Daniele D'Agostino

• PhD
• Professor (Associate) at University of Genoa

High-throughput clonal tracking in patients under hematopoietic stem cell gene therapy with integrating vector is instrumental in assessing bio-safety and efficacy. Monitoring the fate of millions of transplanted clones and their progeny across differentiation and proliferation over time leverages the identification of the vector integration sites,...

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 and d...

Temporal variability in flux and spectral shape is ubiquitous in the X-ray sky and carries crucial information about the nature and emission physics of the sources. The EPIC instrument on board the XMM-Newton observatory is the most powerful tool for studying variability even in faint sources. Each day, it collects a large amount of information abo...

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 advantageo...

Temporal variability in flux and spectral shape is ubiquitous in the X-ray sky and carries crucial information about the nature and emission physics of the sources. The EPIC instrument on board the XMM-Newton observatory is the most powerful tool for studying variability even in faint sources. Each day, it collects a large amount of information abo...

High-throughput sequencing Chromosome Conformation Capture (Hi-C) allows the study of chromatin interactions and 3D chromosome folding on a larger scale. A graph-based multi-level representation of Hi-C data is essential for proper visualisation of the spatial pattern they represent, in particular for comparing different experiments or for re-mappi...

Ultraluminous X-ray sources (ULXs) are a class of accreting compact objects with X-ray luminosities above 10³⁹ erg s⁻¹. The ULX population counts several hundred objects but only a fraction are well studied. Here we present a detailed analysis of all ULXs hosted in the galaxy NGC 7456. It was observed in X-rays only once in the past (in 2005) by XM...

This editorial introduces the articles selected for the special issue concerning the International Conferences on Parallel, Distributed, and Network‐Based Processing, which provided insights related to the efficient exploitation of parallel and distributed architectures, including power‐aware computing, application scheduling, and application devel...

Ultraluminous X-ray sources (ULXs) are a class of accreting compact objects with X-ray luminosities above 1e39 erg/s. The ULX population counts several hundreds objects but only a minor fraction is well studied. Here we present a detailed analysis of all ULXs hosted in the galaxy NGC 7456. It was observed in X-rays only once in the past (in 2005) b...

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project harvested the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Ima...

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project harvested the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Ima...

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored – and largely unexploited – in data archives. Like a treasure-hunt, the EXTraS project harvested the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Ima...

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 IoT co...

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 succe...

In the perspective of energy‐efficient storage solutions supporting scientific computing, we investigate the possibility of using low‐power Systems‐On‐Chip (SoCs) as storage bricks of a BeeGFS file system in support of a realistic genome sequencing pipeline from Bioinformatics. Metadata and data performances of such a file system made of low‐power...

We discovered 2.8 s pulsations in the X-ray emission of the ultraluminous X-ray source (ULX) M51 ULX-7 within the UNSEeN project, which was designed to hunt for new pulsating ULXs (PULXs) with XMM-Newton. The pulse shape is sinusoidal and large variations of its amplitude were observed even within single exposures (pulsed fraction from less than 5%...

We discovered 2.8 s pulsations in the X-ray emission of the ultraluminous X-ray source (ULX) M51 ULX-7 within the UNSEeN project, which was designed to hunt for new pulsating ULXs (PULXs) with XMM-Newton. The pulse shape is sinusoidal and large variations of its amplitude were observed even within single exposures (pulsed fraction from less than 5%...

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 and...

Json-GUI is an AngularJS front-end module that dynamically generates form-based web interfaces. Starting from a formal JSON configuration object describing a list of inputs, Json-GUI is able to build a form frame interface at runtime, with standard and personalized validation rules, giving the possibility to define constraints between input fields....

Introduction: Computational chemistry dramatically accelerates the drug discovery process and high-performance computing (HPC) can be used to speed up the most expensive calculations. Supporting a local HPC infrastructure is both costly and time consuming and therefore many research groups are moving from in-house solutions to remote distributed co...

