XML-based Systems Research Articles

JSON Schemas with Semantic Annotations Supporting Data Translation

As service-oriented architectures are a solution for large distributed systems, interoperability between these systems, which are often heterogeneous, can be a challenge due to the different syntax and semantics of the exchanged messages or even different data interchange formats. This paper addresses the data interchange format and data interoperability issues between XML-based and JSON-based systems. It proposes novel annotation mechanisms to add semantic annotations and complement date values to JSON Schemas, enabling an interoperability approach for JSON-based systems that, until now, was only possible for XML-based systems. A set of algorithms supporting the translation from JSON Schema to XML Schema, JSON to XML, and XML to JSON is also proposed. These algorithms were implemented in an existing prototype tool, which now supports these systems’ interoperability through semantic compatibility verification and the automatic generation of translators.

A study on parallelizing XML path filtering using accelerators

Publish-subscribe systems present the state of the art in information dissemination to multiple users. Such systems have evolved from simple topic-based to the current XML-based systems. XML-based pub-sub systems provide users with more flexibility by allowing the formulation of complex queries on the content as well as the structure of the streaming messages. Messages that match a given user query are forwarded to the user. This article examines how to exploit the parallelism found in XPath filtering. Using an incoming XML stream, parsing and matching thousands of user profiles are performed simultaneously by matching engines. We show the benefits and trade-offs of mapping the proposed filtering approach onto FPGAs, processing streams of XML at wire speed, and GPUs, providing the flexibility of software. This is in contrast to conventional approaches bound by the sequential aspect of software computing, associated with a large memory footprint. By converting XPath expressions into custom stacks, our solution is the first to provide support for complex XPath structural constructs, such as parent-child and ancestor descendant relations, whilst allowing wildcarding and recursion. The measured speedups resulting from the GPU and FPGA accelerations versus single-core CPUs are up to 6.6X and 2.5 orders of magnitude, respectively. The FPGA approaches are up to 31X faster than software running on 12 CPU cores.

JSBML: a flexible and entirely Java-based library for working with SBML

AbstractThe XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to its clearly defined specifications and the availability of libSBML, a portable, robust, and easy-to-use library.LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is a wrapper around the C/C++ core. The real-world experiences of many software developers has been that the deployment of portable libSBML-based Java applications is difficult. Further, the libSBML API and type hierarchy are not sufficiently intuitive from a Java programmer's perspective just because they were not designed directly for Java. For these reasons, several groups in the SBML community have mounted an open-source effort to develop a pure Java library for SBML. Here we present the JSBML project, whose products are freely available at the web site http://sourceforge.net/projects/jsbml.

Evolution and change management of XML-based systems

XML is de-facto a standard language for data exchange. Structure of XML documents exchanged among different components of a system (e.g. services in a Service-Oriented Architecture) is usually described with XML schemas. It is a common practice that there is not only one but a whole family of XML schemas each applied in a particular logical execution part of the system. In such systems, the design and later maintenance of the XML schemas is not a simple task.In this paper we aim at a part of this problem – evolution of the family of the XML schemas. A single change in user requirements or surrounding environment of the system may influence more XML schemas in the family. A designer needs to identify the XML schemas affected by a change and ensure that they are evolved coherently with each other to meet the new requirement. Doing this manually is very time consuming and error prone. In this paper we show that much of the manual work can be automated. For this, we introduce a technique based on the principles of Model-Driven Development. A designer is required to make a change only once in a conceptual schema of the problem domain and our technique ensures semi-automatic coherent propagation to all affected XML schemas (and vice versa). We provide a formal model of possible evolution changes and their propagation mechanism. We also evaluate the approach on a real-world evolution scenario.

JSBML

AbstractThe XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML's clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use library.LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is a wrapper around the C/C++ core. The real-world experiences of many software developers has been that the deployment of portable libSBML-based Java applications is difficult. Further, the libSBML API and type hierarchy are not sufficiently intuitive from a Java programmer's perspective simply because they were not designed directly for Java.For these reasons, several groups in the SBML community have mounted an open-source effort to develop a pure Java library for SBML. Here we present the JSBML project, whose products are freely available at the website "http://jsbml.sourceforge.net/":http://jsbml.sourceforge.net/. The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other for those who desire it.Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 1 release candidate specification, including an API to add SBML extensions. There are no plans to re-implement some of the more complex functions of libSBML, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions.In summary, JSBML is a young, ongoing software project that provides comprehensive and entirely Java-based data structures to read, write, and manipulate SBML files. Its layered architecture allows for the creation of Java web start applications and CellDesigner plug-ins based on stand-alone programs with very little effort. One program, SBMLsqueezer 1.3, has already been re-implemented and released using JSBML, and many others are planned.

