaries. The specification is through an XML Schema which can be used to validate STMML documents or fragments. Many examples of the language are given.

The geometry description markup language

International Nuclear Information System (INIS)

Chytracek, R.

2001-01-01

Currently, a lot of effort is being put on designing complex detectors. A number of simulation and reconstruction frameworks and applications have been developed with the aim to make this job easier. A very important role in this activity is played by the geometry description of the detector apparatus layout and its working environment. However, no real common approach to represent geometry data is available and such data can be found in various forms starting from custom semi-structured text files, source code (C/C++/FORTRAN), to XML and database solutions. The XML (Extensible Markup Language) has proven to provide an interesting approach for describing detector geometries, with several different but incompatible XML-based solutions existing. Therefore, interoperability and geometry data exchange among different frameworks is not possible at present. The author introduces a markup language for geometry descriptions. Its aim is to define a common approach for sharing and exchanging of geometry description data. Its requirements and design have been driven by experience and user feedback from existing projects which have their geometry description in XML

Field Data and the Gas Hydrate Markup Language

Directory of Open Access Journals (Sweden)

Ralf Löwner

2007-06-01

Full Text Available Data and information exchange are crucial for any kind of scientific research activities and are becoming more and more important. The comparison between different data sets and different disciplines creates new data, adds value, and finally accumulates knowledge. Also the distribution and accessibility of research results is an important factor for international work. The gas hydrate research community is dispersed across the globe and therefore, a common technical communication language or format is strongly demanded. The CODATA Gas Hydrate Data Task Group is creating the Gas Hydrate Markup Language (GHML, a standard based on the Extensible Markup Language (XML to enable the transport, modeling, and storage of all manner of objects related to gas hydrate research. GHML initially offers an easily deducible content because of the text-based encoding of information, which does not use binary data. The result of these investigations is a custom-designed application schema, which describes the features, elements, and their properties, defining all aspects of Gas Hydrates. One of the components of GHML is the "Field Data" module, which is used for all data and information coming from the field. It considers international standards, particularly the standards defined by the W3C (World Wide Web Consortium and the OGC (Open Geospatial Consortium. Various related standards were analyzed and compared with our requirements (in particular the Geographic Markup Language (ISO19136, GML and the whole ISO19000 series. However, the requirements demanded a quick solution and an XML application schema readable for any scientist without a background in information technology. Therefore, ideas, concepts and definitions have been used to build up the modules of GHML without importing any of these Markup languages. This enables a comprehensive schema and simple use.

Efficient Analysis of Systems Biology Markup Language Models of Cellular Populations Using Arrays.

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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.

A two-way interface between limited Systems Biology Markup Language and R

Directory of Open Access Journals (Sweden)

Radivoyevitch Tomas

2004-12-01

Full Text Available Abstract 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.

A two-way interface between limited Systems Biology Markup Language and R.

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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.

SuML: A Survey Markup Language for Generalized Survey Encoding

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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.

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

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

2015-01-01

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

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

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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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

Saadawi, Gilan M; Harrison, James H

2006-10-01

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

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

Directory of Open Access Journals (Sweden)

Gauges Ralph

2015-06-01

Full Text Available 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.

Wanda ML - a markup language for digital annotation

NARCIS (Netherlands)

Franke, K.Y.; Guyon, I.; Schomaker, L.R.B.; Vuurpijl, L.G.

2004-01-01

WANDAML is an XML-based markup language for the annotation and filter journaling of digital documents. It addresses in particular the needs of forensic handwriting data examination, by allowing experts to enter information about writer, material (pen, paper), script and content, and to record chains

The WANDAML Markup Language for Digital Document Annotation

NARCIS (Netherlands)

Franke, K.; Guyon, I.; Schomaker, L.; Vuurpijl, L.

2004-01-01

WANDAML is an XML-based markup language for the annotation and filter journaling of digital documents. It addresses in particular the needs of forensic handwriting data examination, by allowing experts to enter information about writer, material (pen, paper), script and content, and to record chains

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

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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

The Behavior Markup Language: Recent Developments and Challenges

NARCIS (Netherlands)

Vilhjalmsson, Hannes; Cantelmo, Nathan; Cassell, Justine; Chafai, Nicholas E.; Kipp, Michael; Kopp, Stefan; Mancini, Maurizio; Marsella, Stacy; Marshall, Andrew N.; Pelachaud, Catherine; Ruttkay, Z.M.; Thorisson, Kristinn R.; van Welbergen, H.; van der Werf, Rick J.; Pelachaud, Catherine; Martin, Jean-Claude; Andre, Elisabeth; Collet, Gerard; Karpouzis, Kostas; Pele, Danielle

2007-01-01

Since the beginning of the SAIBA effort to unify key interfaces in the multi-modal behavior generation process, the Behavior Markup Language (BML) has both gained ground as an important component in many projects worldwide, and continues to undergo further refinement. This paper reports on the

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

Science.gov (United States)

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

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Instrument Remote Control via the Astronomical Instrument Markup Language

Science.gov (United States)

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.

Genomic Sequence Variation Markup Language (GSVML).

Science.gov (United States)

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

AllerML: markup language for allergens.

Science.gov (United States)

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.

PIML: the Pathogen Information Markup Language.

Science.gov (United States)

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/

The Accelerator Markup Language and the Universal Accelerator Parser

International Nuclear Information System (INIS)

Sagan, D.; Forster, M.; Cornell U., LNS; Bates, D.A.; LBL, Berkeley; Wolski, A.; Liverpool U.; Cockcroft Inst. Accel. Sci. Tech.; Schmidt, F.; CERN; Walker, N.J.; DESY; Larrieu, T.; Roblin, Y.; Jefferson Lab; Pelaia, T.; Oak Ridge; Tenenbaum, P.; Woodley, M.; SLAC; Reiche, S.; UCLA

2006-01-01

A major obstacle to collaboration on accelerator projects has been the sharing of lattice description files between modeling codes. To address this problem, a lattice description format called Accelerator Markup Language (AML) has been created. AML is based upon the standard eXtensible Markup Language (XML) format; this provides the flexibility for AML to be easily extended to satisfy changing requirements. In conjunction with AML, a software library, called the Universal Accelerator Parser (UAP), is being developed to speed the integration of AML into any program. The UAP is structured to make it relatively straightforward (by giving appropriate specifications) to read and write lattice files in any format. This will allow programs that use the UAP code to read a variety of different file formats. Additionally, this will greatly simplify conversion of files from one format to another. Currently, besides AML, the UAP supports the MAD lattice format

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

Directory of Open Access Journals (Sweden)

Bergmann Frank T.

2018-03-01

Full Text Available 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.

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

Science.gov (United States)

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.

Development of the atomic and molecular data markup language for internet data exchange

International Nuclear Information System (INIS)

Ralchenko, Yuri; Clark Robert E.H.; Humbert, Denis; Schultz, David R.; Kato, Takako; Rhee, Yong Joo

2006-01-01

Accelerated development of the Internet technologies, including those relevant to the atomic and molecular physics, poses new requirements for the proper communication between computers, users and applications. To this end, a new standard for atomic and molecular data exchange that would reflect the recent achievements in this field becomes a necessity. We report here on development of the Atomic and Molecular Data Markup Language (AMDML) that is based on eXtensible Markup Language (XML). The present version of the AMDML Schema covers atomic spectroscopic data as well as the electron-impact collisions. (author)

Experimental Applications of Automatic Test Markup Language (ATML)

Science.gov (United States)

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.

The Petri Net Markup Language : concepts, technology, and tools

NARCIS (Netherlands)

Billington, J.; Christensen, S.; Hee, van K.M.; Kindler, E.; Kummer, O.; Petrucci, L.; Post, R.D.J.; Stehno, C.; Weber, M.; Aalst, van der W.M.P.; Best, E.

2003-01-01

The Petri Net Markup Language (PNML) is an XML-based interchange format for Petri nets. In order to support different versions of Petri nets and, in particular, future versions of Petri nets, PNML allows the definition of Petri net types.Due to this flexibility, PNML is a starting point for a

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

National Research Council Canada - National Science Library

Sycara, Katia P

2006-01-01

CMU did research and development on semantic web services using OWL-S, the semantic web service language under the Defense Advanced Research Projects Agency- DARPA Agent Markup Language (DARPA-DAML) program...

ArdenML: The Arden Syntax Markup Language (or Arden Syntax: It's Not Just Text Any More!)

Science.gov (United States)

Sailors, R. Matthew

2001-01-01

It is no longer necessary to think of Arden Syntax as simply a text-based knowledge base format. The development of ArdenML (Arden Syntax Markup Language), an XML-based markup language allows structured access to most of the maintenance and library categories without the need to write or buy a compiler may lead to the development of simple commercial and freeware tools for processing Arden Syntax Medical Logic Modules (MLMs)

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

Science.gov (United States)

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.

Geospatial Visualization of Scientific Data Through Keyhole Markup Language

Science.gov (United States)

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.

Developing a Markup Language for Encoding Graphic Content in Plan Documents

Science.gov (United States)

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…

Systematic reconstruction of TRANSPATH data into cell system markup language.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

FuGEFlow: data model and markup language for flow cytometry

Directory of Open Access Journals (Sweden)

Manion Frank J

2009-06-01

Full Text Available Abstract 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

FuGEFlow: data model and markup language for flow cytometry.

Science.gov (United States)

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

Standard generalized markup language: A guide for transmitting encoded bibliographic records

International Nuclear Information System (INIS)

1994-09-01

This document provides the guidance necessary to transmit to DOE's Office of Scientific and Technical Information (OSTI) an encoded bibliographic record that conforms to International Standard ISO 8879, Information Processing -- Text and office systems -- Standard Generalized Markup Language (SGML). Included in this document are element and attribute tag definitions, sample bibliographic records, the bibliographic document type definition, and instructions on how to transmit a bibliographic record electronically to OSTI

Standard generalized markup language: A guide for transmitting encoded bibliographic records

Energy Technology Data Exchange (ETDEWEB)

1994-09-01

This document provides the guidance necessary to transmit to DOE`s Office of Scientific and Technical Information (OSTI) an encoded bibliographic record that conforms to International Standard ISO 8879, Information Processing -- Text and office systems -- Standard Generalized Markup Language (SGML). Included in this document are element and attribute tag definitions, sample bibliographic records, the bibliographic document type definition, and instructions on how to transmit a bibliographic record electronically to OSTI.

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

Science.gov (United States)

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.

A primer on the Petri Net Markup Language and ISO/IEC 15909-2

DEFF Research Database (Denmark)

Hillah, L. M.; Kindler, Ekkart; Kordon, F.

2009-01-01

Standard, defines a transfer format for high-level nets. The transfer format defined in Part 2 of ISO/IEC 15909 is (or is based on) the \\emph{Petri Net Markup Language} (PNML), which was originally introduced as an interchange format for different kinds of Petri nets. In ISO/IEC 15909-2, however...

QUESTION ANSWERING SYSTEM BERBASIS ARTIFICIAL INTELLIGENCE MARKUP LANGUAGE SEBAGAI MEDIA INFORMASI

OpenAIRE

Fajrin Azwary; Fatma Indriani; Dodon T. Nugrahadi

2016-01-01

Artificial intelligence technology nowadays, can be processed with a variety of forms, such as chatbot, and the various methods, one of them using Artificial Intelligence Markup Language (AIML). AIML using template matching, by comparing the specific patterns in the database. AIML template design process begins with determining the necessary information, then formed into questions, these questions adapted to AIML pattern. From the results of the study, can be known that the Question-Answering...

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

Science.gov (United States)

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.

Pathology data integration with eXtensible Markup Language.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Earth Science Markup Language: Transitioning From Design to Application

Science.gov (United States)

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.

On the Power of Fuzzy Markup Language

CERN Document Server

Loia, Vincenzo; Lee, Chang-Shing; Wang, Mei-Hui

2013-01-01

One of the most successful methodology that arose from the worldwide diffusion of Fuzzy Logic is Fuzzy Control. After the first attempts dated in the seventies, this methodology has been widely exploited for controlling many industrial components and systems. At the same time, and very independently from Fuzzy Logic or Fuzzy Control, the birth of the Web has impacted upon almost all aspects of computing discipline. Evolution of Web, Web 2.0 and Web 3.0 has been making scenarios of ubiquitous computing much more feasible;  consequently information technology has been thoroughly integrated into everyday objects and activities. What happens when Fuzzy Logic meets Web technology? Interesting results might come out, as you will discover in this book. Fuzzy Mark-up Language is a son of this synergistic view, where some technological issues of Web are re-interpreted taking into account the transparent notion of Fuzzy Control, as discussed here.  The concept of a Fuzzy Control that is conceived and modeled in terms...

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

Science.gov (United States)

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)

Semantic markup of nouns and adjectives for the Electronic corpus of texts in Tuvan language

Directory of Open Access Journals (Sweden)

Bajlak Ch. Oorzhak

2016-12-01

Full Text Available The article examines the progress of semantic markup of the Electronic corpus of texts in Tuvan language (ECTTL, which is another stage of adding Tuvan texts to the database and marking up the corpus. ECTTL is a collaborative project by researchers from Tuvan State University (Research and Education Center of Turkic Studies and Department of Information Technologies. Semantic markup of Tuvan lexis will come as a search engine and reference system which will help users find text snippets containing words with desired meanings in ECTTL. The first stage of this process is setting up databases of basic lexemes of Tuvan language. All meaningful lexemes were classified into the following semantic groups: humans, animals, objects, natural objects and phenomena, and abstract concepts. All Tuvan object nouns, as well as both descriptive and relative adjectives, were assigned to one of these lexico-semantic classes. Each class, sub-class and descriptor is tagged in Tuvan, Russian and English; these tags, in turn, will help automatize searching. The databases of meaningful lexemes of Tuvan language will also outline their lexical combinations. The automatized system will contain information on semantic combinations of adjectives with nouns, adverbs with verbs, nouns with verbs, as well as on the combinations which are semantically incompatible.

Automatically Generating a Distributed 3D Battlespace Using USMTF and XML-MTF Air Tasking Order, Extensible Markup Language (XML) and Virtual Reality Modeling Language (VRML)

National Research Council Canada - National Science Library

Murray, Mark

2000-01-01

.... To more effectively exchange and share data, the Defense Information Systems Agency (DISA), the lead agency for the USMTF, is actively engaged in extending the USMTF standard with a new data sharing technology called Extensible Markup Language (XML...

Coding practice of the Journal Article Tag Suite extensible markup language

Directory of Open Access Journals (Sweden)

Sun Huh

2014-08-01

Full Text Available In general, the Journal Article Tag Suite (JATS extensible markup language (XML coding is processed automatically by an XML filtering program. In this article, the basic tagging in JATS is explained in terms of coding practice. A text editor that supports UTF-8 encoding is necessary to input JATS XML data that works in every language. Any character representable in Unicode can be used in JATS XML, and commonly available web browsers can be used to view JATS XML files. JATS XML files can refer to document type definitions, extensible stylesheet language files, and cascading style sheets, but they must specify the locations of those files. Tools for validating JATS XML files are available via the web sites of PubMed Central and ScienceCentral. Once these files are uploaded to a web server, they can be accessed from all over the world by anyone with a browser. Encoding an example article in JATS XML may help editors in deciding on the adoption of JATS XML.

The basics of CrossRef extensible markup language

Directory of Open Access Journals (Sweden)

Rachael Lammey

2014-08-01

Full Text Available CrossRef is an association of scholarly publishers that develops shared infrastructure to support more effective scholarly communications. Launched in 2000, CrossRef’s citation-linking network today covers over 68 million journal articles and other content items (books chapters, data, theses, and technical reports from thousands of scholarly and professional publishers around the globe. CrossRef has over 4,000 member publishers who join as members in order to avail of a number of CrossRef services, reference linking via the Digital Object Identifier (DOI being the core service. To deposit CrossRef DOIs, publishers and editors need to become familiar with the basics of extensible markup language (XML. This article will give an introduction to CrossRef XML and what publishers need to do in order to start to deposit DOIs with CrossRef and thus ensure their publications are discoverable and can be linked to consistently in an online environment.

Extensions to the Dynamic Aerospace Vehicle Exchange Markup Language

Science.gov (United States)

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.

Automatically Generating a Distributed 3D Virtual Battlespace Using USMTF and XML-MTF Air Tasking Orders, Extensible Markup Language (XML) and Virtual Reality Modeling Language (VRML)

National Research Council Canada - National Science Library

Murray, Mark

2000-01-01

.... To more effectively exchange and share data, the Defense Information Systems Agency (DISA), the lead agency for the USMTF, is actively engaged in extending the USMTF standard with a new data sharing technology called Extensible Markup Language (XML...

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

Science.gov (United States)

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…

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

Science.gov (United States)

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.

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

Science.gov (United States)

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

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

Science.gov (United States)

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).

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

Science.gov (United States)

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

2015-01-01

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

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

Science.gov (United States)

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

2015-06-01

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

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

Science.gov (United States)

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…

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

Science.gov (United States)

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.

Managing and Querying Image Annotation and Markup in XML.

Science.gov (United States)

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

Science.gov (United States)

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

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

Directory of Open Access Journals (Sweden)

Phadungsukanan Weerapong

2012-08-01

Full Text Available Abstract 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.

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

Science.gov (United States)

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.

Markups and Exporting Behavior

DEFF Research Database (Denmark)

De Loecker, Jan; Warzynski, Frederic Michel Patrick

2012-01-01

In this paper, we develop a method to estimate markups using plant-level production data. Our approach relies on cost minimizing producers and the existence of at least one variable input of production. The suggested empirical framework relies on the estimation of a production function and provides...... estimates of plant- level markups without specifying how firms compete in the product market. We rely on our method to explore the relationship be- tween markups and export behavior. We find that markups are estimated significantly higher when controlling for unobserved productivity; that exporters charge......, on average, higher markups and that markups increase upon export entry....

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

Science.gov (United States)

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.

CytometryML: a markup language for analytical cytology

Science.gov (United States)

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.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Treatment of Markup in Statistical Machine Translation

OpenAIRE

Müller, Mathias

2017-01-01

We present work on handling XML markup in Statistical Machine Translation (SMT). The methods we propose can be used to effectively preserve markup (for instance inline formatting or structure) and to place markup correctly in a machine-translated segment. We evaluate our approaches with parallel data that naturally contains markup or where markup was inserted to create synthetic examples. In our experiments, hybrid reinsertion has proven the most accurate method to handle markup, while alignm...

Markups and Firm-Level Export Status

DEFF Research Database (Denmark)

De Loecker, Jan; Warzynski, Frederic

We derive an estimating equation to estimate markups using the insight of Hall (1986) and the control function approach of Olley and Pakes (1996). We rely on our method to explore the relationship between markups and export behavior using plant-level data. We find significantly higher markups when...... we control for unobserved productivity shocks. Furthermore, we find significant higher markups for exporting firms and present new evidence on markup-export status dynamics. More specifically, we find that firms' markups significantly increase (decrease) after entering (exiting) export markets. We...... see these results as a first step in opening up the productivity-export black box, and provide a potential explanation for the big measured productivity premia for firms entering export markets....

LOG2MARKUP: State module to transform a Stata text log into a markup document

DEFF Research Database (Denmark)

2016-01-01

log2markup extract parts of the text version from the Stata log command and transform the logfile into a markup based document with the same name, but with extension markup (or otherwise specified in option extension) instead of log. The author usually uses markdown for writing documents. However...

A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

DEFF Research Database (Denmark)

Herrgard, Markus; Swainston, Neil; Dobson, Paul

2008-01-01

and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology...

Hospital markup and operation outcomes in the United States.

Science.gov (United States)

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 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 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.

Endogenous Markups, Firm Productivity and International Trade:

DEFF Research Database (Denmark)

Bellone, Flora; Musso, Patrick; Nesta, Lionel

) markups are positively related to firm productivity; 3) markups are negatively related to import penetration; 4) markups are positively related to firm export intensity and markups are higher on the export market than on the domestic ones in the presence of trade barriers and/or if competitors...... on the export market are less efficient than competitors on the domestic market. We estimate micro-level price cost margins (PCMs) using firm-level data extending the techniques developed by Hall (1986, 1988) and extended by Domowitz et al. (1988) and Roeger (1995) for the French manufacturing industry from......In this paper, we test key micro-level theoretical predictions ofMelitz and Ottaviano (MO) (2008), a model of international trade with heterogenous firms and endogenous mark-ups. At the firm-level, the MO model predicts that: 1) firm markups are negatively related to domestic market size; 2...

Wine Price Markup in California Restaurants

OpenAIRE

Amspacher, William

2011-01-01

The study quantifies the relationship between retail wine price and restaurant mark-up. Ordinary Least Squares regressions were run to estimate how restaurant mark-up responded to retail price. Separate regressions were run for white wine, red wine, and both red and white combined. Both slope and intercept coefficients for each of these regressions were highly significant and indicated the expected inverse relationship between retail price and mark-up.

Markups and Firm-Level Export Status

DEFF Research Database (Denmark)

De Loecker, Jan; Warzynski, Frederic

and export behavior using plant-level data. We find that i) markups are estimated significantly higher when controlling for unobserved productivity, ii) exporters charge on average higher markups and iii) firms' markups increase (decrease) upon export entry (exit).We see these findings as a first step...... in opening up the productivity-export black box, and provide a potential explanation for the big measured productivity premia for firms entering export markets....

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

Science.gov (United States)

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.

TEI Standoff Markup - A work in progress

NARCIS (Netherlands)

Spadini, E.; Turska, Magdalena; Broughton, Misha

2015-01-01

“Markup is said to be standoff, or external, when the markup data is placed outside of the text it is meant to tag” (). One of the most widely recognized limitations of inline XML markup is its inability to cope with element overlap; standoff has been considered as a possible solution to

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

Science.gov (United States)

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.

XML/TEI Stand-off Markup. One step beyond.

NARCIS (Netherlands)

Spadini, E.; Turska, Magdalena

2018-01-01

Stand-off markup is widely considered as a possible solution for overcoming the limitation of inline XML markup, primarily dealing with multiple overlapping hierarchies. Considering previous contributions on the subject and implementations of stand-off markup, we propose a new TEI-based model for

Percentage Retail Mark-Ups

OpenAIRE

Thomas von Ungern-Sternberg

1999-01-01

A common assumption in the literature on the double marginalization problem is that the retailer can set his mark-up only in the second stage of the game after the producer has moved. To the extent that the sequence of moves is designed to reflect the relative bargaining power of the two parties it is just as plausible to let the retailer move first. Furthermore, retailers frequently calculate their selling prices by adding a percentage mark-up to their wholesale prices. This allows a retaile...

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

Energy Technology Data Exchange (ETDEWEB)

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

2013-05-24

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 XML 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.

Histoimmunogenetics Markup Language 1.0: Reporting next generation sequencing-based HLA and KIR genotyping.

Science.gov (United States)

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.

PENDEKATAN MODEL MATEMATIS UNTUK MENENTUKAN PERSENTASE MARKUP HARGA JUAL PRODUK

Directory of Open Access Journals (Sweden)

Oviliani Yenty Yuliana

2002-01-01

Full Text Available The purpose of this research is to design Mathematical models that can determine the selling volume as an alternative to improve the markup percentage. Mathematical models was designed with double regression statistic. Selling volume is a function of markup, market condition, and substitute condition variables. The designed Mathematical model has fulfilled by the test of: error upon assumption, accurate model, validation model, and multi collinear problem. The Mathematical model has applied in application program with expectation that the application program can give: (1 alternative to decide percentage markup for user, (2 Illustration of gross profit estimation that will be achieve for selected percentage markup, (3 Illustration of estimation percentage of the units sold that will be achieve for selected percentage markup, and (4 Illustration of total net income before tax will get for specific period. Abstract in Bahasa Indonesia : Penelitian ini bertujuan untuk merancang model Matematis guna menetapkan volume penjualan, sebagai alternatif untuk menentukan persentase markup harga jual produk. Model Matematis dirancang menggunakan Statistik Regresi Berganda. Volume penjualan merupakan fungsi dari variabel markup, kondisi pasar, dan kondisi pengganti. Model Matematis yang dirancang sudah memenuhi uji: asumsi atas error, akurasi model, validasi model, dan masalah multikolinearitas. Rancangan model Matematis tersebut diterapkan dalam program aplikasi dengan harapan dapat memberi: (1 alternatif bagi pengguna mengenai berapa besar markup yang sebaiknya ditetapkan, (2 gambaran perkiraan laba kotor yang akan diperoleh setiap pemilihan markup, (3 gambaran perkiraan persentase unit yang terjual setiap pemilihan markup, dan (4 gambaran total laba kotor sebelum pajak yang dapat diperoleh pada periode yang bersangkutan. Kata kunci: model Matematis, aplikasi program, volume penjualan, markup, laba kotor.

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

Science.gov (United States)

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.

WaterML: an XML Language for Communicating Water Observations Data

Science.gov (United States)

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.

A standard-enabled workflow for synthetic biology

KAUST Repository

Myers, Chris J.

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.

Programming languages for synthetic biology.

Science.gov (United States)

Umesh, P; Naveen, F; Rao, Chanchala Uma Maheswara; Nair, Achuthsankar S

2010-12-01

In the backdrop of accelerated efforts for creating synthetic organisms, the nature and scope of an ideal programming language for scripting synthetic organism in-silico has been receiving increasing attention. A few programming languages for synthetic biology capable of defining, constructing, networking, editing and delivering genome scale models of cellular processes have been recently attempted. All these represent important points in a spectrum of possibilities. This paper introduces Kera, a state of the art programming language for synthetic biology which is arguably ahead of similar languages or tools such as GEC, Antimony and GenoCAD. Kera is a full-fledged object oriented programming language which is tempered by biopart rule library named Samhita which captures the knowledge regarding the interaction of genome components and catalytic molecules. Prominent feature of the language are demonstrated through a toy example and the road map for the future development of Kera is also presented.

The caBIG annotation and image Markup project.

Science.gov (United States)

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.

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

NARCIS (Netherlands)

Olivier, B.G.; Bergmann, F.T.

2015-01-01

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

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

Science.gov (United States)

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 markup compared to public/private not-for-profit status in unconcentrated markets (95%CI: +45.4% - +81.1%; p 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.

Interexaminer variation of minutia markup on latent fingerprints.

Science.gov (United States)

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.

A standard-enabled workflow for synthetic biology.

Science.gov (United States)

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.

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

Science.gov (United States)

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.

The Long-Run Relationship Between Inflation and the Markup in the U.S.

OpenAIRE

Sandeep Mazumder

2011-01-01

This paper examines the long-run relationship between inflation and a new measure of the price-marginal cost markup. This new markup index is derived while accounting for labor adjustment costs, which a large number of the papers that estimate the markup have ignored. We then examine the long-run relationship between this markup measure, which is estimated using U.S. manufacturing data, and inflation. We find that decreases in the markup that are associated with a percentage point increase in...

Markup heterogeneity, export status ans the establishment of the euro

OpenAIRE

Guillou , Sarah; Nesta , Lionel

2015-01-01

We investigate the effects of the establishment of the euro on the markups of French manufacturing firms. Merging firm-level census data with customs data, we estimate time-varying firm-specific markups and distinguish between eurozone exporters from other firms between 1995 and 2007. We find that the establishment of the euro has had a pronounced pro-competitive impact by reducing firm markups by 14 percentage points. By reducing export costs, the euro represented an opp...

Markup cyclicality, employment adjustment, and financial constraints

OpenAIRE

Askildsen, Jan Erik; Nilsen, Øivind Anti

2001-01-01

We investigate the existence of markups and their cyclical behaviour. Markup is not directly observed. Instead, it is given as a price-cost relation that is estimated from a dynamic model of the firm. The model incorporates potential costly employment adjustments and takes into consideration that firms may be financially constrained. When considering size of the future labour stock, financially constrained firms may behave as if they have a higher discount factor, which may affect the realise...

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

Science.gov (United States)

Sankar, Punnaivanam; Aghila, Gnanasekaran

2007-01-01

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

XML Schema Languages: Beyond DTD.

Science.gov (United States)

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)

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

Science.gov (United States)

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.

Are the determinants of markup size industry-specific? The case of Slovenian manufacturing firms

Directory of Open Access Journals (Sweden)

Ponikvar Nina

2011-01-01

Full Text Available The aim of this paper is to identify factors that affect the pricing policy in Slovenian manufacturing firms in terms of the markup size and, most of all, to explicitly account for the possibility of differences in pricing procedures among manufacturing industries. Accordingly, the analysis of the dynamic panel is carried out on an industry-by-industry basis, allowing the coefficients on the markup determinants to vary across industries. We find that the oligopoly theory of markup determination for the most part holds for the manufacturing sector as a whole, although large variability in markup determinants exists across industries within the Slovenian manufacturing. Our main conclusion is that each industry should be investigated separately in detail in order to assess the precise role of markup factors in the markup-determination process.

The Commercial Office Market and the Markup for Full Service Leases

OpenAIRE

Jonathan A. Wiley; Yu Liu; Dongshin Kim; Tom Springer

2014-01-01

Because landlords assume all of the operating expense risk, rents for gross leases exceed those for net leases. The markup, or spread, for gross leases varies between properties and across markets. Specifically, the markup is expected to increase with the cost of real estate services at the property, and to be influenced by market conditions. A matching procedure is applied to measure the services markup as the percentage difference between the actual rent on a gross lease relative to the act...

Trade reforms, mark-ups and bargaining power of workers: the case ...

African Journals Online (AJOL)

Ethiopian Journal of Economics ... workers between 1996 and 2007, a model of mark-up with labor bargaining power was estimated using random effects and LDPDM. ... Keywords: Trade reform, mark-up, bargaining power, rent, trade unions ...

Deciphering the language between biological and synthetic materials

Directory of Open Access Journals (Sweden)

Paolo A. Netti

2014-06-01

Full Text Available Chemical signals propagating through aqueous environment are at the basis of the language utilized by living systems to exchange information. In the last years, molecular biology has partly disclosed the grammar and the syntax of this complex language revealing the fascinating world of molecular communication that is the foundation of biological development.

