XML-based Language Research Articles

CellML 2.0.1

Abstract We present here CellML 2.0.1, an XML-based language for describing and exchanging mathematical models of physiological systems. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations giving relationships between those variables. Models may import other models to create systems of increasing complexity. CellML 2.0.1 is defined by the normative specification presented here, prescribing the CellML syntax and the rules by which it should be used. The normative specification is intended primarily for the developers of software tools which directly consume CellML syntax. Users of CellML models may prefer to browse the informative rendering of the specification (https://cellml.org/specifications/cellml_2.0/) which extends the normative specification with explanations of the rules combined with examples of their usage. This version improves the identification of rule statements and corrects errata present in the CellML 2.0 specification.

Development of XMLbased Markup Language

Development of XMLbased Markup Language

MAGICPL: A Generic Process Description Language for Distributed Pseudonymization Scenarios.

Pseudonymization is an important aspect of projects dealing with sensitive patient data. Most projects build their own specialized, hard-coded, solutions. However, these overlap in many aspects of their functionality. As any re-implementation binds resources, we would like to propose a solution that facilitates and encourages the reuse of existing components. We analyzed already-established data protection concepts to gain an insight into their common features and the ways in which their components were linked together. We found that we could represent these pseudonymization processes with a simple descriptive language, which we have called MAGICPL, plus a relatively small set of components. We designed MAGICPL as an XML-based language, to make it human-readable and accessible to nonprogrammers. Additionally, a prototype implementation of the components was written in Java. MAGICPL makes it possible to reference the components using their class names, making it easy to extend or exchange the component set. Furthermore, there is a simple HTTP application programming interface (API) that runs the tasks and allows other systems to communicate with the pseudonymization process. MAGICPL has been used in at least three projects, including the re-implementation of the pseudonymization process of the German Cancer Consortium, clinical data flows in a large-scale translational research network (National Network Genomic Medicine), and for our own institute's pseudonymization service. Putting our solution into productive use at both our own institute and at our partner sites facilitated a reduction in the time and effort required to build pseudonymization pipelines in medical research.

상호운용적 제조지능화를 위한 OPC UA 기반 데이터 애널리틱스 모델 표현 방법

Manufacturing intelligence necessitates interoperable data and model exchange so that machines seamlessly collect and share their data to create and use data-driven models for predictive planning and control. Open Platform Communications Unified Architecture (OPC UA) has become a powerful standard for data interoperability, and has been extended to various industrial sectors through publishing OPC UA companion specifications with collaboration of industrial consortiums. However, companion specifications for the interoperability of data analytics models have not been released yet. The present work proposes an OPC UA-based representation method for the data analytics models formalized by Predictive Model Markup Language (PMML), an XML-based language for interchanging data analytics models. This article includes: definition of mapping rules between PMML and OPC UA, design of OPC UA information models compliant with PMML, and implementation of a server-client prototype that publishes and subscribes two OPC UA model instances transformed from PMML-based regression and neural network models.

CellML 2.0.

We present here CellML 2.0, an XML-based language for describing and exchanging mathematical models of physiological systems. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of reusable components, each with variables and equations giving relationships between those variables. Models may import other models to create systems of increasing complexity. CellML 2.0 is defined by the normative specification presented here, prescribing the CellML syntax and the rules by which it should be used. The normative specification is intended primarily for the developers of software tools which directly consume CellML syntax. Users of CellML models may prefer to browse the informative rendering of the specification (https://cellml.org/specifications/cellml_2.0/) which extends the normative specification with explanations of the rules combined with examples of their usage.

