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3,690 results for “Computing”
Die Rolle von Mensch und Computer in den Digital Humanities
<p>The video shows the closing keynote by Daniel A. Keim from the Universität Konstanz and the closing of the DHd 2016 conference.</p> <p>The programme of the closing is available <a href="http://dhd2016.de/?q=Abschluss">here</a>.</p>
Chaotic footprints of a flapping wing: A computational perspective
<p>The lecture will discuss the investigations made on the complex vortex interactions in a flapping wing. The flow-field transitions from periodic to chaotic through a quasi-periodic route as the plunge amplitude is gradually increased. This study unravels the role of the complex interactions that take place among the main vortex structures in making the unsteady flow-field transition from periodicity to chaos.</p> <p>The lecture is available for viewing through youtube at: https://www.youtube.com/watch?v=aQZxxe8YURg</p>
Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabrics reinforced composites
<p>Data behind the publications:</p> <p>Auenhammer, R.M., Mikkelsen, L.P., Asp, L., Blinzler, B. Automated X-ray computer tomography segmentation method for finite element analysis of non-crimp fabric reinforced composites. <em>Composite Structures, </em><strong>256</strong>, 113136, <a href="https://doi.org/10.1016/j.compstruct.2020.113136">https://doi.org/10.1016/j.compstruct.2020.113136</a>, 2021.</p> <p>Auenhammer, Robert M., Lars P. Mikkelsen, Leif E. Asp, Brina J. Blinzler, Dataset of non-crimp fabric reinforced composites for an X-ray computer tomography aided engineering process, <em>Data in Brief, </em><strong>33</strong>, 106518, <a href="https://doi.org/10.1016/j.dib.2020.106518">https://doi.org/10.1016/j.dib.2020.106518</a>, 2020.</p> <p>Auenhammer, R.M., L.P. Mikkelsen, L.E. Asp, B.J. Blinzler, X-ray tomography based numerical analysis of stress concentrations in non-crimp fabric reinforced composites - assessment of segmentation methods. <em>IOP Conf. Ser.: Mater. Sci. Eng.</em> <strong>942</strong>, 012038, <a href="https://doi.org/10.1088/1757-899X/942/1/012038">https://doi.org/10.1088/1757-899X/942/1/012038</a>, 2020</p> <p>The data-set contain data from three samples: A, E and G. </p> <p>For each sample the data are saved in the follow format</p> <ul> <li>X-ray scan: nii-files</li> <li>SEM scan: tif-files</li> <li>Abaqus files: inp-files </li> <li>X-ray setting: pdf-files</li> <li>SEM settings: hdr-ascii files</li> </ul> <p> </p>
The Creative Computing Lab
<p>6<sup>th</sup> Project Presentation</p>
WarpX Accelerated Nodes Parallel Computing Paper
<p>This dataset contains the inputs, outputs, job submission scripts, and executables<br> used to create the Figures in "Porting WarpX to GPU-accelerated platforms" by A. Myers<br> et. al, submitted to Parallel Computing as part of the ECP Special Issue on Transitioning<br> to Accelerated nodes.</p> <p>These results were obtained using the October, 2020 release tags of WarpX and AMReX,<br> available on Github here:</p> <p> https://github.com/ECP-WarpX/WarpX</p> <p>and here:</p> <p> https://github.com/AMReX-Codes/amrex</p> <p>The following module files were loaded on Summit:</p> <p> 1) hsi/5.0.2.p5 2) xalt/1.2.0 3) lsf-tools/2.0 4) darshan-runtime/3.1.7<br> 5) DefApps 6) cuda/10.1.243 7) gcc/6.4.0 8) spectrum-mpi/10.3.1.2-20200121</p> <p>To use nsight-compute for the roofline plots, we also loaded:</p> <p> nsight-compute/2020.1.2</p> <p>Manifest:</p> <p>BinScan: contains material used to make Figure 1. To generate the figure, use the<br> Jupyter notebook called "bin_size.ipynb".</p> <p>StrongScaling: contains material used to make Figure 5. To generate the figure, use the<br> Jupyter notebook called "strong_scaling.ipynb".</p> <p>WeakScalingCPU: contains material used to make Figure 4. To generate the figure, use the<br> Jupyter notebook called "weak_scaling.ipynb".</p> <p>WeakScalingGPU: contains material used to make Figure 5. To generate the figure, use the<br> Jupyter notebook called "weak_scaling.ipynb".</p> <p>Roofline: contains material used to make the roofline plots (Figures 2 and 3). This<br> includes output generated using nsight-compute with WarpX and python scripts for<br> processing and plotting these output files. These scripts and methodology originally<br> come from Charlene Yang at NERSC. The file "script.sh" was used to generate the<br> profiler output</p>
Digital and Computational Palaeography: Some Promises and Problems