SELECTION OF ONTOLOGY FOR WEB SERVICE DESCRIPTION LANGUAGE TO ONTOLOGY WEB LANGUAGE CONVERSION

OpenAIRE

J. Mannar Mannan; M. Sundarambal; S. Raghul

2014-01-01

Semantic web is to extend the current human readable web to encoding some of the semantic of resources in a machine processing form. As a Semantic web component, Semantic Web Services (SWS) uses a mark-up that makes the data into detailed and sophisticated machine readable way. One such language is Ontology Web Language (OWL). Existing conventional web service annotation can be changed to semantic web service by mapping Web Service Description Language (WSDL) with the semantic annotation of O...

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

Science.gov (United States)

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.

Planned growth as a determinant of the markup: the case of Slovenian manufacturing

Directory of Open Access Journals (Sweden)

Maks Tajnikar

2009-11-01

Full Text Available The paper follows the idea of heterodox economists that a cost-plus price is above all a reproductive price and growth price. The authors apply a firm-level model of markup determination which, in line with theory and empirical evidence, contains proposed firm-specific determinants of the markup, including the firm’s planned growth. The positive firm-level relationship between growth and markup that is found in data for Slovenian manufacturing firms implies that retained profits gathered via the markup are an important source of growth financing and that the investment decisions of Slovenian manufacturing firms affect their pricing policy and decisions on the markup size as proposed by Post-Keynesian theory. The authors thus conclude that at least a partial trade-off between a firm’s growth and competitive outcome exists in Slovenian manufacturing.

BetaWB - A language for modular representation of biological systems

DEFF Research Database (Denmark)

Ihekwaba, Adoha; Larcher, Roberto; Mardare, Radu Iulian

2007-01-01

A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007......A. Ihekwaba, R. Larcher, R. Mardare, C. Priami. BetaWB - A language for modular representation of biological systems. In Proc. of International Conference on Systems Biology (ICSB), 2007...

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

Science.gov (United States)

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).

The Price-Marginal Cost Markup and its Determinants in U.S. Manufacturing

OpenAIRE

Mazumder, Sandeep

2009-01-01

This paper estimates the price-marginal cost markup for US manufacturing using a new methodology. Most existing techniques of estimating the markup are a variant on Hall's (1988) framework involving the manipulation of the Solow Residual. However this paper argues that this notion is based on the unreasonable assumption that labor can be costlessly adjusted at a fixed wage rate. By relaxing this assumption, we are able to derive a generalized markup index, which when estimated using manufactu...

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

Science.gov (United States)

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.

An Attempt to Construct a Database of Photographic Data of Radiolarian Fossils with the Hypertext Markup Language

OpenAIRE

磯貝, 芳徳; 水谷, 伸治郎; Yoshinori, Isogai; Shinjiro, Mizutani

1998-01-01

放散虫化石の走査型電子顕微鏡写真のコレクションを，Hypertext Markup Languageを用いてデータベース化した．このデータベースは約千枚の放散虫化石の写真を現時点でもっており，化石名，地質学的年代，発掘地名など多様な視点から検索することができる．このデータベースの構築によって，計算機やデータベースについて特別な技術を持っていない通常の研究者が，自身のデータベースを自らの手で構築しようとするとき，Hypertext Markup Languageが有効であることを示した．さらにインターネットを経由して，誰でもこのデータベースを利用できる点は，Hypertext Markup Languageを用いたデータベースの特筆するき特徴である．データベース構築の過程を記述し，現況を報告する．さらに当データベース構築の背景にある考えや問題点について議論する．...

Cell illustrator 4.0: a computational platform for systems biology.

Science.gov (United States)

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 quality assessment tool for markup-based clinical guidelines.

Science.gov (United States)

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.

[Again on language of biology].

Science.gov (United States)

Morchio, di Renzo

2004-01-01

Some time ago I proposed in an Editorial in this journal some considerations on the language of biology. I concluded that, to realize an autonomy of such a language (and therefore of biology), we have to develop a valid language for biology. In such a context, it seemed to me that the term "metaphors" referred to the concepts concerning the information carried by genetic code, was a reasonable one. However, Barbieri's article in this issue of Rivista di Biologia / Biology Forum calls for a reply. Of course, we do not know very much in this field, even if we have some evidence that a sequence of bases on a DNA is not determined only by chance. In any case we can exclude that nature in this occasion has "invented" a code. Nature doesn't "invent" anything: it only follows its rules, that we name "laws of nature". Barbieri quotes the Morse code, but forgets to say that such a code is "conventional" in the sense that it is valid only because it is the result of an "agreement" between Morse and the users of that code. There is nothing more unnatural than a "code": with whom nature should actually have to "reach an agreement"? As a matter of fact, we interpret as "information" what happens by law of nature. Also Barbieri's thesis that genes and proteins are molecular artifacts, assembled by external agents, whereas generally molecules are determined by their bonds, i.e. by internal factors, is a disputable one. It is examined how much an external structure plays a role in ordinary chemical reactions. The "information" of physics is not a semantic information. For such information we can refer to history of literature, telegraphic offices, genetics or biochemistry.

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

XML schemas and mark-up practices of taxonomic literature.

Science.gov (United States)

Penev, Lyubomir; Lyal, Christopher Hc; Weitzman, Anna; Morse, David R; King, David; Sautter, Guido; Georgiev, Teodor; Morris, Robert A; Catapano, Terry; Agosti, Donat

2011-01-01

We review the three most widely used XML schemas used to mark-up taxonomic texts, TaxonX, TaxPub and taXMLit. These are described from the viewpoint of their development history, current status, implementation, and use cases. The concept of "taxon treatment" from the viewpoint of taxonomy mark-up into XML is discussed. TaxonX and taXMLit are primarily designed for legacy literature, the former being more lightweight and with a focus on recovery of taxon treatments, the latter providing a much more detailed set of tags to facilitate data extraction and analysis. TaxPub is an extension of the National Library of Medicine Document Type Definition (NLM DTD) for taxonomy focussed on layout and recovery and, as such, is best suited for mark-up of new publications and their archiving in PubMedCentral. All three schemas have their advantages and shortcomings and can be used for different purposes.

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

Science.gov (United States)

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)

PENDEKATAN MODEL MATEMATIS UNTUK MENENTUKAN PERSENTASE MARKUP HARGA JUAL PRODUK

OpenAIRE

Oviliani Yenty Yuliana; Yohan Wahyudi; Siana Halim

2002-01-01

The purpose of this research is to design Mathematical models that can determine the selling volume as an alternative to improve the markup percentage. Mathematical models was designed with double regression statistic. Selling volume is a function of markup, market condition, and substitute condition variables. The designed Mathematical model has fulfilled by the test of: error upon assumption, accurate model, validation model, and multi collinear problem. The Mathematical model has applied i...

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

Science.gov (United States)

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.

Language cannot be reduced to biology: perspectives from neuro-developmental disorders affecting language learning.

Science.gov (United States)

Vasanta, D

2005-02-01

The study of language knowledge guided by a purely biological perspective prioritizes the study of syntax. The essential process of syntax is recursion--the ability to generate an infinite array of expressions from a limited set of elements. Researchers working within the biological perspective argue that this ability is possible only because of an innately specified genetic makeup that is specific to human beings. Such a view of language knowledge may be fully justified in discussions on biolinguistics, and in evolutionary biology. However, it is grossly inadequate in understanding language-learning problems, particularly those experienced by children with neurodevelopmental disorders such as developmental dyslexia, Williams syndrome, specific language impairment and autism spectrum disorders. Specifically, syntax-centered definitions of language knowledge completely ignore certain crucial aspects of language learning and use, namely, that language is embedded in a social context; that the role of envrironmental triggering as a learning mechanism is grossly underestimated; that a considerable extent of visuo-spatial information accompanies speech in day-to-day communication; that the developmental process itself lies at the heart of knowledge acquisition; and that there is a tremendous variation in the orthographic systems associated with different languages. All these (socio-cultural) factors can influence the rate and quality of spoken and written language acquisition resulting in much variation in phenotypes associated with disorders known to have a genetic component. Delineation of such phenotypic variability requires inputs from varied disciplines such as neurobiology, neuropsychology, linguistics and communication disorders. In this paper, I discuss published research that questions cognitive modularity and emphasises the role of the environment for understanding linguistic capabilities of children with neuro-developmental disorders. The discussion pertains

XML: Ejemplos de uso (presentación)

OpenAIRE

Luján Mora, Sergio

2011-01-01

XML (eXtensible Markup Language, Lenguaje de marcas extensible) - Aplicación XML = Lenguaje de marcado = Vocabulario - Ejemplos: DocBook, Chemical Markup Language, Keyhole Markup Language, Mathematical Markup Language, Open Document, Open XML Format, Scalable Vector Graphics, Systems Byology Markup Language.

XML: Ejemplos de uso

OpenAIRE

Luján Mora, Sergio

2011-01-01

XML (eXtensible Markup Language, Lenguaje de marcas extensible) - Aplicación XML = Lenguaje de marcado = Vocabulario - Ejemplos: DocBook, Chemical Markup Language, Keyhole Markup Language, Mathematical Markup Language, Open Document, Open XML Format, Scalable Vector Graphics, Systems Byology Markup Language.

Monopoly, Pareto and Ramsey mark-ups

NARCIS (Netherlands)

Ten Raa, T.

2009-01-01

Monopoly prices are too high. It is a price level problem, in the sense that the relative mark-ups have Ramsey optimal proportions, at least for independent constant elasticity demands. I show that this feature of monopoly prices breaks down the moment one demand is replaced by the textbook linear

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2.

Science.gov (United States)

Sorokin, Anatoly; Le Novère, Nicolas; Luna, Augustin; Czauderna, Tobias; Demir, Emek; Haw, Robin; Mi, Huaiyu; Moodie, Stuart; Schreiber, Falk; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Entity Relationship language (ER) represents biological entities and their interactions and relationships within a network. SBGN ER focuses on all potential relationships between entities without considering temporal aspects. The nodes (elements) describe biological entities, such as proteins and complexes. The edges (connections) provide descriptions of interactions and relationships (or influences), e.g., complex formation, stimulation and inhibition. Among all three languages of SBGN, ER is the closest to protein interaction networks in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

PENGUKURAN KINERJA BEBERAPA SISTEM BASIS DATA RELASIONAL DENGAN KEMAMPUAN MENYIMPAN DATA BERFORMAT GML (GEOGRAPHY MARKUP LANGUAGE YANG DAPAT DIGUNAKAN UNTUK MENDASARI APLIKASI-APLIKASI SISTEM INFORMASI GEOGRAFIS

Directory of Open Access Journals (Sweden)

Adi Nugroho

2009-01-01

Full Text Available If we want to represent spatial data to user using GIS (Geographical Information System applications, we have 2 choices about the underlying database, that is general RDBMS (Relational Database Management System for saving general spatial data (number, char, varchar, etc., or saving spatial data in GML (Geography Markup Language format. (GML is an another XML’s special vocabulary for spatial data. If we choose GML for saving spatial data, we also have 2 choices, that is saving spatial data in XML Enabled Database (relational databases that can be use for saving XML data or we can use Native XML Database (NXD, that is special databases that can be use for saving XML data. In this paper, we try to make performance comparison for several XML Enabled Database when we do GML’s CRUD (Create-Read-Update-Delete operations to these databases. On the other side, we also want to see flexibility of XML Enabled Database from programmers view.

HTEL: a HyperText Expression Language

DEFF Research Database (Denmark)

Steensgaard-Madsen, Jørgen

1999-01-01

been submitted.A special tool has been used to build the HTEL-interpreter, as an example belonging a family of interpreters for domain specific languages. Members of that family have characteristics that are closely related to structural patterns found in the mark-ups of HTML. HTEL should also be seen...

Semantic Models of Sentences with Verbs of Motion in Standard Language and in Scientific Language Used in Biology

Directory of Open Access Journals (Sweden)

Vita Banionytė

2016-06-01

Full Text Available The semantic models of sentences with verbs of motion in German standard language and in scientific language used in biology are analyzed in the article. In its theoretic part it is affirmed that the article is based on the semantic theory of the sentence. This theory, in its turn, is grounded on the correlation of semantic predicative classes and semantic roles. The combination of semantic predicative classes and semantic roles is expressed by the main semantic formula – proposition. In its practical part the differences between the semantic models of standard and scientific language used in biology are explained. While modelling sentences with verbs of motion, two groups of semantic models of sentences are singled out: that of action (Handlung and process (Vorgang. The analysis shows that the semantic models of sentences with semantic action predicatives dominate in the text of standard language while the semantic models of sentences with semantic process predicatives dominate in the texts of scientific language used in biology. The differences how the doer and direction are expressed in standard and in scientific language are clearly seen and the semantic cases (Agens, Patiens, Direktiv1 help to determine that. It is observed that in scientific texts of high level of specialization (biology science in contrast to popular scientific literature models of sentences with moving verbs are usually seldom found. They are substituted by denominative constructions. In conclusions it is shown that this analysis can be important in methodics, especially planning material for teaching professional-scientific language.

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

Science.gov (United States)

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.

Systems Biology Graphical Notation: Process Description language Level 1 Version 1.3.

Science.gov (United States)

Moodie, Stuart; Le Novère, Nicolas; Demir, Emek; Mi, Huaiyu; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Process Description language represents biological entities and processes between these entities within a network. SBGN PD focuses on the mechanistic description and temporal dependencies of biological interactions and transformations. The nodes (elements) are split into entity nodes describing, e.g., metabolites, proteins, genes and complexes, and process nodes describing, e.g., reactions and associations. The edges (connections) provide descriptions of relationships (or influences) between the nodes, such as consumption, production, stimulation and inhibition. Among all three languages of SBGN, PD is the closest to metabolic and regulatory pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Non-Stationary Inflation and the Markup: an Overview of the Research and some Implications for Policy

OpenAIRE

Bill Russell

2006-01-01

This paper reports on research into the negative relationship between inflation and the markup. It is argued that this relationship can be thought of as ‘long-run’ in nature which suggests that inflation has a persistent effect on the markup and, therefore, the real wage. A ‘rule of thumb’ from the estimates indicate that a 10 percentage point increase in inflation (as occurred worldwide in the 1970s) is associated with around a 7 per cent fall in the markup accompanied by a similar increase ...

Integrating systems biology models and biomedical ontologies.

Science.gov (United States)

Hoehndorf, Robert; Dumontier, Michel; Gennari, John H; Wimalaratne, Sarala; de Bono, Bernard; Cook, Daniel L; Gkoutos, Georgios V

2011-08-11

Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms.

Learning bias, cultural evolution of language, and the biological evolution of the language faculty.

Science.gov (United States)

Smith, Kenny

2011-04-01

The biases of individual language learners act to determine the learnability and cultural stability of languages: learners come to the language learning task with biases which make certain linguistic systems easier to acquire than others. These biases are repeatedly applied during the process of language transmission, and consequently should effect the types of languages we see in human populations. Understanding the cultural evolutionary consequences of particular learning biases is therefore central to understanding the link between language learning in individuals and language universals, common structural properties shared by all the world’s languages. This paper reviews a range of models and experimental studies which show that weak biases in individual learners can have strong effects on the structure of socially learned systems such as language, suggesting that strong universal tendencies in language structure do not require us to postulate strong underlying biases or constraints on language learning. Furthermore, understanding the relationship between learner biases and language design has implications for theories of the evolution of those learning biases: models of gene-culture coevolution suggest that, in situations where a cultural dynamic mediates between properties of individual learners and properties of language in this way, biological evolution is unlikely to lead to the emergence of strong constraints on learning.

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

DEFF Research Database (Denmark)

Rodriguez, Nicolas; Thomas, Alex; Watanabe, Leandro

2015-01-01

JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active...... open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Source code, binaries and documentation for JSBML can be freely...... obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. jsbml-development@googlegroups.com or andraeger@eng.ucsd.edu Supplementary data are available at Bioinformatics...

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

Science.gov (United States)

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.

Monopoly, Pareto and Ramsey mark-ups

OpenAIRE

Ten Raa, T.

2009-01-01

Monopoly prices are too high. It is a price level problem, in the sense that the relative mark-ups have Ramsey optimal proportions, at least for independent constant elasticity demands. I show that this feature of monopoly prices breaks down the moment one demand is replaced by the textbook linear demand or, even within the constant elasticity framework, dependence is introduced. The analysis provides a single Generalized Inverse Elasticity Rule for the problems of monopoly, Pareto and Ramsey.

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

Science.gov (United States)

Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Recent advances in modeling languages for pathway maps and computable biological networks.

Science.gov (United States)

Slater, Ted

2014-02-01

As our theories of systems biology grow more sophisticated, the models we use to represent them become larger and more complex. Languages necessarily have the expressivity and flexibility required to represent these models in ways that support high-resolution annotation, and provide for simulation and analysis that are sophisticated enough to allow researchers to master their data in the proper context. These languages also need to facilitate model sharing and collaboration, which is currently best done by using uniform data structures (such as graphs) and language standards. In this brief review, we discuss three of the most recent systems biology modeling languages to appear: BEL, PySB and BCML, and examine how they meet these needs. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

Science.gov (United States)

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.

Integrating deep and shallow natural language processing components : representations and hybrid architectures

OpenAIRE

Schäfer, Ulrich

2006-01-01

We describe basic concepts and software architectures for the integration of shallow and deep (linguistics-based, semantics-oriented) natural language processing (NLP) components. The main goal of this novel, hybrid integration paradigm is improving robustness of deep processing. After an introduction to constraint-based natural language parsing, we give an overview of typical shallow processing tasks. We introduce XML standoff markup as an additional abstraction layer that eases integration ...

Biological adaptations for functional features of language in the face of cultural evolution.

Science.gov (United States)

Christiansen, Morten H; Reali, Florencia; Chater, Nick

2011-04-01

Although there may be no true language universals, it is nonetheless possible to discern several family resemblance patterns across the languages of the world. Recent work on the cultural evolution of language indicates the source of these patterns is unlikely to be an innate universal grammar evolved through biological adaptations for arbitrary linguistic features. Instead, it has been suggested that the patterns of resemblance emerge because language has been shaped by the brain, with individual languages representing different but partially overlapping solutions to the same set of nonlinguistic constraints. Here, we use computational simulations to investigate whether biological adaptation for functional features of language, deriving from cognitive and communicative constraints, may nonetheless be possible alongside rapid cultural evolution. Specifically, we focus on the Baldwin effect as an evolutionary mechanism by which previously learned linguistic features might become innate through natural selection across many generations of language users. The results indicate that cultural evolution of language does not necessarily prevent functional features of language from becoming genetically fixed, thus potentially providing a particularly informative source of constraints on cross-linguistic resemblance patterns.

A brief discussion on the biological factors in the acquisition of language

Directory of Open Access Journals (Sweden)

Ronivaldo Braz da Silva

2007-11-01

Full Text Available The understanding of how language is acquired and the role the brain plays in the language acquisition process are crucial because the development of language is one of the most important factcrs in human development. The analysis of language development is intrinsically connected with one's awareness of how human beings or human brains perceive, learn, control, and coordinate elaborate behaviour. The study of language development, therefore, involves research on motor, perceptual, and cognitive development. This paper reviews the three major theories of language acquisition, namely, behaviouristic, psycholinguistic, and interactionistic and examines the biological component of language acquisition and the brain's role in the language development process.

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

Science.gov (United States)

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

1998-01-01

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

Fuzzy Markup language : a new solution for transparent intelligent agents

NARCIS (Netherlands)

Acampora, G.; Loia, V.

2011-01-01

From an industrial and technological point of view, fuzzy control theory deals with the development of a particular system controller on a specific hardware by means of an open or legacy programming language that is useful to address, in a high-level fashion, the hardware constraints. Independently

Medical and biologic factors of speech and language development in children (part 2

Directory of Open Access Journals (Sweden)

Chernov D.N.

2015-03-01

Full Text Available The recent data shows that medico-biological aspects of the study of speech and language development in children should be expanded to include an analysis of various socio-cultural factors as the problem requires an interdisciplinary approach. The review stresses the necessity of methodological approach to study of bio- socio-cultural conditions of emerging speech and language abilities in ontogenesis. Psycho-pedagogical aspect involves: informing parents about the medical and biological aspects of speech and language development in childhood; the active involvement of parents in the remedial and preventive activities carried out by specialists; activities to improve the quality and quantity of child-parent interaction depending on the severity and nature of deviations in child speech and language development.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

Science.gov (United States)

Chaouiya, Claudine; Keating, Sarah M; Berenguier, Duncan; Naldi, Aurélien; Thieffry, Denis; van Iersel, Martijn P; Le Novère, Nicolas; Helikar, Tomáš

2015-09-04

Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.

The DSD Schema Language

DEFF Research Database (Denmark)

Klarlund, Nils; Møller, Anders; Schwartzbach, Michael Ignatieff

2002-01-01

be specified as a set of trees. For example, XHTML is a user domain corresponding to a set of XML documents that make sense as hypertext. A notation for defining such a set of XML trees is called a schema language. We believe that a useful schema notation must identify most of the syntactic requirements......XML (Extensible Markup Language), a linear syntax for trees, has gathered a remarkable amount of interest in industry. The acceptance of XML opens new venues for the application of formal methods such as specification of abstract syntax tree sets and tree transformations. A user domain may...... on tree nodes depend on their context. We also support a general, declarative mechanism for inserting default elements and attributes. Also, we include a simple technique for reusing and evolving DSDs through selective redefinitions. The expressiveness of DSD is comparable to that of the schema language...

The evolution of the Faculty of Language from a Chomskyan perspective: bridging linguistics and biology.

Science.gov (United States)

Longa, Victor Manuel

2013-01-01

While language was traditionally considered a purely cultural trait, the advent of Noam Chomsky's Generative Grammar in the second half of the twentieth century dramatically challenged that view. According to that theory, language is an innate feature, part of the human biological endowment. If language is indeed innate, it had to biologically evolve. This review has two main objectives: firstly, it characterizes from a Chomskyan perspective the evolutionary processes by which language could have come into being. Secondly, it proposes a new method for interpreting the archaeological record that radically differs from the usual types of evidence Paleoanthropology has concentrated on when dealing with language evolution: while archaeological remains have usually been regarded from the view of the behavior they could be associated with, the paper will consider archaeological remains from the view of the computational processes and capabilities at work for their production. This computational approach, illustrated with a computational analysis of prehistoric geometric engravings, will be used to challenge the usual generative thinking on language evolution, based on the high specificity of language. The paper argues that the biological machinery of language is neither specifically linguistic nor specifically human, although language itself can still be considered a species-specific innate trait. From such a view, language would be one of the consequences of a slight modification operated on an ancestral architecture shared with vertebrates.

Systems Biology Graphical Notation: Entity Relationship language Level 1 Version 2

Directory of Open Access Journals (Sweden)

Sorokin Anatoly

2015-06-01

Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

ESL students learning biology: The role of language and social interactions

Science.gov (United States)

Jaipal, Kamini

This study explored three aspects related to ESL students in a mainstream grade 11 biology classroom: (1) the nature of students' participation in classroom activities, (2) the factors that enhanced or constrained ESL students' engagement in social interactions, and (3) the role of language in the learning of science. Ten ESL students were observed over an eight-month period in this biology classroom. Data were collected using qualitative research methods such as participant observation, audio-recordings of lessons, field notes, semi-structured interviews, short lesson recall interviews and students' written work. The study was framed within sociocultural perspectives, particularly the social constructivist perspectives of Vygotsky (1962, 1978) and Wertsch (1991). Data were analysed with respect to the three research aspects. Firstly, the findings showed that ESL students' preferred and exhibited a variety of participation practices that ranged from personal-individual to socio-interactive in nature. Both personal-individual and socio-interactive practices appeared to support science and language learning. Secondly, the findings indicated that ESL students' engagement in classroom social interactions was most likely influenced by the complex interactions between a number of competing factors at the individual, interpersonal and community/cultural levels (Rogoff, Radziszewska, & Masiello, 1995). In this study, six factors that appeared to enhance or constrain ESL students' engagement in classroom social interactions were identified. These factors were socio-cultural factors, prior classroom practice, teaching practices, affective factors, English language proficiency, and participation in the research project. Thirdly, the findings indicated that language played a significant mediational role in ESL students' learning of science. The data revealed that the learning of science terms and concepts can be explained by a functional model of language that includes: (1

Defining Linkages between the GSC and NSF's LTER Program: How the Ecological Metadata Language (EML) Relates to GCDML and Other Outcomes

Science.gov (United States)

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)....

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

Science.gov (United States)

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 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 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

A Generic Language for Biological Systems based on Bigraphs

DEFF Research Database (Denmark)

Damgaard, Troels Christoffer; Krivine, Jean

Several efforts have shown that process calculi developed for reasoning about concurrent and mobile systems may be employed for modelling biological systems at the molecular level. In this paper, we initiate investigation of the meta-language framework bigraphical reactive systems, due to Milner et...

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

Science.gov (United States)

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 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.

The structure of an entry in the National corpus of Tuvan language

Directory of Open Access Journals (Sweden)

Mengi V. Ondar

2016-12-01

Full Text Available Contemporary information technologies and mathematical modelling has made creating corpora of natural languages significantly easier. A corpus is an information and reference system based on a collection of digitally processed texts. A corpus includes various written and oral texts in the given language, a set of dictionaries and markup – information on the properties of the text. It is the presence of the markup which distinguishes a corpus from an electronic library. At the moment, national corpora are being set up for many languages of the Russian Federation, including those of the Turkic peoples. Faculty members, postgraduate and undergraduate students at Tuvan State University and Siberian Federal University are working on the National corpus of Tuvan language. This article describes the structure of a dictionary entry in the National corpus of Tuvan language. The corpus database comprises the following tables: MAIN – the headword table, RUS, ENG, GER — translations of the headword into three languages, MORPHOLOGY — the table containing morphological data on the headword. The database is built in Microsoft Office Access. Working with the corpus dictionary includes the following functions: adding, editing and removing an entry, entry search (with transcription, setting and visualizing morphological features of a headword. The project allows us to view the corpus dictionary as a multi-structure entity with a complex hierarchical structure and a dictionary entry as its key component. The corpus dictionary we developed can be used for studying Tuvan language in its pronunciation, orthography and word analysis, as well as for searching for words and collocations in the texts included into the corpus.

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

Directory of Open Access Journals (Sweden)

Maddix Jason

2010-07-01

Full Text Available Abstract 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 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 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

A natural language interface plug-in for cooperative query answering in biological databases.

Science.gov (United States)

Jamil, Hasan M

2012-06-11

One of the many unique features of biological databases is that the mere existence of a ground data item is not always a precondition for a query response. It may be argued that from a biologist's standpoint, queries are not always best posed using a structured language. By this we mean that approximate and flexible responses to natural language like queries are well suited for this domain. This is partly due to biologists' tendency to seek simpler interfaces and partly due to the fact that questions in biology involve high level concepts that are open to interpretations computed using sophisticated tools. In such highly interpretive environments, rigidly structured databases do not always perform well. In this paper, our goal is to propose a semantic correspondence plug-in to aid natural language query processing over arbitrary biological database schema with an aim to providing cooperative responses to queries tailored to users' interpretations. Natural language interfaces for databases are generally effective when they are tuned to the underlying database schema and its semantics. Therefore, changes in database schema become impossible to support, or a substantial reorganization cost must be absorbed to reflect any change. We leverage developments in natural language parsing, rule languages and ontologies, and data integration technologies to assemble a prototype query processor that is able to transform a natural language query into a semantically equivalent structured query over the database. We allow knowledge rules and their frequent modifications as part of the underlying database schema. The approach we adopt in our plug-in overcomes some of the serious limitations of many contemporary natural language interfaces, including support for schema modifications and independence from underlying database schema. The plug-in introduced in this paper is generic and facilitates connecting user selected natural language interfaces to arbitrary databases using a

Analysis of English language learner performance on the biology Massachusetts comprehensive assessment system: The impact of english proficiency, first language characteristics, and late-entry ELL status

Science.gov (United States)

Mitchell, Mary A.

This study analyzed English language learner (ELL) performance on the June 2012 Biology MCAS, namely on item attributes of domain, cognitive skill, and linguistic complexity. It examined the impact of English proficiency, Latinate first language, first language orthography, and late-entry ELL status. The results indicated that English proficiency was a strong predictor of performance and that ELLs at higher levels of English proficiency overwhelmingly passed. The results further indicated that English proficiency introduced a construct-irrelevant variance on the Biology MCAS and raised validity issues for using this assessment at lower levels of English proficiency. This study also found that ELLs with a Latinate first language consistently had statistically significant lower performance. Late-entry ELL status did not predict Biology MCAS performance.

DEMAND FOR AND SUPPLY OF MARK-UP AND PLS FUNDS IN ISLAMIC BANKING: SOME ALTERNATIVE EXPLANATIONS

OpenAIRE

KHAN, TARIQULLAH

1995-01-01

Profit and loss-sharing (PLS) and bai’ al murabahah lil amir bil shira (mark-up) are the two parent principles of Islamic financing. The use of PLS is limited and that of mark-up overwhelming in the operations of the Islamic banks. Several studies provide different explanations for this phenomenon. The dominant among these is the moral hazard hypothesis. Some alternative explanations are given in the present paper. The discussion is based on both demand (user of funds) and supply (bank) side ...