XML-Based Video Game Description Language

This paper presents the XML-based Video Game Description Language (XVGDL), a new language for specifying Video games which is based on the Extensible Markup Language (XML). The proposal is portable and extensible, and allows games to not only be defined at engine level but also includes specific features that can lead the game design process whilst simultaneously reducing the gap between game specification and its corresponding game implementation. XVGDL is as generic as possible, making it possible to describe different genres of games. This paper focuses on presenting the basis of the language. The paper describes the syntax as well as the components of XVGDL, and provides examples of their use. Defining games via XML structures provides all the advantages of the management of XML files and opens up interesting lines of research. Our proposal provides a number of novel features. So, XVGDL game definitions can be managed as any other XML file, which means that it can be automatically handled by any XML file management software. Another interesting feature is that XVGDL can specify game components (e.g., game Artificial), in-game processes (e.g., the procedural generation of maps) or in-game events (e.g., the checking of the conditions to end a game match) via the association with external (possibly non-XML) files. Moreover, XVGDL files can be easily validated as any XML file what means that validations against a particular Document Type Definition (DTD) or XML Schema Definition (XSD) are possible. In addition, the paper presents a first prototype implementation of a (text-based) interpreter that allows XVGDL game specifications as a playable game to be executed. This tool not only validates our proposal but also represents a first step towards smoothing the path to obtaining an executable version of a game from its game specification.

EXCHANGE REQUIREMENT-BASED DELIVERY METHOD OF STRUCTURAL DESIGN INFORMATION FOR COLLABORATIVE DESIGN USING INDUSTRY FOUNDATION CLASSES

In Architecture, engineering, and construction (AEC) collaboration, exchange requirements (ERs) vary in different projects with different platforms. In order to ensure the completeness and accuracy of data sharing and exchange for structural engineering in collaborative design, an ER-based delivery method was proposed to improve the delivery of structural design information. First, a process map of structural design was developed based on Information Delivery Manual (IDM). Within this process map, an ER Matrix of structural design was proposed to define information required by other disciplines at different stages. This matrix was composed of a set of required structural objects and their attributes, which were mapped to related Industry Foundation Classes (IFC) data. The mapping between the ER Matrix and IFC-based structural model data was implemented by an exchange model generation algorithm. Furthermore, a delivery tool was developed to define the ER Matrix in two ways, including user interface and XML-based language. A practical project was used to illustrate the utility of the proposed method. The results show that the proposed method using IFC is beneficial for structural information delivery.

CODA-ML: context-specific biological knowledge representation for systemic physiology analysis

BackgroundComputational analysis of complex diseases involving multiple organs requires the integration of multiple different models into a unified model. Different models are often constructed in heterogeneous formats. Thus, the integration of the models requires a standard language format that can effectively represent essential biological information. However, the previously introduced formats have limitations that prevent from adequately representing essential biological information, particularly specifications of bio-molecules and biological contexts.ResultsWe defined an XML-based markup language called context-oriented directed association markup language (CODA-ML), which better represents essential biological information. The CODA-ML has two major strengths in designating molecular specifications and biological contexts. It can cover heterogeneous entity types involved in biological events (e.g. gene/protein, compound, cellular function, disease). Molecular types of entities can have molecular specifications which include detailed information of a molecule from isoforms to modifications, enabling high-resolution representation of molecules. In addition, it can distinguish biological events that vary depending on different biological contexts such as cell types or disease conditions. Especially representation of inter-cellular events as well as intra-cellular events is available. These two major strengths can resolve contradictory associations when different models are integrated into one unified model, which improves the accuracy of the model.ConclusionsWith the CODA-ML, diverse models such as signaling pathways, metabolic pathways, and gene regulatory pathways can be represented in a unified language format. Heterogeneous entity types can be covered by the CODA-ML, thus it enables detailed description for the mechanisms of diseases or drugs from multiple perspectives (e.g., molecule, function or disease). The CODA-ML is expected to help integrate different models into one systemic model in an efficient and effective. The unified model can be used to perform computational analysis not only for cancer but also for other complex diseases involving multiple organs beyond a single cell.

NFBLab-A Versatile Software for Neurofeedback and Brain-Computer Interface Research.