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 as th...

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. However...

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project harvested the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Ima...

The development of community-specific user interfaces of a science gateway can be a challenging task for non-IT experts. This contribution proposes an original, easy-to-use solution to tackle this issue based on EasyGateway. EasyGateway is a modern, lightweight solution for the development of science gateway able to interplay with most toolkits. In...

We performed a search for eclipsing and dipping sources in the archive of the EXTraS project - a systematic characterization of the temporal behaviour of XMM-Newton point sources. We discovered dips in the X-ray light curve of 3XMM J004232.1+411314, which has been recently associated with the hard X-ray source dominating the emission of M31. A syst...

We performed a search for eclipsing and dipping sources in the archive of the EXTraS project - a systematic characterization of the temporal behaviour of XMM-Newton point sources. We discovered dips in the X-ray light curve of 3XMM J004232.1+411314, which has been recently associated with the hard X-ray source dominating the emission of M31. A syst...

The continuous technological advances made the energy ef- �ciency a major topic for greener Information Technology systems. Low power Systems-on-Chip (SoC), originally developed in the context of mo- bile and embedded technologies, are becoming attractive also for scien- ti�c and industrial applications given their increasing computing per- formanc...

Over the last two decades, a solid consensus grew in the scientific community that the so-called Citizen Science could contribute to advancing our current knowledge in many disciplines. In particular Hydro-Meteorological (HM) researchers immediately pointed out to the countless advantages of cooperating with Citizen Scientists. In this paper we pre...

Current weather information is one of the facilities supplied to the users by most travel and mobility systems. Most of them relies on one provider, who can deliver a more or less satisfactory coverage on different geographical areas. In this paper, we present the approach and discuss the rationale that drove the design and development of a mashup...

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project is harvesting the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon...

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 particip...

From 1970 to 2012, about 9000 high impact weather events were reported globally causing the loss of 1.94 million lives and damage of US$ 2.4 trillion (United Nations International Strategy for Disaster Reduction, UNISDR report 2014). The scientific community is called to action to improve the predictive ability of such events and communicate foreca...

Spinning up an extragalactic neutron star Ultraluminous x-ray sources (ULXs) are strange objects in other galaxies that cannot be explained by conventional accretion onto stellar-mass objects. This has led to exotic interpretations, such as the long-sought intermediate-mass black holes. Israel et al. observed a ULX in the nearby galaxy NGC 5907 and...

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project is harvesting the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon...

A full hydro-meteorological (HM) simulation, from rainfall to impact on urban areas, is a multidisciplinary activity which consists in the execution of a workflow composed by complex and heterogeneous model engines. Moreover an extensive set of configuration parameters have to be selected consistently among the models, otherwise the simulation can...

Modern soft X-ray observatories can yield unique insights into time domain astrophysics, and a huge amount of information is stored - and largely unexploited - in data archives. Like a treasure-hunt, the EXTraS project is harvesting the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon...

The EXTraS project to explore the X-ray Transient and variable Sky searches for coherent signals in the X-ray archival data of XMM-Newton. XMM-Newton performed more than 400 pointed observations in the region of the Large Magellanic Cloud (LMC). We inspected the results of the EXTraS period search to systematically look for new X-ray pulsators in o...

The EXTraS project to explore the X-ray Transient and variable Sky searches for coherent signals in the X-ray archival data of XMM-Newton. XMM-Newton performed more than 400 pointed observations in the region of the Large Magellanic Cloud (LMC). We inspected the results of the EXTraS period search to systematically look for new X-ray pulsators in o...

Non-nuclear ultraluminous x-ray sources (ULXs) in nearby galaxies shine brighter than any source in our Galaxy. ULXs are usually modeled as stellar-mass black holes accreting at very high rates or intermediate-mass black-holes. We have discovered that ULX-1 in NGC 5907 is an x-ray accreting neutron star (NS) with a spin period evolving from 1.43 s...

