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

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

Evaluating Knowledge Representation and Reasoning Capabilites of Ontology Specification Languages

The interchange of ontologies across the World Wide Web (WWW) and the cooperation among heterogeneous agents placed on it is the main reason for the development of a new set of ontology specification languages, based on new web standards such as XML or RDF. These languages (SHOE, XOL, RDF, OIL, etc) aim to represent the knowledge contained in an ontology in a simple and human-readable way, as well as allow for the interchange of ontologies across the web. In this paper, we establish a common framework to compare the expressiveness of "traditional" ontology languages (Ontolingua, OKBC, OCML, FLogic, LOOM) and "web-based" ontology languages. As a result of this study, we conclude that different needs in KR and reasoning may exist in the building of an ontology-based application, and these needs must be evaluated in order to choose the most suitable ontology language(s)

Active architecture for pervasive contextual services

International Workshop on Middleware for Pervasive and Ad-hoc Computing MPAC 2003), ACM/IFIP/USENIX International Middleware Conference (Middleware 2003), Rio de Janeiro, Brazil This work was supported by the FP5 Gloss project IST2000-26070, with partners at Trinity College Dublin and Université Joseph Fourier, and by EPSRC grants GR/M78403/GR/M76225, Supporting Internet Computation in Arbitrary Geographical Locations, and GR/R45154, Bulk Storage of XML Documents.Pervasive services may be defined as services that are available "to any client (anytime, anywhere)". Here we focus on the software and network infrastructure required to support pervasive contextual services operating over a wide area. One of the key requirements is a matching service capable of as-similating and filtering information from various sources and determining matches relevant to those services. We consider some of the challenges in engineering a globally distributed matching service that is scalable, manageable, and able to evolve incrementally as usage patterns, data formats, services, network topologies and deployment technologies change. We outline an approach based on the use of a peer-to-peer architecture to distribute user events and data, and to support the deployment and evolution of the infrastructure itself.Peer reviewe

Active architecture for pervasive contextual services

Pervasive services may be defined as services that are available to any client (anytime, anywhere). Here we focus on the software and network infrastructure required to support pervasive contextual services operating over a wide area. One of the key requirements is a matching service capable of assimilating and filtering information from various sources and determining matches relevant to those services. We consider some of the challenges in engineering a globally distributed matching service that is scalable, manageable, and able to evolve incrementally as usage patterns, data formats, services, network topologies and deployment technologies change. We outline an approach based on the use of a peer-to-peer architecture to distribute user events and data, and to support the deployment and evolution of the infrastructure itself

Organizing the Internet

This paper examines XML and its relationships with SGML (Standardized General Markup Language) and HTML (HyperText Markup Language). It examines the importance of metatags and the XML Document Type Definition (DTD) and proposed alternatives. It looks at the differences between the two types of XML data: “valid” and “well-formed” documents

SBML models and MathSBML

MathSBML is an open-source, freely-downloadable Mathematica package that facilitates working with Systems Biology Markup Language (SBML) models. SBML is a toolneutral,computer-readable format for representing models of biochemical reaction networks, applicable to metabolic networks, cell-signaling pathways, genomic regulatory networks, and other modeling problems in systems biology that is widely supported by the systems biology community. SBML is based on XML, a standard medium for representing and transporting data that is widely supported on the internet as well as in computational biology and bioinformatics. Because SBML is tool-independent, it enables model transportability, reuse, publication and survival. In addition to MathSBML, a number of other tools that support SBML model examination and manipulation are provided on the sbml.org website, including libSBML, a C/C++ library for reading SBML models; an SBML Toolbox for MatLab; file conversion programs; an SBML model validator and visualizer; and SBML specifications and schemas. MathSBML enables SBML file import to and export from Mathematica as well as providing an API for model manipulation and simulation

A Design Methodology for MPEG-21 based Digital Policy Management Systems

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The Research Object Suite of Ontologies: Sharing and Exchanging Research Data and Methods on the Open Web

Research in life sciences is increasingly being conducted in a digital and online environment. In particular, life scientists have been pioneers in embracing new computational tools to conduct their investigations. To support the sharing of digital objects produced during such research investigations, we have witnessed in the last few years the emergence of specialized repositories, e.g., DataVerse and FigShare. Such repositories provide users with the means to share and publish datasets that were used or generated in research investigations. While these repositories have proven their usefulness, interpreting and reusing evidence for most research results is a challenging task. Additional contextual descriptions are needed to understand how those results were generated and/or the circumstances under which they were concluded. Because of this, scientists are calling for models that go beyond the publication of datasets to systematically capture the life cycle of scientific investigations and provide a single entry point to access the information about the hypothesis investigated, the datasets used, the experiments carried out, the results of the experiments, the people involved in the research, etc. In this paper we present the Research Object (RO) suite of ontologies, which provide a structured container to encapsulate research data and methods along with essential metadata descriptions. Research Objects are portable units that enable the sharing, preservation, interpretation and reuse of research investigation results. The ontologies we present have been designed in the light of requirements that we gathered from life scientists. They have been built upon existing popular vocabularies to facilitate interoperability. Furthermore, we have developed tools to support the creation and sharing of Research Objects, thereby promoting and facilitating their adoption.Comment: 20 page

Bigraphical Logics for XML

Bigraphs have been recently proposed as a meta-model for global computing resources; they are built orthogonally on two structures: a hierarchical ‘place’ graph for locations and a ‘link’ (hyper-)graph for connections. XML is now the standard meta-language for the data exchange and storage on the web. In this paper we address the similarities between bigraphs and XML and we propose bigraphs as a rich model for XML (and XML contexts). Building on this idea we proceed by investigating how the recently proposed logic of BiLog can be instantiated to describe, query and reason about web data (and web contexts)