Neurofeedback (NFB) is a real-time paradigm, where subjects learn to volitionally modulate their own brain activity recorded with electroencephalographic (EEG), magnetoencephalographic (MEG) or other functional brain imaging techniques and presented to them via one of sensory modalities: visual, auditory or tactile. NFB has been proposed as an approach to treat neurological conditions and augment brain functions. Although the early NFB studies date back nearly six decades ago, there is still much debate regarding the efficiency of this approach and the ways it should be implemented. Partly, the existing controversy is due to suboptimal conditions under which the NFB training is undertaken. Therefore, new experimental tools attempting to provide optimal or close to optimal training conditions are needed to further exploration of NFB paradigms and comparison of their effects across subjects and training days. To this end, we have developed open-source NFBLab, a versatile, Python-based software for conducting NFB experiments with completely reproducible paradigms and low-latency feedback presentation. Complex experimental protocols can be configured using the GUI and saved in NFBLab's internal XML-based language that describes signal processing tracts, experimental blocks and sequences including randomization of experimental blocks. NFBLab implements interactive modules that enable individualized EEG/MEG signal processing tracts specification using spatial and temporal filters for feature selection and artifacts removal. NFBLab supports direct interfacing to MNE-Python software to facilitate source-space NFB based on individual head models and properly tailored individual inverse solvers. In addition to the standard algorithms for extraction of brain rhythms dynamics from EEG and MEG data, NFBLab implements several novel in-house signal processing algorithms that afford significant reduction in latency of feedback presentation and may potentially improve training effects. The software also supports several standard BCI paradigms. To interface with external data acquisition devices NFBLab employs Lab Streaming Layer protocol supported by the majority of EEG vendors. MEG devices are interfaced through the Fieldtrip buffer.

Usability assessment of interaction management support in LOUISE, an ECA-based user interface for elders with cognitive impairment

Embodied conversational agents (ECA) are possible enablers of assistive technologies, in particular for older adults with cognitive impairment. Yet, dedicated interaction management techniques addressing the specificities of this public are needed. OBJECTIVES: We assess whether the interaction management framework of the LOUISE (Lovely User Interface for Servicing Elders) ECA has the potential to overcome the user interface constraints linked to cognitive impairment. METHODS: LOUISE supports key target-specific features: personalization; attention management; context reminders; image and video displays; a conversation manager for task-oriented interactions; and the foundations for a domain-specific XML-based language for task-oriented assistive scenarios. LOUISE’s usability and acceptance were evaluated at the Broca geriatric hospital in Paris. with a group of 14 older adults with either mild cognitive impairment (MCI) or Alzheimer’s disease (AD) through four simple but realistic assistive scenarios: drinking, taking medicine, measuring blood pressure and choosing the lunch menu. RESULTS: Most of our participants were able to interact with the ECA, succeeded in completing the proposed tasks and enjoyed our design. CONCLUSION: The field usability evaluation of LOUISE’s interaction management framework suggests that this suite of interaction techniques can be effective in enabling interfaces for users with MCI or AD.

An approach to XBRL interoperability based on Ant Colony Optimization algorithm

Extensible Business Reporting Language (XBRL) is an XML-based language developed for enhancing interoperability among the entities involved in process of business reporting. Although this language is adopted by various regulators all around the world and has contributed greatly to semantic interoperability in this field, the variations between taxonomies and also between elements of instance documents, still cause many inconsistencies between elements. Although some existing approaches suppose the conversion of XBRL to ontologies and then resolve the inconsistencies by applying some mapping techniques, it does not seem practical because of low precision and incompleteness of these conversions. In this paper, a novel approach is proposed which utilizes Ant Colony Optimization (ACO) in order to detect best semantic mappings between inconsistent concepts of two XBRL documents. This approach analyzes the possible mappings with respect to various factors like concept names, all label texts, presentation and calculation hierarchies and so on. This makes the approach capable of finding mappings, which were not easily discoverable otherwise. The proposed approach is implemented and applied to actual XBRL reports. The results are measured with aid of well-known criteria (precision, recall and F-measure) and are compared with the well-known Hungarian algorithm and illustrate the better performance in accordance with these three criteria.

