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Last modified: August 12, 2009
XML Daily Newslink. Wednesday, 12 August 2009

A Cover Pages Publication
Provided by OASIS and Sponsor Members
Edited by Robin Cover

This issue of XML Daily Newslink is sponsored by:
Microsoft Corporation

Systems Biology Graphical Notation (SBGN) Standard Leverages SBML
Kathy Svitil, Caltech Announcement

"Researchers at the California Institute of Technology (Caltech) and their colleagues in 30 laboratories worldwide have announced the release of a new set of standards for graphically representing biological information — the biology equivalent of the circuit diagram in electronics. This visual language should make it easier to exchange complex information, so that biological models are depicted more accurately, consistently, and in a more readily understandable way. The new standard, called the Systems Biology Graphical Notation (SBGN), was published in the journal Nature Biotechnology..."

According to the published article: "Despite having one of the highest ratios of graphical to textual information, biology still lacks standard graphical notations. The recent deluge of biological knowledge makes addressing this deficit a pressing concern. Toward this goal, we present the Systems Biology Graphical Notation (SBGN), a visual language developed by a community of biochemists, modelers and computer scientists. SBGN consists of three complementary languages: process diagram, entity relationship diagram and activity flow diagram. Together they enable scientists to represent networks of biochemical interactions in a standard, unambiguous way. We believe that SBGN will foster efficient and accurate representation, visualization, storage, exchange and reuse of information on all kinds of biological knowledge, from gene regulation, to metabolism, to cellular signaling...

Article Table 3 lists software projects that are already developing support for SBGN process diagram level 1. Some of these rely on manual design of the pathways, whereas others, such as Arcadia, automatically generate SBGN PD from SBML models that have been annotated with terms from the Systems Biology Ontology. The encoding of SBGN diagrams using computer-readable formats, a crucial step toward exchange and reuse of SBGN diagrams, is currently supported in different formats such as SBML, GML, and GraphML by different tools, and a general XML-based exchange format for SBGN is currently under discussion..."

See also: the early history of Systems Biology Markup Language (SBML)

Apache Commons Announces Release of Commons Math Version 2.0
Phil Steitz, Apache Software Foundation Announcement

"The Apache Commons team is pleased to announce the release of version 2.0 of Commons Math. Commons Math is a library of lightweight, self-contained mathematics and statistics components addressing the most common problems not available in the Java programming language or Commons Lang.

Version 2.0 is a major release, including bug fixes, new features and enhancements to existing features. Most notable among the new features are matrix decomposition algorithms, sparse matrices and vectors, genetic algorithms, new optimization algorithms, curve fitting algorithms, state derivatives in ODE step handlers, new multistep integrators, multiple regression, correlation, rank transformations and Mersenne twister pseudo random number generator...

Apache Commons guiding principles for Commons Math: (1) Real-world application use cases determine development priority; (2) Package emphasizes small, easily integrated components rather than large libraries with complex dependencies and configurations; (3) All algorithms are fully documented and follow generally accepted best practices; (4) In situations where multiple standard algorithms exist, a Strategy pattern is used to support multiple implementations; (5) Limited dependencies: no external dependencies beyond Commons components and the core Java platform—at least Java 1.3 up to version 1.2 of the library, at least Java 5 starting with version 2.0 of the library..."

See also: the Apache Commons web site

OGC and MISMO Advance Standards for Real Estate Transactions
Staff, Open Geospatial Consortium Announcement

The Open Geospatial Consortium, Inc. (OGC) and the Mortgage Industry Standards Maintenance Organization (MISMO) have signed a memorandum of understanding (MOU). Under the terms of the MOU, the organizations will collaborate on standards development and outreach to enable and promote the use of Web based geospatial technologies in real property transaction applications.

The Mortgage Industry Standards Maintenance Organization (MISMO), a not-for-profit subsidiary of the Mortgage Bankers Association (MBA) managed by the Mortgage Electronic Registration Systems, Inc. (MERS), is the leading technology standards development body for both the Residential and Commercial industry segments. MISMO promotes data consistency throughout the broader industry, reduces processing costs, increases transparency, and boosts investor confidence in mortgages as an asset class, while passing cost savings on to the consumer.

On April 17, 2009 the MISMO XML Architecture Committee recommended the Version 3.0 Public Review Draft for publication to the Governance Committee. MISMO Version 3.0 is to provide a cohesive foundation to support the creation of the widest array of transactions possible, allowing implementers of the standard to use a variety of XML tools to construct their implementations... MISMO has identified two deliverables that will enable the mortgage industry to share data among trading partners: (1) An XML architecture that encompasses data origination, secondary market and servicing data, (2) A data dictionary to provide business definitions and corresponding architecture data elements...

