Netherlands eScience Center

Amsterdam, Netherlands

Netherlands eScience Center

Amsterdam, Netherlands
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van der Linden E.C.,Royal Netherlands Meteorological Institute | Bintanja R.,Royal Netherlands Meteorological Institute | Bintanja R.,University of Groningen | Hazeleger W.,Wageningen University | Hazeleger W.,Netherlands eScience Center
Journal of Geophysical Research: Atmospheres | Year: 2017

Natural decadal variability of surface air temperature might obscure Arctic temperature trends induced by anthropogenic forcing. It is therefore imperative to know how Arctic decadal variability (ADV) will change as the climate warms. In this study, we evaluate ADV characteristics in three equilibrium climates with present-day, double, and quadrupled atmospheric CO2 forcing. The dominant region of variability, which is located over the Barents and Greenland Sea at present, shifts to the central Arctic and Siberian regions as the climate warms. The maximum variability in sea ice cover and surface air temperature occurs in the CO2 doubling climate when sea ice becomes more vulnerable to melt over vast stretches of the Arctic. Furthermore, the links between dominant atmospheric circulation modes and Arctic surface climate characteristics vary strongly with climate change. For instance, a positive Arctic Oscillation index is associated with a colder Arctic in warmer climates, instead of a warmer Arctic at present. Such changing relationships are partly related to the retreat of sea ice because altered wind patterns influence the sea ice distribution and hence the associated local surface fluxes. The atmospheric pressure distributions governing ADV and the associated large-scale dynamics also change with climate warming. The changing character of the ADV shows that it is vital to consider (changes in) ADV when addressing Arctic warming in climate model projections. ©2017. American Geophysical Union. All Rights Reserved.

Borgdorff J.,Netherlands eScience Center | Krishna H.,Fields of View | Lees M.H.,University of Amsterdam
Procedia Computer Science | Year: 2015

Urban areas are characterised by high population densities and the resulting complex social dynamics. For urban planners to evaluate, analyse, and predict complex urban dynamics, a lot of scenarios and a large parameter space must be explored. In urban disasters, complex situations must be assessed in short notice. We propose the concept of an assisted decision support system to aid in these situations The system interactively runs a scenario exploration, which evaluates scenarios and optimize for desired properties. We introduce the SIM-CITY architecture to run such interactive scenario explorations and highlight a use case for the architecture, an urban fire emergency response simulation in Bangalore. © The Authors. Published by Elsevier B.V.

PubMed | Phortos Consultants, Stanford University, Cray, TU Eindhoven and 30 more.
Type: | Journal: Scientific data | Year: 2016

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders-representing academia, industry, funding agencies, and scholarly publishers-have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

Van Der Zwaan J.M.,Netherlands eScience Center | Marx M.,University of Amsterdam | Kamps J.,University of Amsterdam
Frontiers in Artificial Intelligence and Applications | Year: 2016

In the literature, different topic models have been introduced that target the task of viewpoint extraction. Because, generally, these studies do not present thorough validations of the models they introduce, it is not clear in advance which topic modeling technique will work best for our use case of extracting viewpoints of political parties from parliamentary proceedings. We argue that the usefulness of methods like topic modeling depend on whether they yield valid and reliable results on real world data. This means that there is a need for validation studies. In this paper, we present such a study for an existing topic model for viewpoint extraction called cross-perspective topic modeling [11]. The model is applied to Dutch parliamentary proceedings, and the resulting topics and opinions are validated using external data. The results of our validation show that the model yields valid topics (content and criterion validity), and opinions with content validity. We conclude that cross-perspective topic modeling is a promising technique for extracting political parties' positions from parliamentary proceedings. Second, by exploring a number of validation methods, we demonstrate that validating topic models is feasible, even without extensive domain knowledge. © 2016 The Authors and IOS Press.

Pelupessy F.I.,Leiden University | Van Elteren A.,Leiden University | De Vries N.,Leiden University | McMillan S.L.W.,Drexel University | And 2 more authors.
Astronomy and Astrophysics | Year: 2013

We present the open source Astrophysical Multi-purpose Software Environment (AMUSE), a component library for performing astrophysical simulations involving different physical domains and scales. It couples existing codes within a Python framework based on a communication layer using MPI. The interfaces are standardized for each domain and their implementation based on MPI guarantees that the whole framework is well-suited for distributed computation. It includes facilities for unit handling and data storage. Currently it includes codes for gravitational dynamics, stellar evolution, hydrodynamics and radiative transfer. Within each domain the interfaces to the codes are as similar as possible. We describe the design and implementation of AMUSE, as well as the main components and community codes currently supported and we discuss the code interactions facilitated by the framework. Additionally, we demonstrate how AMUSE can be used to resolve complex astrophysical problems by presenting example applications. © ESO, 2013.

