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/.

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UCSF Chimera--a visualization system for exploratory research and analysis.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.

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Bioconductor: open software development for computational biology and bioinformatics

The OWL Web Ontology Language is designed for use by applications that need to process the content of information instead of just presenting information to humans. OWL facilitates greater machine interpretability of Web content than that supported by XML, RDF, and RDF Schema (RDF-S) by providing additional vocabulary along with a formal semantics. OWL has three increasingly-expressive sublanguages: OWL Lite, OWL DL, and OWL Full. This document is written for readers who want a first impression of the capabilities of OWL. It provides an introduction to OWL by informally describing the features of each of the sublanguages of OWL. Some knowledge of RDF Schema is useful for understanding this document, but not essential. After this document, interested readers may turn to the OWL Guide for more detailed descriptions and extensive examples on the features of OWL. The normative formal definition of OWL can be found in the OWL Semantics and Abstract Syntax. Status of this document OWL Web Ontology Language Overview https://www.w3.org/TR/owl-features/ 1 de 14 09/05/2017 08:32 a.m. This document has been reviewed by W3C Members and other interested parties, and it has been endorsed by the Director as a W3C Recommendation. W3C's role in making the Recommendation is to draw attention to the specification and to promote its widespread deployment. This enhances the functionality and interoperability of the Web. This is one of six parts of the W3C Recommendation for OWL, the Web Ontology Language. It has been developed by the Web Ontology Working Group as part of the W3C Semantic Web Activity (Activity Statement, Group Charter) for publication on 10 February 2004. The design of OWL expressed in earlier versions of these documents has been widely reviewed and satisfies the Working Group's technical requirements. The Working Group has addressed all comments received, making changes as necessary. Changes to this document since the Proposed Recommendation version are detailed in the change log. Comments are welcome at public-webont-comments@w3.org (archive) and general discussion of related technology is welcome at www-rdf-logic@w3.org (archive). A list of implementations is available. The W3C maintains a list of any patent disclosures related to this work. This section describes the status of this document at the time of its publication. Other documents may supersede this document. A list of current W3C publications and the latest revision of this technical report can be found in the W3C technical reports index at http://www.w3.org/TR/.

OWL Web ontology language overview

In both e-business and e-science, we often need to integrate services across distributed, heterogeneous, dynamic “virtual organizations” formed from the disparate resources within a single enterprise and/or from external resource sharing and service provider relationships. This integration can be technically challenging because of the need to achieve various qualities of service when running on top of different native platforms. We present an Open Grid Services Architecture that addresses these challenges. Building on concepts and technologies from the Grid and Web services communities, this architecture defines a uniform exposed service semantics (the Grid service); defines standard mechanisms for creating, naming, and discovering transient Grid service instances; provides location transparency and multiple protocol bindings for service instances; and supports integration with underlying native platform facilities. The Open Grid Services Architecture also defines, in terms of Web Services Description Language (WSDL) interfaces and associated conventions, mechanisms required for creating and composing sophisticated distributed systems, including lifetime management, change management, and notification. Service bindings can support reliable invocation, authentication, authorization, and delegation, if required. Our presentation complements an earlier foundational article, “The Anatomy of the Grid,” by describing how Grid mechanisms can implement a service-oriented architecture, explaining how Grid functionality can be incorporated into a Web services framework, and illustrating how our architecture can be applied within commercial computing as a basis for distributed system integration—within and across organizational domains. This is a DRAFT document and continues to be revised. The latest version can be found at http://www.globus.org/research/papers/ogsa.pdf. Please send comments to foster@mcs.anl.gov, carl@isi.edu, jnick@us.ibm.com, tuecke@mcs.anl.gov Physiology of the Grid 2

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The Physiology of the Grid An Open Grid Services Architecture for Distributed Systems Integration

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/.

The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Extensible Markup Language (XML) is an extremely simple dialect of SGML which is completely described in this document. The goal is to enable generic SGML to be served, received, and processed on the Web in the way that is now possible with HTML. For this reason, XML has been designed for ease of implementation, and for interoperability with both SGML and HTML. Note on status of this document: This is even more of a moving target than the typical W3C working draft. Several important decisions on the details of XML are still outstanding members of the W3C SGML Working Group will recognize these areas of particular volatility in the spec, but those who are not intimately familiar with the deliberative process should be careful to avoid actions based on the content of this document, until the notice you are now reading has been removed.

Extensible Markup Language (XML).

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.

Extensible markup language

JavaScript Object Notation (JSON) is a lightweight, text-based,
language-independent data interchange format. It was derived from the
ECMAScript Programming Language Standard. JSON defines a small set of
formatting rules for the portable representation of structured data.
This document removes inconsistencies with other specifications of
JSON, repairs specification errors, and offers experience-based
interoperability guidance.

The JavaScript Object Notation (JSON) Data Interchange Format

“When you can measure what you are speaking about, and express it in numbers, you know something about it; but when you cannot express it in numbers, your knowledge is of a meager and unsatisfactory kind; it may be the beginning of knowledge, but you have scarcely in your thoughts advanced to the state of science.” — Lord Kelvin This paper presents some difficult qualitative questions concerning the Web, and attempts to provide some partial quantitative answers to them. It uses the numbers in these answers to drive some 3-D visualizations of localities in the Web.

Tim Bray

Papers

Extensible Markup Language (XML).

Extensible markup language

The JavaScript Object Notation (JSON) Data Interchange Format

Measuring the Web

Extensible markup language (XML) part 2: linking