Agents in Bioinformatics

The scope of the Technical Forum Group (TFG) on Agents in Bioinformatics (BIOAGENTS) was to inspire collaboration between the agent and bioinformatics communities with the aim of creating an opportunity to propose a different (agent-based) approach to the development of computational frameworks both for data analysis in bioinformatics and for system modelling in computational biology. During the day, the participants examined the future of research on agents in bioinformatics primarily through 12 invited talks selected to cover the most relevant topics. From the discussions, it became clear that there are many perspectives to the field, ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages for use by information agents, and to the use of Grid agents, each of which requires further exploration. The interactions between participants encouraged the development of applications that describe a way of creating agent-based simulation models of biological systems, starting from an hypothesis and inferring new knowledge (or relations) by mining and analysing the huge amount of public biological data. In this report we summarise and reflect on the presentations and discussions

A Taxonomy of Data Grids for Distributed Data Sharing, Management and Processing

Data Grids have been adopted as the platform for scientific communities that need to share, access, transport, process and manage large data collections distributed worldwide. They combine high-end computing technologies with high-performance networking and wide-area storage management techniques. In this paper, we discuss the key concepts behind Data Grids and compare them with other data sharing and distribution paradigms such as content delivery networks, peer-to-peer networks and distributed databases. We then provide comprehensive taxonomies that cover various aspects of architecture, data transportation, data replication and resource allocation and scheduling. Finally, we map the proposed taxonomy to various Data Grid systems not only to validate the taxonomy but also to identify areas for future exploration. Through this taxonomy, we aim to categorise existing systems to better understand their goals and their methodology. This would help evaluate their applicability for solving similar problems. This taxonomy also provides a "gap analysis" of this area through which researchers can potentially identify new issues for investigation. Finally, we hope that the proposed taxonomy and mapping also helps to provide an easy way for new practitioners to understand this complex area of research.Comment: 46 pages, 16 figures, Technical Repor

Leveraging the Grid to Provide a Global Platform for Ubiquitous Computing Research

The requirement for distributed systems support for Ubicomp has led to the development of numerous platforms, each addressing a subset of the overall requirements of ubiquitous systems. In contrast, many other scientific disciplines have embraced the vision of a global distributed computing platform, i.e. the Grid. We believe that the Grid has the potential to evolve into an ideal platform for building ubiquitous computing applications. In this paper we explore in detail the areas of synergy between Grid computing and ubiquitous computing and highlight a series of research challenges in this space

Data-Intensive architecture for scientific knowledge discovery

This paper presents a data-intensive architecture that demonstrates the ability to support applications from a wide range of application domains, and support the different types of users involved in defining, designing and executing data-intensive processing tasks. The prototype architecture is introduced, and the pivotal role of DISPEL as a canonical language is explained. The architecture promotes the exploration and exploitation of distributed and heterogeneous data and spans the complete knowledge discovery process, from data preparation, to analysis, to evaluation and reiteration. The architecture evaluation included large-scale applications from astronomy, cosmology, hydrology, functional genetics, imaging processing and seismology