Machine learning is a widely used technique in structural biology, since the analysis of large conformational ensembles originated from single protein structures (e.g. derived from NMR experiments or molecular dynamics simulations) can be approached by partitioning the original dataset into sensible subsets, revealing important structural and dynam...

The flexible and pay-as-you-go computing capabilities offered by Cloud infrastructures are nowadays very attractive, and widely adopted by many organizations and enterprises. In particular this is true for those having periodical or variable tasks to execute, and, choose to not or cannot afford the expenses of buying and managing computing faciliti...

MicroRNAs (or miRNA) are key regulators of gene expression, but the precise mechanisms underlying their interaction with their mRNA-targets are still poorly understood. Since miRNA are involved in the onset of many different diseases, the study of their interaction with the genome is very important to study. Different approaches can be used to reco...

The EXTraS project (“Exploring the X-ray Transient and variable Sky”) will characterise the temporal behaviour of the largest ever sample of objects in the soft X-ray range (0.1–12 keV) with a complex, systematic and consistent analysis of all data collected by the European Photon Imaging Camera (EPIC) instrument onboard the ESA XMM-Newton X-ray ob...

During a search for coherent signals in the X-ray archival data of XMM–Newton, we discovered a modulation at 1.2 s in 3XMM J004301.4+413017 (3X J0043), a source lying in the direction of an external arm of M 31. This short period indicates a neutron star (NS). Between 2000 and 2013, the position of 3X J0043 was imaged by public XMM–Newton observati...

X-ray emission from Young Stellar Objects (YSOs) is crucial to understand star formation. A very limited amount of X-ray results is available for the protostellar (ClassI) phase. A systematic search of transient X-ray phenomena combined with a careful evaluation of the evolutionary stage offer a widely unexplored window to our understanding of YSOs...

X-ray emission from Young Stellar Objects (YSOs) is crucial to understand star formation. A very limited amount of X-ray results is available for the protostellar (ClassI) phase. A systematic search of transient X-ray phenomena combined with a careful evaluation of the evolutionary stage offer a widely unexplored window to our understanding of YSOs...

A full hydrometeorological (HM) simulation, from rainfall to impact on urban areas, is a multidisciplinary job, which relies on the execution of a workflow composed of complex and heterogeneous model engines. Moreover, the accuracy of the simulation is strongly dependent on an extensive set of configuration parameters, which have to be selected in...

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 conf...

Many computational and systems biology challenges, in particular those related to big data analysis, can be formulated as optimization problems and therefore can be addressed using heuristics. Beside the typical optimization problems, formulated with respect to a single target, the possibility of optimizing multiple objectives (MO) is rapidly becom...

The e-Science environment developed in the framework of the EU-funded DRIHM project was used to demonstrate its capability to provide relevant, meaningful hydrometeorological forecasts. This was illustrated for the tragic case of 4 November 2011, when Genoa, Italy, was flooded as the result of heavy, convective precipitation that inundated the Bisa...

The EXTraS project (Exploring the X-ray Transient and variable Sky) will harvest the hitherto unexplored temporal domain information buried in the serendipitous data collected by the European Photon Imaging Camera (EPIC) instrument onboard the ESA XMM-Newton X-ray observatory since its launch. This will include a search for fast transients, as well...

The flexible and pay-as-you-go computing capabilities offered by Cloud infrastructures are very attractive for high-demanding e-Science applications like weather prediction simulators. For their ability to couple the scalability offered by public service provider with the greater control and customization provided by Private Clouds, Hybrid Clouds s...

Scientific image processing is a topic of interest for a broad scientific community since it is a mean of gaining understanding and insight into the data for a growing number of applications. Furthermore, the technological evolution permits large data acquisition, with sophisticated instruments, and their elaboration through complex multidisciplina...

