Monitoring-Oriented Programming: A Tool-Supported Methodology for Higher Quality Object-Oriented Software

This paper presents a tool-supported methodological paradigm for object-oriented software development, called monitoring-oriented programming and abbreviated MOP, in which runtime monitoring is a basic software design principle. The general idea underlying MOP is that software developers insert specifications in their code via annotations. Actual monitoring code is automatically synthesized from these annotations before compilation and integrated at appropriate places in the program, according to user-defined configuration attributes. This way, the specification is checked at runtime against the implementation. Moreover, violations and/or validations of specifications can trigger user-defined code at any points in the program, in particular recovery code, outputting or sending messages, or raising exceptions. The MOP paradigm does not promote or enforce any specific formalism to specify requirements: it allows the users to plug-in their favorite or domain-specific specification formalisms via logic plug-in modules. There are two major technical challenges that MOP supporting tools unavoidably face: monitor synthesis and monitor integration. The former is heavily dependent on the specification formalism and comes as part of the corresponding logic plug-in, while the latter is uniform for all specification formalisms and depends only on the target programming language. An experimental prototype tool, called Java-MOP, is also discussed, which currently supports most but not all of the desired MOP features. MOP aims at reducing the gap between formal specification and implementation, by integrating the two and allowing them together to form a system

Iris: an Extensible Application for Building and Analyzing Spectral Energy Distributions

Iris is an extensible application that provides astronomers with a user-friendly interface capable of ingesting broad-band data from many different sources in order to build, explore, and model spectral energy distributions (SEDs). Iris takes advantage of the standards defined by the International Virtual Observatory Alliance, but hides the technicalities of such standards by implementing different layers of abstraction on top of them. Such intermediate layers provide hooks that users and developers can exploit in order to extend the capabilities provided by Iris. For instance, custom Python models can be combined in arbitrary ways with the Iris built-in models or with other custom functions. As such, Iris offers a platform for the development and integration of SED data, services, and applications, either from the user's system or from the web. In this paper we describe the built-in features provided by Iris for building and analyzing SEDs. We also explore in some detail the Iris framework and software development kit, showing how astronomers and software developers can plug their code into an integrated SED analysis environment.Comment: 18 pages, 8 figures, accepted for publication in Astronomy & Computin

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Background. 
The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration. There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics community. Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.

Description. 
SADI – Semantic Automated Discovery and Integration – is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers.

Conclusions.
SADI Services are fully compliant with, and utilize only foundational Web standards; are simple to create and maintain for service providers; and can be discovered and utilized in a very intuitive way by biologist end-users. In addition, the SADI design patterns significantly improve the ability of software to automatically discover appropriate services based on user-needs, and automatically chain these into complex analytical workflows. We show that, when resources are exposed through SADI, data compliant with a given ontological model can be automatically gathered, or generated, from these distributed, non-coordinating resources - a behavior we have not observed in any other Semantic system. Finally, we show that, using SADI, data dynamically generated from Web services can be explored in a manner very similar to data housed in static triple-stores, thus facilitating the intersection of Web services and Semantic Web technologies