Extensible markup language
TL;DR: XML is the lingua franca of the wireless Web and is already being used for a host of server-server communication applications, which make it possible for different data servers to easily exchange information.
Abstract: XML is the lingua franca of the wireless Web. Its strength is in its generality: XML can describe virtually any kind of structured data. Once described, the data can be presented in other formats. Moreover, XML is already being used for a host of server-server communication applications, which make it possible for different data servers to easily exchange information. The trend toward a common format for representing data will doubtlessly present new opportunities for both Web and wireless Web clients.
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TL;DR: Two unusual extensions are presented: Multiscale, which adds the ability to visualize large‐scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales.
Abstract: The design, implementation, and capabilities of an extensible visualization system, UCSF Chimera, are discussed. Chimera is segmented into a core that provides basic services and visualization, and extensions that provide most higher level functionality. This architecture ensures that the extension mechanism satisfies the demands of outside developers who wish to incorporate new features. Two unusual extensions are presented: Multiscale, which adds the ability to visualize large-scale molecular assemblies such as viral coats, and Collaboratory, which allows researchers to share a Chimera session interactively despite being at separate locales. Other extensions include Multalign Viewer, for showing multiple sequence alignments and associated structures; ViewDock, for screening docked ligand orientations; Movie, for replaying molecular dynamics trajectories; and Volume Viewer, for display and analysis of volumetric data. A discussion of the usage of Chimera in real-world situations is given, along with anticipated future directions. Chimera includes full user documentation, is free to academic and nonprofit users, and is available for Microsoft Windows, Linux, Apple Mac OS X, SGI IRIX, and HP Tru64 Unix from http://www.cgl.ucsf.edu/chimera/.
35,698 citations
California Institute of Technology1, University of Hertfordshire2, University of California, Berkeley3, Jet Propulsion Laboratory4, University of Cambridge5, Centre national de la recherche scientifique6, University of Auckland7, GlaxoSmithKline8, Max Planck Society9, Stellenbosch University10, University of Connecticut Health Center11, Virginia Bioinformatics Institute12, University of California, Irvine13, Keio University14, Princeton University15
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Abstract: Motivation: Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. Results: We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. ∗ To whom correspondence should be addressed. Availability: The specification of SBML Level 1 is freely available from http://www.sbml.org/.
3,205 citations
Additional excerpts
...In addition, the 13 following quoting rules specified by XML for character data (Bray et al., 2000) must be obeyed: 14...
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TL;DR: The main objective of this survey is to present the work that has been conducted in the area of graph database modeling, concentrating on data structures, query languages, and integrity constraints.
Abstract: Graph database models can be defined as those in which data structures for the schema and instances are modeled as graphs or generalizations of them, and data manipulation is expressed by graph-oriented operations and type constructors. These models took off in the eighties and early nineties alongside object-oriented models. Their influence gradually died out with the emergence of other database models, in particular geographical, spatial, semistructured, and XML. Recently, the need to manage information with graph-like nature has reestablished the relevance of this area. The main objective of this survey is to present the work that has been conducted in the area of graph database modeling, concentrating on data structures, query languages, and integrity constraints.
1,669 citations
Book•
01 Jan 2004
TL;DR: The third edition of this widely used text has been thoroughly updated, with significant new material that reflects a rapidly developing field.
Abstract: The development of the Semantic Web, with machine-readable content, has the potential to revolutionize the World Wide Web and its uses. A Semantic Web Primer provides an introduction and guide to this continuously evolving field, describing its key ideas, languages, and technologies. Suitable for use as a textbook or for independent study by professionals, it concentrates on undergraduate-level fundamental concepts and techniques that will enable readers to proceed with building applications on their own and includes exercises, project descriptions, and annotated references to relevant online materials.The third edition of this widely used text has been thoroughly updated, with significant new material that reflects a rapidly developing field. Treatment of the different languages (OWL2, rules) expands the coverage of RDF and OWL, defining the data model independently of XML and including coverage of N3/Turtle and RDFa. A chapter is devoted to OWL2, the new W3C standard. This edition also features additional coverage of the query language SPARQL, the rule language RIF and the possibility of interaction between rules and ontology languages and applications. The chapter on Semantic Web applications reflects the rapid developments of the past few years. A new chapter offers ideas for term projects. Additional material, including updates on the technological trends and research directions, can be found at http://www.semanticwebprimer.org.
1,634 citations
12 May 2002
TL;DR: This paper presents an automated technique for generating and analyzing attack graphs, based on symbolic model checking algorithms, letting us construct attack graphs automatically and efficiently.
Abstract: An integral part of modeling the global view of network security is constructing attack graphs. Manual attack graph construction is tedious, error-prone, and impractical for attack graphs larger than a hundred nodes. In this paper we present an automated technique for generating and analyzing attack graphs. We base our technique on symbolic model checking algorithms, letting us construct attack graphs automatically and efficiently. We also describe two analyses to help decide which attacks would be most cost-effective to guard against. We implemented our technique in a tool suite and tested it on a small network example, which includes models of a firewall and an intrusion detection system.
1,302 citations