<p>Video, abstract and draft transcript of presentation given at the 13th Annual (Virtual) Schoenberg Symposium on Manuscript Studies in the Digital Age.</p> <p>As the Schoenberg Symposium and the Schoenberg Institute for Manuscript Studies have long been demonstrating, access to digital images of manuscripts has grown enormously in recent years, particularly with IIIF and the movement towards increasingly open and rights-free content. At the same time, we also have increasing access to relatively powerful computers, fast internet connections, and now access even to hardware and software for deep learning such as free software libraries, increasingly affordable GPUs and, in some cases, high-performance computing clusters. At the same time, however, librarians are often reporting less time for cataloguing and metadata, and at least in some cases access to original items is becoming increasingly difficult, not to mention the increasing complexity of computational methods and the widely-recognised fact that the ‘reasoning’ of modern machine learning is inaccessible even to specialists. The current health crisis seems to be accelerating these trends, which leaves the question: what of palaeography? Looking at the past and present of digital and computational methods, in this talk I attempt to identify some of the promises and problems of where we are now and where we seem to be going.</p>
Computational Musicology – Distant Reading of Sheet Music
<p>2<sup>nd </sup>Lecture</p>
Dataset for: Trust Trackers for Computation Offloading in Edge-Based IoT Networks
<p>The dataset used to generate graphs for: Matthew Bradbury, Arshad Jhumka and Tim Watson.<br> Trust Trackers for Computation Offloading in Edge-Based IoT Networks. In IEEE INFOCOM, 1–10. IEEE, 10–13 May 2021.</p> <p>Also includes instructions for experiment setup.</p> <p>Scripts from https://github.com/MBradbury/iot-trust-task-alloc are required to analyse and graph these results.</p>
Raw data on computational analysis the relationships of energy and mechanical properties with sensitivity for 1, 1-diamino-2, 2-dinitroethene based polymer bonded explosives
<p>The dataset provides raw data on key properties in the text as well as raw data on the temperature and energy balances of the P, P1, P2, P3 and P4 systems at room temperature. These data allow the results obtained in the article to be reproduced, while the reader can obtain the raw data for the plots not labeled with data in the article and thus quantify the exact magnitude of the changes shown in the plots. The main work of the article is: Molecular dynamics (MD) simulations have been applied to investigate 1, 1-diamino-2, 2-dinitroethene (FOX-7) crystal and FOX-7(011)-based polymer-bonded explosives (PBXs) with four typical polymers, polyethylene glycol (PEG), fluorine-polymer (F<sub>2603</sub>), ethylene-vinyl acetate copolymer (EVA) and ester urethane (ESTANE5703) under COMPASS force field. Binding energy (E<sub>bind</sub>), cohesive energy density (CED), initiation bond length distribution, radial distribution function, and isotropic mechanical properties of FOX-7 and its PBXs at different temperatures were reported for the first time, and the relationship between them and sensitivity. Using quantum chemistry, FOX-7 was optimized with the four polymers at the B3LYP/6-311++G(d,p) level, and the structure and RDG of the optimized composite system were analyzed.</p>
Data from: Approximate Bayesian computation reveals the crucial role of oceanic islands for the assembly of continental biodiversity
The perceived low levels of genetic diversity, poor interspecific competitive and defensive ability, and loss of dispersal capacities of insular lineages have driven the view that oceanic islands are evolutionary dead ends. Focusing on the Atlantic bryophyte flora distributed across the archipelagos of the Azores, Madeira, the Canary Islands, Western Europe, and northwestern Africa, we used an integrative approach with species distribution modeling and population genetic analyses based on approximate Bayesian computation to determine whether this view applies to organisms with inherent high dispersal capacities. Genetic diversity was found to be higher in island than in continental populations, contributing to mounting evidence that, contrary to theoretical expectations, island populations are not necessarily genetically depauperate. Patterns of genetic variation among island and continental populations consistently fitted those simulated under a scenario of de novo foundation of continental populations from insular ancestors better than those expected if islands would represent a sink or a refugium of continental biodiversity. We, suggest that the northeastern Atlantic archipelagos have played a key role as a stepping stone for transoceanic migrants. Our results challenge the traditional notion that oceanic islands are the end of the colonization road and illustrate the significant role of oceanic islands as reservoirs of novel biodiversity for the assembly of continental floras.
