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| 2. |
- Grüning, Björn, et al.
(author)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Other publication (other academic/artistic)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 3. |
- Aumayr, Friedrich, et al.
(author)
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Roadmap on photonic, electronic and atomic collision physics : III. Heavy particles
- 2019
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In: Journal of Physics B. - : IOP Publishing. - 0953-4075 .- 1361-6455. ; 52:17
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Journal article (peer-reviewed)abstract
- We publish three Roadmaps on photonic, electronic and atomic collision physics in order to celebrate the 60th anniversary of the ICPEAC conference. Roadmap III focusses on heavy particles: with zero to relativistic speeds. Modern theoretical and experimental approaches provide detailed insight into the wide range of many-body interactions involving projectiles and targets of varying complexity ranging from simple atoms, through molecules and clusters, complex biomolecules and nanoparticles to surfaces and crystals. These developments have been driven by technological progress and future developments will expand the horizon of the systems that can be studied. This Roadmap aims at looking back along the road, explaining the evolution of the field, and looking forward, collecting nineteen contributions from leading scientists in the field.
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| 4. |
- Ahlkrona, Josefin, et al.
(author)
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Dynamically coupling the non-linear Stokes equations with the shallow ice approximation in glaciology : Description and first applications of the ISCAL method
- 2016
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In: Journal of Computational Physics. - : Elsevier BV. - 0021-9991 .- 1090-2716. ; 308, s. 1-19
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Journal article (peer-reviewed)abstract
- We propose and implement a new method, called the Ice Sheet Coupled Approximation Levels (ISCAL) method, for simulation of ice sheet flow in large domains during long time-intervals. The method couples the full Stokes (FS) equations with the Shallow Ice Approximation (SIA). The part of the domain where SIA is applied is determined automatically and dynamically based on estimates of the modeling error. For a three dimensional model problem, ISCAL computes the solution substantially faster with a low reduction in accuracy compared to a monolithic FS. Furthermore, ISCAL is shown to be able to detect rapid dynamic changes in the flow. Three different error estimations are applied and compared. Finally, ISCAL is applied to the Greenland Ice Sheet on a quasi-uniform grid, proving ISCAL to be a potential valuable tool for the ice sheet modeling community.
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| 5. |
- Blösch, Günter, et al.
(author)
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Twenty-three unsolved problems in hydrology (UPH) - a community perspective
- 2019
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In: Hydrological Sciences Journal. - : Informa UK Limited. - 0262-6667 .- 2150-3435. ; 64:10, s. 1141-1158
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Journal article (peer-reviewed)abstract
- This paper is the outcome of a community initiative to identify major unsolved scientific problems in hydrology motivated by a need for stronger harmonisation of research efforts. The procedure involved a public consultation through online media, followed by two workshops through which a large number of potential science questions were collated, prioritised, and synthesised. In spite of the diversity of the participants (230 scientists in total), the process revealed much about community priorities and the state of our science: a preference for continuity in research questions rather than radical departures or redirections from past and current work. Questions remain focused on the process-based understanding of hydrological variability and causality at all space and time scales. Increased attention to environmental change drives a new emphasis on understanding how change propagates across interfaces within the hydrological system and across disciplinary boundaries. In particular, the expansion of the human footprint raises a new set of questions related to human interactions with nature and water cycle feedbacks in the context of complex water management problems. We hope that this reflection and synthesis of the 23 unsolved problems in hydrology will help guide research efforts for some years to come.
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| 6. |
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| 7. |
- O'Regan, Matt, et al.
(author)
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The De Long Trough: A newly discovered glacial trough on the East Siberian continental margin
- 2017
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In: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 13:9, s. 1269-1284
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Journal article (peer-reviewed)abstract
- Ice sheets extending over parts of the East Siberian continental shelf have been proposed for the last glacial period and during the larger Pleistocene glaciations. The sparse data available over this sector of the Arctic Ocean have left the timing, extent and even existence of these ice sheets largely unresolved. Here we present new geophysical mapping and sediment coring data from the East Siberian shelf and slope collected during the 2014 SWERUS-C3 expedition (SWERUS-C3: Swedish - Russian - US Arctic Ocean Investigation of Climate-Cryosphere-Carbon Interactions). The multibeam bathymetry and chirp sub-bottom profiles reveal a set of glacial landforms that include grounding zone formations along the outer continental shelf, seaward of which lies a > 65m thick sequence of glacio-genic debris flows. The glacial landforms are interpreted to lie at the seaward end of a glacial trough - the first to be reported on the East Siberian margin, here referred to as the De Long Trough because of its location due north of the De Long Islands. Stratigraphy and dating of sediment cores show that a drape of acoustically laminated sediments covering the glacial deposits is older than similar to 50 cal kyr BP. This provides direct evidence for extensive glacial activity on the Siberian shelf that predates the Last Glacial Maximum and most likely occurred during the Saalian (Marine Isotope Stage (MIS) 6).