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2

Directory of Open Access Journals (Sweden)

Mi Huaiyu

2015-06-01

Full Text Available The Systems Biological Graphical Notation (SBGN is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD, Entity Relationship (ER and Activity Flow (AF, allow for the representation of different aspects of biological and biochemical systems at different levels of detail.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0

KAUST Repository

Cox, Robert Sidney

2018-03-24

People who are engineering biological organisms often find it useful to communicate in diagrams, both about the structure of the nucleic acid sequences that they are engineering and about the functional relationships between sequence features and other molecular species. Some typical practices and conventions have begun to emerge for such diagrams. The Synthetic Biology Open Language Visual (SBOL Visual) has been developed as a standard for organizing and systematizing such conventions in order to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.0 of SBOL Visual, which builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions and molecular species, making the relationship between diagrams and the SBOL data model explicit, supporting families of symbol variants, clarifying a number of requirements and best practices, and significantly expanding the collection of diagram glyphs.

Synthetic Biology Open Language (SBOL) Version 2.2.0.

Science.gov (United States)

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grünberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H; Myers, Chris; Sauro, Herbert; Wipat, Anil

2018-04-02

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL) Version 2.2.0

KAUST Repository

Cox, Robert Sidney

2018-04-04

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year\\'s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL Version 2.2.0

Directory of Open Access Journals (Sweden)

Cox Robert Sidney

2018-04-01

Full Text Available Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year’s JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Synthetic Biology Open Language (SBOL) Version 2.2.0

KAUST Repository

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James Alastair; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Beal, Jacob; Bissell, Michael; Choi, Kiri; Clancy, Kevin; Grunberg, Raik; Macklin, Chris; Misirli, Goksel; Oberortner, Ernst; Pocock, Matthew; Samineni, Meher; Zhang, Michael; Zhang, Zhen; Zundel, Zach; Gennari, John H.; Myers, Chris; Sauro, Herbert; Wipat, Anil

2018-01-01

Synthetic biology builds upon the techniques and successes of genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. The field still faces substantial challenges, including long development times, high rates of failure, and poor reproducibility. One method to ameliorate these problems would be to improve the exchange of information about designed systems between laboratories. The synthetic biology open language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing standards. This document details version 2.2.0 of SBOL that builds upon version 2.1.0 published in last year's JIB special issue. In particular, SBOL 2.2.0 includes improved description and validation rules for genetic design provenance, an extension to support combinatorial genetic designs, a new class to add non-SBOL data as attachments, a new class for genetic design implementations, and a description of a methodology to describe the entire design-build-test-learn cycle within the SBOL data model.

Student and Teacher Perceptions of a Mobile-Based Biology Vocabulary Study Tool for English Language Learners

Science.gov (United States)

Cruz, Maria B.

English language learners studying biology face a dual challenge of mastering both content and language. Teaching ELLs how to engage in scientific discourse using appropriate language to ask, answer, explain, and make predictions about science requires a foundational knowledge of content-specific vocabulary. This study used qualitative interviews with intermediate-level ELLs at an American high school to learn how a supplemental iPod-based vocabulary review tool influenced their perceptions of learning biology vocabulary outside of classroom hours. Interviews with their biology teacher were also used to complement student testimony from the point of view of an educational professional with ELL teaching experience. Past studies in the area of mobile learning have primarily employed questionnaires to gather feedback from participants. This research study adds greater participant voice to the body of literature that encompasses mobile language learning, second language acquisition, and science education by presenting nuanced opinions from both students and teachers. This dissertation concludes with a discussion on the influence that this study could have on further research in the fields of mobile learning, academic vocabulary, and student learning behaviors.

The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology.

Science.gov (United States)

Galdzicki, Michal; Clancy, Kevin P; Oberortner, Ernst; Pocock, Matthew; Quinn, Jacqueline Y; Rodriguez, Cesar A; Roehner, Nicholas; Wilson, Mandy L; Adam, Laura; Anderson, J Christopher; Bartley, Bryan A; Beal, Jacob; Chandran, Deepak; Chen, Joanna; Densmore, Douglas; Endy, Drew; Grünberg, Raik; Hallinan, Jennifer; Hillson, Nathan J; Johnson, Jeffrey D; Kuchinsky, Allan; Lux, Matthew; Misirli, Goksel; Peccoud, Jean; Plahar, Hector A; Sirin, Evren; Stan, Guy-Bart; Villalobos, Alan; Wipat, Anil; Gennari, John H; Myers, Chris J; Sauro, Herbert M

2014-06-01

The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

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

Science.gov (United States)

Zschocke, Thomas

2012-01-01

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

Modularization and Structured Markup for Learning Content in an Academic Environment

Science.gov (United States)

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

2006-01-01

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

Systematic integration of experimental data and models in systems biology.

Science.gov (United States)

Li, Peter; Dada, Joseph O; Jameson, Daniel; Spasic, Irena; Swainston, Neil; Carroll, Kathleen; Dunn, Warwick; Khan, Farid; Malys, Naglis; Messiha, Hanan L; Simeonidis, Evangelos; Weichart, Dieter; Winder, Catherine; Wishart, Jill; Broomhead, David S; Goble, Carole A; Gaskell, Simon J; Kell, Douglas B; Westerhoff, Hans V; Mendes, Pedro; Paton, Norman W

2010-11-29

The behaviour of biological systems can be deduced from their mathematical models. However, multiple sources of data in diverse forms are required in the construction of a model in order to define its components and their biochemical reactions, and corresponding parameters. Automating the assembly and use of systems biology models is dependent upon data integration processes involving the interoperation of data and analytical resources. Taverna workflows have been developed for the automated assembly of quantitative parameterised metabolic networks in the Systems Biology Markup Language (SBML). A SBML model is built in a systematic fashion by the workflows which starts with the construction of a qualitative network using data from a MIRIAM-compliant genome-scale model of yeast metabolism. This is followed by parameterisation of the SBML model with experimental data from two repositories, the SABIO-RK enzyme kinetics database and a database of quantitative experimental results. The models are then calibrated and simulated in workflows that call out to COPASIWS, the web service interface to the COPASI software application for analysing biochemical networks. These systems biology workflows were evaluated for their ability to construct a parameterised model of yeast glycolysis. Distributed information about metabolic reactions that have been described to MIRIAM standards enables the automated assembly of quantitative systems biology models of metabolic networks based on user-defined criteria. Such data integration processes can be implemented as Taverna workflows to provide a rapid overview of the components and their relationships within a biochemical system.

[Use of the 2D:4D digit ratio as a biological marker of specific language disorders].

Science.gov (United States)

Font-Jordà, Antònia; Gamundí, Antoni; Nicolau Llobera, María Cristina; Aguilar-Mediavilla, Eva

2018-04-03

The finding of biological markers of specific language impairment would facilitate their detection and early intervention. In this sense, the 2D:4D finger ratio is considered an indirect indicator of prenatal exposure to testosterone. Previous studies have related it to linguistic competence and aggressive behaviour, and could be a candidate for a biological marker of language impairment. The aim was to compare the value of the 2D:4D ratio in children with Specific Language Impairment (SLI) with those of children with typical language development, as well as to establish to what extent this biological index correlates with the behaviour (linguistic, cognitive, social,...) in both groups. 2D:4D ratio, language, cognition and social behaviour were compared in a group of children with SLI (n=15), with a group of children without language difficulties (n=16) of the same age (between 5-8 years), gender (male), and socio-cultural level. Children with SLI showed significantly higher values of 2D:4D ratio of the right hand, and a negative correlation between this ratio and their linguistic competence. Although the children with SLI showed impaired adaptive abilities, but not more aggressive behaviour, these measurements did not correlate with the 2D:4D index. Nevertheless, social behaviour correlated with language and cognition competence. A higher value of the biological 2D:4D ration (lower intrauterine exposure to testosterone) seems to be associated with language difficulties in boys with SLI, but not with their behavioural difficulties. Their behavioural difficulties seem to be a consequence of their linguistic difficulties and their level of cognition. Copyright © 2018. Publicado por Elsevier España, S.L.U.

Hyper Text Mark-up Language and Dublin Core metadata element set usage in websites of Iranian State Universities’ libraries

Science.gov (United States)

Zare-Farashbandi, Firoozeh; Ramezan-Shirazi, Mahtab; Ashrafi-Rizi, Hasan; Nouri, Rasool

2014-01-01

Introduction: Recent progress in providing innovative solutions in the organization of electronic resources and research in this area shows a global trend in the use of new strategies such as metadata to facilitate description, place for, organization and retrieval of resources in the web environment. In this context, library metadata standards have a special place; therefore, the purpose of the present study has been a comparative study on the Central Libraries’ Websites of Iran State Universities for Hyper Text Mark-up Language (HTML) and Dublin Core metadata elements usage in 2011. Materials and Methods: The method of this study is applied-descriptive and data collection tool is the check lists created by the researchers. Statistical community includes 98 websites of the Iranian State Universities of the Ministry of Health and Medical Education and Ministry of Science, Research and Technology and method of sampling is the census. Information was collected through observation and direct visits to websites and data analysis was prepared by Microsoft Excel software, 2011. Results: The results of this study indicate that none of the websites use Dublin Core (DC) metadata and that only a few of them have used overlaps elements between HTML meta tags and Dublin Core (DC) elements. The percentage of overlaps of DC elements centralization in the Ministry of Health were 56% for both description and keywords and, in the Ministry of Science, were 45% for the keywords and 39% for the description. But, HTML meta tags have moderate presence in both Ministries, as the most-used elements were keywords and description (56%) and the least-used elements were date and formatter (0%). Conclusion: It was observed that the Ministry of Health and Ministry of Science follows the same path for using Dublin Core standard on their websites in the future. Because Central Library Websites are an example of scientific web pages, special attention in designing them can help the researchers

Hyper Text Mark-up Language and Dublin Core metadata element set usage in websites of Iranian State Universities' libraries.

Science.gov (United States)

Zare-Farashbandi, Firoozeh; Ramezan-Shirazi, Mahtab; Ashrafi-Rizi, Hasan; Nouri, Rasool

2014-01-01

Recent progress in providing innovative solutions in the organization of electronic resources and research in this area shows a global trend in the use of new strategies such as metadata to facilitate description, place for, organization and retrieval of resources in the web environment. In this context, library metadata standards have a special place; therefore, the purpose of the present study has been a comparative study on the Central Libraries' Websites of Iran State Universities for Hyper Text Mark-up Language (HTML) and Dublin Core metadata elements usage in 2011. The method of this study is applied-descriptive and data collection tool is the check lists created by the researchers. Statistical community includes 98 websites of the Iranian State Universities of the Ministry of Health and Medical Education and Ministry of Science, Research and Technology and method of sampling is the census. Information was collected through observation and direct visits to websites and data analysis was prepared by Microsoft Excel software, 2011. The results of this study indicate that none of the websites use Dublin Core (DC) metadata and that only a few of them have used overlaps elements between HTML meta tags and Dublin Core (DC) elements. The percentage of overlaps of DC elements centralization in the Ministry of Health were 56% for both description and keywords and, in the Ministry of Science, were 45% for the keywords and 39% for the description. But, HTML meta tags have moderate presence in both Ministries, as the most-used elements were keywords and description (56%) and the least-used elements were date and formatter (0%). It was observed that the Ministry of Health and Ministry of Science follows the same path for using Dublin Core standard on their websites in the future. Because Central Library Websites are an example of scientific web pages, special attention in designing them can help the researchers to achieve faster and more accurate information resources

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

Science.gov (United States)

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/.

An online model composition tool for system biology models.

Science.gov (United States)

Coskun, Sarp A; Cicek, A Ercument; Lai, Nicola; Dash, Ranjan K; Ozsoyoglu, Z Meral; Ozsoyoglu, Gultekin

2013-09-05

There are multiple representation formats for Systems Biology computational models, and the Systems Biology Markup Language (SBML) is one of the most widely used. SBML is used to capture, store, and distribute computational models by Systems Biology data sources (e.g., the BioModels Database) and researchers. Therefore, there is a need for all-in-one web-based solutions that support advance SBML functionalities such as uploading, editing, composing, visualizing, simulating, querying, and browsing computational models. We present the design and implementation of the Model Composition Tool (Interface) within the PathCase-SB (PathCase Systems Biology) web portal. The tool helps users compose systems biology models to facilitate the complex process of merging systems biology models. We also present three tools that support the model composition tool, namely, (1) Model Simulation Interface that generates a visual plot of the simulation according to user's input, (2) iModel Tool as a platform for users to upload their own models to compose, and (3) SimCom Tool that provides a side by side comparison of models being composed in the same pathway. Finally, we provide a web site that hosts BioModels Database models and a separate web site that hosts SBML Test Suite models. Model composition tool (and the other three tools) can be used with little or no knowledge of the SBML document structure. For this reason, students or anyone who wants to learn about systems biology will benefit from the described functionalities. SBML Test Suite models will be a nice starting point for beginners. And, for more advanced purposes, users will able to access and employ models of the BioModels Database as well.

The evolution of the CUAHSI Water Markup Language (WaterML)

Science.gov (United States)

Zaslavsky, I.; Valentine, D.; Maidment, D.; Tarboton, D. G.; Whiteaker, T.; Hooper, R.; Kirschtel, D.; Rodriguez, M.

2009-04-01

The CUAHSI Hydrologic Information System (HIS, his.cuahsi.org) uses web services as the core data exchange mechanism which provides programmatic connection between many heterogeneous sources of hydrologic data and a variety of online and desktop client applications. The service message schema follows the CUAHSI Water Markup Language (WaterML) 1.x specification (see OGC Discussion Paper 07-041r1). Data sources that can be queried via WaterML-compliant water data services include national and international repositories such as USGS NWIS (National Water Information System), USEPA STORET (Storage & Retrieval), USDA SNOTEL (Snowpack Telemetry), NCDC ISH and ISD(Integrated Surface Hourly and Daily Data), MODIS (Moderate Resolution Imaging Spectroradiometer), and DAYMET (Daily Surface Weather Data and Climatological Summaries). Besides government data sources, CUAHSI HIS provides access to a growing number of academic hydrologic observation networks. These networks are registered by researchers associated with 11 hydrologic observatory testbeds around the US, and other research, government and commercial groups wishing to join the emerging CUAHSI Water Data Federation. The Hydrologic Information Server (HIS Server) software stack deployed at NSF-supported hydrologic observatory sites and other universities around the country, supports a hydrologic data publication workflow which includes the following steps: (1) observational data are loaded from static files or streamed from sensors into a local instance of an Observations Data Model (ODM) database; (2) a generic web service template is configured for the new ODM instance to expose the data as a WaterML-compliant water data service, and (3) the new water data service is registered at the HISCentral registry (hiscentral.cuahsi.org), its metadata are harvested and semantically tagged using concepts from a hydrologic ontology. As a result, the new service is indexed in the CUAHSI central metadata catalog, and becomes

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

Science.gov (United States)

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

2008-11-06

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

Medico-biological factors of speech and language development in young children (part 1

Directory of Open Access Journals (Sweden)

Chernov D.N.

2015-03-01

Full Text Available The article analyzed the main results of medico-biological directions in the study of the factors of children's speech and language. It shows that a variety of pre-, peri-and neonatal developmental factors (teratogenic effects, prematurity, low birth weight, maternal diseases during pregnancy, and chronic diseases of the child had a negative impact on the child-parent relationship that has a lasting influence on child speech and language development.

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

Science.gov (United States)

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.

"Knight in shining armour" or "Frankenstein's creation"? The coverage of synthetic biology in German-language media.

Science.gov (United States)

Gschmeidler, Brigitte; Seiringer, Alexandra

2012-02-01

Although still a side issue in the German-language media, attention towards synthetic biology has risen clearly during the last years, in line with the first applications being presented. This paper presents findings from a content analysis of synthetic biology coverage in German-language media over the years 2004-2009. In the media, synthetic biology is not clearly separated from gene technology. News value is attributed to established categories such as persons and events. Many metaphors and analogies used in describing gene technology can also be found in the coverage of synthetic biology; however, engineering metaphors are more prominent. In addition, playfulness constitutes an aspect rarely found in genetic engineering coverage. Overall, the picture emerging is ambivalent, which leaves prospects for the further development of public debate ambiguous.

A Card-Sorting Activity to Engage Students in the Academic Language of Biology.

Science.gov (United States)

Wallon, Robert C; Jasti, Chandana; Hug, Barbara

2017-03-01

The activity described in this article is designed to provide biology students with opportunities to engage in a range of academic language as they learn the discipline-specific meanings of the terms "drug," "poison," "toxicant," and "toxin." Although intended as part of an introductory lesson in a comprehensive unit for the high school level, this approach to teaching academic language can be adapted for use with older or younger students and can be modified to teach other terms.

Network File - TP Atlas | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available at file For CSML (Cell System Markup Language), see also the CSML website. CSML files may be graphically vie... and simulated at Cell Illustrator Online. For these pieces of software, see also the Cell Illustrator websi...te or the Cell Illustrator Online website. Legend in Fundamental Biology Legend in Medicine/Pharmacology Leg

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

Science.gov (United States)

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.

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

Science.gov (United States)

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.

Biocoder: A programming language for standardizing and automating biology protocols.

Science.gov (United States)

Ananthanarayanan, Vaishnavi; Thies, William

2010-11-08

Published descriptions of biology protocols are often ambiguous and incomplete, making them difficult to replicate in other laboratories. However, there is increasing benefit to formalizing the descriptions of protocols, as laboratory automation systems (such as microfluidic chips) are becoming increasingly capable of executing them. Our goal in this paper is to improve both the reproducibility and automation of biology experiments by using a programming language to express the precise series of steps taken. We have developed BioCoder, a C++ library that enables biologists to express the exact steps needed to execute a protocol. In addition to being suitable for automation, BioCoder converts the code into a readable, English-language description for use by biologists. We have implemented over 65 protocols in BioCoder; the most complex of these was successfully executed by a biologist in the laboratory using BioCoder as the only reference. We argue that BioCoder exposes and resolves ambiguities in existing protocols, and could provide the software foundations for future automation platforms. BioCoder is freely available for download at http://research.microsoft.com/en-us/um/india/projects/biocoder/. BioCoder represents the first practical programming system for standardizing and automating biology protocols. Our vision is to change the way that experimental methods are communicated: rather than publishing a written account of the protocols used, researchers will simply publish the code. Our experience suggests that this practice is tractable and offers many benefits. We invite other researchers to leverage BioCoder to improve the precision and completeness of their protocols, and also to adapt and extend BioCoder to new domains.

Harnessing QbD, Programming Languages, and Automation for Reproducible Biology.

Science.gov (United States)

Sadowski, Michael I; Grant, Chris; Fell, Tim S

2016-03-01

Building robust manufacturing processes from biological components is a task that is highly complex and requires sophisticated tools to describe processes, inputs, and measurements and administrate management of knowledge, data, and materials. We argue that for bioengineering to fully access biological potential, it will require application of statistically designed experiments to derive detailed empirical models of underlying systems. This requires execution of large-scale structured experimentation for which laboratory automation is necessary. This requires development of expressive, high-level languages that allow reusability of protocols, characterization of their reliability, and a change in focus from implementation details to functional properties. We review recent developments in these areas and identify what we believe is an exciting trend that promises to revolutionize biotechnology. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

49 CFR 1580.103 - Location and shipping information for certain rail cars.

Science.gov (United States)

2010-10-01

... the following methods: (1) Electronic data transmission in spreadsheet format. (2) Electronic data transmission in Hyper Text Markup Language (HTML) format. (3) Electronic data transmission in Extensible Markup Language (XML). (4) Facsimile transmission of a hard copy spreadsheet in tabular format. (5) Posting the...

XML and E-Journals: The State of Play.

Science.gov (United States)

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…

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

Science.gov (United States)

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

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

Science.gov (United States)

Bai, Ge; Anderson, Gerard F

2015-06-01

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

Review of Russian language studies on radionuclide behaviour in agricultural animals: biological half-lives

International Nuclear Information System (INIS)

Fesenko, S.; Isamov, N.; Barnett, C.L.; Beresford, N.A.; Howard, B.J.; Sanzharova, N.; Fesenko, E.

2015-01-01

Extensive studies on transfer of radionuclides to animals were carried out in the USSR from the 1950s. Few of these studies were published in the international refereed literature or taken into account in international reviews. This paper continues a series of reviews of Russian language literature on radionuclide transfer to animals, providing information on biological half-lives of radionuclides in various animal tissues. The data are compared, where possible, with those reported in other countries. The data are normally quantified using a single or double exponential accounting for different proportions of the loss. For some products, such as milk, biological half-lives tend to be rapid at 1–3 d for most radionuclides and largely described by a single exponential. However, for other animal products biological half-lives can vary widely as they are influenced by many factors such as the age and size of the animal. Experimental protocols, such as the duration of the study, radionuclide administration and/or sample collection protocol also influence the value of biological half-lives estimated. - Highlights: • The data on biological half-lives from Russian language literature were reviewed. • Radionuclides with the shortest half-lives in animals are those which accumulate in soft tissues. • Short term behaviour is affected by the form in which radionuclides are administered. • There is a tendency for more rapid radionuclide turnover in younger animals

Free Trade Agreements and Firm-Product Markups in Chilean Manufacturing

DEFF Research Database (Denmark)

Lamorgese, A.R.; Linarello, A.; Warzynski, Frederic Michel Patrick

In this paper, we use detailed information about firms' product portfolio to study how trade liberalization affects prices, markups and productivity. We document these effects using firm product level data in Chilean manufacturing following two major trade agreements with the EU and the US....... The dataset provides information about the value and quantity of each good produced by the firm, as well as the amount of exports. One additional and unique characteristic of our dataset is that it provides a firm-product level measure of the unit average cost. We use this information to compute a firm...

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

Science.gov (United States)

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

2016-10-01

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

Firm Dynamics and Markup Variations: Implications for Sunspot Equilibria and Endogenous Economic Fluctuation

OpenAIRE

Nir Jaimovich

2007-01-01

This paper analyzes how the interaction between firms’ entry-and-exit decisions and variations in competition gives rise to self-fulfilling, expectation-driven fluctuations in aggregate economic activity and in measured total factor productivity (TFP). The analysis is based on a dynamic general equilibrium model in which net business formation is endogenously procyclical and leads to endogenous countercyclical variations in markups. This interaction leads to indeterminacy in which economic fl...

Head First HTML5 Programming Building Web Apps with JavaScript

CERN Document Server

Freeman, Eric

2011-01-01

HTML has been on a wild ride. Sure, HTML started as a mere markup language, but more recently HTML's put on some major muscle. Now we've got a language tuned for building web applications with Web storage, 2D drawing, offline support, sockets and threads, and more. And to speak this language you've got to go beyond HTML5 markup and into the world of the DOM, events, and JavaScript APIs. Now you probably already know all about HTML markup (otherwise known as structure) and you know all aboutCSS style (presentation), but what you've been missing is JavaScript (behavior). If all you know about

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

Directory of Open Access Journals (Sweden)

Bergmann Frank T.

2015-06-01

Full Text Available 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.

Handheld Computing

National Research Council Canada - National Science Library

Alford, Kenneth L

2005-01-01

.... It outlines some of the considerations involved in a PDA procurement, discusses four tools for developing PDA resource materials -- programming tools, hypertext markup language- and eXtensible markup...

A Conversion Tool for Mathematical Expressions in Web XML Files.

Science.gov (United States)

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.…

Domain-specific markup languages and descriptive metadata: their functions in scientific resource discoveryLinguagens de marcação específicas por domínio e metadados descritivos: funções para a descoberta de recursos científicos

Directory of Open Access Journals (Sweden)

Marcia Lei Zeng

2010-01-01

Full Text Available While metadata has been a strong focus within information professionals‟ publications, projects, and initiatives during the last two decades, a significant number of domain-specific markup languages have also been developing on a parallel path at the same rate as metadata standards; yet, they do not receive comparable attention. This essay discusses the functions of these two kinds of approaches in scientific resource discovery and points out their potential complementary roles through appropriate interoperability approaches.Enquanto os metadados tiveram grande foco em publicações, projetos e iniciativas dos profissionais da informação durante as últimas duas décadas, um número significativo de linguagens de marcação específicas por domínio também se desenvolveram paralelamente a uma taxa equivalente aos padrões de metadados; mas ainda não recebem atenção comparável. Esse artigo discute as funções desses dois tipos de abordagens na descoberta de recursos científicos e aponta papéis potenciais e complementares por meio de abordagens de interoperabilidade apropriadas.

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

Science.gov (United States)

2012-05-22

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

Beacon Editor: Capturing Signal Transduction Pathways Using the Systems Biology Graphical Notation Activity Flow Language.

Science.gov (United States)

Elmarakeby, Haitham; Arefiyan, Mostafa; Myers, Elijah; Li, Song; Grene, Ruth; Heath, Lenwood S

2017-12-01

The Beacon Editor is a cross-platform desktop application for the creation and modification of signal transduction pathways using the Systems Biology Graphical Notation Activity Flow (SBGN-AF) language. Prompted by biologists' requests for enhancements, the Beacon Editor includes numerous powerful features for the benefit of creation and presentation.

Building blocks of e-commerce

Indian Academy of Sciences (India)

R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

e-commerce possible are: html (hyper text markup language), XML (extensible markup .... Standard word processor outputs can be converted to ..... various types of transactions between organizations and it requires an expert to understand.

GIBS Keyhole Markup Language (KML)

Data.gov (United States)

National Aeronautics and Space Administration — The KML documentation standard provides a solution for imagery integration into mapping tools that utilize support the KML standard, specifically Google Earth. Using...

A polythematic real-time synergistic hybrid data telecommunication system for scientific research with bidirectional fuzzy feedback peer review by expert referees

Directory of Open Access Journals (Sweden)

Panagiotis Petratos

2003-02-01

Full Text Available Heterogeneous research environments, interests and locations do not necessarily coincide, thus hitherto the primary method of communication amongst researchers has been email. In this article a novel unified polythematic, real-time, synergistic, data telecommunication system is proposed with peer-reviewed, bidirectional fuzzy feedback for research scientists, to facilitate scientific information exchange via the extensible markup language (XML on multiple scientific topics, e.g. in mathematics, physics, biology and chemistry.

Automatic compilation from high-level biologically-oriented programming language to genetic regulatory networks.

Science.gov (United States)

Beal, Jacob; Lu, Ting; Weiss, Ron

2011-01-01

The field of synthetic biology promises to revolutionize our ability to engineer biological systems, providing important benefits for a variety of applications. Recent advances in DNA synthesis and automated DNA assembly technologies suggest that it is now possible to construct synthetic systems of significant complexity. However, while a variety of novel genetic devices and small engineered gene networks have been successfully demonstrated, the regulatory complexity of synthetic systems that have been reported recently has somewhat plateaued due to a variety of factors, including the complexity of biology itself and the lag in our ability to design and optimize sophisticated biological circuitry. To address the gap between DNA synthesis and circuit design capabilities, we present a platform that enables synthetic biologists to express desired behavior using a convenient high-level biologically-oriented programming language, Proto. The high level specification is compiled, using a regulatory motif based mechanism, to a gene network, optimized, and then converted to a computational simulation for numerical verification. Through several example programs we illustrate the automated process of biological system design with our platform, and show that our compiler optimizations can yield significant reductions in the number of genes (~ 50%) and latency of the optimized engineered gene networks. Our platform provides a convenient and accessible tool for the automated design of sophisticated synthetic biological systems, bridging an important gap between DNA synthesis and circuit design capabilities. Our platform is user-friendly and features biologically relevant compiler optimizations, providing an important foundation for the development of sophisticated biological systems.

Visualization Development of the Ballistic Threat Geospatial Optimization

Science.gov (United States)

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

High-Bandwidth Tactical-Network Data Analysis in a High-Performance-Computing (HPC) Environment: Packet-Level Analysis

Science.gov (United States)

2015-09-01

individual fragments using the hash-based method. In general, fragments 6 appear in order and relatively close to each other in the file. A fragment...data product derived from the data model is shown in Fig. 5, a Google Earth12 Keyhole Markup Language (KML) file. This product includes aggregate...System BLOb binary large object FPGA field-programmable gate array HPC high-performance computing IP Internet Protocol KML Keyhole Markup Language

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

Science.gov (United States)

Boucheron, Laura E

2013-07-16

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

Review of Russian language studies on radionuclide behaviour in agricultural animals: biological half-lives.

Science.gov (United States)

Fesenko, S; Isamov, N; Barnett, C L; Beresford, N A; Howard, B J; Sanzharova, N; Fesenko, E

2015-04-01

Extensive studies on transfer of radionuclides to animals were carried out in the USSR from the 1950s. Few of these studies were published in the international refereed literature or taken into account in international reviews. This paper continues a series of reviews of Russian language literature on radionuclide transfer to animals, providing information on biological half-lives of radionuclides in various animal tissues. The data are compared, where possible, with those reported in other countries. The data are normally quantified using a single or double exponential accounting for different proportions of the loss. For some products, such as milk, biological half-lives tend to be rapid at 1-3 d for most radionuclides and largely described by a single exponential. However, for other animal products biological half-lives can vary widely as they are influenced by many factors such as the age and size of the animal. Experimental protocols, such as the duration of the study, radionuclide administration and/or sample collection protocol also influence the value of biological half-lives estimated. Copyright © 2015 Elsevier Ltd. All rights reserved.

The countries and languages that dominate biological research at the beginning of the 21st century.

Science.gov (United States)

Monge-Nájera, Julian; Nielsen, Vanessa

2005-01-01

Traditionally, studies of scientific productivity are biased in two ways: they are based on Current Contents, an index centered in British and American journals, and they seldom correct for population size, ignoring the relative effort that each society places in research. We studied national productivity for biology using a more representative index, the Biological Abstracts, and analyzed both total and relative productivity. English dominates biological publications with 87% (no other individual language reaches 2%). If the USA is considered a region by itself, it occupies the first place in per capita production of biology papers, with at least twice the productivity of either Asia or Europe. Canada, Oceania and Latin America occupy an intermediate position. The global output of scientific papers is dominated by Europe, USA. Japan, Canada, China and India. When corrected for population size, the countries with the greatest productivity of biology papers are the Nordic nations, Israel, Switzerland, Netherlands, Australia, Saint Lucia and Montserrat. The predominance of English as the language of biological research found in this study shows a continuation of the trend initiated around the year 1900. The large relative productivity of the USA reflects the importance that American society gives to science as the basis for technological and economic development, but the USA's share of total scientific output has decreased from 44% in 1983 to 34% in 2002, while there is a greater growth of science in India, Japan and Latin America, among others. The increasing share obtained by China and India may reflect a recent change in attitude towards funding science. The leadership of Nordic nations, Israel, Switzerland, Netherlands and Australia can be explained by cultural attitude. Apparently, a positive trend is emerging in Latin America, where Chile improved its ranking in per capita productivity but Argentina, Costa Rica, Uruguay, Brazil and Cuba fell. Nevertheless, the

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

Science.gov (United States)

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

2015-08-01

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

The "New Oxford English Dictionary" Project.