Isosurface extraction is a fundamental operation for the analysis and visualization of 3D scalar fields, and the marching cubes technique is the de facto standard to implement it. The processing of large datasets can be a very time-consuming task, and for this reason a number of parallel implementations have been proposed in the literature. In this...

A proper representation of protein surfaces is an important task in bioinformatics and biophysics. In a previous work we described a parallel workflow, based on the isosurface extraction and the CUDA architecture, able to produce high-resolution molecular surfaces based on the Van der Waals, Solvent Accessible, Richards-Connolly and Blobby definiti...

The distributed research infrastructure for hydrometeorology (DRIHM) project focuses on the development of an e-Science infrastructure to provide end-to-end hydro meteorological research (HMR) services (models, data, and post processing tools) by exploiting HPC, Grid and Cloud facilities. In particular, the DRIHM infrastructure supports the executi...

The e-Science environment developed in the framework of the EU-funded DRIHM project was used to demonstrate its capability to provide relevant, meaningful hydrometeorological forecasts. This was illustrated for the tragic case of 4 November 2011, when Genoa, Italy, was flooded as the result of heavy, convective precipitation that inundated the Bisa...

Besides core project partners, the SCI-BUS project also supported several external user communities in developing and setting up customized science gateways. The focus was on large communities typically represented by other European research projects. However, smaller local efforts with the potential of generalizing the solution to wider communitie...

Predicting weather and climate and its impacts on the environment, including hazards such as floods and landslides, is a big challenge that can be efficiently supported by a distributed and heterogeneous infrastructure, exploiting several kinds of computational resources: HPC, Grids and Clouds. This can help researchers in speeding up experiments,...

The explosion of the data both in the biomedical research and in the healthcare systems demands urgent solutions. In particular, the research in omics sciences is moving from a hypothesis-driven to a data-driven approach. Healthcare is additionally always asking for a tighter integration with biomedical data in order to promote personalized medicin...

In a Business-to-Business (B2B) scenario strategic goals are integration and interoperability. Integration regards the process, within an enterprise, of linking different software systems to become part of larger systems. Interoperability is strictly linked to the standardization of commercial messages and communication protocols. In this work we p...

The special issue of Concurrency And Computation: Practice And Experience deals with latest advances in distributed, parallel, and graphic processing unit accelerated approaches to computational biology. This trend is motivated by the lightening improvement of novel molecular biology high-throughput technologies, such as next generation sequencing,...

SUMMARYA proper and efficient representation of possibly complex and large molecular surfaces is an important task in bioinformatics and biophysics. Molecular surfaces indeed are used for different aims, in particular, for computation, as visual support tools for biologists, in electrostatics problems involving implicit solvents (e.g. while solving...

Predicting weather and climate and its impacts on the environment, including hazards such as floods and landslides, is one of the main challenges of the 21st century with significant societal and economic implications. To advance the state of the art in forecasting extreme events, an effective collaboration with the Information and Communication Te...

There is an increasing awareness of the pivotal role of noise in biochemical processes and of the effect of molecular crowding on the dynamics of biochemical systems. This necessity has given rise to a strong need for suitable and sophisticated algorithms for the simulation of biological phenomena taking into account both spatial effects and noise....

This chapter analyzes some of the programming models and tools, both commercial and freely available, in terms of the provided support and achievable performance with respect to some widely used compute-intensive algorithms such as the N-body and the convolution algorithms. It focuses on providing a clear measure of the different efficiency figures...

Resources benchmarking is a promising though challenging opportunity for research communities to better exploit e-Science infrastructures. The paper investigates the suitability of an integrated two-level benchmarking approach in supporting resources ranking on a performance basis. The coupling of different benchmarking techniques i.e. kernel and a...

The Grid infrastructures, such as the one provided by the European Grid Infrastructure, represent suitable solutions to achieve cost effective computational power. However, these solutions present to Grid users some challenges, i.e. to create a customized computing environment and its management. For this reason a Cloud-like approach is for certain...