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| 8. |
- Stokes, Chris R., et al.
(author)
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On the reconstruction of palaeo-ice sheets : Recent advances and future challenges
- 2015
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In: Quaternary Science Reviews. - : Elsevier BV. - 0277-3791 .- 1873-457X. ; 125, s. 15-49
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Research review (peer-reviewed)abstract
- Reconstructing the growth and decay of palaeo-ice sheets is critical to understanding mechanisms of global climate change and associated sea-level fluctuations in the past, present and future. The significance of palaeo-ice sheets is further underlined by the broad range of disciplines concerned with reconstructing their behaviour, many of which have undergone a rapid expansion since the 1980s. In particular, there has been a major increase in the size and qualitative diversity of empirical data used to reconstruct and date ice sheets, and major improvements in our ability to simulate their dynamics in numerical ice sheet models. These developments have made it increasingly necessary to forge interdisciplinary links between sub-disciplines and to link numerical modelling with observations and dating of proxy records. The aim of this paper is to evaluate recent developments in the methods used to reconstruct ice sheets and outline some key challenges that remain, with an emphasis on how future work might integrate terrestrial and marine evidence together with numerical modelling. Our focus is on pan-ice sheet reconstructions of the last deglaciation, but regional case studies are used to illustrate methodological achievements, challenges and opportunities. Whilst various disciplines have made important progress in our understanding of ice-sheet dynamics, it is clear that data-model integration remains under-used, and that uncertainties remain poorly quantified in both empirically-based and numerical ice-Sheet reconstructions. The representation of past climate will continue to be the largest source of uncertainty for numerical modelling. As such, palaeo-observations are critical to constrain and validate modelling. State-of-the-art numerical models will continue to improve both in model resolution and in the breadth of inclusion of relevant processes, thereby enabling more accurate and more direct comparison with the increasing range of palaeo-observations. Thus, the capability is developing to use all relevant palaeo-records to more strongly constrain deglacial (and to a lesser extent pre-LGM) ice sheet evolution. In working towards that goal, the accurate representation of uncertainties is required for both constraint data and model outputs. Close cooperation between modelling and data-gathering communities is essential to ensure this capability is realised and continues to progress.
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| 9. |
- van Dongen, Eef C. H., et al.
(author)
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Dynamically coupling full Stokes and shallow shelf approximation for marine ice sheet flow using Elmer/Ice (v8.3)
- 2018
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In: Geoscientific Model Development. - : Copernicus GmbH. - 1991-959X .- 1991-9603. ; 11:11, s. 4563-4576
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Journal article (peer-reviewed)abstract
- Ice flow forced by gravity is governed by the full Stokes (FS) equations, which are computationally expensive to solve due to the nonlinearity introduced by the rheology. Therefore, approximations to the FS equations are commonly used, especially when modeling a marine ice sheet (ice sheet, ice shelf, and/or ice stream) for 103 years or longer. The shallow ice approximation (SIA) and shallow shelf approximation (SSA) are commonly used but are accurate only for certain parts of an ice sheet. Here, we report a novel way of iteratively coupling FS and SSA that has been implemented in Elmer/Ice and applied to conceptual marine ice sheets. The FS-SSA coupling appears to be very accurate; the relative error in velocity compared to FS is below 0.5% for diagnostic runs and below 5% for prognostic runs. Results for grounding line dynamics obtained with the FS-SSA coupling are similar to those obtained from an FS model in an experiment with a periodical temperature forcing over 3000 years that induces grounding line advance and retreat. The rapid convergence of the FS-SSA coupling shows a large potential for reducing computation time, such that modeling a marine ice sheet for thousands of years should become feasible in the near future. Despite inefficient matrix assembly in the current implementation, computation time is reduced by 32 %, when the coupling is applied to a 3-D ice shelf.
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