Mark Reichardt, CEO and president of the OGC: "Real estate by definition is a highly place-based activity. With so many actors involved in real estate development, transactions and forms of management, Web-based geospatial standards can help to further advance the industry in its modernization..."

See also: the MISMO specifications listing

Monitoring and Control of Large Systems with MonALISA
Iosif Legrand, Ramiro Voicu, Catalin Cirstoiu (et al); ACM Queue

The High Energy Physics (HEP) group at the California Institute of Technology started developing the MonALISA (Monitoring Agents using a Large Integrated Services Architecture) framework in 2002, aiming to provide a distributed service system capable of controlling and optimizing large-scale, data-intensive applications...

An essential part of managing large-scale, distributed data-processing facilities is a monitoring system for computing facilities, storage, networks, and the very large number of applications running on these systems in near realtime. Current applications of MonALISA's higher-level services include optimized dynamic routing, control, and optimization for large-scale data transfers on dedicated circuits, data-transfer scheduling, distributed job scheduling, and automated management of remote services among a large set of grid facilities.

One of the most difficult parts in developing the MonALISA system was the communication mechanism for all these services in the wide area network. The system tries to establish and maintain reliable communication among services, using the ability to reconnect automatically or find alternative services in case of network or hardware problems. Although the fashion of the time was to implement remote call protocols over XML and to use Web services, we decided to use a binary protocol to avoid the overhead of wrapping everything in a text-based protocol and because of the lack of remote notification except for a pull-based approach — the OASIS Web Services Notification (WS Notification) — appeared later and still used a pull-based approach in the first implementations... Implementing our own communication protocol over standard TCP sockets helped us to have finer control in case of network I/O errors for quick and clean recovery... At the other end, for the LAN communication between thousands of monitored entities and the local MonALISA service, we decided to use a highly portable protocol employing XDR (IETF External Data Representation Standard, RFC 4506) for data encoding; this choice proved to be effective and allowed the service to collect more than 5,000 messages per second without any loss...

See also: Monitoring Agents using a Large Integrated Services Architecture

Semantics-Based Software Boosts Company Performance
Staff, CORDIS ITC Results

New semantics-based software tools that accelerate the speed companies can develop or adjust their processes—while slashing costs—have resulted from a major European research project. Tools developed by SUPER, a European research project, greatly enhance the business usefulness of the service-oriented architecture (SOA) approach to software development. The new tools raise business process management (BPM) to the business level where it belongs, from the IT level where it mostly resides now...

The EU-funded SUPER project applied semantics and semantic web technology to the problem...Ontologies are the backbone of the SUPER tools. Ontologies define 'meanings' through formal descriptions of concepts and relationships in an industry as well as carefully defined industry terms. For SUPER, that industry was telecommunications. Using the SUPER ontologies, telecoms business managers can model new business processes, search for existing process fragments, automatically fill in the missing elements in the process model, search for semantic web services that will deliver the functionality, compose business processes out of available web services and execute implemented business process models.

Global giant Telefonica sees SUPER tools as important in its drive into the ICT outsourcing market. SUPER will help it stay ahead of the game with leading-edge IT solutions. Members of the research consortium, such as Polish Telecom, part of France Telecom, are also looking to exploit the developments commercially. SAP, IBM, and IDS Scheer are incorporating SUPER findings into their software offering..."

See also: the Integrated Project SUPER

Announcing a New Product Line: Telerik Extensions for ASP.NET MVC
Atanas Korchev, Telerik Blog

"[We hereby announce] Telerik Extensions for ASP.NET MVC, a new UI component suite targeting the ASP.NET MVC framework. The new product line will not be based on RadControls for ASP.NET Ajax nor will it depend on ASP.NET Ajax or ASP.NET WebForms. No page lifecycle, ScriptManager dependency, viewstate or postback... Telerik Extensions for ASP.NET MVC is available as an open source product under the Ms-PL license. For the first time Telerik will be releasing a free and open source product. The code can be used, modified and redistributed. You can even start your own open source project built upon Telerik Extensions for ASP.NET MVC...

We are adopting jQuery as our primary client-side framework and will build exclusively on top of it. Not only that—we are providing a sample class library which offers a few server-side components based on jQuery UI. This serves as a proof of concept for our server-side framework. The client-side and theming are from the jQuery UI suite — without any modification...

The first CTP of Telerik Extensions for ASP.NET MVC includes the following unique features: (1) Rich server side framework for developing view components with fluent interface; (2) Rich web asset management — you can register, combine, cache and compress JavaScript and CSS files; (3) Tested with the default view engine, Spark and NHaml—sample projects are included; (4) Sample class library based on Telerik Extensions for ASP.NET MVC and jQuery UI—provides Accordion, DatePicker, MessageBox, ProgressBar, Tab and Slider components; (5) All of this comes with full source code and unit tests..."

See also: the Telerik product description


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