Science.gov (United States)

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…

Geoinformation perspectives on innovation and economic growth

CSIR Research Space (South Africa)

Cooper, Antony K

2009-03-01

Full Text Available driving patterns, monitored through a tracking device placed in the insured person’s vehicle. circle6 Real estate: Real estate agencies have been pioneers of incorporating multimedia into a GIS, to link photographs and video footage of properties... geobrowsers. With markup languages such as the Keyhole Markup Language (KML), geobrowsers can be customised to drape one’s geoinformation over the virtual globe, attach one’s content (eg: photographs, video or sound recordings) to locations in the virtual...

A general lexicographic model for a typological variety of ...

African Journals Online (AJOL)

eXtensible Markup Language/Web Ontology Language) representation model. This article follows another route in describing a model based on entities and relations between them; MySQL (usually referred to as: Structured Query Language) ...

Data Display Markup Language (DDML) Handbook

Science.gov (United States)

2017-01-31

purpose of this handbook is to improve the use of DDML as a standard by presenting clear guidelines and thereby eliminating any misinterpretations ...code is slightly different for internal translators than for external translators. Like external translators, special considerations must be accounted

Rethinking foundations of language from a multidisciplinary perspective.

Science.gov (United States)

Gong, Tao; Shuai, Lan; Wu, Yicheng

2018-04-21

The issue of language foundations has been of great controversy ever since it was first raised in Lenneberg's (1967) monograph Biological Foundations of Language. Based on a survey of recent findings relevant to the study of language acquisition and evolution, we propose that: (i) the biological predispositions for language are largely domain-general, not necessarily language-specific or human-unique; (ii) the socio-cultural environment of language serves as another important foundation of language, which helps shape language components, induce and drive language shift; and (iii) language must have coevolved with the cognitive mechanisms associated with it through intertwined biological and cultural evolution. In addition to theoretical issues, this paper also evaluates the primary approaches recently joining the endeavor of studying language foundations and evolution, including human experiments and computer simulations. Most of the evidence surveyed in this paper comes from a variety of disciplines, and methodology therein complements each other to form a global picture of language foundations. These reflect the complexity of the issue of language foundations and the necessity of taking a multidisciplinary perspective to address it. Copyright © 2018 Elsevier B.V. All rights reserved.

XForms 2.0

NARCIS (Netherlands)

S. Pemberton (Steven); J.M. Boyer; L.L. Klotz; N. van den Bleeken

2012-01-01

htmlabstractXForms is an XML markup for a new generation of forms and form-like applications on the Web. XForms is not a free-standing document type, but is integrated into other markup languages, such as [XHTML], [ODF] or [SVG]. An XForms-based application gathers and processes data using an

Ontology-Driven Translator Generator for Data Display Configurations

National Research Council Canada - National Science Library

Jones, Charles

2004-01-01

.... In addition, the method includes the specification of mappings between a language-specific ontology and its corresponding syntax specification, that is, either an eXtensible Markup Language (XML...

Modeling of the bacterial mechanism of methicillin-resistance by a systems biology approach.

Directory of Open Access Journals (Sweden)

Ida Autiero

Full Text Available BACKGROUND: A microorganism is a complex biological system able to preserve its functional features against external perturbations and the ability of the living systems to oppose to these external perturbations is defined "robustness". The antibiotic resistance, developed by different bacteria strains, is a clear example of robustness and of ability of the bacterial system to acquire a particular functional behaviour in response to environmental changes. In this work we have modeled the whole mechanism essential to the methicillin-resistance through a systems biology approach. The methicillin is a beta-lactamic antibiotic that act by inhibiting the penicillin-binding proteins (PBPs. These PBPs are involved in the synthesis of peptidoglycans, essential mesh-like polymers that surround cellular enzymes and are crucial for the bacterium survival. METHODOLOGY: The network of genes, mRNA, proteins and metabolites was created using CellDesigner program and the data of molecular interactions are stored in Systems Biology Markup Language (SBML. To simulate the dynamic behaviour of this biochemical network, the kinetic equations were associated with each reaction. CONCLUSIONS: Our model simulates the mechanism of the inactivation of the PBP by methicillin, as well as the expression of PBP2a isoform, the regulation of the SCCmec elements (SCC: staphylococcal cassette chromosome and the synthesis of peptidoglycan by PBP2a. The obtained results by our integrated approach show that the model describes correctly the whole phenomenon of the methicillin resistance and is able to respond to the external perturbations in the same way of the real cell. Therefore, this model can be useful to develop new therapeutic approaches for the methicillin control and to understand the general mechanism regarding the cellular resistance to some antibiotics.

Systems biology of host-mycobiota interactions: dissecting Dectin-1 and Dectin-2 signalling in immune cells with DC-ATLAS.

Science.gov (United States)

Rizzetto, Lisa; De Filippo, Carlotta; Rivero, Damariz; Riccadonna, Samantha; Beltrame, Luca; Cavalieri, Duccio

2013-11-01

Modelling the networks sustaining the fruitful coexistence between fungi and their mammalian hosts is becoming increasingly important to control emerging fungal pathogens. The C-type lectins Dectin-1 and Dectin-2 are involved in host defense mechanisms against fungal infection driving inflammatory and adaptive immune responses and complement in containing fungal burdens. Recognizing carbohydrate structures in pathogens, their engagement induces maturation of dendritic cells (DCs) into potent immuno-stimulatory cells endowed with the capacity to efficiently prime T cells. Owing to these properties, Dectin-1 and Dectin-2 agonists are currently under investigation as promising adjuvants in vaccination procedures for the treatment of fungal infection. Thus, a detailed understanding of events' cascade specifically triggered in DCs upon engagement is of great interest in translational research. Here, we summarize the current knowledge on Dectin-1 and Dectin-2 signalling in DCs highlighting similarities and differences. Detailed maps are annotated, using the Biological Connection Markup Language (BCML) data model, and stored in DC-ATLAS, a versatile resource for the interpretation of high-throughput data generated perturbing the signalling network of DCs. Copyright © 2013 Elsevier GmbH. All rights reserved.

Mark-up bancário, conflito distributivo e utilização da capacidade produtiva: uma macrodinâmica pós-keynesiana

Directory of Open Access Journals (Sweden)

Lima Gilberto Tadeu

2003-01-01

Full Text Available Elabora-se um modelo macrodinâmico pós-keynesiano de utilização da capacidade, distribuição e inflação por conflito, no qual a oferta de moeda de crédito é endógena. A taxa nominal de juros é determinada pela aplicação de um mark-up sobre a taxa básica fixada pela autoridade monetária. Ao longo do tempo, o mark-up bancário varia com a taxa de lucro sobre o capital físico, enquanto a taxa básica varia com excessos de demanda que não são acomodáveis pela utilização da capacidade. São analisados os casos em que a demanda é suficiente ou não para gerar a plena utilização da capacidade.

GAIML: A New Language for Verbal and Graphical Interaction in Chatbots

Directory of Open Access Journals (Sweden)

Roberto Pirrone

2008-01-01

Full Text Available Natural and intuitive interaction between users and complex systems is a crucial research topic in human-computer interaction. A major direction is the definition and implementation of systems with natural language understanding capabilities. The interaction in natural language is often performed by means of systems called chatbots. A chatbot is a conversational agent with a proper knowledge base able to interact with users. Chatbots appearance can be very sophisticated with 3D avatars and speech processing modules. However the interaction between the system and the user is only performed through textual areas for inputs and replies. An interaction able to add to natural language also graphical widgets could be more effective. On the other side, a graphical interaction involving also the natural language can increase the comfort of the user instead of using only graphical widgets. In many applications multi-modal communication must be preferred when the user and the system have a tight and complex interaction. Typical examples are cultural heritages applications (intelligent museum guides, picture browsing or systems providing the user with integrated information taken from different and heterogenous sources as in the case of the iGoogle™ interface. We propose to mix the two modalities (verbal and graphical to build systems with a reconfigurable interface, which is able to change with respect to the particular application context. The result of this proposal is the Graphical Artificial Intelligence Markup Language (GAIML an extension of AIML allowing merging both interaction modalities. In this context a suitable chatbot system called Graphbot is presented to support this language. With this language is possible to define personalized interface patterns that are the most suitable ones in relation to the data types exchanged between the user and the system according to the context of the dialogue.

Modeling biology with HDL languages: a first step toward a genetic design automation tool inspired from microelectronics.

Science.gov (United States)

Gendrault, Yves; Madec, Morgan; Lallement, Christophe; Haiech, Jacques

2014-04-01

Nowadays, synthetic biology is a hot research topic. Each day, progresses are made to improve the complexity of artificial biological functions in order to tend to complex biodevices and biosystems. Up to now, these systems are handmade by bioengineers, which require strong technical skills and leads to nonreusable development. Besides, scientific fields that share the same design approach, such as microelectronics, have already overcome several issues and designers succeed in building extremely complex systems with many evolved functions. On the other hand, in systems engineering and more specifically in microelectronics, the development of the domain has been promoted by both the improvement of technological processes and electronic design automation tools. The work presented in this paper paves the way for the adaptation of microelectronics design tools to synthetic biology. Considering the similarities and differences between the synthetic biology and microelectronics, the milestones of this adaptation are described. The first one concerns the modeling of biological mechanisms. To do so, a new formalism is proposed, based on an extension of the generalized Kirchhoff laws to biology. This way, a description of all biological mechanisms can be made with languages widely used in microelectronics. Our approach is therefore successfully validated on specific examples drawn from the literature.

Epilepsy, language, and social skills.

Science.gov (United States)

Caplan, Rochelle

2017-10-04

Language and social skills are essential for intrapersonal and interpersonal functioning and quality of life. Since epilepsy impacts these important domains of individuals' functioning, understanding the psychosocial and biological factors involved in the relationship among epilepsy, language, and social skills has important theoretical and clinical implications. This review first describes the psychosocial and biological factors involved in the association between language and social behavior in children and in adults and their relevance for epilepsy. It reviews the findings of studies of social skills and the few studies conducted on the inter-relationship of language and social skills in pediatric and adult epilepsy. The paper concludes with suggested future research and clinical directions that will enhance early identification and treatment of epilepsy patients at risk for impaired language and social skills. Copyright © 2017 Elsevier Inc. All rights reserved.

Bigraphical Languages and their Simulation

DEFF Research Database (Denmark)

Højsgaard, Espen

-trivial. A key problem is that of matching: deciding if and how a reaction rule applies to a bigraph. In this dissertation, we study bigraphs and their simulation for two types of practical formal languages: programming languages and languages for cell biology. First, we study programming languages and binding...... bigraphs, a variant of bigraphs with a facility for modeling the binders found in most programming languages. We construct and implement a provably correct term-based matching algorithm resulting in the BPL Tool, a first tool for binding bigraphs, which provides facilities for modeling, simulation...... of stochastic behavior which is useful in cell biology. We generalize an efficient and scalable stochastic simulation algorithm for the k-calculus to bigraphs. For this purpose, we develop and implement a number of theories for (stochastic) bigraphs: a formulation of the theory that is amenable...

Towards programming languages for genetic engineering of living cells.

Science.gov (United States)

Pedersen, Michael; Phillips, Andrew

2009-08-06

Synthetic biology aims at producing novel biological systems to carry out some desired and well-defined functions. An ultimate dream is to design these systems at a high level of abstraction using engineering-based tools and programming languages, press a button, and have the design translated to DNA sequences that can be synthesized and put to work in living cells. We introduce such a programming language, which allows logical interactions between potentially undetermined proteins and genes to be expressed in a modular manner. Programs can be translated by a compiler into sequences of standard biological parts, a process that relies on logic programming and prototype databases that contain known biological parts and protein interactions. Programs can also be translated to reactions, allowing simulations to be carried out. While current limitations on available data prevent full use of the language in practical applications, the language can be used to develop formal models of synthetic systems, which are otherwise often presented by informal notations. The language can also serve as a concrete proposal on which future language designs can be discussed, and can help to guide the emerging standard of biological parts which so far has focused on biological, rather than logical, properties of parts.

Model-based development of robotic systems and services in construction robotics

DEFF Research Database (Denmark)

Schlette, Christian; Roßmann, Jürgen

2017-01-01

More and more of our indoor/outdoor environments are available as 3D digital models. In particular, digital models such as the CityGML (City Geography Markup Language) format for cities and the BIM (Building Information Modeling) methodology for buildings are becoming important standards for proj......More and more of our indoor/outdoor environments are available as 3D digital models. In particular, digital models such as the CityGML (City Geography Markup Language) format for cities and the BIM (Building Information Modeling) methodology for buildings are becoming important standards...

XML in an Adaptive Framework for Instrument Control

Science.gov (United States)

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.

Treating metadata as annotations: separating the content markup from the content

Directory of Open Access Journals (Sweden)

Fredrik Paulsson

2007-11-01

Full Text Available The use of digital learning resources creates an increasing need for semantic metadata, describing the whole resource, as well as parts of resources. Traditionally, schemas such as Text Encoding Initiative (TEI have been used to add semantic markup for parts of resources. This is not sufficient for use in a ”metadata ecology”, where metadata is distributed, coherent to different Application Profiles, and added by different actors. A new methodology, where metadata is “pointed in” as annotations, using XPointers, and RDF is proposed. A suggestion for how such infrastructure can be implemented, using existing open standards for metadata, and for the web is presented. We argue that such methodology and infrastructure is necessary to realize the decentralized metadata infrastructure needed for a “metadata ecology".

Developmental language and speech disability.

Science.gov (United States)

Spiel, G; Brunner, E; Allmayer, B; Pletz, A

2001-09-01

Speech disabilities (articulation deficits) and language disorders--expressive (vocabulary) receptive (language comprehension) are not uncommon in children. An overview of these along with a global description of the impairment of communication as well as clinical characteristics of language developmental disorders are presented in this article. The diagnostic tables, which are applied in the European and Anglo-American speech areas, ICD-10 and DSM-IV, have been explained and compared. Because of their strengths and weaknesses an alternative classification of language and speech developmental disorders is proposed, which allows a differentiation between expressive and receptive language capabilities with regard to the semantic and the morphological/syntax domains. Prevalence and comorbidity rates, psychosocial influences, biological factors and the biological social interaction have been discussed. The necessity of the use of standardized examinations is emphasised. General logopaedic treatment paradigms, specific therapy concepts and an overview of prognosis have been described.

Toward the Language-Ready Brain: Biological Evolution and Primate Comparisons.

Science.gov (United States)

Arbib, Michael A

2017-02-01

The approach to language evolution suggested here focuses on three questions: How did the human brain evolve so that humans can develop, use, and acquire languages? How can the evolutionary quest be informed by studying brain, behavior, and social interaction in monkeys, apes, and humans? How can computational modeling advance these studies? I hypothesize that the brain is language ready in that the earliest humans had protolanguages but not languages (i.e., communication systems endowed with rich and open-ended lexicons and grammars supporting a compositional semantics), and that it took cultural evolution to yield societies (a cultural constructed niche) in which language-ready brains could become language-using brains. The mirror system hypothesis is a well-developed example of this approach, but I offer it here not as a closed theory but as an evolving framework for the development and analysis of conflicting subhypotheses in the hope of their eventual integration. I also stress that computational modeling helps us understand the evolving role of mirror neurons, not in and of themselves, but only in their interaction with systems "beyond the mirror." Because a theory of evolution needs a clear characterization of what it is that evolved, I also outline ideas for research in neurolinguistics to complement studies of the evolution of the language-ready brain. A clear challenge is to go beyond models of speech comprehension to include sign language and models of production, and to link language to visuomotor interaction with the physical and social world.

EVALUATION OF SEMANTIC SIMILARITY FOR SENTENCES IN NATURAL LANGUAGE BY MATHEMATICAL STATISTICS METHODS

Directory of Open Access Journals (Sweden)

A. E. Pismak

2016-03-01

Full Text Available Subject of Research. The paper is focused on Wiktionary articles structural organization in the aspect of its usage as the base for semantic network. Wiktionary community references, article templates and articles markup features are analyzed. The problem of numerical estimation for semantic similarity of structural elements in Wiktionary articles is considered. Analysis of existing software for semantic similarity estimation of such elements is carried out; algorithms of their functioning are studied; their advantages and disadvantages are shown. Methods. Mathematical statistics methods were used to analyze Wiktionary articles markup features. The method of semantic similarity computing based on statistics data for compared structural elements was proposed.Main Results. We have concluded that there is no possibility for direct use of Wiktionary articles as the source for semantic network. We have proposed to find hidden similarity between article elements, and for that purpose we have developed the algorithm for calculation of confidence coefficients proving that each pair of sentences is semantically near. The research of quantitative and qualitative characteristics for the developed algorithm has shown its major performance advantage over the other existing solutions in the presence of insignificantly higher error rate. Practical Relevance. The resulting algorithm may be useful in developing tools for automatic Wiktionary articles parsing. The developed method could be used in computing of semantic similarity for short text fragments in natural language in case of algorithm performance requirements are higher than its accuracy specifications.

Original Dataset - dbQSNP | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available English ]; } else { document.getElementById(lang).innerHTML= '[ Japanese | English ]'; } } window.onload = switchLanguage... included - the subdirectory old/ is not included - pml/ includes data in PML (Polymorphism Markup Language)

Modeling of the positioning system and visual mark-up of historical cadastral maps

Directory of Open Access Journals (Sweden)

Tomislav Jakopec

2013-03-01

Full Text Available The aim of the paper is to present of the possibilities of positioning and visual markup of historical cadastral maps onto Google maps using open source software. The corpus is stored in the Croatian State Archives in Zagreb, in the Maps Archive for Croatia and Slavonia. It is part of cadastral documentation that consists of cadastral material from the period of first cadastral survey conducted in the Kingdom of Croatia and Slavonia from 1847 to 1877, and which is used extensively according to the data provided by the customer service of the Croatian State Archives. User needs on the one side and the possibilities of innovative implementation of ICT on the other have motivated the development of the system which would use digital copies of original cadastral maps and connect them with systems like Google maps, and thus both protect the original materials and open up new avenues of research related to the use of originals. With this aim in mind, two cadastral map presentation models have been created. Firstly, there is a detailed display of the original, which enables its viewing using dynamic zooming. Secondly, the interactive display is facilitated through blending the cadastral maps with Google maps, which resulted in establishing links between the coordinates of the digital and original plans through transformation. The transparency of the original can be changed, and the user can intensify the visibility of the underlying layer (Google map or the top layer (cadastral map, which enables direct insight into parcel dynamics over a longer time-span. The system also allows for the mark-up of cadastral maps, which can lead to the development of the cumulative index of all terms found on cadastral maps. The paper is an example of the implementation of ICT for providing new services, strengthening cooperation with the interested public and related institutions, familiarizing the public with the archival material, and offering new possibilities for

Crowdsourcing and curation: perspectives from biology and natural language processing.

Science.gov (United States)

Hirschman, Lynette; Fort, Karën; Boué, Stéphanie; Kyrpides, Nikos; Islamaj Doğan, Rezarta; Cohen, Kevin Bretonnel

2016-01-01

Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodology and its applicability to biocuration. This paper explores crowdsourcing for biocuration through several case studies that highlight different ways of leveraging 'the crowd'; these raise issues about the kind(s) of expertise needed, the motivations of participants, and questions related to feasibility, cost and quality. The paper is an outgrowth of a panel session held at BioCreative V (Seville, September 9-11, 2015). The session consisted of four short talks, followed by a discussion. In their talks, the panelists explored the role of expertise and the potential to improve crowd performance by training; the challenge of decomposing tasks to make them amenable to crowdsourcing; and the capture of biological data and metadata through community editing.Database URL: http://www.mitre.org/publications/technical-papers/crowdsourcing-and-curation-perspectives. © The Author(s) 2016. Published by Oxford University Press.

XML — an opportunity for data standards in the geosciences

Science.gov (United States)

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.

Language architecture and its import for evolution.

Science.gov (United States)

Chomsky, Noam

2017-10-01

Inquiry into the evolution of some biological system evidently can proceed only as far as its nature is understood. Lacking such understanding, its manifestations are likely to appear to be chaotic, highly variable, and lacking significant general properties; and, accordingly, study of its evolution cannot be seriously undertaken. These truisms hold of the study of the human faculty of language FL just as for other biological systems. As discussed below, FL appears to be a shared human capacity in essentials, with options of variation of a kind to which we return. After a long lapse, the problem of evolution of language arose in mid-twentieth century when the first efforts were made to construct accounts of FL as a biological object, internal to an individual, with particular internal languages - I-languages in current terminology - as manifestations of FL. Copyright © 2017. Published by Elsevier Ltd.

Bibliometry of the Revista de Biología Tropical / International Journal of Tropical Biology and Conservation: document types, languages, countries, institutions, citations and article lifespan.

Science.gov (United States)

Monge-Nájera, Julián; Ho, Yuh-Shan

2016-09-01

The Revista de Biología Tropical / International Journal of Tropical Biology and Conservation, founded in 1953, publishes feature articles about tropical nature and is considered one of the leading journals in Latin America. This article analyzes document type, language, countries, institutions, citations and for the first time article lifespan, from 1976 through 2014. We analyzed 3 978 documents from the Science Citation Index Expanded. Articles comprised 88 % of the total production and had 3.7 citations on average, lower than reviews. Spanish and English articles were nearly equal in numbers and citation for English articles was only slightly higher. Costa Rica, Mexico, and the USA are the countries with more articles, and the leading institutions were Universidad de Costa Rica, Universidad Nacional, Universidad Nacional Autónoma de Mexico and Universidad de Oriente (Venezuela). The citation lifespan of articles is long, around 37 years. It is not surprising that Costa Rica, Mexico, and Venezuela lead in productivity and cooperation, because they are mostly covered by tropical ecosystems and share a common culture and a tradition of scientific cooperation. The same applies to the leading institutions, which are among the largest Spanish language universities in the neotropical region. American output can be explained by the regional presence of the Smithsonian Tropical Research Institute and the Organization for Tropical Studies. Tropical research does not have the rapid change typical of medical research, and for this reason, the impact factor misses most of citations for the Revista, which are made after the two-year window used by the Web of Science. This issue is especially damaging for the Revista because most journals that deal with tropical biology are never checked when citations are counted for by the Science Citation Index.

Biological origins of color categorization.

Science.gov (United States)

Skelton, Alice E; Catchpole, Gemma; Abbott, Joshua T; Bosten, Jenny M; Franklin, Anna

2017-05-23

The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants' categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mapped infants' categorical recognition memory for hue onto a stimulus array used previously to document the color lexicons of 110 nonindustrialized languages. Following familiarization to a given hue, infants' response to a novel hue indicated that their recognition memory parses the hue continuum into red, yellow, green, blue, and purple categories. Infants' categorical distinctions aligned with common distinctions in color lexicons and are organized around hues that are commonly central to lexical categories across languages. The boundaries between infants' categorical distinctions also aligned, relative to the adaptation point, with the cardinal axes that describe the early stages of color representation in retinogeniculate pathways, indicating that infant color categorization may be partly organized by biological mechanisms of color vision. The findings suggest that color categorization in language and thought is partially biologically constrained and have implications for broader debate on how biology, culture, and communication interact in human cognition.

Fuzzy markup language for malware behavioral analysis

NARCIS (Netherlands)

Huang, H.-D.; Acampora, G.; Loia, V.; Lee, C.-S.; Hagras, H.; Wang, M.-H.; Kao, H.-Y.; Chang, J.-G.; Acampora, G.; Loia, V.; Lee, Ch.-Sh.; Wang, M.-H.

2013-01-01

In recent years, antimalware applications represented one of the most important research topics in the area of network security threat. In addition, malware have become a growing important problem for governments and commercial organizations. The key point of the research on the network security is

PERBANDINGAN ANTARA “BIG” WEB SERVICE DENGAN RESTFUL WEB SERVICE UNTUK INTEGRASI DATA BERFORMAT GML

Directory of Open Access Journals (Sweden)

Adi Nugroho

2012-01-01

Full Text Available Web Service with Java: SOAP (JAX-WS/Java API for XML Web Services and Java RESTful Web Service (JAX-RS/Java RESTful API for XML Web Services are now a technology competing with each other in terms of their use for integrates data residing in different systems. Both Web Service technologies, of course, have advantages and disadvantages. In this paper, we discuss the comparison of the two technologies is a Java Web Service in relation to the development of GIS application (Geographic Information System integrates the use of data-formatted GML (Geography Markup Language, which is stored in the system database XML (eXtensible Markup Language.

Implementing ATML in Distributed ATS for SG-III Prototype

International Nuclear Information System (INIS)

Chen Ming; Yang Cunbang; Lu Junfeng; Ding Yongkun; Yin Zejie; Zheng Zhijian

2007-01-01

With the forthcoming large-scale scientific experimental systems, we are looking for ways to construct an open, distributed architecture within the new and the existing automatic test systems. The new standard of Automatic Test Markup Language meets our demand for data exchange for this architecture through defining the test routines and resultant data in the XML format. This paper introduces the concept of ATML(Automatic Test Markup Language) and related standards, and the significance of these new standards for a distributed automatic test system. It also describes the implementation of ATML through the integration of this technology among the existing and new test systems

Teach Yourself VISUALLY HTML5

CERN Document Server

Wooldridge, Mike

2011-01-01

Make mark-up language more manageable with this visual guide HTML5 is the next-generation of web standard mark-up language, and among other things, it offers amazing new avenues for incorporating multimedia into your sites. What easier way to master all of HTML5's new bells and whistles than with a guide that shows you, screenshot by screenshot, just what to do? Over a hundred tasks that web designers need to know most are explained using, full-color screenshots and how-to steps. From the easy stuff like revised new header and footer elements to complex updates such as canvas and audio, this

Toward an interactive article: integrating journals and biological databases

Directory of Open Access Journals (Sweden)

Marygold Steven J

2011-05-01

Full Text Available Abstract Background Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. Results We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD and FlyBase, and has been implemented in marking up a paper with links to multiple databases. Conclusions Our semi-automated pipeline hyperlinks articles published in GENETICS to

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

Science.gov (United States)

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)

Multilingual Federated Searching Across Heterogeneous Collections.

Science.gov (United States)

Powell, James; Fox, Edward A.

1998-01-01

Describes a scalable system for searching heterogeneous multilingual collections on the World Wide Web. Details Searchable Database Markup Language (SearchDB-ML) for describing the characteristics of a search engine and its interface, and a protocol for requesting word translations between languages. (Author)

Mirror Neurons and the Evolution of Language

Science.gov (United States)

Corballis, Michael C.

2010-01-01

The mirror system provided a natural platform for the subsequent evolution of language. In nonhuman primates, the system provides for the understanding of biological action, and possibly for imitation, both prerequisites for language. I argue that language evolved from manual gestures, initially as a system of pantomime, but with gestures…

Modeling Coevolution between Language and Memory Capacity during Language Origin

Science.gov (United States)

Gong, Tao; Shuai, Lan

2015-01-01

Memory is essential to many cognitive tasks including language. Apart from empirical studies of memory effects on language acquisition and use, there lack sufficient evolutionary explorations on whether a high level of memory capacity is prerequisite for language and whether language origin could influence memory capacity. In line with evolutionary theories that natural selection refined language-related cognitive abilities, we advocated a coevolution scenario between language and memory capacity, which incorporated the genetic transmission of individual memory capacity, cultural transmission of idiolects, and natural and cultural selections on individual reproduction and language teaching. To illustrate the coevolution dynamics, we adopted a multi-agent computational model simulating the emergence of lexical items and simple syntax through iterated communications. Simulations showed that: along with the origin of a communal language, an initially-low memory capacity for acquired linguistic knowledge was boosted; and such coherent increase in linguistic understandability and memory capacities reflected a language-memory coevolution; and such coevolution stopped till memory capacities became sufficient for language communications. Statistical analyses revealed that the coevolution was realized mainly by natural selection based on individual communicative success in cultural transmissions. This work elaborated the biology-culture parallelism of language evolution, demonstrated the driving force of culturally-constituted factors for natural selection of individual cognitive abilities, and suggested that the degree difference in language-related cognitive abilities between humans and nonhuman animals could result from a coevolution with language. PMID:26544876

New Frontiers in Language Evolution and Development.

Science.gov (United States)

Oller, D Kimbrough; Dale, Rick; Griebel, Ulrike

2016-04-01

This article introduces the Special Issue and its focus on research in language evolution with emphasis on theory as well as computational and robotic modeling. A key theme is based on the growth of evolutionary developmental biology or evo-devo. The Special Issue consists of 13 articles organized in two sections: A) Theoretical foundations and B) Modeling and simulation studies. All the papers are interdisciplinary in nature, encompassing work in biological and linguistic foundations for the study of language evolution as well as a variety of computational and robotic modeling efforts shedding light on how language may be developed and may have evolved. Copyright © 2016 Cognitive Science Society, Inc.