JSBML

The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML's clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use library.LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is a wrapper around the C/C++ core. The real-world experiences of many software developers has been that the deployment of portable libSBML-based Java applications is difficult. Further, the libSBML API and type hierarchy are not sufficiently intuitive from a Java programmer's perspective simply because they were not designed directly for Java.For these reasons, several groups in the SBML community have mounted an open-source effort to develop a pure Java library for SBML. Here we present the JSBML project, whose products are freely available at the website "http://jsbml.sourceforge.net/":http://jsbml.sourceforge.net/. The JSBML project's aim is to provide an SBML parser and programming library that maps all SBML elements to a flexible and extended type hierarchy. Where possible, JSBML strives to attain 100% API compatibility with the libSBML Java API, to facilitate a switch from one library to the other for those who desire it.Currently, JSBML supports all constructs for SBML up to the latest Level 3 Version 1 release candidate specification, including an API to add SBML extensions. There are no plans to re-implement some of the more complex functions of libSBML, since separate community efforts are expected to make them available to JSBML via web services. These more complex functions include model consistency checking, SBML validation, and the conversion between different SBML Levels and Versions.In summary, JSBML is a young, ongoing software project that provides comprehensive and entirely Java-based data structures to read, write, and manipulate SBML files. Its layered architecture allows for the creation of Java web start applications and CellDesigner plug-ins based on stand-alone programs with very little effort. One program, SBMLsqueezer 1.3, has already been re-implemented and released using JSBML, and many others are planned.

SBML2LaTEX: Conversion of SBML files into human-readable reports

Summary: The XML-based Systems Biology Markup Language (SBML) has emerged as a standard for storage, communication and interchange of models in systems biology. As a machine-readable format XML is difficult for humans to read and understand. Many tools are available that visualize the reaction pathways stored in SBML files, but many components, e.g. unit declarations, complex kinetic equations or links to MIRIAM resources, are often not made visible in these diagrams. For a broader understanding of the models, support in scientific writing and error detection, a human-readable report of the complete model is needed. We present SBML2LaTEX, a Java-based stand-alone program to fill this gap. A convenient web service allows users to directly convert SBML to various formats, including DVI, LaTEX and PDF, and provides many settings for customization.Availability: Source code, documentation and a web service are freely available at http://www.ra.cs.uni-tuebingen.de/software/SBML2LaTeX.Contact:andreas.draeger@uni-tuebingen.deSupplementary information:Supplementary data are available at Bioinformatics online.

BP's multi-enterprise asset management system

BP is one of the largest energy companies in the world with 2003 revenues of $233 billion. In this paper, we analyse its use of an innovative ‘multi-enterprise asset management system’ that supports and enables the asset management strategy of BP's exploration and production division on the UK continental shelf (UKCS). The analysis focuses on how BP connects its business processes with over 1500 suppliers to co-ordinate the maintenance, operation and repair of specialised exploration and production equipment. The systems strategy is novel because it takes the enterprise computing concept and implements it across organisational boundaries—hence the term ‘multi-enterprise system’. This use of a shared system with all of its suppliers is distinctive from the most common way of connecting with economic partners which is to use shared data systems based on common data standards and communication technologies such as EDI and more recently XML-based systems within vertical industries such as RosettaNet. The design of the multi-enterprise system is based on a sophisticated business process management system called Maximo and this is used to illustrate the systems design aspect of the overall information system in the broader contexts of business strategy and information technology infrastructure.

FORMALISED MODEL REPRESENTATION FOR WASTEWATER SYSTEMS

A fundamental pre-condition for the application of simulation is the availability of reliable models. Particular problems arise in the application of simulation for integrated process design of complex wastewater systems. The models necessary for this task have to include different sub-processes such as biological wastewater treatment, anaerobic digestion processes and also models of the control system. To deal with this problem this paper describes an approach on how (1) to follow strict mass conservation principles during model development and (2) how to use formalised model representation methods for model creation, exchange and analysis. The adaptation of the XML-based Systems Biology Mark-Up Language (SBML) to the area of wastewater modelling is proposed. The implementation of this approach in a simulation environment for practical control engineering tasks is demonstrated.

Integrating SNMP agents with XML-based management systems

XML-based network management systems are becoming more and more popular these days. However, it has to be taken into account that there is a broad existing management infrastructure based on non-XML protocols. Today, the most dominant technology in Internet management is based on the SNMP framework. This article presents an approach for seamless integration of management information supplied by SNMP agents into XML-based systems. This is done by an automated transformation of SMI MIB definitions into XML schema definitions, which implies a corresponding transformation of SNMP management information into XML documents. Furthermore, we present an SNMP-to-XML gateway that allows retrieval of such XML management information at runtime.

Discussion of CAWS model for XML-based accounting systems

Discussion of CAWS model for XML-based accounting systems

Reply to the discussions of a Continuous Auditing Web Services model for XML-based accounting systems

Reply to the discussions of a Continuous Auditing Web Services model for XML-based accounting systems

Discussion of a continuous auditing Web Services model for XML-based accounting systems

Discussion of a continuous auditing Web Services model for XML-based accounting systems

XML-Based Network Management for IP Networks

XML-based network management, which applies XML technologies to network management, has been proposed as an alternative to existing network management. The use of XML in network management offers many advantages. However, most existing network devices are already embedded with simple network management protocol (SNMP) agents and managed by SNMP managers. For integrated network management, we present the architectures of an XML-based manager, an XML-based agent, and an XML/SNMP gateway for legacy SNMP agents. We describe our experience of developing an XML-based network management system (XNMS), XML-based agent, and an XML/SNMP gateway. We also verify the effectiveness of our XML-based agent and XML/SNMP gateway through performance tests. Our experience with developing XNMS and XML-based agents can be used as a guideline for development of XML-based management systems that fully take advantage of the strengths of XML technologies.