Haren R.,Royal Netherlands Meteorological Institute | Haren R.,Netherlands eScience Center | Haarsma R.J.,Netherlands eScience Center | Oldenborgh G.J.,Netherlands eScience Center | And 3 more authors.
Journal of Climate | Year: 2015

In this study, the authors investigate the effect of GCM spatial resolution on modeled precipitation over Europe. The objectives of the analysis are to determine whether climate models have sufficient spatial resolution to have an accurate representation of the storm tracks that affect precipitation. They investigate if there is a significant statistical difference in modeled precipitation between a medium-resolution (~ 112-km horizontal resolution) and a high-resolution (~ 25-km horizontal resolution) version of a state-of-the-art AGCM (EC-EARTH), if either model resolution gives a better representation of precipitation in the current climate, and what processes are responsible for the differences inmodeled precipitation. The authors find that the highresolution model gives a more accurate representation of northern and central European winter precipitation. The medium-resolution model has a larger positive bias in precipitation inmost of the northern half of Europe. Storm tracks are better simulated in the high-resolution model, providing for a more accurate horizontal moisture transport and moisture convergence. Using a decomposition of the precipitation difference between the medium- and high-resolution model in a part related and a part unrelated to a difference in the distribution of vertical atmospheric velocity, the authors find that the smaller precipitation bias in central and northern Europe is largely unrelated to a difference in vertical velocity distribution. The smaller precipitation amount in these areas is in agreementwith lessmoisture transport over this area in the high-resolution model. In areas with orography the change in vertical velocity distribution is found to be more important. © 2015 American Meteorological Society.

Fleuren W.W.M.,Computational Discovery and oDesign Group CMBI | Fleuren W.W.M.,Netherlands eScience Center | Alkema W.,Computational Discovery and oDesign Group CMBI | Alkema W.,NIZO Food Research BV
Methods | Year: 2015

In recent years the amount of experimental data that is produced in biomedical research and the number of papers that are being published in this field have grown rapidly. In order to keep up to date with developments in their field of interest and to interpret the outcome of experiments in light of all available literature, researchers turn more and more to the use of automated literature mining. As a consequence, text mining tools have evolved considerably in number and quality and nowadays can be used to address a variety of research questions ranging from de novo drug target discovery to enhanced biological interpretation of the results from high throughput experiments. In this paper we introduce the most important techniques that are used for a text mining and give an overview of the text mining tools that are currently being used and the type of problems they are typically applied for. © 2015 Elsevier Inc.

Sang E.T.K.,Netherlands eScience Center | Van Den Bosch A.,Radboud University Nijmegen
Computational Linguistics in the Netherlands Journal | Year: 2013

As data sets keep growing, computational linguists are experiencing more big data problems: challenging demands on storage and processing caused by very large data sets. An example of this is dealing with social media data: including metadata, the messages of the social media site Twitter in 2012 comprise more than 250 terabytes of structured text. Handling data volumes like this requires parallel computing architectures with appropriate software tools. In this paper we present our experiences in working with such a big data set, a collection of two billion Dutch tweets. We show how we collected and stored the data. Next we deal with searching in the data using the Hadoop framework and visualizing search results. In order to determine the usefulness of this tweet analysis resource, we have performed three case studies based on the data: relating word frequency to real-life events, finding words related to a topic, and gathering information about conversations. The three case studies are presented in this paper. Access to this current and expanding tweet data set is offered via the website © 2013 Erik Tjong Kim Sang and Antal van den Bosch.

Shamoun-Baranes J.,University of Amsterdam | Bouten W.,University of Amsterdam | Van Loon E.E.,University of Amsterdam | Meijer C.,Netherlands eScience Center | Camphuysen C.J.,University Utrecht
Philosophical Transactions of the Royal Society B: Biological Sciences | Year: 2016

The aerial environment is heterogeneous in space and time and directly influences the costs of animal flight. Volant animals can reduce these costs by using different flight modes, each with their own benefits and constraints. However, the extent to which animals alter their flight modes in response to environmental conditions has rarely been studied in the wild. To provide insight into how a flight generalist can reduce the energetic cost of movement, we studied flight behaviour in relation to the aerial environmental and landscape using hundreds of hours of global positioning system and triaxial acceleration measurements of the lesser black-backed gull (Larus fuscus). Individuals differed largely in the time spent in flight, which increased linearly with the time spent in flight at sea. In general, flapping was used more frequently than more energetically efficient soaring flight. The probability of soaring increased with increasing boundary layer height and time closer to midday, reflecting improved convective conditions supportive of thermal soaring. Other forms of soaring flight were also used, including fine-scale use of orographic lift. We explore the energetic consequences of behavioural adaptations to the aerial environment and underlying landscape and implications for individual energy budgets, foraging ecology and reproductive success. © 2016 The Author(s) Published by the Royal Society. All rights reserved.

PubMed | University of Glasgow, Netherlands eScience Center and Laboratory of Biochemistry
Type: Journal Article | Journal: Mass spectrometry (Tokyo, Japan) | Year: 2016

The MAGMa software for automatic annotation of mass spectrometry based fragmentation data was applied to 16 MS/MS datasets of the CASMI 2013 contest. Eight solutions were submitted in category 1 (molecular formula assignments) and twelve in category 2 (molecular structure assignment). The MS/MS peaks of each challenge were matched with in silico generated substructures of candidate molecules from PubChem, resulting in penalty scores that were used for candidate ranking. In 6 of the 12 submitted solutions in category 2, the correct chemical structure obtained the best score, whereas 3 molecules were ranked outside the top 5. All top ranked molecular formulas submitted in category 1 were correct. In addition, we present MAGMa results generated retrospectively for the remaining challenges. Successful application of the MAGMa algorithm required inclusion of the relevant candidate molecules, application of the appropriate mass tolerance and a sufficient degree of in silico fragmentation of the candidate molecules. Furthermore, the effect of the exhaustiveness of the candidate lists and limitations of substructure based scoring are discussed.

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