Language, Thought, and Culture: Views and Arguments

Directory of Open Access Journals (Sweden)

Keyvan Zahedi

2009-07-01

Full Text Available This study follows two aims: one to review some late views on the relations among language, thought, and culture; and the other, to offer a new strategy, in a novel model, based on last achievements in the minimalist approach. Studying views and arguments, three dichotomies are discussed: 1 the views which confirm the relation between culture and language in opposition to the views that deny this; 2 distinguishing the symmetry-procedural view and the transforming views of language; and 3 distinction among the social-communicational, and the biological-genetic motivations of language. The hypothesis for the novel strategy is that considering what the minimalist program has offered, especially from 2000 onwards, it is possible that language affects thought, while coding the and that culture affects language (which is called ethno-grammar . This is in addition to the biological-genetic base. From this point of view, language’s main function is neither to provide communication, nor to express thought, but to connect cognitive and socio-cultural terminals together.

An Intranet for the Systems Management Curricular Office

National Research Council Canada - National Science Library

Morgan, Reece

1997-01-01

...), hypertext markup language (HTML) pages, and search engines. Many organizations are now using or building intranets to distribute, collect, and share timely, consistent, and accurate information...

A Google Earth Grand Tour of the Terrestrial Planets

Science.gov (United States)

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 Wonder Years" of XML.

Science.gov (United States)

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…

Bio-ecology and language: a necessary unity

DEFF Research Database (Denmark)

Cowley, Stephen

2014-01-01

-ecology. While shaped by discourse and beliefs about language-systems (and representations), the language and actions of human organism–environment systems change the world. As Garner (2004) argues, ecolinguistics can do more than invoke ‘interaction’ between language and ecology. While ‘realities’ are partly...... shared, much is biophysical. Living subjects link language and languaging with experience and technologies that have transformed the bio-ecology. Once these dynamics are subject to investigation, macrosocial issues can be reconnected with biological, human and linguistic concerns. Ecolinguistics can thus...

What Constitutes Successful Format Conversion? Towards a Formalization of 'Intellectual Content'

Directory of Open Access Journals (Sweden)

C. M. Sperberg-McQueen

2011-03-01

Full Text Available Recent work in the semantics of markup languages may offer a way to achieve more reliable results for format conversion, or at least a way to state the goal more explicitly. In the work discussed, the meaning of markup in a document is taken as the set of things accepted as true because of the markup's presence, or equivalently, as the set of inferences licensed by the markup in the document. It is possible, in principle, to apply a general semantic description of a markup vocabulary to documents encoded using that vocabulary and to generate a set of inferences (typically rather large, but finite as a result. An ideal format conversion translating a digital object from one vocabulary to another, then, can be characterized as one which neither adds nor drops any licensed inferences; it is possible to check this equivalence explicitly for a given conversion of a digital object, and possible in principle (although probably beyond current capabilities in practice to prove that a given transformation will, if given valid and semantically correct input, always produce output that is semantically equivalent to its input. This approach is directly applicable to the XML formats frequently used for scientific and other data, but it is also easily generalized from SGML/XML-based markup languages to digital formats in general; at a high level, it is equally applicable to document markup, to database exchanges, and to ad hoc formats for high-volume scientific data.Some obvious complications and technical difficulties arising from this approach are discussed, as are some important implications. In most real-world format conversions, the source and target formats differ at least somewhat in their ontology, either in the level of detail they cover or in the way they carve reality into classes; it is thus desirable not only to define what a perfect format conversion looks like, but to quantify the loss or distortion of information resulting from the conversion.

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

Science.gov (United States)

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

2017-06-24

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

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

Directory of Open Access Journals (Sweden)

Wei Tian

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

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

Science.gov (United States)

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

2016-01-01

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

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

Science.gov (United States)

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.

Three forms of assessment of prior knowledge, and improved performance following an enrichment programme, of English second language biology students within the context of a marine theme

Science.gov (United States)

Feltham, Nicola F.; Downs, Colleen T.

2002-02-01

The Science Foundation Programme (SFP) was launched in 1991 at the University of Natal, Pietermaritzburg, South Africa in an attempt to equip a selected number of matriculants from historically disadvantaged schools with the skills, resources and self-confidence needed to embark on their tertiary studies. Previous research within the SFP biology component suggests that a major contributor to poor achievement and low retention rates among English second language (ESL) students in the Life Sciences is the inadequate background knowledge in natural history. In this study, SFP student background knowledge was assessed along a continuum of language dependency using a set of three probes. Improved student performance in each of the respective assessments examined the extent to which a sound natural history background facilitated meaningful learning relative to ESL proficiency. Student profiles and attitudes to biology were also examined. Results indicated that students did not perceive language to be a problem in biology. However, analysis of the student performance in the assessment probes indicated that, although the marine course provided the students with the background knowledge that they were initially lacking, they continued to perform better in the drawing and MCQ tools in the post-tests, suggesting that it is their inability to express themselves in the written form that hampers their development. These results have implications for curriculum development within the constructivist framework of the SFP.

Enhancing transparent fuzzy controllers through temporal concepts : an application to computer games

NARCIS (Netherlands)

Acampora, G.; Loia, V.; Vitiello, A.

2010-01-01

In the last years, FML (Fuzzy Markup Language) is emerging as one of the most efficient and useful language to define a fuzzy control thanks to its capability of modeling Fuzzy Logic Controllers in a human-readable and hardware independent way, i.e. the so-called Transparent Fuzzy Controllers

76 FR 2677 - Request Facilities To Report Toxics Release Inventory Information Electronically or Complete Fill...

Science.gov (United States)

2011-01-14

... reflected by the generally increasing percentage of facilities that submit TRI reporting forms... ability to submit valid chemical data files from third party software using eXtensible Markup Language...

A Visual Language for Protein Design

KAUST Repository

Cox, Robert Sidney

2017-02-08

As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with easy-to draw glyphs, intended to be compatible with other biological diagram languages such as SBOL Visual and SBGN. Protein Language consists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams. To support Protein Language we have implemented an extensible web-based software diagram tool, Protein Designer, that uses Protein Language in a

A Visual Language for Protein Design

KAUST Repository

Cox, Robert Sidney; McLaughlin, James Alastair; Grunberg, Raik; Beal, Jacob; Wipat, Anil; Sauro, Herbert M.

2017-01-01

As protein engineering becomes more sophisticated, practitioners increasingly need to share diagrams for communicating protein designs. To this end, we present a draft visual language, Protein Language, that describes the high-level architecture of an engineered protein with easy-to draw glyphs, intended to be compatible with other biological diagram languages such as SBOL Visual and SBGN. Protein Language consists of glyphs for representing important features (e.g., globular domains, recognition and localization sequences, sites of covalent modification, cleavage and catalysis), rules for composing these glyphs to represent complex architectures, and rules constraining the scaling and styling of diagrams. To support Protein Language we have implemented an extensible web-based software diagram tool, Protein Designer, that uses Protein Language in a

XBRL: Beyond Basic XML

Science.gov (United States)

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…

BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language.

Science.gov (United States)

Rinaldi, Fabio; Ellendorff, Tilia Renate; Madan, Sumit; Clematide, Simon; van der Lek, Adrian; Mevissen, Theo; Fluck, Juliane

2016-01-01

Automatic extraction of biological network information is one of the most desired and most complex tasks in biological and medical text mining. Track 4 at BioCreative V attempts to approach this complexity using fragments of large-scale manually curated biological networks, represented in Biological Expression Language (BEL), as training and test data. BEL is an advanced knowledge representation format which has been designed to be both human readable and machine processable. The specific goal of track 4 was to evaluate text mining systems capable of automatically constructing BEL statements from given evidence text, and of retrieving evidence text for given BEL statements. Given the complexity of the task, we designed an evaluation methodology which gives credit to partially correct statements. We identified various levels of information expressed by BEL statements, such as entities, functions, relations, and introduced an evaluation framework which rewards systems capable of delivering useful BEL fragments at each of these levels. The aim of this evaluation method is to help identify the characteristics of the systems which, if combined, would be most useful for achieving the overall goal of automatically constructing causal biological networks from text. © The Author(s) 2016. Published by Oxford University Press.

Bibliography of Research in Natural Language Generation

Science.gov (United States)

1993-11-01

593], pages International Conference of the IEEE Engineer- 351-363. ing in Medicine and Biology Society, volume 3, pages 1347-1348, New Orleans, LA...Conference on Machine Translation of Languages and Applied [1218] Ingrid Zukerman. Koalas are not bears: Gener- Language Analysis. pages 66-80. Her

Issues in Scientific Terminology in African / Bantu Languages

OpenAIRE

Taljard , Elsabé

2007-01-01

In 2006, the South African Department of Education initiated a pilot project in which the Matric or Senior Certificate papers for Science, Maths, Biology and History were translated into the nine official African/Bantu languages of the country. Grade 12 learners who use these languages as home languages therefore received a question paper containing questions in English, where every question was followed by its translation into the relevant language. Taking into consideration that these learn...

Air Force Information Workflow Automation through Synchronized Air Power Management (SAPM)

National Research Council Canada - National Science Library

Benkley, Carl; Chang, Irene; Crowley, John; Oristian, Thomas

2004-01-01

.... Implementing Extensible Markup Language (XML) messages, web services, and workflow automation, SAPM expands existing web-based capabilities, enables machine-to-machine interfaces, and streamlines the war fighter kill chain process...

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

Science.gov (United States)

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.

IMPROVING THE INTEROPERABILITY OF DISASTER MODELS: A CASE STUDY OF PROPOSING FIREML FOR FOREST FIRE MODEL

Directory of Open Access Journals (Sweden)

W. Jiang

2018-04-01

Full Text Available 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.

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

Science.gov (United States)

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.

Diabetes mellitus: preliminary health-promotion activity based on ...

African Journals Online (AJOL)

2011-05-10

May 10, 2011 ... mark-up language (XML). For the analysis of the logged. XML, an interpreter was written in the Python® programming language to convert the raw logs into tables of responses that could be analysed statistically. The pharmacy students also prepared a poster, interactive models and a bilingual English and ...

PML:PAGE-OM Markup Language: About PAGE-OM [

Lifescience Database Archive (English)

Full Text Available he Object Management Group (OMG) standardization organization, and this was approved in 2006. The latest meeting... to continue this model development was held in Tokyo in September 2007. The meeting discussed extension...ation as well as modeling experimental results for associations between genotype and phenotype. The outcome of that meeting

Webscripter: End-User Tools for Composition Ontology-Enabled Web Services

National Research Council Canada - National Science Library

Frank, Martin

2005-01-01

... (schemes or ontologies) with respect to objects. The DARPA Agent Markup Language (DAML), through the use of ontologies, provides a very powerful way to describe objects and their relationships to other objects...

Core Semantics for Public Ontologies

National Research Council Canada - National Science Library

Suni, Niranjan

2005-01-01

... (schemas or ontologies) with respect to objects. The DARPA Agent Markup Language (DAML) through the use of ontologies provides a very powerful way to describe objects and their relationships to other objects...

Language structure is partly determined by social structure.

Directory of Open Access Journals (Sweden)

Gary Lupyan

Full Text Available BACKGROUND: Languages differ greatly both in their syntactic and morphological systems and in the social environments in which they exist. We challenge the view that language grammars are unrelated to social environments in which they are learned and used. METHODOLOGY/PRINCIPAL FINDINGS: We conducted a statistical analysis of >2,000 languages using a combination of demographic sources and the World Atlas of Language Structures--a database of structural language properties. We found strong relationships between linguistic factors related to morphological complexity, and demographic/socio-historical factors such as the number of language users, geographic spread, and degree of language contact. The analyses suggest that languages spoken by large groups have simpler inflectional morphology than languages spoken by smaller groups as measured on a variety of factors such as case systems and complexity of conjugations. Additionally, languages spoken by large groups are much more likely to use lexical strategies in place of inflectional morphology to encode evidentiality, negation, aspect, and possession. Our findings indicate that just as biological organisms are shaped by ecological niches, language structures appear to adapt to the environment (niche in which they are being learned and used. As adults learn a language, features that are difficult for them to acquire, are less likely to be passed on to subsequent learners. Languages used for communication in large groups that include adult learners appear to have been subjected to such selection. Conversely, the morphological complexity common to languages used in small groups increases redundancy which may facilitate language learning by infants. CONCLUSIONS/SIGNIFICANCE: We hypothesize that language structures are subjected to different evolutionary pressures in different social environments. Just as biological organisms are shaped by ecological niches, language structures appear to adapt to the

Emergence of communication in socio-biological networks

CERN Document Server

Berea, Anamaria

2018-01-01

This book integrates current advances in biology, economics of information and linguistics research through applications using agent-based modeling and social network analysis to develop scenarios of communication and language emergence in the social aspects of biological communications. The book presents a model of communication emergence that can be applied both to human and non-human living organism networks. The model is based on economic concepts and individual behavior fundamental for the study of trust and reputation networks in social science, particularly in economics; it is also based on the theory of the emergence of norms and historical path dependence that has been influential in institutional economics. Also included are mathematical models and code for agent-based models to explore various scenarios of language evolution, as well as a computer application that explores language and communication in biological versus social organisms, and the emergence of various meanings and grammars in human ...

NAEP Literacy Data: Students Deficient in Using Language. Why?

Science.gov (United States)

Williamson, Leon E.

Concerned with what can be done to help produce more thoughtful, critical readers, this report first presents an historical overview of theories on the origin of language, referring to B. F. Skinner, Noam Chomsky, and Jean Piaget, among others. It then discusses biological reasons for the evolution of language and the impact of verbal language on…

HDF-EOS Web Server

Science.gov (United States)

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.

On HTML and XML based web design and implementation techniques

International Nuclear Information System (INIS)

Bezboruah, B.; Kalita, M.

2006-05-01

Web implementation is truly a multidisciplinary field with influences from programming, choosing of scripting languages, graphic design, user interface design, and database design. The challenge of a Web designer/implementer is his ability to create an attractive and informative Web. To work with the universal framework and link diagrams from the design process as well as the Web specifications and domain information, it is essential to create Hypertext Markup Language (HTML) or other software and multimedia to accomplish the Web's objective. In this article we will discuss Web design standards and the techniques involved in Web implementation based on HTML and Extensible Markup Language (XML). We will also discuss the advantages and disadvantages of HTML over its successor XML in designing and implementing a Web. We have developed two Web pages, one utilizing the features of HTML and the other based on the features of XML to carry out the present investigation. (author)

XML DTD and Schemas for HDF-EOS

Science.gov (United States)

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.

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African Journals Online (AJOL)

pc

2018-03-05

Mar 5, 2018 ... embedded, extended with sensors or automated visual inspection. Keywords: ... influential for mobile as well as for manufacturing oriented. Robotic .... integration with web services and Internet of Things a markup language ...

Nassi-Schneiderman Diagram in HTML Based on AML

Science.gov (United States)

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…

Adding XML to the MIS Curriculum: Lessons from the Classroom

Science.gov (United States)

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"…

Applications of Natural Language Processing in Biodiversity Science

Directory of Open Access Journals (Sweden)

Anne E. Thessen

2012-01-01

A computer can handle the volume but cannot make sense of the language. This paper reviews and discusses the use of natural language processing (NLP and machine-learning algorithms to extract information from systematic literature. NLP algorithms have been used for decades, but require special development for application in the biological realm due to the special nature of the language. Many tools exist for biological information extraction (cellular processes, taxonomic names, and morphological characters, but none have been applied life wide and most still require testing and development. Progress has been made in developing algorithms for automated annotation of taxonomic text, identification of taxonomic names in text, and extraction of morphological character information from taxonomic descriptions. This manuscript will briefly discuss the key steps in applying information extraction tools to enhance biodiversity science.

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

Science.gov (United States)

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.

Cultural and climatic changes shape the evolutionary history of the Uralic languages.

Science.gov (United States)

Honkola, T; Vesakoski, O; Korhonen, K; Lehtinen, J; Syrjänen, K; Wahlberg, N

2013-06-01

Quantitative phylogenetic methods have been used to study the evolutionary relationships and divergence times of biological species, and recently, these have also been applied to linguistic data to elucidate the evolutionary history of language families. In biology, the factors driving macroevolutionary processes are assumed to be either mainly biotic (the Red Queen model) or mainly abiotic (the Court Jester model) or a combination of both. The applicability of these models is assumed to depend on the temporal and spatial scale observed as biotic factors act on species divergence faster and in smaller spatial scale than the abiotic factors. Here, we used the Uralic language family to investigate whether both 'biotic' interactions (i.e. cultural interactions) and abiotic changes (i.e. climatic fluctuations) are also connected to language diversification. We estimated the times of divergence using Bayesian phylogenetics with a relaxed-clock method and related our results to climatic, historical and archaeological information. Our timing results paralleled the previous linguistic studies but suggested a later divergence of Finno-Ugric, Finnic and Saami languages. Some of the divergences co-occurred with climatic fluctuation and some with cultural interaction and migrations of populations. Thus, we suggest that both 'biotic' and abiotic factors contribute either directly or indirectly to the diversification of languages and that both models can be applied when studying language evolution. © 2013 The Authors. Journal of Evolutionary Biology © 2013 European Society For Evolutionary Biology.

Introduction to Beautiful Soup

Directory of Open Access Journals (Sweden)

Jeri Wieringa

2012-12-01

Full Text Available Beautiful Soup is a Python library for getting data out of HTML, XML, and other markup languages. Say you’ve found some webpages that display data relevant to your research, such as date or address information, but that do not provide any way of downloading the data directly. Beautiful Soup helps you pull particular content from a webpage, remove the HTML markup, and save the information. It is a tool for web scraping that helps you clean up and parse the documents you have pulled down from the web.

Introduction to Beautiful Soup

OpenAIRE

Jeri Wieringa

2012-01-01

Beautiful Soup is a Python library for getting data out of HTML, XML, and other markup languages. Say you’ve found some webpages that display data relevant to your research, such as date or address information, but that do not provide any way of downloading the data directly. Beautiful Soup helps you pull particular content from a webpage, remove the HTML markup, and save the information. It is a tool for web scraping that helps you clean up and parse the documents you have pulled down from t...

JSBML: a flexible Java library for working with SBML.

Science.gov (United States)

Dräger, Andreas; Rodriguez, Nicolas; Dumousseau, Marine; Dörr, Alexander; Wrzodek, Clemens; Le Novère, Nicolas; Zell, Andreas; Hucka, Michael

2011-08-01

The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version 1, and we have strived to maintain the highest possible degree of compatibility with the popular library libSBML. JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend. Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML.

The sound symbolism bootstrapping hypothesis for language acquisition and language evolution.

Science.gov (United States)

Imai, Mutsumi; Kita, Sotaro

2014-09-19

Sound symbolism is a non-arbitrary relationship between speech sounds and meaning. We review evidence that, contrary to the traditional view in linguistics, sound symbolism is an important design feature of language, which affects online processing of language, and most importantly, language acquisition. We propose the sound symbolism bootstrapping hypothesis, claiming that (i) pre-verbal infants are sensitive to sound symbolism, due to a biologically endowed ability to map and integrate multi-modal input, (ii) sound symbolism helps infants gain referential insight for speech sounds, (iii) sound symbolism helps infants and toddlers associate speech sounds with their referents to establish a lexical representation and (iv) sound symbolism helps toddlers learn words by allowing them to focus on referents embedded in a complex scene, alleviating Quine's problem. We further explore the possibility that sound symbolism is deeply related to language evolution, drawing the parallel between historical development of language across generations and ontogenetic development within individuals. Finally, we suggest that sound symbolism bootstrapping is a part of a more general phenomenon of bootstrapping by means of iconic representations, drawing on similarities and close behavioural links between sound symbolism and speech-accompanying iconic gesture. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications.

Science.gov (United States)

Khomtchouk, Bohdan B; Weitz, Edmund; Karp, Peter D; Wahlestedt, Claes

2016-12-31

We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research. Put simply, Lisp-family languages enable programmers to more quickly write programs that run faster than in other languages. Languages such as Common Lisp, Scheme and Clojure facilitate the creation of powerful and flexible software that is required for complex and rapidly evolving domains like biology. We will point out several important key features that distinguish languages of the Lisp family from other programming languages, and we will explain how these features can aid researchers in becoming more productive and creating better code. We will also show how these features make these languages ideal tools for artificial intelligence and machine learning applications. We will specifically stress the advantages of domain-specific languages (DSLs): languages that are specialized to a particular area, and thus not only facilitate easier research problem formulation, but also aid in the establishment of standards and best programming practices as applied to the specific research field at hand. DSLs are particularly easy to build in Common Lisp, the most comprehensive Lisp dialect, which is commonly referred to as the 'programmable programming language'. We are convinced that Lisp grants programmers unprecedented power to build increasingly sophisticated artificial intelligence systems that may ultimately transform machine learning and artificial intelligence research in bioinformatics and computational biology. © The Author 2016. Published by Oxford University Press.

THE NORMALIZATION OF FINANCIAL DATA EXCHANGE OVER THE INTERNET: ADOPTING INTERNATIONAL STANDARD XBRL

Directory of Open Access Journals (Sweden)

Catalin Georgel Tudor

2009-05-01

Full Text Available The development of a common syntax for EDI (Electronic Data Interchange, XML (eXtensible Markup Language, opened new formalization perspectives for interorganizational data exchanges over the Internet. Many of the organizations involved in the normaliza

The XML approach to implementing space link extension service management

Science.gov (United States)

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.

Principles of parametric estimation in modeling language competition.

Science.gov (United States)

Zhang, Menghan; Gong, Tao

2013-06-11

It is generally difficult to define reasonable parameters and interpret their values in mathematical models of social phenomena. Rather than directly fitting abstract parameters against empirical data, we should define some concrete parameters to denote the sociocultural factors relevant for particular phenomena, and compute the values of these parameters based upon the corresponding empirical data. Taking the example of modeling studies of language competition, we propose a language diffusion principle and two language inheritance principles to compute two critical parameters, namely the impacts and inheritance rates of competing languages, in our language competition model derived from the Lotka-Volterra competition model in evolutionary biology. These principles assign explicit sociolinguistic meanings to those parameters and calculate their values from the relevant data of population censuses and language surveys. Using four examples of language competition, we illustrate that our language competition model with thus-estimated parameter values can reliably replicate and predict the dynamics of language competition, and it is especially useful in cases lacking direct competition data.

Graphical abstract - AT Atlas | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available ML (Cell System Markup Language), see also the CSML website. CSML files may be graphically viewed on Cell Il.... For these pieces of software, see also the Cell Illustrator website or the Cell Illustrator Online web

Biolinguistics or Physicolinguistics? Is the Third Factor Helpful or Harmful in Explaining Language?

Directory of Open Access Journals (Sweden)

Sverker Johansson

2013-10-01

Full Text Available Noam Chomsky (2005 proposed that a ‘third factor’, consisting of general principles and natural laws, may explain core properties of language in a principled manner, minimizing the need for either genetic endowment or experience. But the focus on third-factor patterns in much recent bio-linguistic work is misguided for several reasons: First, ‘the’ third factor is a vague and disparate collection of unrelated components, useless as an analytical tool. Second, the vagueness of the third factor, together with the desire for principled explanations, too often leads to sweeping claims, such as syntax “coming for free, directly from physics”, that are unwarranted without a case-by-case causal analysis. Third, attention is diverted away from a proper causal analysis of language as a biological feature. The point with biolinguistics is to acknowledge the language faculty as a biological feature. The best way forward towards an understanding of language is to take the biology connection seriously, instead of dabbling with physics.

PSL Chemical Biology Symposia First 2016 Edition: When Chemistry and Biology Share the Language of Discovery.

Science.gov (United States)

Gautier, Arnaud; Rodriguez, Raphaël

2017-05-18

Chemical biology, the science of understanding biological processes at the molecular level, has grown exponentially with the development of chemical strategies to manipulate and quantify biology with unprecedented precision. Recent advances presented at the Université Paris Sciences et Lettres symposium are discussed. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

HTML 5 up and running

CERN Document Server

Pilgrim, Mark

2010-01-01

If you don't know about the new features available in HTML5, now's the time to find out. This book provides practical information about how and why the latest version of this markup language will significantly change the way you develop for the Web. HTML5 is still evolving, yet browsers such as Safari, Mozilla, Opera, and Chrome already support many of its features -- and mobile browsers are even farther ahead. HTML5: Up & Running carefully guides you though the important changes in this version with lots of hands-on examples, including markup, graphics, and screenshots. You'll learn how to

Biological origins of color categorization

OpenAIRE

Skelton, Alice E.; Catchpole, Gemma; Abbott, Joshua T.; Bosten, Jenny M.; Franklin, Anna

2017-01-01

The biological basis of the commonality in color lexicons across languages has been hotly debated for decades. Prior evidence that infants categorize color could provide support for the hypothesis that color categorization systems are not purely constructed by communication and culture. Here, we investigate the relationship between infants’ categorization of color and the commonality across color lexicons, and the potential biological origin of infant color categories. We systematically mappe...

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

Science.gov (United States)

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.

Impact of specific language impairment and type of school on different language subsystems.

Science.gov (United States)

Puglisi, Marina Leite; Befi-Lopes, Debora Maria

2016-01-01

This study aimed to explore quantitative and qualitative effects of type of school and specific language impairment (SLI) on different language abilities. 204 Brazilian children aged from 4 to 6 years old participated in the study. Children were selected to form three groups: 1) 63 typically developing children studying in private schools (TDPri); 2) 102 typically developing children studying in state schools (TDSta); and 39 children with SLI studying in state schools (SLISta). All individuals were assessed regarding expressive vocabulary, number morphology and morphosyntactic comprehension. All language subsystems were vulnerable to both environmental (type of school) and biological (SLI) effects. The relationship between the three language measures was exactly the same to all groups: vocabulary growth correlated with age and with the development of morphological abilities and morphosyntactic comprehension. Children with SLI showed atypical errors in the comprehension test at the age of 4, but presented a pattern of errors that gradually resembled typical development. The effect of type of school was marked by quantitative differences, while the effect of SLI was characterised by both quantitative and qualitative differences.

DESENVOLVIMENTO DE UM SIMULADOR DE DIÁLOGO UTILIZANDO A LINGUAGEM AIML COM BANCO DE DADOS

Directory of Open Access Journals (Sweden)

André Damasceno Aoki

2011-12-01

Full Text Available This paper presents an application to simulate dialogues (chatterbot using the AIML language (Artificial Intelligence Markup Language with a new functionality to provide dynamic answers to database queries. This kind of applications is used to answer questions or doubts that are asked by people. Traditional systems are based in fixed answers using AIML language and they search answers in knowledge bases that offer low maintainability, compromising responses that require periodic updates. The AIML language has been extended to be applied to a greater source of knowledge (database.

A systematic review of context bias in invasion biology.

Directory of Open Access Journals (Sweden)

Robert J Warren

Full Text Available The language that scientists use to frame biological invasions may reveal inherent bias-including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.

A systematic review of context bias in invasion biology.

Science.gov (United States)

Warren, Robert J; King, Joshua R; Tarsa, Charlene; Haas, Brian; Henderson, Jeremy

2017-01-01

The language that scientists use to frame biological invasions may reveal inherent bias-including how data are interpreted. A frequent critique of invasion biology is the use of value-laden language that may indicate context bias. Here we use a systematic study of language and interpretation in papers drawn from invasion biology to evaluate whether there is a link between the framing of papers and the interpretation of results. We also examine any trends in context bias in biological invasion research. We examined 651 peer-reviewed invasive species competition studies and implemented a rigorous systematic review to examine bias in the presentation and interpretation of native and invasive competition in invasion biology. We predicted that bias in the presentation of invasive species is increasing, as suggested by several authors, and that bias against invasive species would result in misinterpreting their competitive dominance in correlational observational studies compared to causative experimental studies. We indeed found evidence of bias in the presentation and interpretation of invasive species research; authors often introduced research with invasive species in a negative context and study results were interpreted against invasive species more in correlational studies. However, we also found a distinct decrease in those biases since the mid-2000s. Given that there have been several waves of criticism from scientists both inside and outside invasion biology, our evidence suggests that the subdiscipline has somewhat self-corrected apparent biases.

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

Science.gov (United States)

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.

THE DESCENT OF LANGUAGE. A CONVERSATION BETWEEN TWO JOBLESS BIOLOGISTS

Directory of Open Access Journals (Sweden)

D'Angelo Giovanni

2013-12-01

Full Text Available Seen from the perspective of a biologist, the issue of the origin of language contains an inherent ambiguity. On the one hand, one might think to explore the cognitive features or even the anatomical structures related to communication through the peculiar medium called verbal language, a characteristic property emergent among the Homo sapiens. On the other hand, if one decides to restrict oneself to the formal definition of language as a system of signs for encoding information, then, the human-specific nature of language becomes less convincing and the temptation to look into non-human languages allows a provocative question. Was human verbal language an invention or a discovery? In the following two biologists informally discuss about the concept of non-verbal biological languages.

A comparison of biological and cultural evolution.

Science.gov (United States)

Portin, Petter

2015-03-01

This review begins with a definition of biological evolution and a description of its general principles. This is followed by a presentation of the biological basis of culture, specifically the concept of social selection. Further, conditions for cultural evolution are proposed, including a suggestion for language being the cultural replicator corresponding to the concept of the gene in biological evolution. Principles of cultural evolution are put forward and compared to the principles of biological evolution. Special emphasis is laid on the principle of selection in cultural evolution, including presentation of the concept of cultural fitness. The importance of language as a necessary condition for cultural evolution is stressed. Subsequently, prime differences between biological and cultural evolution are presented, followed by a discussion on interaction of our genome and our culture. The review aims at contributing to the present discussion concerning the modern development of the general theory of evolution, for example by giving a tentative formulation of the necessary and sufficient conditions for cultural evolution, and proposing that human creativity and mind reading or theory of mind are motors specific for it. The paper ends with the notion of the still ongoing coevolution of genes and culture.

How will XML impact industrial automation?

CERN Multimedia

Pinceti, P

2002-01-01

A working group of the World Wide Web Consortium (W3C) has overcome the limits of both HTML and SGML with the definition of the extensible markup language - XML. This article looks at how XML will affect industrial automation (2 pages).

The Processing of Biologically Plausible and Implausible forms in American Sign Language: Evidence for Perceptual Tuning.

