Abstract

Materials Cloud is a platform designed to enable open and seamless sharing of resources for computational science, driven by applications in materials modelling. It hosts 1) archival and dissemination services for raw and curated data, together with their provenance graph, 2) modelling services and virtual machines, 3) tools for data analytics, and pre-/post-processing, and 4) educational materials. Data is citable and archived persistently, providing a comprehensive embodiment of the FAIR principles that extends to computational workflows. Materials Cloud leverages the AiiDA framework to record the provenance of entire simulation pipelines (calculations performed, codes used, data generated) in the form of graphs that allow to retrace and reproduce any computed result. When an AiiDA database is shared on Materials Cloud, peers can browse the interconnected record of simulations, download individual files or the full database, and start their research from the results of the original authors. The infrastructure is agnostic to the specific simulation codes used and can support diverse applications in computational science that transcend its initial materials domain. Comment: 19 pages, 8 figure Document type: Article

Abstract

The emergence of large, fine-grained mobility datasets offers significant opportunities for the development and application of new methodologies for transportation analysis. In this paper, the link between routing behaviour and traffic patterns in urban areas is examined, introducing a method to derive estimates of traffic patterns from a large collection of fine-grained routing data. Using this dataset, the interconnectivity between road network junctions is extracted in the form of a Markov chain. This representation encodes the probability of the successive usage of adjacent road junctions, encoding routes as flows between decision points rather than flows along road segments. This network of functional interactions is then integrated within a modified Markov chain Monte Carlo (MCMC) framework, adapted for the estimation of urban traffic patterns. As part of this approach, the data-derived links between major junctions influence the movement of directed random walks executed across the network to model origin-destination journeys. The simulation process yields estimates of traffic distribution across the road network. The paper presents an implementation of the modified MCMC approach for London, United Kingdom, building an MCMC model based on a dataset of nearly 700000 minicab routes. Validation of the approach clarifies how each element of the MCMC framework contributes to junction prediction performance, and finds promising results in relation to the estimation of junction choice and minicab traffic distribution. The paper concludes by summarising the potential for the development and extension of this approach to the wider urban modelling domain. Document type: Article

Abstract

Natural disasters like floods are a worldwide phenomenon and a serious threat to mankind. Flood simulations are applications of disaster control, which are used for the development of appropriate flood protection. Adequate simulations require not only the geometry but also the roughness of the Earth’s surface, as well as the roughness of the objects hereon. Usually, the floodplain roughness is based on land use/land cover maps derived from orthophotos. This study analyses the applicability of roughness map derivation approaches for flood simulations based on different datasets: orthophotos, LiDAR data, official land use data, OpenStreetMap data and CORINE Land Cover data. Object-based image analysis is applied to orthophotos and LiDAR raster data in order to generate land cover maps, which enable a roughness parameterization. The vertical vegetation structure within the LiDAR point cloud is used to derive an additional floodplain roughness map. Further roughness maps are derived from official land use data, OpenStreetMap and CORINE Land Cover datasets. Six different flood simulations are applied based on one elevation data but with the different roughness maps. The results of the hydrodynamic–numerical models include information on flow velocity and water depth from which the additional attribute flood intensity is calculated of. The results based on roughness maps derived from LiDAR data and OpenStreetMap data are comparable, whereas the results of the other datasets differ significantly. Document type: Article

Abstract

The introduction and spread of emerging infectious diseases is increasing in both prevalence and scale. Whether naturally, accidentally or maliciously introduced, the substantial uncertainty surrounding the emergence of novel viruses, specifically where they may come from and how they will spread, demands robust and quantifiably validated outbreak control policies that can be implemented in real time. This work presents a novel mathematical modeling framework that integrates both outbreak dynamics and outbreak control into a decision support tool for mitigating infectious disease pandemics that spread through passenger air travel. An ensemble of border control strategies that exploit properties of the air traffic network structure and expected outbreak behavior are proposed. A stochastic metapopulation epidemic model is developed to evaluate and rank the control strategies based on their effectiveness in reducing the spread of outbreaks. Sensitivity analyses are conducted to illustrate the robustness of the proposed control strategies across a range of outbreak scenarios, and a case study is presented for the 2009 H1N1 influenza pandemic. This study highlights the importance of strategically allocating outbreak control resources, and the results can be used to identify the most robust border control policy that can be implemented in the early stages of an outbreak. Document type: Preprint