Application of XML-based Language for Digital Representation of Crochet Symbols

This paper views the problems related to the development of crochet software. It presents an extension of PKF - XML-based language for digital representation of crochet patterns. Its purpose is to develop a uniform and platform independent description of simple graphic primitives corresponding to different types of stitches. Due to the crochet symbols’ features the suggested format is particularly suitable for their description. Graphic primitives are described in vector format, character transformations are allowed, and there are possibilities for creating combinations of symbols, called clusters – major components in crochet diagram.The XML language can be built on crochet software.

An approach to build XML-based domain specific languages solutions for client-side web applications

Summary Domain-Specific Languages (DSLs) allow for the building of applications that ease the labour of both software engineers and domain experts thanks to the level of abstraction they provide. In cases where the domain is restricted to Client-Side Web Applications (CSWA), XML-based languages, frameworks and widgets are commonly combined in order to provide fast, robust and flexible solutions. This article presents an approach designed to create XML-based DSL solutions for CSWA that includes an evaluation engine, a programming model and a lightweight development environment. The approach is able to evaluate multiple XML-based DSL programs simultaneously to provide solutions to those Domain Specific Problems for CSWAs. To better demonstrate the capabilities and potential of this novel approach, we will employ a couple of case studies, namely Anisha and FeedPsi .

Development of custom notation for XML-based language: A model-driven approach

In spite of its popularity, XML provides poor user experience and a lot of domain-specific languages can be improved by introducing custom, more humanfriendly notation. This paper presents an approach for design and development of the custom notation for existing XML-based language together with a translator between the new notation and XML. The approach supports iterative design of the language concrete syntax, allowing its modification based on users feedback. The translator is developed using a model-driven approach. It is based on explicit representation of language abstract syntax (metamodel) that can be augmented with mappings to both XML and the custom notation. We provide recommendations for application of the approach and demonstrate them on a case study of a language for definition of graphs.

Partov: a network simulation and emulation tool

Network protocol design and evaluation requires either full implementation of the considered protocol and evaluation in a real network, or a simulation based on a model. There is also a middle approach in which both simulation and emulation are used to evaluate a protocol. In this article the Partov engine, which provides both simulation and emulation capabilities simultaneously, is presented. Partov benefits from a layered and platform-independent architecture. As a pure simulator, it provides an extensible plugin-based platform that can be configured to perform both real-time and non-real-time discrete-event simulations. It also acts as an emulator, making interaction with real networks possible in real time. Additionally, a declarative XML-based language is used, acting as a glue between simulation and emulation modules and plugins. It supports dynamic network modelling and simulation based on continuous time Markov chains. Partov is compared with other well-known tools such as NS-3 and real processes such as Hping3. It is shown that Partov requires less overhead and is much more scalable than NS-3.

A Formal Language For Specifying Visual Interface Signifiers

User interfaces are often designed with signifiers that support end-users in understanding the function and meaning of device components. Formal methods have been successfully applied to support computational usability analyses early in the interface design cycle, without the need for a physical interface prototype. However limited support exists for applying formal methods to the analysis of signifiers. This paper presents the XML-based language of Browser-Integrated Guidance for Specifying Interface Signifiers (BIGSIS), a new approach that supports such an analysis. We employ BIGSIS-XML in a smart phone alarm clock case study to provide insight into the use of formal signifier specifications to inform the design of visual interface properties that operate as signifiers.