Science.gov (United States)

Almeida, Diogo; Poeppel, David; Corina, David

The human auditory system distinguishes speech-like information from general auditory signals in a remarkably fast and efficient way. Combining psychophysics and neurophysiology (MEG), we demonstrate a similar result for the processing of visual information used for language communication in users of sign languages. We demonstrate that the earliest visual cortical responses in deaf signers viewing American Sign Language (ASL) signs show specific modulations to violations of anatomic constraints that would make the sign either possible or impossible to articulate. These neural data are accompanied with a significantly increased perceptual sensitivity to the anatomical incongruity. The differential effects in the early visual evoked potentials arguably reflect an expectation-driven assessment of somatic representational integrity, suggesting that language experience and/or auditory deprivation may shape the neuronal mechanisms underlying the analysis of complex human form. The data demonstrate that the perceptual tuning that underlies the discrimination of language and non-language information is not limited to spoken languages but extends to languages expressed in the visual modality.

Synthetic Biology Open Language Visual (SBOL Visual) Version 2.0

KAUST Repository

Cox, Robert Sidney; Madsen, Curtis; McLaughlin, James; Nguyen, Tramy; Roehner, Nicholas; Bartley, Bryan; Bhatia, Swapnil; Bissell, Mike; Clancy, Kevin; Gorochowski, Thomas; Grunberg, Raik; Luna, Augustin; Le Novè re, Nicolas; Pocock, Matthew; Sauro, Herbert; Sexton, John T.; Stan, Guy-Bart; Tabor, Jeffrey J.; Voigt, Christopher A.; Zundel, Zach; Myers, Chris; Beal, Jacob; Wipat, Anil

2018-01-01

to produce a coherent language for expressing the structure and function of genetic designs. This document details version 2.0 of SBOL Visual, which builds on the prior SBOL Visual 1.0 standard by expanding diagram syntax to include functional interactions

Simulation for competition of languages with an ageing sexual population

OpenAIRE

Schwämmle, Veit

2005-01-01

Recently, individual-based models originally used for biological purposes revealed interesting insights into processes of the competition of languages. Within this new field of population dynamics a model considering sexual populations with ageing is presented. The agents are situated on a lattice and each one speaks one of two languages or both. The stability and quantitative structure of an interface between two regions, initially speaking different languages, is studied. We find that indiv...

ADASS Web Database XML Project

Science.gov (United States)

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.

Converting biomolecular modelling data based on an XML representation.

Science.gov (United States)

Sun, Yudong; McKeever, Steve

2008-08-25

Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language). BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

MOCCASIN: converting MATLAB ODE models to SBML.

Science.gov (United States)

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.

Converting Biomolecular Modelling Data Based on an XML Representation

Directory of Open Access Journals (Sweden)

Sun Yudong

2008-06-01

Full Text Available Biomolecular modelling has provided computational simulation based methods for investigating biological processes from quantum chemical to cellular levels. Modelling such microscopic processes requires atomic description of a biological system and conducts in fine timesteps. Consequently the simulations are extremely computationally demanding. To tackle this limitation, different biomolecular models have to be integrated in order to achieve high-performance simulations. The integration of diverse biomolecular models needs to convert molecular data between different data representations of different models. This data conversion is often non-trivial, requires extensive human input and is inevitably error prone. In this paper we present an automated data conversion method for biomolecular simulations between molecular dynamics and quantum mechanics/molecular mechanics models. Our approach is developed around an XML data representation called BioSimML (Biomolecular Simulation Markup Language. BioSimML provides a domain specific data representation for biomolecular modelling which can effciently support data interoperability between different biomolecular simulation models and data formats.

Social interaction, languaging and the operational conditions for the emergence of observing.

Science.gov (United States)

Raimondi, Vincenzo

2014-01-01

In order to adequately understand the foundations of human social interaction, we need to provide an explanation of our specific mode of living based on linguistic activity and the cultural practices with which it is interwoven. To this end, we need to make explicit the constitutive conditions for the emergence of the phenomena which relate to language and joint activity starting from their operational-relational matrix. The approach presented here challenges the inadequacy of mentalist models to explain the relation between language and interaction. Recent empirical studies concerning joint attention and language acquisition have led scholars such as Tomasello et al. (2005) to postulate the existence of a universal human "sociocognitive infrastructure" that drives joint social activities and is biologically inherited. This infrastructure would include the skill of precocious intention-reading, and is meant to explain human linguistic development and cultural learning. However, the cognitivist and functionalist assumptions on which this model relies have resulted in controversial hypotheses (i.e., intention-reading as the ontogenetic precursor of language) which take a contentious conception of mind and language for granted. By challenging this model, I will show that we should instead turn ourselves towards a constitutive explanation of language within a "bio-logical" understanding of interactivity. This is possible only by abandoning the cognitivist conception of organism and traditional views of language. An epistemological shift must therefore be proposed, based on embodied, enactive and distributed approaches, and on Maturana's work in particular. The notions of languaging and observing that will be discussed in this article will allow for a bio-logically grounded, theoretically parsimonious alternative to mentalist and spectatorial approaches, and will guide us towards a wider understanding of our sociocultural mode of living.

Social interaction, languaging and the operational conditions for the emergence of observing

Directory of Open Access Journals (Sweden)

Vincenzo eRaimondi

2014-08-01

Full Text Available In order to adequately understand the foundations of human social interaction, we need to provide an explanation of our specific mode of living based on linguistic activity and the cultural practices with which it is interwoven. To this end, we need to make explicit the constitutive conditions for the emergence of the phenomena which relate to language and joint activity starting from their operational-relational matrix. The approach presented here challenges the inadequacy of mentalist models to explain the relation between language and interaction. Recent empirical studies concerning joint attention and language acquisition have led scholars such as Tomasello and his colleagues to postulate the existence of a universal human sociocognitive infrastructure that drives joint social activities and is biologically inherited. This infrastructure would include the skill of precocious intention-reading, and is meant to explain human linguistic development and cultural learning. However, the cognitivist and functionalist assumptions on which this model relies have resulted in controversial hypotheses (i.e., intention-reading as the ontogenetic precursor of language which take a contentious conception of mind and language for granted. By challenging this model, I will show that we should instead turn ourselves towards a constitutive explanation of language within a bio-logical understanding of interactivity. This is possible only by abandoning the cognitivist conception of organism and traditional views of language. An epistemological shift must therefore be proposed, based on embodied, enactive and distributed approaches, and on Maturana’s work in particular. The notions of languaging and observing that will be discussed in this article will allow for a bio-logically grounded, theoretically parsimonious alternative to mentalist and spectatorial approaches, and will guide us towards a wider understanding of our sociocultural mode of living.

Q&A: What is human language, when did it evolve and why should we care?

OpenAIRE

Pagel, Mark

2017-01-01

Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign 'language' in Great Apes is nothing like human language. Language evolution shares many features with biological evolution, and this has made it useful for tracing recent human history and for studying how culture evolves among groups of people with related languages. A case can be made that languag...

Capital Markets and E-fraud Policy Note and Concept Paper for Future Study

OpenAIRE

Kellermann, Tom; McNevin, Valerie

2005-01-01

The technological dependency of securities exchanges on internet-based (IP) platforms has dramatically increased the industry's exposure to reputation, market, and operational risks. In addition, the convergence of several innovations in the market are adding stress to these systems. These innovations affect everything from software to system design and architecture. These include the use of XML (extensible markup language) as the industry IP language, STP or straight through processing of da...

Performance analysis of Java APIS for XML processing

OpenAIRE

Oliveira, Bruno; Santos, Vasco; Belo, Orlando

2013-01-01

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, such as ...

Processing XML with Java – a performance benchmark

OpenAIRE

Oliveira, Bruno; Santos, Vasco; Belo, Orlando

2013-01-01

Over time, XML markup language has acquired a considerable importance in applications development, standards definition and in the representation of large volumes of data, such as databases. Today, processing XML documents in a short period of time is a critical activity in a large range of applications, which imposes choosing the most appropriate mechanism to parse XML documents quickly and efficiently. When using a programming language for XML processing, suc...

Standard biological parts knowledgebase.

Directory of Open Access Journals (Sweden)

Michal Galdzicki

2011-02-01

Full Text Available We have created the Knowledgebase of Standard Biological Parts (SBPkb as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org. The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org. SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL, a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

Standard Biological Parts Knowledgebase

Science.gov (United States)

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M.; Gennari, John H.

2011-01-01

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate “promoter” parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible. PMID:21390321

Standard biological parts knowledgebase.

Science.gov (United States)

Galdzicki, Michal; Rodriguez, Cesar; Chandran, Deepak; Sauro, Herbert M; Gennari, John H

2011-02-24

We have created the Knowledgebase of Standard Biological Parts (SBPkb) as a publically accessible Semantic Web resource for synthetic biology (sbolstandard.org). The SBPkb allows researchers to query and retrieve standard biological parts for research and use in synthetic biology. Its initial version includes all of the information about parts stored in the Registry of Standard Biological Parts (partsregistry.org). SBPkb transforms this information so that it is computable, using our semantic framework for synthetic biology parts. This framework, known as SBOL-semantic, was built as part of the Synthetic Biology Open Language (SBOL), a project of the Synthetic Biology Data Exchange Group. SBOL-semantic represents commonly used synthetic biology entities, and its purpose is to improve the distribution and exchange of descriptions of biological parts. In this paper, we describe the data, our methods for transformation to SBPkb, and finally, we demonstrate the value of our knowledgebase with a set of sample queries. We use RDF technology and SPARQL queries to retrieve candidate "promoter" parts that are known to be both negatively and positively regulated. This method provides new web based data access to perform searches for parts that are not currently possible.

ASPASIA: A toolkit for evaluating the effects of biological interventions on SBML model behaviour.

Science.gov (United States)

Evans, Stephanie; Alden, Kieran; Cucurull-Sanchez, Lourdes; Larminie, Christopher; Coles, Mark C; Kullberg, Marika C; Timmis, Jon

2017-02-01

A calibrated computational model reflects behaviours that are expected or observed in a complex system, providing a baseline upon which sensitivity analysis techniques can be used to analyse pathways that may impact model responses. However, calibration of a model where a behaviour depends on an intervention introduced after a defined time point is difficult, as model responses may be dependent on the conditions at the time the intervention is applied. We present ASPASIA (Automated Simulation Parameter Alteration and SensItivity Analysis), a cross-platform, open-source Java toolkit that addresses a key deficiency in software tools for understanding the impact an intervention has on system behaviour for models specified in Systems Biology Markup Language (SBML). ASPASIA can generate and modify models using SBML solver output as an initial parameter set, allowing interventions to be applied once a steady state has been reached. Additionally, multiple SBML models can be generated where a subset of parameter values are perturbed using local and global sensitivity analysis techniques, revealing the model's sensitivity to the intervention. To illustrate the capabilities of ASPASIA, we demonstrate how this tool has generated novel hypotheses regarding the mechanisms by which Th17-cell plasticity may be controlled in vivo. By using ASPASIA in conjunction with an SBML model of Th17-cell polarisation, we predict that promotion of the Th1-associated transcription factor T-bet, rather than inhibition of the Th17-associated transcription factor RORγt, is sufficient to drive switching of Th17 cells towards an IFN-γ-producing phenotype. Our approach can be applied to all SBML-encoded models to predict the effect that intervention strategies have on system behaviour. ASPASIA, released under the Artistic License (2.0), can be downloaded from http://www.york.ac.uk/ycil/software.

Syntactic priming in American Sign Language.

Science.gov (United States)

Hall, Matthew L; Ferreira, Victor S; Mayberry, Rachel I

2015-01-01

Psycholinguistic studies of sign language processing provide valuable opportunities to assess whether language phenomena, which are primarily studied in spoken language, are fundamentally shaped by peripheral biology. For example, we know that when given a choice between two syntactically permissible ways to express the same proposition, speakers tend to choose structures that were recently used, a phenomenon known as syntactic priming. Here, we report two experiments testing syntactic priming of a noun phrase construction in American Sign Language (ASL). Experiment 1 shows that second language (L2) signers with normal hearing exhibit syntactic priming in ASL and that priming is stronger when the head noun is repeated between prime and target (the lexical boost effect). Experiment 2 shows that syntactic priming is equally strong among deaf native L1 signers, deaf late L1 learners, and hearing L2 signers. Experiment 2 also tested for, but did not find evidence of, phonological or semantic boosts to syntactic priming in ASL. These results show that despite the profound differences between spoken and signed languages in terms of how they are produced and perceived, the psychological representation of sentence structure (as assessed by syntactic priming) operates similarly in sign and speech.

Developing Intranets: Practical Issues for Implementation and Design.

Science.gov (United States)

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,…

CMD2RDF: Building a Bridge from CLARIN to Linked Open Data

NARCIS (Netherlands)

Windhouwer, M.; Indarto, E.; Broeder, D.; Odijk, Jan; Van Hessen, Arjan

2017-01-01

Metadata can be represented in many different ways. CLARIN’s Component Metadata Infrastructure (CMDI) uses the eXtensible Markup Language (XML) as the representation format for metadata records. However, the Resource Description Format (RDF) as used by Linked Open Data (LOD) is gaining more

Indoor Multi-Dimensional Location GML and Its Application for Ubiquitous Indoor Location Services

NARCIS (Netherlands)

Zhu, Qing; Li, Yun; Xiong, Qing; Zlatanova, S.; Ding, Yulin; Zhang, Yeting; Zhou, Yan

2016-01-01

The Open Geospatial Consortium (OGC) Geography Markup Language (GML) standard provides basic types and a framework for defining geo-informational data models such as CityGML and IndoorGML, which provide standard information models for 3D city modelling and lightweight indoor network navigation.

77 FR 20835 - National Customs Automation Program (NCAP) Test Concerning Automated Commercial Environment (ACE...

Science.gov (United States)

2012-04-06

... Interchange (EDI). This notice also describes test particulars including commencement date, eligibility... Electronic Data Interchange (EDI) as part of the Document Image System (DIS) test. DIS is currently a stand... with supporting information via EDI in an Extensible Markup Language (XML) format, in lieu of...

Cornerstone: Foundational Models and Services for Integrated Battle Planning

Science.gov (United States)

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

Modeling biochemical transformation processes and information processing with Narrator.

Science.gov (United States)

Mandel, Johannes J; Fuss, Hendrik; Palfreyman, Niall M; Dubitzky, Werner

2007-03-27

Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs), which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Narrator is a flexible and intuitive systems biology tool. It is

CWRML: representing crop wild relative conservation and use data in XML.

Science.gov (United States)

Moore, Jonathan D; Kell, Shelagh P; Iriondo, Jose M; Ford-Lloyd, Brian V; Maxted, Nigel

2008-02-25

Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange. Crop Wild Relative Markup Language (CWRML) was developed to represent the data necessary for crop wild relative conservation and ensure that they can be effectively utilised for crop improvement. The schema partitions data into taxon-, site-, and population-specific elements, to allow for integration with other more general conservation biology schemata which may emerge as accepted standards in the future. These elements are composed of sub-elements, which are structured in order to facilitate the use of the schema in a variety of crop wild relative conservation and use contexts. Pre-existing standards for data representation in conservation biology were reviewed and incorporated into the schema as restrictions on element data contents, where appropriate. CWRML provides a flexible data communication format for representing in situ and ex situ conservation status of individual taxa as well as their utilisation potential. The development of the schema highlights a number of instances where additional standards-development may

Biological data integration: wrapping data and tools.

Science.gov (United States)

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.

Co-occurrence of linguistic and biological diversity in biodiversity hotspots and high biodiversity wilderness areas.

Science.gov (United States)

Gorenflo, L J; Romaine, Suzanne; Mittermeier, Russell A; Walker-Painemilla, Kristen

2012-05-22

As the world grows less biologically diverse, it is becoming less linguistically and culturally diverse as well. Biologists estimate annual loss of species at 1,000 times or more greater than historic rates, and linguists predict that 50-90% of the world's languages will disappear by the end of this century. Prior studies indicate similarities in the geographic arrangement of biological and linguistic diversity, although conclusions have often been constrained by use of data with limited spatial precision. Here we use greatly improved datasets to explore the co-occurrence of linguistic and biological diversity in regions containing many of the Earth's remaining species: biodiversity hotspots and high biodiversity wilderness areas. Results indicate that these regions often contain considerable linguistic diversity, accounting for 70% of all languages on Earth. Moreover, the languages involved are frequently unique (endemic) to particular regions, with many facing extinction. Likely reasons for co-occurrence of linguistic and biological diversity are complex and appear to vary among localities, although strong geographic concordance between biological and linguistic diversity in many areas argues for some form of functional connection. Languages in high biodiversity regions also often co-occur with one or more specific conservation priorities, here defined as endangered species and protected areas, marking particular localities important for maintaining both forms of diversity. The results reported in this article provide a starting point for focused research exploring the relationship between biological and linguistic-cultural diversity, and for developing integrated strategies designed to conserve species and languages in regions rich in both.

Rosen's (M,R) system in Unified Modelling Language.

Science.gov (United States)

Zhang, Ling; Williams, Richard A; Gatherer, Derek

2016-01-01

Robert Rosen's (M,R) system is an abstract biological network architecture that is allegedly non-computable on a Turing machine. If (M,R) is truly non-computable, there are serious implications for the modelling of large biological networks in computer software. A body of work has now accumulated addressing Rosen's claim concerning (M,R) by attempting to instantiate it in various software systems. However, a conclusive refutation has remained elusive, principally since none of the attempts to date have unambiguously avoided the critique that they have altered the properties of (M,R) in the coding process, producing merely approximate simulations of (M,R) rather than true computational models. In this paper, we use the Unified Modelling Language (UML), a diagrammatic notation standard, to express (M,R) as a system of objects having attributes, functions and relations. We believe that this instantiates (M,R) in such a way than none of the original properties of the system are corrupted in the process. Crucially, we demonstrate that (M,R) as classically represented in the relational biology literature is implicitly a UML communication diagram. Furthermore, since UML is formally compatible with object-oriented computing languages, instantiation of (M,R) in UML strongly implies its computability in object-oriented coding languages. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Formal analysis of XACML policies using SMT

NARCIS (Netherlands)

Turkmen, F.; den Hartog, J.; Ranise, S.; Zannone, N.

2017-01-01

The eXtensible Access Control Markup Language (XACML) has attracted significant attention from both industry and academia, and has become the de facto standard for the specification of access control policies. However, its XML-based verbose syntax and rich set of constructs make the authoring of

Utilizing Structural Knowledge for Information Retrieval in XML Databases

NARCIS (Netherlands)

Mihajlovic, V.; Hiemstra, Djoerd; Blok, H.E.; Apers, Peter M.G.

In this paper we address the problem of immediate translation of eXtensible Mark-up Language (XML) information retrieval (IR) queries to relational database expressions and stress the benefits of using an intermediate XML-specific algebra over relational algebra. We show how adding an XML-specific

Modeling views in the layered view model for XML using UML

NARCIS (Netherlands)

Rajugan, R.; Dillon, T.S.; Chang, E.; Feng, L.

In data engineering, view formalisms are used to provide flexibility to users and user applications by allowing them to extract and elaborate data from the stored data sources. Conversely, since the introduction of Extensible Markup Language (XML), it is fast emerging as the dominant standard for

Relational Data Modelling of Textual Corpora: The Skaldic Project and its Extensions

DEFF Research Database (Denmark)

Wills, Tarrin Jon

2015-01-01

Skaldic poetry is a highly complex textual phenomenon both in terms of the intricacy of the poetry and its contextual environment. Extensible Markup Language (XML) applications such as that of the Text Encoding Initiative provide a means of semantic representation of some of these complexities. XML...

78 FR 46005 - NPDES Electronic Reporting Rule

Science.gov (United States)

2013-07-30

.... B. Does this action apply to me? Entities potentially affected by this action would include all... Compliance System (ICIS-NPDES) is the transmission of eXtensible Markup Language (XML) data files through a... system that allocates points against various factors including flow, pollutant loadings, and water...

XML Views: Part 1

NARCIS (Netherlands)

Rajugan, R.; Marik, V.; Retschitzegger, W.; Chang, E.; Dillon, T.; Stepankova, O.; Feng, L.

The exponential growth and the nature of Internet and web-based applications made eXtensible Markup Language (XML) as the de-facto standard for data exchange and data dissemination. Now it is gaining momentum in replacing conventional data models for data representation. XML with its self-describing

Dictionary as Database.

Science.gov (United States)

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)

Multicultural science education in Lesotho high school biology classrooms

Science.gov (United States)

Nthathakane, Malefu Christina

2001-12-01

This study investigated how Basotho high school biology students responded to a multicultural science education (MCSE) approach. Students' home language---Sesotho---and cultural experiences were integrated into the teaching of a unit on alcohol, tobacco and other drugs (ATOD) abuse. The focus was on students whose cultural background is African and who are English second language users. The study was conducted in three high school biology classrooms in Lesotho where the ATOD unit was taught using MCSE. A fourth biology classroom was observed for comparison purposes. In this classroom the regular biology teacher taught ATOD using typical instructional strategies. The study was framed by the general question: How does a multicultural science education approach affect Basotho high school biology students? More specifically: How does the use of Sesotho (or code-switching between Sesotho and English) and integration of Basotho students' cultural knowledge and experiences with respect to ATOD affect students' learning? In particular how does the approach affect students' participation and academic performance? A qualitative research method was used in this study. Data were drawn from a number of different sources and analyzed inductively. The data sources included field-notes, transcripts of ATOD lessons, research assistant lesson observation notes and interviews, regular biology teachers' interviews and notes from observing a few of their lessons, students' interviews and pre and posttest scripts, and other school documents that recorded students' performance throughout the year. Using the students' home language---Sesotho---was beneficial in that it enabled them to share ideas, communicate better and understand each other, the teacher and the material that was taught. Integrating students' cultural and everyday experiences was beneficial because it enabled students to anchor the new ATOD ideas in what was familiar and helped them find the relevance of the unit by

XML Based Scientific Data Management Facility

Science.gov (United States)

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.

Growth and development and their environmental and biological determinants

Directory of Open Access Journals (Sweden)

Kelly da Rocha Neves

2016-05-01

Conclusion: The results showed a high prevalence of stunting and below‐average results for cognitive/language development among the participating children. Both environmental and biological factors were related to growth and development. However, biological variables showed a greater association with growth, whereas environmental variables were associated with development.

Language in Comparative Perspective. Chapter 11

Science.gov (United States)

Rumbaugh, Duane M.; Savage-Rumbaugh, E. Sue

1994-01-01

The twentieth century will be noted for a wide variety of scientific and technological advancements, including powered flight, antibiotics, space travel, and the breaking of the genetic code. It also should be noted as the century in which major psychological, as well as biological, continuities between animal and human have been defined. Charles Darwin (1859) was quite right when he anticipated continuity in mental processes, some of which provide for language. Though none will argue that any animal has the full capacity of humans for language, none should deny that at least some animals have quite impressive competencies for language skills, including speech comprehension. The finding that the language skills in the bonobo and the chimpanzee are likely more fully and efficiently developed as a result of early rearing than by formal training at a later age declares a continuity even stronger than that defined by the language acquisition potential of the ape. To clarify, because early rearing facilitates the emergence of language in ape as well as in child, a naturalness to the familiar course of language acquisition, whereby comprehension precedes production, is also corroborated. In turn, the continuity and the shared naturalness of language acquisition serve jointly to define an advanced and critical point of linkage between the genera Pan and Homo - and, as concluded by Domjan (1993), one worthy of contributing to the series of reconceptions of ourselves as anticipated by Ploog and Melnechuk (1971).

Testing a model of science process skills acquisition: An interaction with parents' education, preferred language, gender, science attitude, cognitive development, academic ability, and biology knowledge

Science.gov (United States)

Germann, Paul J.

Path analysis techniques were used to test a hypothesized structural model of direct and indirect causal effects of student variables on science process skills. The model was tested twice using data collected at the beginning and end of the school year from 67 9th- and 10th-grade biology students who lived in a rural Franco-American community in New England. Each student variable was found to have significant effects, accounting for approximately 80% of the variance in science process skills achievement. Academic ability, biology knowledge, and language preference had significant direct effects. There were significant mediated effects by cognitive development, parents' education, and attitude toward science in school. The variables of cognitive development and academic ability had the greatest total effects on science process skills. Implications for practitioners and researchers are discussed.

Syntactic priming in American Sign Language.

Directory of Open Access Journals (Sweden)

Matthew L Hall

Full Text Available Psycholinguistic studies of sign language processing provide valuable opportunities to assess whether language phenomena, which are primarily studied in spoken language, are fundamentally shaped by peripheral biology. For example, we know that when given a choice between two syntactically permissible ways to express the same proposition, speakers tend to choose structures that were recently used, a phenomenon known as syntactic priming. Here, we report two experiments testing syntactic priming of a noun phrase construction in American Sign Language (ASL. Experiment 1 shows that second language (L2 signers with normal hearing exhibit syntactic priming in ASL and that priming is stronger when the head noun is repeated between prime and target (the lexical boost effect. Experiment 2 shows that syntactic priming is equally strong among deaf native L1 signers, deaf late L1 learners, and hearing L2 signers. Experiment 2 also tested for, but did not find evidence of, phonological or semantic boosts to syntactic priming in ASL. These results show that despite the profound differences between spoken and signed languages in terms of how they are produced and perceived, the psychological representation of sentence structure (as assessed by syntactic priming operates similarly in sign and speech.

ppropriation of scientific discourse by protestant biology students: the contribution of Bakhtin's language theory to educational research and culture

Directory of Open Access Journals (Sweden)

Claudia Sepulveda

2006-03-01

Full Text Available Studies about the relations between classroom discourse interactions and processes of teaching and learning show that science learning is related to a process structured by speech genres and ways of establishing semantic links between events, objects, and people. Accordingly, it has been emphasized that science education research needs to incorporate theories and methods developed for the interpretative analysis of discourse. This paper shows the heuristic power that an interpretative analysis of discourse based on Bakhtin’s theory of language can have in the investigation of meaning making in science education in multicultural contexts. With this purpose, we discuss here results obtained in the analysis of the discourse about “nature” or “natural world” of protestant Biology preservice teachers of a Brazilian university, produced in the context of semi-structured interviews.

The countries and languages that dominate biological research at the beginning of the 21st century

Directory of Open Access Journals (Sweden)

Julián Monge-Nájera

2005-06-01

Full Text Available Traditionally,studies of scientific productivity are biased in two ways: they are based on Current Contents, an index centered in British and American journals, and they seldom correct for population size, ignoring the relative effort that each society places in research. We studied national productivity for biology using a more representative index, the Biological Abstracts, and analyzed both total and relative productivity. English dominates biological publications with 87% (no other individual language reaches 2%. If the USA is considered a region by itself, it occupies the first place in per capita production of biology papers, with at least twice the productivity of either Asia or Europe. Canada, Oceania and Latin America occupy an intermediate position. The global output of scientific papers is dominated by Europe, USA, Japan, Canada, China and India. When corrected for population size, the countries with the greatest productivity of biology papers are the Nordic nations, Israel, Switzerland, Netherlands, Australia, Saint Lucia and Montserrat. The predominance of English as the language of biological research found in this study shows a continuation of the trend initiated around the year 1900. The large relative productivity of the USA reflects the importance that American society gives to science as the basis for technological and economic development, but the USA’s share of total scientific output has decreased from 44% in 1983 to 34% in 2002, while there is a greater growth of science in India, Japan and Latin America, among others. The increasing share obtained by China and India may reflect a recent change in attitude towards funding science. The leadership of Nordic nations, Israel, Switzerland, Netherlands and Australia can be explained by cultural attitude. Apparently, a positive trend is emerging in Latin America, where Chile improved its ranking in per capita productivity but Argentina, Costa Rica, Uruguay, Brazil and Cuba fell

Intentions and actions in molecular self-assembly: perspectives on students' language use

Science.gov (United States)

Höst, Gunnar E.; Anward, Jan

2017-04-01

Learning to talk science is an important aspect of learning to do science. Given that scientists' language frequently includes intentions and purposes in explanations of unobservable objects and events, teachers must interpret whether learners' use of such language reflects a scientific understanding or inaccurate anthropomorphism and teleology. In the present study, a framework consisting of three 'stances' (Dennett, 1987) - intentional, design and physical - is presented as a powerful tool for analysing students' language use. The aim was to investigate how the framework can be differentiated and used analytically for interpreting students' talk about a molecular process. Semi-structured group discussions and individual interviews about the molecular self-assembly process were conducted with engineering biology/chemistry (n = 15) and biology/chemistry teacher students (n = 6). Qualitative content analysis of transcripts showed that all three stances were employed by students. The analysis also identified subcategories for each stance, and revealed that intentional language with respect to molecular movement and assumptions about design requirements may be potentially problematic areas. Students' exclusion of physical stance explanations may indicate literal anthropomorphic interpretations. Implications for practice include providing teachers with a tool for scaffolding their use of metaphorical language and for supporting students' metacognitive development as scientific language users.

A BML Based Embodied Conversational Agent for a Personality Detection Program

NARCIS (Netherlands)

Solano Méndez, Guillermo; Reidsma, Dennis; Vilhjálmsson, Hannes Högni; Kopp, Stefan; Marsella, Stacy; Thórisson, Kristinn R.

2011-01-01

This paper presents a project in which an Embodied Conversational Agent (ECA) attemtps to detect the personality of the user by asking him (or her) a series of questions. The project uses the Elckerlyc platform, a Behavior Markup Language (BML) compliant behavior realizer for ECAs [1]. BML allows

A Courseware to Script Animated Pedagogical Agents in Instructional Material for Elementary Students in English Education

Science.gov (United States)

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…

Silicon Graphics' IRIS InSight: An SGML Success Story.

Science.gov (United States)

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…

Migrating an Online Service to WAP - A Case Study.

Science.gov (United States)

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)

Design And Implementation Of An Interactive Website; A Case Study ...