Data from: A new approach using high-resolution computed tomography to test the buoyant properties of chambered cephalopod shells
The chambered shell of modern cephalopods functions as a buoyancy apparatus, allowing the animal to enter the water column without expending a large amount of energy to overcome its own weight. Indeed, the chambered shell is largely considered a key adaptation that allowed the earliest cephalopods to leave the ocean floor and enter the water column. It has been argued by some, however, that the iconic chambered shell of Paleozoic and Mesozoic ammonoids did not provide a sufficiently buoyant force to compensate for the weight of the entire animal, thus restricting ammonoids to a largely benthic lifestyle reminiscent of some octopods. Here we develop a technique using high-resolution computed tomography to quantify the buoyant properties of chambered shells without reducing the shell to ideal spirals or eliminating inherent biological variability by using mathematical models that characterize past work in this area. This technique has been tested on Nautilus pompilius and is now extended to the extant deep-sea squid Spirula spirula and the Jurassic ammonite Cadoceras sp. hatchling. Cadoceras is found to have possessed near-neutral to positive buoyancy if hatched when the shell possessed between three and five chambers. However, we show that the animal could also overcome degrees of negative buoyancy through swimming, similar to the paralarvae of modern squids. These calculations challenge past inferences of benthic life habits based solely on calculations of negative buoyancy. The calculated buoyancy of Cadoceras supports the possibility of planktonic dispersal of ammonite hatchlings. This information is essential to understanding ammonoid ecology as well as biotic interactions and has implications for the interpretation of geochemical data gained from the isotopic analysis of the shell.
Data from: Predicting classifier performance with limited training data: applications to computer-aided diagnosis in breast and prostate cancer
Clinical trials increasingly employ medical imaging data in conjunction with supervised classifiers, where the latter require large amounts of training data to accurately model the system. Yet, a classifier selected at the start of the trial based on smaller and more accessible datasets may yield inaccurate and unstable classification performance. In this paper, we aim to address two common concerns in classifier selection for clinical trials: (1) predicting expected classifier performance for large datasets based on error rates calculated from smaller datasets and (2) the selection of appropriate classifiers based on expected performance for larger datasets. We present a framework for comparative evaluation of classifiers using only limited amounts of training data by using random repeated sampling (RRS) in conjunction with a cross-validation sampling strategy. Extrapolated error rates are subsequently validated via comparison with leave-one-out cross-validation performed on a larger dataset. The ability to predict error rates as dataset size increases is demonstrated on both synthetic data as well as three different computational imaging tasks: detecting cancerous image regions in prostate histopathology, differentiating high and low grade cancer in breast histopathology, and detecting cancerous metavoxels in prostate magnetic resonance spectroscopy. For each task, the relationships between 3 distinct classifiers (k-nearest neighbor, naive Bayes, Support Vector Machine) are explored. Further quantitative evaluation in terms of interquartile range (IQR) suggests that our approach consistently yields error rates with lower variability (mean IQRs of 0.0070, 0.0127, and 0.0140) than a traditional RRS approach (mean IQRs of 0.0297, 0.0779, and 0.305) that does not employ cross-validation sampling for all three datasets.
