XML and Web Services In The News - 01 June 2004

NSF Middleware Initiative Goes Beyond Science. Effort Spreads to Corporate Use.
Nancy Weil, InfoWorld
A multifaceted, federally funded initiative aimed at developing and deploying open-source, open-standards middleware and services so that scientists can share data and collaborate on research has released the fifth version of its software, as the effort spreads into corporate use and beyond U.S. borders. Last week, NMI Release 5 rolled out as part of the initiative's twice-annual update of software, services and documentation. The software suite and individual components, tested and debugged before release, are distributed for free at the NMI Web site. Penn State is using Shibboleth, a federated ID management environment based on Security Assertion Markup Language (SAML), to allow its students access to physics class material at North Carolina State University and also for single sign-on and password access to the Napster music download service. NMI components have begun taking hold globally; this is occurring in large measure because of the growing clamor for federated identity services, which let domains share local identity and security information, while keeping their own internal directory, metadirectory, public-key infrastructure and account provisioning.
See also: SAML References

Web Services for Bioinformatics, Part 1
Chetna Warade, Virinder Batra, and Rick Runyan; IBM developerWorks
Bioinformatics research applications exist in various stages of completeness in many different languages. Furthermore, building a workflow from several different applications requires installing applications locally, copying input and output data by hand, and often modifying source code for adapting changes in output and input data format. When the services can communicate by producing and consuming compatible XML documents, then the process of orchestrating these services can be automated. Our proof-of-concept example Web Service for Basic Local Alignment Search Tool (BLAST) is hosted on the NC BioGrid. This article provides directions for how to deploy a service and present a new implementation of document-style Web services extensions to the BioPerl module that will allow a wide range of existing applications to consume such services. The series describes the process of building, deploying, and using high-throughput Web services for bioinformatics applications. This is meant to serve as a guide for development of software based on the Open-Bioinformatics Foundations software toolkits with packages such as BioPerl, BioJava, and BioPython.

Adding XML 1.1 to a Java Application
Rick Jelliffe, O'Reilly Developer Weblogs
XML 1.1 is fairly controversial: it just adds some niche features that most people don't need. We recently added some XML 1.1 support to Topologi's XML editor; I was surprised by how straightforward it was, but also perhaps premature. XML 1.1 has four aspects: NELS (a newline on some IBM mainframes), extra name characters (some pretty obscure characters), improved rules for control characters (more controls allowed, but safer because they must be references not literals), and coping with the different version number. Moving our product to XML 1.1 was not disruptive or difficult. We use the latest version of Xerces for XML processing; the latest version of Xerces can detect and switch to XML 1.1, and we didn't find any problems. One thing XML 1.1 does expose is that XML's simple n.n versioning system didn't come with enough policy to make it convenient: it would be better if there were a policy such as "XML processors must fail with a WF error when there is a different major number; XML processors must not fail only because of a difference in the minor number", so that an XML 1.0 processor would only fail on an XML 1.1 document when there is some syntax apart from the version number that fails.

To Tag or Not to Tag: The New Variorum Shakespeare and XML
Patrick O'Kelley, XML.com
Every generation remakes Shakespeare for itself with new costumes, new set designs, and new interpretations. Despite numerous advances in humanities computing, variorum editions of the works of Shakespeare have relied on models established well before the digital age. Since the nineteenth century, scholars have slowly worked through the plays and sonnets to create definitive, variorum editions that include the variations of each line of each play as well as all of the major critical commentary. The undertaking, which was assumed by the Modern Language Association (MLA) in 1936, is obviously mammoth. The variorum editions, thick with special typographical marks and a complex web of cross-references, were prepared solely as print texts running hundreds of pages long. Later this year the MLA will bring the New Variorum Shakespeare (NVS) project into the world of XML for the first time.

Sun Adds Java Tools to RFID Menu
Matt Hines, CNET News.com
Sun Microsystems plans to launch a software package aimed at the RFID market. Built on Sun's Java programming architecture and Jini networking technology, the software attempts to simplify integration of data collected via radio frequency identification (RFID) systems into other software applications. Managing the massive amounts of information generated by RFID tools ranks among one of the greatest hurdles faced by radio tag systems today. The package, dubbed Sun Java System RFID Software, is made up of two primary elements. An event manager promises to help process information collected from RFID tags, or sensors, and filter the data based on customers' needs. An information server captures and stores information garnered using RFID technology and makes that data available to other applications such as supply chain management systems.
See also: the announcement

Open Mobile Alliance Releases Working Drafts for OMA DRM Version 2.0.
XML Cover Pages
OMA has published draft specifications for the OMA DRM 2.0 Enabler Release. OMA DRM 2.0 takes advantage of expanded device capabilities and offers improved support for audio/video rendering, streaming content, and access to protected content using multiple devices. OMA's DRM Rights Expression Language (REL) is a mobile profile of the royalty-free XML-based Open Digital Rights Language (ODRL).