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.

Automated Negotiation Between Publishers And Consumers Of Grid Notifications

Notification Services mediate between information publishers and consumers that wish to subscribe to periodic updates. In many cases, however, there is a mismatch between the dissemination of these updates and the delivery preferences of the consumer, often in terms of frequency of delivery, quality, etc. In this paper, we present an automated negotiation engine that identifies mutually acceptable terms; we study its performance, and discuss its application to a Grid Notification Service. We also demonstrate how the negotiation engine enables users to control the Quality of Service levels they require.

Automated Negotiation for Grid Notification Services

Notification Services mediate between information publishers and consumers that wish to subscribe to periodic updates. In many cases, however, there is a mismatch between the dissemination of these updates and the delivery preferences of the consumer, often in terms of frequency of delivery, quality, etc. In this paper, we present an automated negotiation engine that identifies mutually acceptable terms; we study its performance, and discuss its application to a Grid Notification Service. We also demonstrate how the negotiation engine enables users to control the Quality of Service levels they require.