Abstract

The Landsat archives have been made freely available in 2008, allowing the production of high resolution built-up maps at the regional or global scale. In this context, most of the classification algorithms rely on supervised learning to tackle the heterogeneity of the urban environments. However, at a large scale, the process of collecting training samples becomes a huge project in itself. This leads to a growing interest from the remote sensing community toward Volunteered Geographic Information (VGI) projects such as OpenStreetMap (OSM). Despite the spatial heterogeneity of its contribution patterns, OSM provides an increasing amount of information on the earth’s surface. More interestingly, the community has moved beyond street mapping to collect a wider range of spatial data such as building footprints, land use, or points of interest. In this paper, we propose a classification method that makes use of OSM to automatically collect training samples for supervised learning of built-up areas. To take into account a wide range of potential issues, the approach is assessed in ten Sub-Saharan African urban areas from various demographic profiles and climates. The obtained results are compared with: (1) existing high resolution global urban maps such as the Global Human Settlement Layer (GHSL) or the Human Built-up and Settlements Extent (HBASE); and (2) a supervised classification based on manually digitized training samples. The results suggest that automated supervised classifications based on OSM can provide performances similar to manual approaches, provided that OSM training samples are sufficiently available and correctly pre-processed. Moreover, the proposed method could reach better results in the near future, given the increasing amount and variety of information in the OSM database. SCOPUS: ar.j info:eu-repo/semantics/published Document type: Article

Abstract

utonomous driving technology offers a promising solution to reduce road accidents, traffic congestion, and fuel consumption. The management of vehicular networks is challenging as it demands mobility, location awareness, high reliability and low latency of data traffic. In this paper, we propose a novel communication architecture for vehicular network with 5G Mobile Networks and SDN technologies to support multiple core networks for autonomous vehicles and to tackle the potential challenges raised by the autonomous driving vehicles. Data requirements are evaluated for vehicular networks with respect to number of lanes and cluster size, to efficiently use the frequency and bandwidth. Also, the network latency requirements are analysed, which are mandatory constraints for all the applications where real time end-to-end communication is necessary. A test environment is also formulated to evaluate improvement in vehicular network using SDN-based approach over traditional core networks. Document type: Article

Abstract

"jats:p"This research is focused on understanding the phase behavior of gas hydrate formation in the gas dominant multiphase pipelines containing mixed gas with high CO"jats:sub"2"/jats:sub", crude oil, and deionized water. The experimental conditions are in the pressure range of 3–7 MPa with water cut as 20% of the volume. Initially, the effect of high CO"jats:sub"2"/jats:sub" content in natural gas on the phase boundary conditions of hydrates is studied through simulation (CSMGEM software) and experiments. Later, an additional phase of crude oil was introduced, with 15% of the volume to study the multiphase system. From the experimental analysis, thermodynamic equilibrium conditions were found, and the hydrate-liquid–vapor-equilibrium (HLVE) curves were drawn. The phase behavior is comprehended by comparing the HLVE curves of pure and multiphase systems. It is found that the high CO"jats:sub"2"/jats:sub" content tends to promote the gas hydrate formation. Based on the results, temperature variance and enthalpy of formation were calculated for the multiphase system. With a difference of 1.32 average temperature variance, the multiphase system exhibits inhibition. A basic statistical regression model was made to predict the gas hydrate formation in multiphase transmission pipelines. This work helps in understanding the effect of a new phase on gas hydrate formation. Document type: Article

