A Molecular Biology Database Digest

Computational Biology or Bioinformatics has been defined as the application of mathematical and Computer Science methods to solving problems in Molecular Biology that require large scale data, computation, and analysis [18]. As expected, Molecular Biology databases play an essential role in Computational Biology research and development. This paper introduces into current Molecular Biology databases, stressing data modeling, data acquisition, data retrieval, and the integration of Molecular Biology data from different sources. This paper is primarily intended for an audience of computer scientists with a limited background in Biology

Querying Large Physics Data Sets Over an Information Grid

Optimising use of the Web (WWW) for LHC data analysis is a complex problem and illustrates the challenges arising from the integration of and computation across massive amounts of information distributed worldwide. Finding the right piece of information can, at times, be extremely time-consuming, if not impossible. So-called Grids have been proposed to facilitate LHC computing and many groups have embarked on studies of data replication, data migration and networking philosophies. Other aspects such as the role of 'middleware' for Grids are emerging as requiring research. This paper positions the need for appropriate middleware that enables users to resolve physics queries across massive data sets. It identifies the role of meta-data for query resolution and the importance of Information Grids for high-energy physics analysis rather than just Computational or Data Grids. This paper identifies software that is being implemented at CERN to enable the querying of very large collaborating HEP data-sets, initially being employed for the construction of CMS detectors.Comment: 4 pages, 3 figure

Open-source digital technologies for low-cost monitoring of historical constructions

This paper shows new possibilities of using novel, open-source, low-cost platforms for the structural health monitoring of heritage structures. The objective of the study is to present an assessment of increasingly available open-source digital modeling and fabrication technologies in order to identify the suitable counterparts of the typical components of a continuous static monitoring system for a historical construction. The results of the research include a simple case-study, which is presented with low-cost, open-source, calibrated components, as well as an assessment of different alternatives for deploying basic structural health monitoring arrangements. The results of the research show the great potential of these existing technologies that may help to promote a widespread and cost-efficient monitoring of the built cultural heritage. Such scenario may contribute to the onset of commonplace digital records of historical constructions in an open-source, versatile and reliable fashion.Peer ReviewedPostprint (author's final draft

Logic-Based Specification Languages for Intelligent Software Agents

The research field of Agent-Oriented Software Engineering (AOSE) aims to find abstractions, languages, methodologies and toolkits for modeling, verifying, validating and prototyping complex applications conceptualized as Multiagent Systems (MASs). A very lively research sub-field studies how formal methods can be used for AOSE. This paper presents a detailed survey of six logic-based executable agent specification languages that have been chosen for their potential to be integrated in our ARPEGGIO project, an open framework for specifying and prototyping a MAS. The six languages are ConGoLog, Agent-0, the IMPACT agent programming language, DyLog, Concurrent METATEM and Ehhf. For each executable language, the logic foundations are described and an example of use is shown. A comparison of the six languages and a survey of similar approaches complete the paper, together with considerations of the advantages of using logic-based languages in MAS modeling and prototyping.Comment: 67 pages, 1 table, 1 figure. Accepted for publication by the Journal "Theory and Practice of Logic Programming", volume 4, Maurice Bruynooghe Editor-in-Chie

Predicting Intermediate Storage Performance for Workflow Applications

Configuring a storage system to better serve an application is a challenging task complicated by a multidimensional, discrete configuration space and the high cost of space exploration (e.g., by running the application with different storage configurations). To enable selecting the best configuration in a reasonable time, we design an end-to-end performance prediction mechanism that estimates the turn-around time of an application using storage system under a given configuration. This approach focuses on a generic object-based storage system design, supports exploring the impact of optimizations targeting workflow applications (e.g., various data placement schemes) in addition to other, more traditional, configuration knobs (e.g., stripe size or replication level), and models the system operation at data-chunk and control message level. This paper presents our experience to date with designing and using this prediction mechanism. We evaluate this mechanism using micro- as well as synthetic benchmarks mimicking real workflow applications, and a real application.. A preliminary evaluation shows that we are on a good track to meet our objectives: it can scale to model a workflow application run on an entire cluster while offering an over 200x speedup factor (normalized by resource) compared to running the actual application, and can achieve, in the limited number of scenarios we study, a prediction accuracy that enables identifying the best storage system configuration

Towards a Distributed Quantum Computing Ecosystem

The Quantum Internet, by enabling quantum communications among remote quantum nodes, is a network capable of supporting functionalities with no direct counterpart in the classical world. Indeed, with the network and communications functionalities provided by the Quantum Internet, remote quantum devices can communicate and cooperate for solving challenging computational tasks by adopting a distributed computing approach. The aim of this paper is to provide the reader with an overview about the main challenges and open problems arising with the design of a Distributed Quantum Computing ecosystem. For this, we provide a survey, following a bottom-up approach, from a communications engineering perspective. We start by introducing the Quantum Internet as the fundamental underlying infrastructure of the Distributed Quantum Computing ecosystem. Then we go further, by elaborating on a high-level system abstraction of the Distributed Quantum Computing ecosystem. Such an abstraction is described through a set of logical layers. Thereby, we clarify dependencies among the aforementioned layers and, at the same time, a road-map emerges