The increasing awareness of the pivotal role of noise in biochemical systems has given rise to a strong need for suitable stochastic algorithms for the description and the simulation of biological phenomena. However, the high computational demand that characterizes stochastic simulation approaches coupled with the necessity to simulate the models s...

Current workstations can offer really amazing raw computational power, in the order of TFlops on a single machine equipped with multiple CPUs and accelerators, which means less than half a dollar for a GFlop. Such result can only be achieved with a massive parallelism of the computational devices, but unfortunately not every application is able to...

Hybrid Clouds couple the scalability offered by public Clouds with the greater control supplied by private ones. A (hybrid) Cloud broker acting as an intermediary between users and providers of public Cloud services, may support customers in the selection of the most suitable offers, optionally adding the provisioning of dedicated services with hig...

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 simulation can r...

Cloud computing opens new perspectives for small-medium biotechnology laboratories that need to perform bioinformatics analysis in a flexible and effective way. This seems particularly true for hybrid clouds that couple the scalability offered by general-purpose public clouds with the greater control and ad hoc customizations supplied by the privat...

Hybrid Clouds seems able to offer their customers with differentiate solutions capable of providing more and personalized guarantees with respect to the basic service availability generally supplied. In the context of an Italian research project aimed to transfer ICT advancements from research centers towards ICT SMEs, the paper focuses on the desi...

The acknowledged success and diffusion of Cloud computing is due to its great potential in terms of improving companies' business model. Notwithstanding this opportunity, two main issues arise: the need of brokers supporting users in the selection of the most suitable offers, and the provisioning of dedicated services with higher levels of quality...

One of the main challenges of the 21st century is represented by accurate weather predictions together with the estimate of extreme phenomena and their impacts on the environment and on the society. The key point of this challenge is to enable the acceleration of advances in hydrometeorological research, and to integrate these advances in the every...

Grid portals and related technologies represent an easy and transparent way for scientists to interact with Distributed Computing Infrastructures (DCIs) as the Grid and the Cloud. Many toolkits and frameworks are available, both commercial and open source, but there is a lack of best practices, customization methodologies and dedicated high-level s...

Present advances in sequencing technology make possible to generate large amounts of data in short time. However one major issue is represented by the fact that fragments produced by these high-throughput methods are short and in very high number, resulting in a difficult analytical task. Two different approaches are currently applied to genome ass...

The allocation of jobs to a set of heterogeneous resources, as in common e-Science environments, is a key issue for their efficient use. To reach a better coupling and improve execution times of applications, a consolidated though challenging opportunity is the benchmarking of resources. In this direction, we propose to exploit two complementary ap...

A proper and efficient representation of molecular surfaces is an important issue in biophysics from several view points. Molecular surfaces indeed are used for different aims, in particular for visualization, as support tools for biologists, computation, in electrostatics problems involving implicit solvents (e.g. while solving the Poisson-Boltzma...

Emerging technologies for structure matching based on surface descriptions have demonstrated their effectiveness in many research fields. In particular, they can be successfully applied to in silico studies of structural biology. Protein activities, in fact, are related to the external characteristics of these macromolecules and the ability to matc...

In this paper we discuss the issues related to the development of efficient parallel implementations of the Marching Cubes algorithm, one of the most used methods for isosurface extraction, which is a fundamental operation for 3D data analysis and visualization. We present three possible parallelization strategies and we outline the pros and cons o...

Present advances in sequencing technology make possible to generate large amounts of data in short time. The problem is that fragments produced by these high-throughput methods are much shorter than in traditional Sanger sequencing, and this makes stringent the issue of exploiting an efficient sequence assembly algorithm. While two common approache...

The Distributed Research Infrastructure for Hydro-Meteorological Study (DRIHMS) is a coordinated action co-funded by the European Commission. DRIHMS analyzes the main issues that arise when designing and setting up a pan-European Grid-based e-Infrastructure for research activities in the hydrologic and meteorological fields. The main outcome of the...