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.

Implementing Policy Management through BDI

The requirement for Grid middleware to be largely transparent to individual users and at the same time act in accordance with their personal needs is a difficult challenge. In e-science scenarios, users cannot be repeatedly interrogated for each operational decision made when enacting experiments on the Grid. It is thus important to specify and enforce policies that enable the environment to be configured to take user preferences into account automatically. In particular, we need to consider the context in which these policies are applied, because decisions are based not only on the rules of the policy but also on the current state of the system. Consideration of context is explicitly addressed, in the agent perspective, when deciding how to balance the achievement of goals and reaction to the environment. One commonly-applied abstraction that balances reaction to multiple events with context-based reasoning in the way suggested by our requirements is the belief-desire-intention (BDI) architecture, which has proven successful in many applications. In this paper, we argue that BDI is an appropriate model for policy enforcement, and describe the application of BDI to policy enforcement in personalising Grid service discovery. We show how this has been implemented in the myGrid registry to provide bioinformaticians with control over the services returned to them by the service discovery process.