African Journals Online (AJOL)

An interactive website has been designed for the Department of Physics, University of Uyo, using Hypertext Markup Language (HTML) involving structuring, coding, and testing. This will enable the Department to gather, process, store and disseminate an up- to- date information to the whole world on the academic ...

Inducing Head-Driven PCFGs with Latent Heads: Refining a Tree-bank Grammar for Parsing

NARCIS (Netherlands)

Prescher, D.; Gama, J.; Camacho, R.; Brazdil, P.; Jorge, A.; Torgo, L.

2005-01-01

Although state-of-the-art parsers for natural language are lexicalized, it was recently shown that an accurate unlexicalized parser for the Penn tree-bank can be simply read off a manually refined tree-bank. While lexicalized parsers often suffer from sparse data, manual mark-up is costly and

XML under the Hood.

Science.gov (United States)

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…

An Electronic Publishing Model for Academic Publishers.

Science.gov (United States)

Gold, Jon D.

1994-01-01

Describes an electronic publishing model based on Standard Generalized Markup Language (SGML) and considers its use by an academic publisher. Highlights include how SGML is used to produce an electronic book, hypertext, methods of delivery, intellectual property rights, and future possibilities. Sample documents are included. (two references) (LRW)

Molecular biology of the cell

CERN Document Server

Alberts, Bruce; Lewis, Julian

2000-01-01

Molecular Biology of the Cell is the classic in-dept text reference in cell biology. By extracting the fundamental concepts from this enormous and ever-growing field, the authors tell the story of cell biology, and create a coherent framework through which non-expert readers may approach the subject. Written in clear and concise language, and beautifully illustrated, the book is enjoyable to read, and it provides a clear sense of the excitement of modern biology. Molecular Biology of the Cell sets forth the current understanding of cell biology (completely updated as of Autumn 2001), and it explores the intriguing implications and possibilities of the great deal that remains unknown. The hallmark features of previous editions continue in the Fourth Edition. The book is designed with a clean and open, single-column layout. The art program maintains a completely consistent format and style, and includes over 1,600 photographs, electron micrographs, and original drawings by the authors. Clear and concise concept...

Computerized tomographic simulation compared with clinical mark-up in palliative radiotherapy: A prospective study

International Nuclear Information System (INIS)

Haddad, Peiman; Cheung, Fred; Pond, Gregory; Easton, Debbie; Cops, Frederick; Bezjak, Andrea; McLean, Michael; Levin, Wilfred; Billingsley, Susan; Williams, Diane; Wong, Rebecca

2006-01-01

Purpose To evaluate the impact of computed tomographic (CT) planning in comparison to clinical mark-up (CM) for palliative radiation of chest wall metastases. Methods and Materials In patients treated with CM for chest wall bone metastases (without conventional simulation/fluoroscopy), two consecutive planning CT scans were acquired with and without an external marker to delineate the CM treatment field. The two sets of scans were fused for evaluation of clinical tumor volume (CTV) coverage by the CM technique. Under-coverage was defined as the proportion of CTV not covered by the CM 80% isodose. Results Twenty-one treatments (ribs 17, sternum 2, and scapula 2) formed the basis of our study. Due to technical reasons, comparable data between CM and CT plans were available for 19 treatments only. CM resulted in a mean CTV under-coverage of 36%. Eleven sites (58%) had an under-coverage of >20%. Mean volume of normal tissues receiving ≥80% of the dose was 5.4% in CM and 9.3% in CT plans (p = 0.017). Based on dose-volume histogram comparisons, CT planning resulted in a change of treatment technique from direct apposition to a tangential pair in 7 of 19 cases. Conclusions CT planning demonstrated a 36% under-coverage of CTV with CM of ribs and chest wall metastases

Language Teachers' Target Language Project: Language for Specific Purposes of Language Teaching

Science.gov (United States)

Korenev, Alexey; Westbrook, Carolyn; Merry, Yvonne; Ershova, Tatiana

2016-01-01

The Language Teachers' Target Language project (LTTL) aims to describe language teachers' target language use domain (Bachman & Palmer 2010) and to develop a language test for future teachers of English. The team comprises four researchers from Moscow State University (MSU) and Southampton Solent University.

In silico Evolutionary Developmental Neurobiology and the Origin of Natural Language

Science.gov (United States)

Szathmáry, Eörs; Szathmáry, Zoltán; Ittzés, Péter; Orbaán, Geroő; Zachár, István; Huszár, Ferenc; Fedor, Anna; Varga, Máté; Számadó, Szabolcs

It is justified to assume that part of our genetic endowment contributes to our language skills, yet it is impossible to tell at this moment exactly how genes affect the language faculty. We complement experimental biological studies by an in silico approach in that we simulate the evolution of neuronal networks under selection for language-related skills. At the heart of this project is the Evolutionary Neurogenetic Algorithm (ENGA) that is deliberately biomimetic. The design of the system was inspired by important biological phenomena such as brain ontogenesis, neuron morphologies, and indirect genetic encoding. Neuronal networks were selected and were allowed to reproduce as a function of their performance in the given task. The selected neuronal networks in all scenarios were able to solve the communication problem they had to face. The most striking feature of the model is that it works with highly indirect genetic encoding--just as brains do.

Q&A: What is human language, when did it evolve and why should we care?

Science.gov (United States)

Pagel, Mark

2017-07-24

Human language is unique among all forms of animal communication. It is unlikely that any other species, including our close genetic cousins the Neanderthals, ever had language, and so-called sign 'language' in Great Apes is nothing like human language. Language evolution shares many features with biological evolution, and this has made it useful for tracing recent human history and for studying how culture evolves among groups of people with related languages. A case can be made that language has played a more important role in our species' recent (circa last 200,000 years) evolution than have our genes.

Growth and development and their environmental and biological determinants.

Science.gov (United States)

da Rocha Neves, Kelly; de Souza Morais, Rosane Luzia; Teixeira, Romero Alves; Pinto, Priscilla Avelino Ferreira

2016-01-01

To investigate child growth, cognitive/language development, and their environmental and biological determinants. This was a cross-sectional, predictive correlation study with all 92 children aged 24-36 months who attended the municipal early childhood education network in a town in the Vale do Jequitinhonha region, in 2011. The socioeconomic profile was determined using the questionnaire of the Associação Brasileira de Empresas de Pesquisa. The socio-demographicand maternal and child health profiles were created through a self-prepared questionnaire. The height-for-age indicator was selected to represent growth. Cognitive/language development was assessed through the Bayley Scale of Infant and Toddler Development. The quality of educational environments was assessed by Infant/Toddler Environment Scale; the home environment was assessed by the Home Observation for Measurement of the Environment. The neighborhood quality was determined by a self-prepared questionnaire. A multivariate linear regression analysis was performed. Families were predominantly from socioeconomic class D, with low parental education. The prevalence of stunted growth was 14.1%; cognitive and language development were below average at 28.6% and 28.3%, respectively. Educational institutions were classified as inadequate, and 69.6% of homes were classified as presenting a risk for development. Factors such as access to parks and pharmacies and perceived security received the worst score regarding neighborhood environment. Biological variables showed a greater association with growth and environmental variables with development. The results showed a high prevalence of stunting and below-average results for cognitive/language development among the participating children. Both environmental and biological factors were related to growth and development. However, biological variables showed a greater association with growth, whereas environmental variables were associated with development

Growth and development and their environmental and biological determinants

Directory of Open Access Journals (Sweden)

Kelly da Rocha Neves

2016-06-01

Full Text Available Abstract Objective To investigate child growth, cognitive/language development, and their environmental and biological determinants. Methods This was a cross-sectional, predictive correlation study with all 92 children aged 24-36 months who attended the municipal early childhood education network in a town in the Vale do Jequitinhonha region, in 2011. The socioeconomic profile was determined using the questionnaire of the Associação Brasileira de Empresas de Pesquisa. The socio-demographicand maternal and child health profiles were created through a self-prepared questionnaire. The height-for-age indicator was selected to represent growth. Cognitive/language development was assessed through the Bayley Scale of Infant and Toddler Development. The quality of educational environments was assessed by Infant/Toddler Environment Scale; the home environment was assessed by the Home Observation for Measurement of the Environment. The neighborhood quality was determined by a self-prepared questionnaire. A multivariate linear regression analysis was performed. Results Families were predominantly from socioeconomic class D, with low parental education. The prevalence of stunted growth was 14.1%; cognitive and language development were below average at 28.6% and 28.3%, respectively. Educational institutions were classified as inadequate, and 69.6% of homes were classified as presenting a risk for development. Factors such as access to parks and pharmacies and perceived security received the worst score regarding neighborhood environment. Biological variables showed a greater association with growth and environmental variables with development. Conclusion The results showed a high prevalence of stunting and below-average results for cognitive/language development among the participating children. Both environmental and biological factors were related to growth and development. However, biological variables showed a greater association with growth, whereas

Chargaff's "Grammar of Biology": New Fractal-like Rules

OpenAIRE

Yamagishi, Michel Eduardo Beleza; Herai, Roberto H.

2011-01-01

Chargaff once said that "I saw before me in dark contours the beginning of a grammar of Biology". In linguistics, "grammar" is the set of natural language rules, but we do not know for sure what Chargaff meant by "grammar" of Biology. Nevertheless, assuming the metaphor, Chargaff himself started a "grammar of Biology" discovering the so called Chargaff's rules. In this work, we further develop his grammar. Using new concepts, we were able to discovery new genomic rules that seem to be invaria...

CURIE Syntax 1.0, A syntax for expressing Compact URIs

NARCIS (Netherlands)

institution W3C; M. Birbeck (Mark); not CWI et al

2007-01-01

textabstractThe aim of this document is to outline a syntax for expressing URIs in a generic, abbreviated syntax. While it has been produced in conjunction with the HTML Working Group, it is not specifically targeted at use by XHTML Family Markup Languages. Note that the target audience for this

XML in Libraries.

Science.gov (United States)

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…

How Does XML Help Libraries?

Science.gov (United States)

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.…

Modeling the Emergence of Contact Languages

Science.gov (United States)

Tria, Francesca; Servedio, Vito D.P.; Mufwene, Salikoko S.; Loreto, Vittorio

2015-01-01

Contact languages are born out of the non-trivial interaction of two (or more) parent languages. Nowadays, the enhanced possibility of mobility and communication allows for a strong mixing of languages and cultures, thus raising the issue of whether there are any pure languages or cultures that are unaffected by contact with others. As with bacteria or viruses in biological evolution, the evolution of languages is marked by horizontal transmission; but to date no reliable quantitative tools to investigate these phenomena have been available. An interesting and well documented example of contact language is the emergence of creole languages, which originated in the contacts of European colonists and slaves during the 17th and 18th centuries in exogenous plantation colonies of especially the Atlantic and Indian Ocean. Here, we focus on the emergence of creole languages to demonstrate a dynamical process that mimics the process of creole formation in American and Caribbean plantation ecologies. Inspired by the Naming Game (NG), our modeling scheme incorporates demographic information about the colonial population in the framework of a non-trivial interaction network including three populations: Europeans, Mulattos/Creoles, and Bozal slaves. We show how this sole information makes it possible to discriminate territories that produced modern creoles from those that did not, with a surprising accuracy. The generality of our approach provides valuable insights for further studies on the emergence of languages in contact ecologies as well as to test specific hypotheses about the peopling and the population structures of the relevant territories. We submit that these tools could be relevant to addressing problems related to contact phenomena in many cultural domains: e.g., emergence of dialects, language competition and hybridization, globalization phenomena. PMID:25875371

Simplicity and Specificity in Language: Domain-General Biases Have Domain-Specific Effects

Science.gov (United States)

Culbertson, Jennifer; Kirby, Simon

2016-01-01

The extent to which the linguistic system—its architecture, the representations it operates on, the constraints it is subject to—is specific to language has broad implications for cognitive science and its relation to evolutionary biology. Importantly, a given property of the linguistic system can be “specific” to the domain of language in several ways. For example, if the property evolved by natural selection under the pressure of the linguistic function it serves then the property is domain-specific in the sense that its design is tailored for language. Equally though, if that property evolved to serve a different function or if that property is domain-general, it may nevertheless interact with the linguistic system in a way that is unique. This gives a second sense in which a property can be thought of as specific to language. An evolutionary approach to the language faculty might at first blush appear to favor domain-specificity in the first sense, with individual properties of the language faculty being specifically linguistic adaptations. However, we argue that interactions between learning, culture, and biological evolution mean any domain-specific adaptations that evolve will take the form of weak biases rather than hard constraints. Turning to the latter sense of domain-specificity, we highlight a very general bias, simplicity, which operates widely in cognition and yet interacts with linguistic representations in domain-specific ways. PMID:26793132

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

Science.gov (United States)

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

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

Science.gov (United States)

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.

Epigenetics: the language of the cell?

Science.gov (United States)

Huang, Biao; Jiang, Cizhong; Zhang, Rongxin

2014-02-01

Epigenetics is one of the most rapidly developing fields of biological research. Breakthroughs in several technologies have enabled the possibility of genome-wide epigenetic research, for example the mapping of human genome-wide DNA methylation. In addition, with the development of various high-throughput and high-resolution sequencing technologies, a large number of functional noncoding RNAs have been identified. Massive studies indicated that these functional ncRNA also play an important role in epigenetics. In this review, we gain inspiration from the recent proposal of the ceRNAs hypothesis. This hypothesis proposes that miRNAs act as a language of communication. Accordingly, we further deduce that all of epigenetics may functionally acquire such a unique language characteristic. In summary, various epigenetic markers may not only participate in regulating cellular processes, but they may also act as the intracellular 'language' of communication and are involved in extensive information exchanges within cell.

ShinyKGode: an Interactive Application for ODE Parameter Inference Using Gradient Matching.

Science.gov (United States)

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

2018-02-27

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 visualised 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. dirk.husmeier@glasgow.ac.uk. None.

Genes, language, cognition, and culture: towards productive inquiry.

Science.gov (United States)

Fitch, W Tecumseh

2011-04-01

The Queen Mary conference on “Integrating Genetic and Cultural Evolutionary Approaches to Language,” and the papers in this special issue, clearly illustrate the excitement and potential of trans-disciplinary approaches to language as an evolved biological capacity (phylogeny) and an evolving cultural entity (glossogeny). Excepting the present author, the presenters/authors are mostly young rising stars in their respective fields, and include scientists with backgrounds in linguistics, animal communication, neuroscience, evolutionary biology, anthropology, and computer science. On display was a clear willingness to engage with different approaches and terminology and a commitment to shared standards of scientific rigor, empirically driven theory, and logical argument. Because the papers assembled here, together with the introduction, speak for themselves, I will focus in this “extro-duction” on some of the terminological and conceptual difficulties which threaten to block this exciting wave of scientific progress in understanding language evolution, in both senses of that term. In particular I will first argue against the regrettably widespread practice of opposing cultural and genetic explanations of human cognition as if they were dichotomous. Second, I will unpack the debate concerning “general-purpose” and “domain-specific” mechanisms, which masquerades as a debate about nativism but is nothing of the sort. I believe that framing discussions of language in these terms has generated more heat than light, and that a modern molecular understanding of genes, development, behavior, and evolution renders many of the assumptions underlying this debate invalid.

Spoken language achieves robustness and evolvability by exploiting degeneracy and neutrality.

Science.gov (United States)

Winter, Bodo

2014-10-01

As with biological systems, spoken languages are strikingly robust against perturbations. This paper shows that languages achieve robustness in a way that is highly similar to many biological systems. For example, speech sounds are encoded via multiple acoustically diverse, temporally distributed and functionally redundant cues, characteristics that bear similarities to what biologists call "degeneracy". Speech is furthermore adequately characterized by neutrality, with many different tongue configurations leading to similar acoustic outputs, and different acoustic variants understood as the same by recipients. This highlights the presence of a large neutral network of acoustic neighbors for every speech sound. Such neutrality ensures that a steady backdrop of variation can be maintained without impeding communication, assuring that there is "fodder" for subsequent evolution. Thus, studying linguistic robustness is not only important for understanding how linguistic systems maintain their functioning upon the background of noise, but also for understanding the preconditions for language evolution. © 2014 WILEY Periodicals, Inc.

Detecting evolutionary forces in language change.

Science.gov (United States)

Newberry, Mitchell G; Ahern, Christopher A; Clark, Robin; Plotkin, Joshua B

2017-11-09

Both language and genes evolve by transmission over generations with opportunity for differential replication of forms. The understanding that gene frequencies change at random by genetic drift, even in the absence of natural selection, was a seminal advance in evolutionary biology. Stochastic drift must also occur in language as a result of randomness in how linguistic forms are copied between speakers. Here we quantify the strength of selection relative to stochastic drift in language evolution. We use time series derived from large corpora of annotated texts dating from the 12th to 21st centuries to analyse three well-known grammatical changes in English: the regularization of past-tense verbs, the introduction of the periphrastic 'do', and variation in verbal negation. We reject stochastic drift in favour of selection in some cases but not in others. In particular, we infer selection towards the irregular forms of some past-tense verbs, which is likely driven by changing frequencies of rhyming patterns over time. We show that stochastic drift is stronger for rare words, which may explain why rare forms are more prone to replacement than common ones. This work provides a method for testing selective theories of language change against a null model and reveals an underappreciated role for stochasticity in language evolution.

The language capacity: architecture and evolution.

Science.gov (United States)

Chomsky, Noam

2017-02-01

There is substantial evidence that the human language capacity (LC) is a species-specific biological property, essentially unique to humans, invariant among human groups, and dissociated from other cognitive systems. Each language, an instantiation of LC, consists of a generative procedure that yields a discrete infinity of hierarchically structured expressions with semantic interpretations, hence a kind of "language of thought" (LOT), along with an operation of externalization (EXT) to some sensory-motor system, typically sound. There is mounting evidence that generation of LOT observes language-independent principles of computational efficiency and is based on the simplest computational operations, and that EXT is an ancillary process not entering into the core semantic properties of LOT and is the primary locus of the apparent complexity, diversity, and mutability of language. These conclusions are not surprising, since the internal system is acquired virtually without evidence in fundamental respects, and EXT relates it to sensory-motor systems that are unrelated to it. Even such properties as the linear order of words appear to be reflexes of the sensory motor system, not available to generation of LOT. The limited evidence from the evolutionary record lends support to these conclusions, suggesting that LC emerged with Homo sapiens or not long after, and has not evolved since human groups dispersed.

Designing a framework for a unified electronic identity system ...

African Journals Online (AJOL)

In this paper, a Unified Identity System is proposed where single electronic identity (eID) is issued that can be used across the various platforms of business transaction. The activity/state diagram of the model is presented, and the means of authentication is based on the Secure Assertion Markup Language (SAML) ...

XForms 1.1 candidate recommendation

NARCIS (Netherlands)

J.M. Boyer

2007-01-01

textabstractXForms is an XML application that represents the next generation of forms for the Web. XForms is not a free-standing document type, but is intended to be integrated into other markup languages, such as XHTML, ODF or SVG. An XForms-based web form gathers and processes XML data using an

The ePNK: An Extensible Petri Net Tool for PNML

DEFF Research Database (Denmark)

Kindler, Ekkart

2011-01-01

The Petri Net Markup Language (PNML) is an XML-based interchange format for all kinds of Petri nets, which is an ISO/IEC International Standard 15909-2 now. The focus of this standard is on PNML as an interchange format for high-level Petri nets. PNML, however, is more general and allows exchanging...

Converting from XML to HDF-EOS

Science.gov (United States)

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.

A high-level language for rule-based modelling.

Science.gov (United States)

Pedersen, Michael; Phillips, Andrew; Plotkin, Gordon D

2015-01-01

Rule-based languages such as Kappa excel in their support for handling the combinatorial complexities prevalent in many biological systems, including signalling pathways. But Kappa provides little structure for organising rules, and large models can therefore be hard to read and maintain. This paper introduces a high-level, modular extension of Kappa called LBS-κ. We demonstrate the constructs of the language through examples and three case studies: a chemotaxis switch ring, a MAPK cascade, and an insulin signalling pathway. We then provide a formal definition of LBS-κ through an abstract syntax and a translation to plain Kappa. The translation is implemented in a compiler tool which is available as a web application. We finally demonstrate how to increase the expressivity of LBS-κ through embedded scripts in a general-purpose programming language, a technique which we view as generally applicable to other domain specific languages.

Spatial congruence in language and species richness but not threat in the world's top linguistic hotspot.

Science.gov (United States)

Turvey, Samuel T; Pettorelli, Nathalie

2014-12-07

Languages share key evolutionary properties with biological species, and global-level spatial congruence in richness and threat is documented between languages and several taxonomic groups. However, there is little understanding of the functional connection between diversification or extinction in languages and species, or the relationship between linguistic and species richness across different spatial scales. New Guinea is the world's most linguistically rich region and contains extremely high biological diversity. We demonstrate significant positive relationships between language and mammal richness in New Guinea across multiple spatial scales, revealing a likely functional relationship over scales at which infra-island diversification may occur. However, correlations are driven by spatial congruence between low levels of language and species richness. Regional biocultural richness may have showed closer congruence before New Guinea's linguistic landscape was altered by Holocene demographic events. In contrast to global studies, we demonstrate a significant negative correlation across New Guinea between areas with high levels of threatened languages and threatened mammals, indicating that landscape-scale threats differ between these groups. Spatial resource prioritization to conserve biodiversity may not benefit threatened languages, and conservation policy must adopt a multi-faceted approach to protect biocultural diversity as a whole.

Language and life history: a new perspective on the development and evolution of human language.

Science.gov (United States)

Locke, John L; Bogin, Barry

2006-06-01

It has long been claimed that Homo sapiens is the only species that has language, but only recently has it been recognized that humans also have an unusual pattern of growth and development. Social mammals have two stages of pre-adult development: infancy and juvenility. Humans have two additional prolonged and pronounced life history stages: childhood, an interval of four years extending between infancy and the juvenile period that follows, and adolescence, a stage of about eight years that stretches from juvenility to adulthood. We begin by reviewing the primary biological and linguistic changes occurring in each of the four pre-adult ontogenetic stages in human life history. Then we attempt to trace the evolution of childhood and juvenility in our hominin ancestors. We propose that several different forms of selection applied in infancy and childhood; and that, in adolescence, elaborated vocal behaviors played a role in courtship and intrasexual competition, enhancing fitness and ultimately integrating performative and pragmatic skills with linguistic knowledge in a broad faculty of language. A theoretical consequence of our proposal is that fossil evidence of the uniquely human stages may be used, with other findings, to date the emergence of language. If important aspects of language cannot appear until sexual maturity, as we propose, then a second consequence is that the development of language requires the whole of modern human ontogeny. Our life history model thus offers new ways of investigating, and thinking about, the evolution, development, and ultimately the nature of human language.

Processing sequence annotation data using the Lua programming language.

Science.gov (United States)

Ueno, Yutaka; Arita, Masanori; Kumagai, Toshitaka; Asai, Kiyoshi

2003-01-01

The data processing language in a graphical software tool that manages sequence annotation data from genome databases should provide flexible functions for the tasks in molecular biology research. Among currently available languages we adopted the Lua programming language. It fulfills our requirements to perform computational tasks for sequence map layouts, i.e. the handling of data containers, symbolic reference to data, and a simple programming syntax. Upon importing a foreign file, the original data are first decomposed in the Lua language while maintaining the original data schema. The converted data are parsed by the Lua interpreter and the contents are stored in our data warehouse. Then, portions of annotations are selected and arranged into our catalog format to be depicted on the sequence map. Our sequence visualization program was successfully implemented, embedding the Lua language for processing of annotation data and layout script. The program is available at http://staff.aist.go.jp/yutaka.ueno/guppy/.

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.

Science.gov (United States)

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.

Handwritten-word spotting using biologically inspired features

NARCIS (Netherlands)

van der Zant, Tijn; Schomaker, Lambert; Haak, Koen

For quick access to new handwritten collections, current handwriting recognition methods are too cumbersome. They cannot deal with the lack of labeled data and would require extensive laboratory training for each individual script, style, language, and collection. We propose a biologically inspired

PathwayAccess: CellDesigner plugins for pathway databases.

Science.gov (United States)

Van Hemert, John L; Dickerson, Julie A

2010-09-15

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

Computer simulation as an important approach to explore language universal. Comment on "Dependency distance: a new perspective on syntactic patterns in natural languages" by Haitao Liu et al.

Science.gov (United States)

Lu, Qian

2017-07-01

Exploring language universal is one of the major goals of linguistic researches, which are largely devoted to answering the ;Platonic questions; in linguistics, that is, what is the language knowledge, how to get and use this knowledge. However, if solely guided by linguistic intuition, it is very difficult for syntactic studies to answer these questions, or to achieve abstractions in the scientific sense. This suggests that linguistic analyses based on the probability theory may provide effective ways to investigate into language universals in terms of biological motivations or cognitive psychological mechanisms. With the view that ;Language is a human-driven system;, Liu, Xu & Liang's review [1] pointed out that dependency distance minimization (DDM), which has been corroborated by big data analysis of corpus, may be a language universal shaped in language evolution, a universal that has profound effect on syntactic patterns.

Introduction: integrating genetic and cultural evolutionary approaches to language.

Science.gov (United States)

Mesoudi, Alex; McElligott, Alan G; Adger, David

2011-04-01

The papers in this special issue of Human Biology address recent research in the field of language evolution, both the genetic evolution of the language faculty and the cultural evolution of specific languages. While both of these areas have received increasing interest in recent years, there is also a need to integrate these somewhat separate efforts and explore the relevant gene-culture coevolutionary interactions. Here we summarize the individual contributions, set them in the context of the wider literature, and identify outstanding future research questions. The first set of papers concerns the comparative study of nonhuman communication in primates and birds from both a behavioral and neurobiological perspective, revealing evidence for several common language-related traits in various nonhuman species and providing clues as to the evolutionary origin and function of the human language faculty. The second set of papers discusses the consequences of viewing language as a culturally evolving system in its own right, including claims that this removes the need for strong genetic biases for language acquisition, and that phylogenetic evolutionary methods can be used to reconstruct language histories. We conclude by highlighting outstanding areas for future research, including identifying the precise selection pressures that gave rise to the language faculty in ancestral hominin species, and determining the strength, domain specificity, and origin of the cultural transmission biases that shape languages as they pass along successive generations of language learners.

The price of surgery: markup of operative procedures in the United States.

Science.gov (United States)

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

2017-02-01

Despite cost containment efforts, the price for surgery is not subject to any regulations. We sought to characterize and compare variability in pricing for commonly performed major surgical procedures across the United States. Medicare claims corresponding to eight major surgical procedures (aortic aneurysm repair, aortic valvuloplasty, carotid endartectomy, coronary artery bypass grafting, esophagectomy, pancreatectomy, liver resection, and colectomy) were identified using the Medicare Provider Utilization and Payment Data Physician and Other Supplier Public Use File for 2013. For each procedure, total charges, Medicare-allowable costs, and total payments were recorded. A procedure-specific markup ratio (MR; ratio of total charges to Medicare-allowable costs) was calculated and compared between procedures and across states. Variation in MR was compared using a coefficient of variation (CoV). Among all providers, the median MR was 3.5 (interquartile range: 3.1-4.0). MR was noted to vary by procedure; ranging from 3.0 following colectomy to 6.0 following carotid endartectomy (P < 0.001). MR also varied for the same procedure; varying the least after liver resection (CoV = 0.24), while coronary artery bypass grafting pricing demonstrated the greatest variation in MR (CoV = 0.53). Compared with the national average, MR varied by 36% between states ranging from 1.8 to 13.0. Variation in MR was also noted within the same state varying by 15% within the state of Arkansas (CoV = 0.15) compared with 51% within the state of Wisconsin (CoV = 0.51). Significant variation was noted for the price of surgery by procedure as well as between and within different geographical regions. Greater scrutiny and transparency in the price of surgery is required to promote cost containment. Copyright © 2016 Elsevier Inc. All rights reserved.

Language variety, language hierarchy, and language choice in the international university

DEFF Research Database (Denmark)

Haberland, Hartmut; Mortensen, Janus

2012-01-01

Introduction to thematic issue on Language variety, language hierarchy, and language choice in the international university......Introduction to thematic issue on Language variety, language hierarchy, and language choice in the international university...

XML Based Course Websites.

Science.gov (United States)

Wollowski, Michael

XML, the extensible markup language, is a quickly evolving technology that presents a viable alternative to courseware products and promises to ease the burden of Web authors, who edit their course pages directly. XML uses tags to label kinds of contents, rather than format information. The use of XML enables faculty to focus on providing…

Information Security and Wireless: Alternate Approaches for Controlling Access to Critical Information

National Research Council Canada - National Science Library

Nandram, Winsome

2004-01-01

.... Typically, network managers implement countermeasures to augment security. The goal of this thesis is to research approaches that compliment existing security measures with fine grain access control measures. The Extensible Markup Language (XML) is adopted to accommodate such granular access control as it provides the mechanisms for scaling security down to the document content level.

Global Situational Awareness with Free Tools

Science.gov (United States)

2015-01-15

also be use in a closed environment • It’s cool, and people like cool 14© 2015 Carnegie Mellon University Google Earth Demo attempted-recon Signature...multiple data sources • Snort (Snorby on Security Onion) • Nagios • SharePoint RSS • Flow • Others • Leverage standard data formats • Keyhole Markup Language

Optimality and Plausibility in Language Design

Directory of Open Access Journals (Sweden)

Michael R. Levot

2016-12-01

Full Text Available The Minimalist Program in generative syntax has been the subject of much rancour, a good proportion of it stoked by Noam Chomsky’s suggestion that language may represent “a ‘perfect solution’ to minimal design specifications.” A particular flash point has been the application of Minimalist principles to speculations about how language evolved in the human species. This paper argues that Minimalism is well supported as a plausible approach to language evolution. It is claimed that an assumption of minimal design specifications like that employed in MP syntax satisfies three key desiderata of evolutionary and general scientific plausibility: Physical Optimism, Rational Optimism, and Darwin’s Problem. In support of this claim, the methodologies employed in MP to maximise parsimony are characterised through an analysis of recent theories in Minimalist syntax, and those methodologies are defended with reference to practices and arguments from evolutionary biology and other natural sciences.