Abstract

Prep is a high-performance tool for preparing sequence alignment/map files for variant calling in sequencing pipelines. It can be used as a replacement for SAMtools and Picard for preparation steps such as filtering, sorting, marking duplicates, reordering contigs, and so on, while producing identical results. What sets elPrep apart is its software architecture that allows executing preparation pipelines by making only a single pass through the data, no matter how many preparation steps are used in the pipeline. elPrep is designed as a multithreaded application that runs entirely in memory, avoids repeated file I/O, and merges the computation of several preparation steps to significantly speed up the execution time. For example, for a preparation pipeline of five steps on a whole-exome BAM file (NA12878), we reduce the execution time from about 1: 40 hours, when using a combination of SAMtools and Picard, to about 15 minutes when using elPrep, while utilising the same server resources, here 48 threads and 23GB of RAM. For the same pipeline on whole-genome data (NA12878), elPrep reduces the runtime from 24 hours to less than 5 hours. As a typical clinical study may contain sequencing data for hundreds of patients, elPrep can remove several hundreds of hours of computing time, and thus substantially reduce analysis time and cost. Document type: Article

Abstract

Global navigation satellite system (GNSS) is widely regarded as the primary positioning solution for intelligent transport system (ITS) applications. However, its performance could degrade, due to signal outages and faulty-signal contamination, including multipath and non-line-of-sight reception. Considering the limitation of the performance and computation loads in mass-produced automotive products, this research investigates the methods for enhancing GNSS-based solutions without significantly increasing the cost for vehicular navigation system. In this study, the measurement technique of the odometer in modern vehicle designs is selected to integrate the GNSS information, without using an inertial navigation system. Three techniques are implemented to improve positioning accuracy; (a) Time-differenced carrier phase (TDCP) based filter: A state-augmented extended Kalman filter is designed to incorporate TDCP measurements for maximizing the effectiveness of phase-smoothing; (b) odometer-aided constraints: The aiding measurement from odometer utilizing forward speed with the lateral constraint enhances the state estimation; the information based on vehicular motion, comprising the zero-velocity constraint, fault detection and exclusion, and dead reckoning, maintains the stability of the positioning solution; (c) robust regression: A weighted-least-square based robust regression as a measurement-quality assessment is applied to adjust the weightings of the measurements adaptively. Experimental results in a GNSS-challenging environment indicate that, based on the single-point-positioning mode with an automotive-grade receiver, the combination of the proposed methods presented a root-mean-square error of 2.51 m, 3.63 m, 1.63 m, and 1.95 m for the horizontal, vertical, forward, and lateral directions, with improvements of 35.1%, 49.6%, 45.3%, and 21.1%, respectively. The statistical analysis exhibits 97.3% state estimation result in the horizontal direction for the percentage of epochs that had errors of less than 5 m, presenting that after the intervention of proposed methods, the positioning performance can fulfill the requirements for road level applications. Document type: Article

Abstract

ns4:p"Pipeline tools are becoming increasingly important within the field of bioinformatics. Using a pipeline manager to manage and run workflows comprised of multiple tools reduces workload and makes analysis results more reproducible. Existing tools require significant work to install and get running, typically needing pipeline scripts to be written from scratch before running any analysis. We present Cluster Flow, a simple and flexible bioinformatics pipeline tool designed to be quick and easy to install. Cluster Flow comes with 40 modules for common NGS processing steps, ready to work out of the box. Pipelines are assembled using these modules with a simple syntax that can be easily modified as required. Core helper functions automate many common NGS procedures, making running pipelines simple. Cluster Flow is available with an GNU GPLv3 license on GitHub. Documentation, examples and an online demo are available at "ns4:ext-link xmlns:ns3="http://www.w3.org/1999/xlink" ext-link-type="uri" ns3:href="http://clusterflow.io""http://clusterflow.io"/ns4:ext-link"."/ns4 Document type: Article