Implementation of a Test Data Generator based on DSL Files

IntroductionSoftware testing represents an important step in software development [1], [2] and the testing process is thoroughly presented in books like [3] and [4]. Like other applications, mobile applications require testing in order to achieve a required level of quality. This can be done using similar tools and frameworks and also specific and dedicated tools, depending on the platform. Some of the mobile application testing types are shortly described in [5].During the testing process, test data generation has its own role for testing success. Test data generation is made using different tools and techniques. The paper continues the research presented in [6], [7] and [17] and focuses on template generation for test data based on Android layout files. Test data templates are XML-based files written using DSL (Data Specification Language). The generated test data can be used by own testing tools or frameworks or can be used as inputs for existing testing frameworks and tools.The paper is structured as follows. The section Android testing frameworks and tools presents the most important aspects related to Android applications testing. It also make a short presentation of the Android testing instruments. Data Specification Language (DSL) section describes the proposed system for test data generator based on Android layout files and details the XML-based language used for test data specification. The proposed parser for Android layout files is presented in the last section, Android layout files parser. The section Random test data generator based on pragmatic testing (RIGHT-BICEP) presents a test data generator, based on DSL files, that allows to generate data that conform to selected principles. The paper ends with conclusion and future work.2 Android Testing Frameworks and ToolsAndroid applications being developed using Java programming language, JUnit testing framework is suitable for the automated testing of functional issues. JUnit is a testing framework for regressive unit testing of Java programs [8]. The main Java classes used by the framework are associated to test cases and suites.The Android platform includes several tools and frameworks. Also, third party developers have built such tools and framework for Android applications testing. In [9] are presented the fundamentals of Android applications testing.Table 1 summarizes the most used Android testing tools and frameworks. Many of these are based on JUnit.Espresso is a testing framework used for UI testing. It is based on JUnit and it is included in Android Support Repository.Android Instrumentation framework is developed by Google for testing Android applications. It allows to control the life cycle of the Android applications and components during the tests.Monkey is a testing tool that runs within the emulator or on the mobile device. It is used to send random events to the Android device (user or system).monkeyrunner provides an API that can be used to control an Android device by installing applications, sending commands and taking and saving screenshots.Robotium is a testing framework for Android and hybrid application. It is based on Android Instrumentation and it is used to automate UI testing.Robolectric is framework that allows testing on a JVM running on a computer. This will speed-up the testing process.UI Automator framework provides an API that allows to control user and system applications for UI testing.In [10] there is a short presentation of several other Android testing frameworks and tools:* Mockito - a framework for testing Java and Android applications; it allows creation of mock objects for testing and it is used in unit testing;* EasyMock - a testing framework used in unit testing; it uses mock objects;* PowerMock - a framework based on Mockito and EasyMock;* Inifinitest - a testing plugin for Eclipse and IntelliJ; it is a continuous test runner. …

MT4WS: an automated metamorphic testing system for web services

The use of web services has been growing significantly, with increasingly large numbers of applications being implemented through the web. A difficulty associated with this development is the quality assurance of these services, specifically the challenges encountered when testing the applications - amongst other things, testers may not have access to the source code, and the correctness of the output may not be easily ascertained known as the oracle problem. Metamorphic testing MT has been introduced as a technique to alleviate the oracle problem. MT makes use of properties of the software under test, known as metamorphic relations, and checks whether or not these relations are violated. Since MT does not require source code to generate the metamorphic relations, it is suitable for testing web services-based applications. We have designed an XML-based language representation to facilitate the formalisation of metamorphic relations, the generation of follow-up test cases, and the verification of the test results. Based on this, we have also developed a tool to support the automation of MT for web service applications. This tool has been used in an experiment to test web services, the evaluation of which is reported in this paper.

The CellML 1.1 Specification

Summary This document specifies CellML 1.1, an XML-based language for describing and exchanging models of cellular and subcellular processes. MathML embedded in CellML documents is used to define the underlying mathematics of models. Models consist of a network of re- usable components, each with variables and equations manipulating those variables. Models may import other models to create systems of increasing complexity. Metadata may be embedded in CellML documents using RDF.

XML jako formát vyjádření objektových Petriho sítí

A number of object-oriented (OO) variants have so far been devised for Petri Nets (PN). However, none of these variants has ever been described using an open, independent format – such as XML. This article suggests several possibilities and advantages of such a description. The outlined XML language definition for the description of object-oriented Petri Nets (OOPN) is based on XMI (description of UML object-oriented models), SOX (simple description of general OO systems) and PNML (an XML-based language used for the description of structured and modular PN). For OOPN, the XML form of description represents a standard format for storing as well as for transfer between various OOPN-processing (analysis, simulation, ...) tools.