The marine biological week as an approach to science

Science.gov (United States)

Ransdorf, Angela; Satzinger, Viktoria

2017-04-01

The "Wiedner Gymnasium" is an academic high school with two branches: one focusses on languages and the other one on science. In the language branch the students learn at least three languages; one of which is Latin, whereas the students of the scientific branch can learn geometrical drawing and have to attend a scientific laboratory throughout the last four upper classes. As incentive highlights the language classes have a one week's school trip to France, Italy or Spain at the beginning of their 7th form in order to attend a language school and to practice their language skills. As a counterbalance, there was introduced the "marine biological week" several years ago, in which the students of the scientific branch take part whilst their colleagues have their language trips. The marine biological week takes place in Rovinj, Croatia. A team of biologists and divers leads through a programme, by which the students get an overview of different habitats, their conditions and the different ways of adaptation organisms find. Thus, they also become acquainted with several species of animals and plants which are characteristic for this area. They become familiar with some methods of scientific work and also get to know some of the problems marine ecosystems are confronted with. They also learn a little bit if the Mediterranean history and culture. Back in school all the findings are reviewed and brought into an ecological context. The insights can be used for many other topics, too, such as e.g. evolution. This week has proved to be a good start as well for the topic of ecology as for learning to think scientifically in general. So, you can call it a pivot for the scientific branch of our school.

Trends in programming languages for neuroscience simulations.

Science.gov (United States)

Davison, Andrew P; Hines, Michael L; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing.

Trends in Programming Languages for Neuroscience Simulations

Science.gov (United States)

Davison, Andrew P.; Hines, Michael L.; Muller, Eilif

2009-01-01

Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing. PMID:20198154

Trends in programming languages for neuroscience simulations

Directory of Open Access Journals (Sweden)

Andrew P Davison

2009-12-01

Full Text Available Neuroscience simulators allow scientists to express models in terms of biological concepts, without having to concern themselves with low-level computational details of their implementation. The expressiveness, power and ease-of-use of the simulator interface is critical in efficiently and accurately translating ideas into a working simulation. We review long-term trends in the development of programmable simulator interfaces, and examine the benefits of moving from proprietary, domain-specific languages to modern dynamic general-purpose languages, in particular Python, which provide neuroscientists with an interactive and expressive simulation development environment and easy access to state-of-the-art general-purpose tools for scientific computing.

Modeling biochemical transformation processes and information processing with Narrator

Directory of Open Access Journals (Sweden)

Palfreyman Niall M

2007-03-01

Full Text Available Abstract Background Software tools that model and simulate the dynamics of biological processes and systems are becoming increasingly important. Some of these tools offer sophisticated graphical user interfaces (GUIs, which greatly enhance their acceptance by users. Such GUIs are based on symbolic or graphical notations used to describe, interact and communicate the developed models. Typically, these graphical notations are geared towards conventional biochemical pathway diagrams. They permit the user to represent the transport and transformation of chemical species and to define inhibitory and stimulatory dependencies. A critical weakness of existing tools is their lack of supporting an integrative representation of transport, transformation as well as biological information processing. Results Narrator is a software tool facilitating the development and simulation of biological systems as Co-dependence models. The Co-dependence Methodology complements the representation of species transport and transformation together with an explicit mechanism to express biological information processing. Thus, Co-dependence models explicitly capture, for instance, signal processing structures and the influence of exogenous factors or events affecting certain parts of a biological system or process. This combined set of features provides the system biologist with a powerful tool to describe and explore the dynamics of life phenomena. Narrator's GUI is based on an expressive graphical notation which forms an integral part of the Co-dependence Methodology. Behind the user-friendly GUI, Narrator hides a flexible feature which makes it relatively easy to map models defined via the graphical notation to mathematical formalisms and languages such as ordinary differential equations, the Systems Biology Markup Language or Gillespie's direct method. This powerful feature facilitates reuse, interoperability and conceptual model development. Conclusion Narrator is a

Enablers and Inhibitors to English Language Learners' Research Process in a High School Setting

Science.gov (United States)

Kim, Sung Un

2015-01-01

This researcher sought to examine enablers and inhibitors to English language learner (ELL) students' research process within the framework of Carol C. Kuhlthau's Information Search Process (ISP). At a high school forty-eight ELL students in three classes, an English as a Second Language (ESL) teacher, and a biology teacher participated in the…

Biological time series analysis using a context free language: applicability to pulsatile hormone data.

Directory of Open Access Journals (Sweden)

Dennis A Dean

Full Text Available We present a novel approach for analyzing biological time-series data using a context-free language (CFL representation that allows the extraction and quantification of important features from the time-series. This representation results in Hierarchically AdaPtive (HAP analysis, a suite of multiple complementary techniques that enable rapid analysis of data and does not require the user to set parameters. HAP analysis generates hierarchically organized parameter distributions that allow multi-scale components of the time-series to be quantified and includes a data analysis pipeline that applies recursive analyses to generate hierarchically organized results that extend traditional outcome measures such as pharmacokinetics and inter-pulse interval. Pulsicons, a novel text-based time-series representation also derived from the CFL approach, are introduced as an objective qualitative comparison nomenclature. We apply HAP to the analysis of 24 hours of frequently sampled pulsatile cortisol hormone data, which has known analysis challenges, from 14 healthy women. HAP analysis generated results in seconds and produced dozens of figures for each participant. The results quantify the observed qualitative features of cortisol data as a series of pulse clusters, each consisting of one or more embedded pulses, and identify two ultradian phenotypes in this dataset. HAP analysis is designed to be robust to individual differences and to missing data and may be applied to other pulsatile hormones. Future work can extend HAP analysis to other time-series data types, including oscillatory and other periodic physiological signals.

OpenCOR: a modular and interoperable approach to computational biology

Directory of Open Access Journals (Sweden)

Alan eGarny

2015-02-01

Full Text Available 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.

Language Planning and Planned Languages: How Can Planned Languages Inform Language Planning?

Directory of Open Access Journals (Sweden)

Humphrey Tonkin

2015-04-01

Full Text Available The field of language planning (LP has largely ignored planned languages. Of classic descriptions of LP processes, only Tauli (preceded by Wüster suggests that planned languages (what Wüster calls Plansprache might bear on LP theory and practice. If LP aims "to modify the linguistic behaviour of some community for some reason," as Kaplan and Baldauf put it, creating a language de novo is little different. Language policy and planning are increasingly seen as more local and less official, and occasionally more international and cosmopolitan. Zamenhof's work on Esperanto provides extensive material, little studied, documenting the formation of the language and linking it particularly to issues of supranational LP. Defining LP decision-making, Kaplan & Baldauf begin with context and target population. Zamenhof's Esperanto came shortly before Ben-Yehuda's revived Hebrew. His target community was (mostly the world's educated elite; Ben-Yehuda's was worldwide Jewry. Both planners were driven not by linguistic interest but by sociopolitical ideology rooted in reaction to anti-Semitism and imbued with the idea of progress. Their territories had no boundaries, but were not imaginary. Function mattered as much as form (Haugen's terms, status as much as corpus. For Zamenhof, status planning involved emphasis on Esperanto's ownership by its community - a collective planning process embracing all speakers (cf. Hebrew. Corpus planning included a standardized European semantics, lexical selectivity based not simply on standardization but on representation, and the development of written, and literary, style. Esperanto was successful as linguistic system and community language, less as generally accepted lingua franca. Its terminology development and language cultivation offers a model for language revival, but Zamenhof's somewhat limited analysis of language economy left him unprepared to deal with language as power.

Taming Log Files from Game/Simulation-Based Assessments: Data Models and Data Analysis Tools. Research Report. ETS RR-16-10

Science.gov (United States)

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…

Markdoc

DEFF Research Database (Denmark)

Haghish, E. F.

2016-01-01

for typesetting the document. In this article, I introduce markdoc, a software package for interactive literate programming and generating dynamic-analysis documents in Stata. markdoc recognizes Markdown, LATEX, and HTML markup languages and can export documents in several formats, such as PDF, Microsoft Office.......docx, OpenOffice and LibreOffice.odt, LATEX, HTML, ePub, and Markdown....

Dependency Tree Annotation Software

Science.gov (United States)

2015-11-01

extended markup language [XML] format), PNG+XML (.png) file or .vdx file (XML drawing file) from their files.* o “Open .conll File” allows the user to...to zoom the graph to. The user can also select “Custom” and enter in a customized zoom percentage .* o “Zoom in” and “Zoom out” cause the graph to

Using XML to Separate Content from the Presentation Software in eLearning Applications

Science.gov (United States)

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…

PORIDGE: Postmodern Rhizomatics in Digitally Generated Environments--Do We Need a Metatheory for W3?

Science.gov (United States)

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)…

Cognitive Neuroscience of Foreign Language Education: Myths and Realities

Directory of Open Access Journals (Sweden)

Ali Nouri

2015-04-01

Full Text Available This paper summarizes the educational implications of current research on cognitive neuroscience for foreign-language learning to provide an overview of myths and realities in this appealing area of research. Although the potential benefits of neuroscientific research into language acquisition are great, there are a number of popular myths that none of which are supported by scientific evidence. In this paper, three prominent examples of these myths are introduced and discussed how they are based on misinterpretation and misapplication from neuroscience research. The first pervasive example of such misconception is the prevalent belief of being the certain critical periods for learning a second language. It implies that the opportunity to acquire foreign languages is lost forever by missing these biological windows. In fact, however, extensive research shows that there are sensitive periods, but not critical periods, during which an individual can acquire certain aspects of language with greater ease than at other times. Another example of myths is a false conclusion implies that exposing children to a foreign language too early interrupts knowledge of their first language. The reality is that learning a second language not only improves language abilities in the first language, but also positively affects reading abilities and general literacy in school. Like the other myths, there is also a popular conception about ability to learn second language during sleep. It is demonstrated that previously acquired memories are consolidated and new association are learned during sleep, but learning a foreign language requires conscious effort and available data do not support this hypothesis that second language acquire during sleep. The main conclusion arising from this argument is that, while our understanding of the neural bases of language learning is continually evolving, our interpretation of the implications of these findings for foreign language

Language comprehension warps the mirror neuron system

Directory of Open Access Journals (Sweden)

Noah eZarr

2013-12-01

Full Text Available Is the mirror neuron system (MNS used in language understanding? According to embodied accounts of language comprehension, understanding sentences describing actions makes use of neural mechanisms of action control, including the MNS. Consequently, repeatedly comprehending sentences describing similar actions should induce adaptation of the MNS thereby warping its use in other cognitive processes such as action recognition and prediction. To test this prediction, participants read blocks of multiple sentences where each sentence in the block described transfer of objects in a direction away or toward the reader. Following each block, adaptation was measured by having participants predict the end-point of videotaped actions. The adapting sentences disrupted prediction of actions in the same direction, but a only for videos of biological motion, and b only when the effector implied by the language (e.g., the hand matched the videos. These findings are signatures of the mirror neuron system.

Language comprehension warps the mirror neuron system.

Science.gov (United States)

Zarr, Noah; Ferguson, Ryan; Glenberg, Arthur M

2013-01-01

Is the mirror neuron system (MNS) used in language understanding? According to embodied accounts of language comprehension, understanding sentences describing actions makes use of neural mechanisms of action control, including the MNS. Consequently, repeatedly comprehending sentences describing similar actions should induce adaptation of the MNS thereby warping its use in other cognitive processes such as action recognition and prediction. To test this prediction, participants read blocks of multiple sentences where each sentence in the block described transfer of objects in a direction away or toward the reader. Following each block, adaptation was measured by having participants predict the end-point of videotaped actions. The adapting sentences disrupted prediction of actions in the same direction, but (a) only for videos of biological motion, and (b) only when the effector implied by the language (e.g., the hand) matched the videos. These findings are signatures of the MNS.

New software tools for evaluating and disseminating nuclear data

International Nuclear Information System (INIS)

Langlands, Tracy L.M.; Miyake, Erik E.; Stone, Craig A.

2001-01-01

Three new related technologies that offer real promise for modeling, processing, and disseminating nuclear data are explored. Extensible Markup Language (XML) provides a simple method of describing nuclear data. Extensible Style Language (XSL) supports XML data searching, filtering and processing. It is shown how the technology can be used to transform an XML-formatted ENSDF file into a table of similar form to those found in the Nuclear Data Sheets. Scalable Vector Graphics (SVG) has been used to convert XML formatted ENSDF files into interactive level scheme

The Bilingual Brain: Human Evolution and Second Language Acquisition

Directory of Open Access Journals (Sweden)

L. Kirk Hagen

2008-01-01

Full Text Available For the past half-century, psycholinguistic research has concerned itself with two mysteries of human cognition: (1 that children universally acquire a highly abstract, computationally complex set of linguistic rules rapidly and effortlessly, and (2 that second language acquisition (SLA among adults is, conversely, slow, laborious, highly variable, and virtually never results in native fluency. We now have a decent, if approximate, understanding of the biological foundations of first language acquisition, thanks in large part to Lenneberg's (1964, 1984 seminal work on the critical period hypothesis. More recently, the elements of a promising theory of language and evolution have emerged as well (see e.g. Bickerton, 1981, 1990; Leiberman, 1984, 1987. I argue here that the empirical foundations of an evolutionary theory of language are now solid enough to support an account of bilingualism and adult SLA as well. Specifically, I will show that evidence from the environment of evolutionary adaptation of paleolithic humans suggests that for our nomadic ancestors, the ability to master a language early in life was an eminently useful adaptation. However, the ability to acquire another language in adulthood was not, and consequently was not selected for propagation.

The language of the protein universe.

Science.gov (United States)

Scaiewicz, Andrea; Levitt, Michael

2015-12-01

Proteins, the main cell machinery which play a major role in nearly every cellular process, have always been a central focus in biology. We live in the post-genomic era, and inferring information from massive data sets is a steadily growing universal challenge. The increasing availability of fully sequenced genomes can be regarded as the 'Rosetta Stone' of the protein universe, allowing the understanding of genomes and their evolution, just as the original Rosetta Stone allowed Champollion to decipher the ancient Egyptian hieroglyphics. In this review, we consider aspects of the protein domain architectures repertoire that are closely related to those of human languages and aim to provide some insights about the language of proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Dependency distance: A new perspective on syntactic patterns in natural languages

Science.gov (United States)

Liu, Haitao; Xu, Chunshan; Liang, Junying

2017-07-01

Dependency distance, measured by the linear distance between two syntactically related words in a sentence, is generally held as an important index of memory burden and an indicator of syntactic difficulty. Since this constraint of memory is common for all human beings, there may well be a universal preference for dependency distance minimization (DDM) for the sake of reducing memory burden. This human-driven language universal is supported by big data analyses of various corpora that consistently report shorter overall dependency distance in natural languages than in artificial random languages and long-tailed distributions featuring a majority of short dependencies and a minority of long ones. Human languages, as complex systems, seem to have evolved to come up with diverse syntactic patterns under the universal pressure for dependency distance minimization. However, there always exist a small number of long-distance dependencies in natural languages, which may reflect some other biological or functional constraints. Language system may adapt itself to these sporadic long-distance dependencies. It is these universal constraints that have shaped such a rich diversity of syntactic patterns in human languages.

Human biological rhythm in traditional Chinese medicine

Directory of Open Access Journals (Sweden)

Tianxing Zhang

2016-10-01

Full Text Available Traditional Chinese medicine (TCM has a comprehensive and thorough understanding of biological rhythm. Biological rhythm is an inherent connotation of “harmony between human and nature”, one of the thoughts in TCM. TCM discusses emphatically circadian rhythm, syzygial rhythm and seasonal rhythm, and particularly circadian and seasonal rhythms. Theories of Yin Yang and Five Elements are the principles and methods, with which TCM understands biological rhythms. Based on theories in TCM, biological rhythm in essence is a continuous variation of the human body state synchronized with natural rhythms, and theories of Yin Yang and Five Elements are both language tools to describe this continuous variation and theoretical tools for its investigation and application. The understandings of biological rhythm in TCM can be applied to etiology, health care, disease control and treatment. Many understandings in TCM have been confirmed by modern research and clinical reports, but there are still some pending issues. TCM is distinguished for its holistic viewpoint on biological rhythms.

A new instrument to assess physician skill at thoracic ultrasound, including pleural effusion markup.

Science.gov (United States)

Salamonsen, Matthew; McGrath, David; Steiler, Geoff; Ware, Robert; Colt, Henri; Fielding, David

2013-09-01

To reduce complications and increase success, thoracic ultrasound is recommended to guide all chest drainage procedures. Despite this, no tools currently exist to assess proceduralist training or competence. This study aims to validate an instrument to assess physician skill at performing thoracic ultrasound, including effusion markup, and examine its validity. We developed an 11-domain, 100-point assessment sheet in line with British Thoracic Society guidelines: the Ultrasound-Guided Thoracentesis Skills and Tasks Assessment Test (UGSTAT). The test was used to assess 22 participants (eight novices, seven intermediates, seven advanced) on two occasions while performing thoracic ultrasound on a pleural effusion phantom. Each test was scored by two blinded expert examiners. Validity was examined by assessing the ability of the test to stratify participants according to expected skill level (analysis of variance) and demonstrating test-retest and intertester reproducibility by comparison of repeated scores (mean difference [95% CI] and paired t test) and the intraclass correlation coefficient. Mean scores for the novice, intermediate, and advanced groups were 49.3, 73.0, and 91.5 respectively, which were all significantly different (P < .0001). There were no significant differences between repeated scores. Procedural training on mannequins prior to unsupervised performance on patients is rapidly becoming the standard in medical education. This study has validated the UGSTAT, which can now be used to determine the adequacy of thoracic ultrasound training prior to clinical practice. It is likely that its role could be extended to live patients, providing a way to document ongoing procedural competence.

Simulating the Effects of Cross-Generational Cultural Transmission on Language Change

Science.gov (United States)

Gong, Tao; Shuai, Lan

Language evolves in a socio-cultural environment. Apart from biological evolution and individual learning, cultural transmission also casts important influence on many aspects of language evolution. In this paper, based on the lexicon-syntax coevolution model, we extend the acquisition framework in our previous work to examine the roles of three forms of cultural transmission spanning the offspring, parent, and grandparent generations in language change. These transmissions are: those between the parent and offspring generations (PO), those within the offspring generation (OO), and those between the grandparent and offspring generations (GO). The simulation results of the considered model and relevant analyses illustrate not only the necessity of PO and OO transmissions for language change, thus echoing our previous findings, but also the importance of GO transmission, a form of cross-generational cultural transmission, on preserving the mutual understandability of the communal language across generations of individuals.

Music and language: relations and disconnections.

Science.gov (United States)

Kraus, Nina; Slater, Jessica

2015-01-01

Music and language provide an important context in which to understand the human auditory system. While they perform distinct and complementary communicative functions, music and language are both rooted in the human desire to connect with others. Since sensory function is ultimately shaped by what is biologically important to the organism, the human urge to communicate has been a powerful driving force in both the evolution of auditory function and the ways in which it can be changed by experience within an individual lifetime. This chapter emphasizes the highly interactive nature of the auditory system as well as the depth of its integration with other sensory and cognitive systems. From the origins of music and language to the effects of auditory expertise on the neural encoding of sound, we consider key themes in auditory processing, learning, and plasticity. We emphasize the unique role of the auditory system as the temporal processing "expert" in the brain, and explore relationships between communication and cognition. We demonstrate how experience with music and language can have a significant impact on underlying neural function, and that auditory expertise strengthens some of the very same aspects of sound encoding that are deficient in impaired populations. © 2015 Elsevier B.V. All rights reserved.

Textbook language: Incentive or obstacle

Directory of Open Access Journals (Sweden)

Šefer Jasmina

2008-01-01

Full Text Available The criticism of the current language in school textbooks indicates the gravity of this problem in our environment and the need to solve it. The first step in approaching this problem is studying the reception of primary school textbooks. In the first part of the paper we discuss all primary school textbooks from the fifth to the eighth grade with regard to the frequency of textbook usage and the perception of the difficulty of textbook language. In the second part of the paper there is an additional analysis of history, geography, biology, physics and chemistry textbooks from the fifth to the eighth grade with regard to the reasons for which pupils find them difficult. This preliminary research comprised in total 120 pupils from an urban school, thirty from each fifth to eighth grade. We analyzed the textbooks of the Institute for Textbook Publishing and Teaching Aids, which are used most frequently in our educational practice, and hence can represent the general situation of the problem. Bearing in mind the limited size of the sample of pupils, the results are used only as an illustration and should encourage new studies on a more extensive sample. Textbook language is often difficult since it is mostly insufficiently comprehensible, longwinded and with many data. In natural sciences, physics and chemistry, pupils give up studying from the textbook. The textbooks in narrative subjects lead the way with respect to their usage, among which everybody finds history textbooks most difficult. Geography and biology textbooks were evaluated differently, depending on the grade and success of the pupils declaring themselves. The results present a guideline to the current and new writers of our textbooks, critics and publishing houses.

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

Science.gov (United States)

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

2013-09-01

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

Using XML technology for the ontology-based semantic integration of life science databases.

Science.gov (United States)

Philippi, Stephan; Köhler, Jacob

2004-06-01

Several hundred internet accessible life science databases with constantly growing contents and varying areas of specialization are publicly available via the internet. Database integration, consequently, is a fundamental prerequisite to be able to answer complex biological questions. Due to the presence of syntactic, schematic, and semantic heterogeneities, large scale database integration at present takes considerable efforts. As there is a growing apprehension of extensible markup language (XML) as a means for data exchange in the life sciences, this article focuses on the impact of XML technology on database integration in this area. In detail, a general architecture for ontology-driven data integration based on XML technology is introduced, which overcomes some of the traditional problems in this area. As a proof of concept, a prototypical implementation of this architecture based on a native XML database and an expert system shell is described for the realization of a real world integration scenario.

Integration, warehousing, and analysis strategies of Omics data.

Science.gov (United States)

Gedela, Srinubabu

2011-01-01

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

Metingear: a development environment for annotating genome-scale metabolic models.

Science.gov (United States)

May, John W; James, A Gordon; Steinbeck, Christoph

2013-09-01

Genome-scale metabolic models often lack annotations that would allow them to be used for further analysis. Previous efforts have focused on associating metabolites in the model with a cross reference, but this can be problematic if the reference is not freely available, multiple resources are used or the metabolite is added from a literature review. Associating each metabolite with chemical structure provides unambiguous identification of the components and a more detailed view of the metabolism. We have developed an open-source desktop application that simplifies the process of adding database cross references and chemical structures to genome-scale metabolic models. Annotated models can be exported to the Systems Biology Markup Language open interchange format. Source code, binaries, documentation and tutorials are freely available at http://johnmay.github.com/metingear. The application is implemented in Java with bundles available for MS Windows and Macintosh OS X.

A state-of-the-art review of interoperability amongst heterogeneous software systems

Directory of Open Access Journals (Sweden)

Carlos Mario Zapata Jaramillo

2009-05-01

Full Text Available Information systems are sets of interacting elements aimed at supporting entrepreneurial or business activities; they cannot thus coexist in an isolated way but require their data to be shared so as to increase their productivity. Such systems’ interoperability is normally accomplished through mark-up standards, query languages and web services. The literature contains work related to software system interoperability; however, it presents some difficulties, such as the need for using the same platforms and different programming languages, the use of read only languages and the deficiencies in the formalism used for achieving it. This paper presents a critical review of the advances made regarding heterogeneous software systems’ interoperability.

Microsoft Biology Initiative: .NET Bioinformatics Platform and Tools

Science.gov (United States)

Diaz Acosta, B.

2011-01-01

The Microsoft Biology Initiative (MBI) is an effort in Microsoft Research to bring new technology and tools to the area of bioinformatics and biology. This initiative is comprised of two primary components, the Microsoft Biology Foundation (MBF) and the Microsoft Biology Tools (MBT). MBF is a language-neutral bioinformatics toolkit built as an extension to the Microsoft .NET Framework—initially aimed at the area of Genomics research. Currently, it implements a range of parsers for common bioinformatics file formats; a range of algorithms for manipulating DNA, RNA, and protein sequences; and a set of connectors to biological web services such as NCBI BLAST. MBF is available under an open source license, and executables, source code, demo applications, documentation and training materials are freely downloadable from http://research.microsoft.com/bio. MBT is a collection of tools that enable biology and bioinformatics researchers to be more productive in making scientific discoveries.

Environmental factors influence language development in children with autism spectrum disorders.

Directory of Open Access Journals (Sweden)

Marine Grandgeorge

Full Text Available BACKGROUND: While it is clearly admitted that normal behavioural development is determined by the interplay of genetic and environmental influences, this is much less the case for psychiatric disorders for which more emphasis has been given in the past decades on biological determinism. Thus, previous studies have shown that Autistic Spectrum Disorders (ASD were not affected by parental style. However, animal research suggests that different behavioural traits can be differentially affected by genetic/environmental factors. METHODOLOGY/ PRINCIPAL FINDINGS: In the present study we hypothesized that amongst the ASD, language disorders may be more sensitive to social factors as language is a social act that develops under social influences. Using the Autism Diagnostic Interview-Revised, we compared the early characteristics of sensori-motor and language development in a large sample of children with ASD (n = 162 with parents belonging to different levels of education. The results showed that children raised by parents with a high level of education displayed earlier language development. Moreover, they showed earlier first words and phrases if their mother was at a high level of education, which reveals an additional gender effect. CONCLUSIONS/SIGNIFICANCE: To our knowledge this study may trigger important new lines of thought and research, help equilibrate social and purely biological perspectives regarding ASD and bring new hopes for environmentally based therapies.

OWL Reasoning Framework over Big Biological Knowledge Network

Science.gov (United States)

Chen, Huajun; Chen, Xi; Gu, Peiqin; Wu, Zhaohui; Yu, Tong

2014-01-01

Recently, huge amounts of data are generated in the domain of biology. Embedded with domain knowledge from different disciplines, the isolated biological resources are implicitly connected. Thus it has shaped a big network of versatile biological knowledge. Faced with such massive, disparate, and interlinked biological data, providing an efficient way to model, integrate, and analyze the big biological network becomes a challenge. In this paper, we present a general OWL (web ontology language) reasoning framework to study the implicit relationships among biological entities. A comprehensive biological ontology across traditional Chinese medicine (TCM) and western medicine (WM) is used to create a conceptual model for the biological network. Then corresponding biological data is integrated into a biological knowledge network as the data model. Based on the conceptual model and data model, a scalable OWL reasoning method is utilized to infer the potential associations between biological entities from the biological network. In our experiment, we focus on the association discovery between TCM and WM. The derived associations are quite useful for biologists to promote the development of novel drugs and TCM modernization. The experimental results show that the system achieves high efficiency, accuracy, scalability, and effectivity. PMID:24877076

Preschool language interventions for latino dual language learners with language disorders: what, in what language, and how.

Science.gov (United States)

Simon-Cereijido, Gabriela

2015-05-01

About a quarter of young children in the United States are dual language learners. The large majority are Latino children who are exposed to Spanish in their homes. The language needs of Latino dual language preschoolers are different from the needs of monolingual English-speaking children. As a group, they are likely to live in environments that put them at risk of delays in language development. This situation is direr for dual language preschoolers with language impairment. Recent findings from studies on interventions for Spanish-English preschoolers with language impairment suggest that a bilingual approach does not delay English vocabulary and oral language learning and promotes Spanish maintenance. Targets and strategies for different language domains are described. The effects of pullout versus push-in interventions for this population are preliminarily explored. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

An XML-Based Protocol for Distributed Event Services

Science.gov (United States)

Smith, Warren; Gunter, Dan; Quesnel, Darcy; Biegel, Bryan (Technical Monitor)

2001-01-01

This viewgraph presentation provides information on the application of an XML (extensible mark-up language)-based protocol to the developing field of distributed processing by way of a computational grid which resembles an electric power grid. XML tags would be used to transmit events between the participants of a transaction, namely, the consumer and the producer of the grid scheme.

Mission Assurance, Threat Alert, Disaster Resiliency and Response (MATADRR) Product Reference Guide

Science.gov (United States)

2014-06-01

the world. Keystone implants the Google Earth KML ( Keyhole Markup Language) publishing interface to consume the Keystone Work Product sharing. Client...multiple Cores; display, close and archive incidents and work products; and monitor the health and status of the Core. Agreement Services are...to protect forces, mitigate threats, close protection gaps, and provide increased situational awareness by linking the disparate physical

Indo-European languages tree by Levenshtein distance

Science.gov (United States)

Serva, M.; Petroni, F.

2008-03-01

The evolution of languages closely resembles the evolution of haploid organisms. This similarity has been recently exploited (Gray R. D. and Atkinson Q. D., Nature, 426 (2003) 435; Gray R. D. and Jordan F. M., Nature, 405 (2000) 1052) to construct language trees. The key point is the definition of a distance among all pairs of languages which is the analogous of a genetic distance. Many methods have been proposed to define these distances; one of these, used by glottochronology, computes the distance from the percentage of shared "cognates". Cognates are words inferred to have a common historical origin, and subjective judgment plays a relevant role in the identification process. Here we push closer the analogy with evolutionary biology and we introduce a genetic distance among language pairs by considering a renormalized Levenshtein distance among words with same meaning and averaging on all words contained in a Swadesh list (Swadesh M., Proc. Am. Philos. Soc., 96 (1952) 452). The subjectivity of process is consistently reduced and the reproducibility is highly facilitated. We test our method against the Indo-European group considering fifty different languages and the two hundred words of the Swadesh list for any of them. We find out a tree which closely resembles the one published in Gray and Atkinson (2003), with some significant differences.