D'AGOSTINO D.

Energy consumption is one of the major issues in today's computer science, and an increasing number of scientific communities are interested in evaluating the tradeoff between time-to-solution and energy-to-solution. Despite, in the last two decades, computing which revolved around centralized computing infrastructures, such as supercomputing...

In this paper we describe our experience in exploiting different cloud-based environments for an actual use case taken from the bioinformatics domain - the molecular surfaces analysis - that identifies similarities and possible complementarities in the protein surfaces. The analysis of macromolecular surfaces is important since protein surface...

In the last two decades deep learning has attracted a lot of attention internationally, solving problems in different application domains and achieving results beyond expectations. For example it has been applied in bioinformatics, game playing, imaging processing, object detection, robotic and drug discovery. One of the main reasons for the...

Metagenomic studies are becoming increasingly widespread, yielding important insights into microbial communities covering diverse environments from terrestrial to aquatic ecosystems. This also because genome sequencing is likely to become a routinely and ubiquitous analysis in a near future thanks to a new generation of portable devices, such...

Many bioinformatic applications require to exploit the capabilities of several computational resources to effectively access and process large and distributed datasets. In this context, Grid computing has been largely used to face unprecedented challenges in Computational Biology, at the cost of complex workarounds needed to make applications...

In the last decade, different computing paradigms and modelling frameworks for the description and simulation of biochemical systems based on stochastic modelling have been proposed. From a computational point of view, many simulations of the model are necessary to identify the behaviour of the system. The execution of thousands of simulations...

Portable sequencing machines, such as the Oxford Nanopore MinION, are making the genome sequencing ubiquitous. Consequently, metagenomic studies are becoming increasingly popular, yielding important insights into microbial communities covering diverse environments from terrestrial to aquatic ecosystems. Furthermore, the adoption of low-power...

The purpose of this paper is to report on and analyse an international consultation into hydro-meteorological e-Science environments with the objective of identifying key functions and features together with exploring show-stopping issues and organisational structure. Transatlantic experiences were compared and contrasted. Including strong...

Background: High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of DNA interactions and 3D chromosome folding at the genome-wide scale. Usually, these data are represented as matrices describing the binary contacts among the different chromosome regions. On the other hand, a graph-based representation can be...

Portable sequencing machines, such as the Oxford Nanopore MinION, are making the genome sequencing ubiquitous. This can be particularly interesting for identifying specific bacteria in air-filters or waters and for monitoring the microbioma composition in cultivated soils or in different animal samples, using a simple and portable approach....

Energy consumption represents one of the most relevant issues by now in operating computing infrastructures, from traditional High Performance Computing Centers to Cloud Data Centers. Low power System-on-Chip (SoC) architectures, originally developed in the context of mobile and embedded technologies, are becoming attractive also for scientific...