Agent-Oriented Data Curation in Bioinformatics

The practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view.

Agent-Oriented Data Curation in Bioinformatics

The practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view.

Designing Agent-Oriented Systems by Analysing Agent Interactions

We propose a preliminary methodology for agent-oriented software engineering based on the idea of agent interaction analysis. This approach uses interactions between undetermined agents as the primary component of analysis and design. Agents as a basis for software engineering are useful because they provide a powerful and intuitive abstraction which can increase the comprehensiblity of a complex design. The paper describes a process by which the designer can derive the interactions that can occur in a system satisfying the given requirements and use them to design the structure of an agent-based system, including the identification of the agents themselves. We suggest that this approach has the flexibility necessary to provide agent-oriented designs for open and complex applications, and has value for future maintenance and extension of these systems.

Security Issues in a SOA-based Provenance System

Recent work has begun exploring the characterization and utilization of provenance in systems based on the Service Oriented Architecture (such as Web Services and Grid based environments). One of the salient issues related to provenance use within any given system is its security. In a broad sense, security requirements arise within any data archival and retrieval system, however provenance presents unique requirements of its own. These requirements are additionally dependent on the architectural and environmental context that a provenance system operates in. We seek to analyze the security considerations pertaining to a Service Oriented Architecture based provenance system. Towards this end, we describe the components of such a system and illustrate the security considerations that arise within it. Concurrently, we outline possible approaches to address them.