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

Middleware architectures for the smart grid: A survey on the state-of-the-art, taxonomy and main open issues

The integration of small-scale renewable energy sources in the smart grid depends on several challenges that must be overcome. One of them is the presence of devices with very different characteristics present in the grid or how they can interact among them in terms of interoperability and data sharing. While this issue is usually solved by implementing a middleware layer among the available pieces of equipment in order to hide any hardware heterogeneity and offer the application layer a collection of homogenous resources to access lower levels, the variety and differences among them make the definition of what is needed in each particular case challenging. This paper offers a description of the most prominent middleware architectures for the smart grid and assesses the functionalities they have, considering the performance and features expected from them in the context of this application domain

Global Grids and Software Toolkits: A Study of Four Grid Middleware Technologies

Grid is an infrastructure that involves the integrated and collaborative use of computers, networks, databases and scientific instruments owned and managed by multiple organizations. Grid applications often involve large amounts of data and/or computing resources that require secure resource sharing across organizational boundaries. This makes Grid application management and deployment a complex undertaking. Grid middlewares provide users with seamless computing ability and uniform access to resources in the heterogeneous Grid environment. Several software toolkits and systems have been developed, most of which are results of academic research projects, all over the world. This chapter will focus on four of these middlewares--UNICORE, Globus, Legion and Gridbus. It also presents our implementation of a resource broker for UNICORE as this functionality was not supported in it. A comparison of these systems on the basis of the architecture, implementation model and several other features is included.Comment: 19 pages, 10 figure

Many-Task Computing and Blue Waters

This report discusses many-task computing (MTC) generically and in the context of the proposed Blue Waters systems, which is planned to be the largest NSF-funded supercomputer when it begins production use in 2012. The aim of this report is to inform the BW project about MTC, including understanding aspects of MTC applications that can be used to characterize the domain and understanding the implications of these aspects to middleware and policies. Many MTC applications do not neatly fit the stereotypes of high-performance computing (HPC) or high-throughput computing (HTC) applications. Like HTC applications, by definition MTC applications are structured as graphs of discrete tasks, with explicit input and output dependencies forming the graph edges. However, MTC applications have significant features that distinguish them from typical HTC applications. In particular, different engineering constraints for hardware and software must be met in order to support these applications. HTC applications have traditionally run on platforms such as grids and clusters, through either workflow systems or parallel programming systems. MTC applications, in contrast, will often demand a short time to solution, may be communication intensive or data intensive, and may comprise very short tasks. Therefore, hardware and software for MTC must be engineered to support the additional communication and I/O and must minimize task dispatch overheads. The hardware of large-scale HPC systems, with its high degree of parallelism and support for intensive communication, is well suited for MTC applications. However, HPC systems often lack a dynamic resource-provisioning feature, are not ideal for task communication via the file system, and have an I/O system that is not optimized for MTC-style applications. Hence, additional software support is likely to be required to gain full benefit from the HPC hardware

Forum Session at the First International Conference on Service Oriented Computing (ICSOC03)

The First International Conference on Service Oriented Computing (ICSOC) was held in Trento, December 15-18, 2003. The focus of the conference ---Service Oriented Computing (SOC)--- is the new emerging paradigm for distributed computing and e-business processing that has evolved from object-oriented and component computing to enable building agile networks of collaborating business applications distributed within and across organizational boundaries. Of the 181 papers submitted to the ICSOC conference, 10 were selected for the forum session which took place on December the 16th, 2003. The papers were chosen based on their technical quality, originality, relevance to SOC and for their nature of being best suited for a poster presentation or a demonstration. This technical report contains the 10 papers presented during the forum session at the ICSOC conference. In particular, the last two papers in the report ere submitted as industrial papers

Analysis of current middleware used in peer-to-peer and grid implementations for enhancement by catallactic mechanisms

This deliverable describes the work done in task 3.1, Middleware analysis: Analysis of current middleware used in peer-to-peer and grid implementations for enhancement by catallactic mechanisms from work package 3, Middleware Implementation. The document is divided in four parts: The introduction with application scenarios and middleware requirements, Catnets middleware architecture, evaluation of existing middleware toolkits, and conclusions. -- Die Arbeit definiert Anforderungen an Grid und Peer-to-Peer Middleware Architekturen und analysiert diese auf ihre Eignung für die prototypische Umsetzung der Katallaxie. Eine Middleware-Architektur für die Umsetzung der Katallaxie in Application Layer Netzwerken wird vorgestellt.Grid Computing