Data from: The Shortlist Method for fast computation of the Earth Mover's Distance and finding optimal solutions to transportation problems
Finding solutions to the classical transportation problem is of great importance, since this optimization problem arises in many engineering and computer science applications. Especially the Earth Mover's Distance is used in a plethora of applications ranging from content-based image retrieval, shape matching, fingerprint recognition, object tracking and phishing web page detection to computing color differences in linguistics and biology. Our starting point is the well-known revised simplex algorithm, which iteratively improves a feasible solution to optimality. The Shortlist Method that we propose substantially reduces the number of candidates inspected for improving the solution, while at the same time balancing the number of pivots required. Tests on simulated benchmarks demonstrate a considerable reduction in computation time for the new method as compared to the usual revised simplex algorithm implemented with state-of-the-art initialization and pivot strategies. As a consequence, the Shortlist Method facilitates the computation of large scale transportation problems in viable time. In addition we describe a novel method for finding an initial feasible solution which we coin Modified Russell's Method.
Data from: Enhanced computational methods for quantifying the effect of geographic and environmental isolation on genetic differentiation
1. In a recent paper, Bradburd et al. (Evolution, 67, 2013, 3258) proposed a model to quantify the relative effect of geographic and environmental distance on genetic differentiation. Here, we enhance this method in several ways. 2. We modify the covariance model so as to fit better with mainstream geostatistical models and avoid mathematically ill-behaved covariance functions. We extend the model – initially implemented only for co-dominant bi-allelic markers such as single nucleotide polymorphisms – to encompass highly polymorphic markers such as microsatellites. We implement and test a model selection procedure that allows users to assess which model (e.g. with or without an environment effect) is most suited. We code all our MCMC algorithms in a mix of compiled languages which allows us to decrease computing time by at least one order of magnitude. We propose an approximate inference and model selection method allowing us to deal with genomic data sets (several hundred thousands loci). 3. We also illustrate the potential of the method by re-analysing three data sets, namely harbour porpoises in Europe, coyotes in California and herrings in the Baltic Sea. 4. The computer program developed here is freely available as an r package called sunder. It takes as input georeferenced allele counts at the individual or population level for co-dominant markers. Program homepage: http://www2.imm.dtu.dk/~gigu/Sunder/.
Data from: The demographic history of Atlantic salmon (Salmo salar) across its distribution range reconstructed from approximate Bayesian computations
Understanding the dual roles of demographic and selective processes in the buildup of population divergence is one of the most challenging tasks in evolutionary biology. Here, we investigated the demographic history of Atlantic Salmon across the entire species range using 2035 anadromous individuals from North America and Eurasia. By combining results from admixture graphs, geo-genetic maps and an Approximate Bayesian Computation (ABC) framework, we validated previous hypotheses pertaining to secondary contact between European and Northern American populations, but also identified secondary contacts in European populations from different glacial refugia. We further identified the major sources of admixture from the southern range of North America into more northern populations along with a strong signal of secondary gene flow between genetic regional groups. We hypothesize that these patterns reflects the spatial redistribution of ancestral variation across the entire North American range. Results also support a role for linked selection and differential introgression that likely played an under-appreciated role in shaping the genomic landscape of species in the Northern hemisphere. We conclude that studies between partially isolated populations should systematically include heterogeneity in selective and introgressive effects among loci to perform more rigorous demographic inferences of the divergence process.
Data from: Modeling the internet of things, self-organizing and other complex adaptive communication networks: a cognitive agent-based computing approach
Background: Computer Networks have a tendency to grow at an unprecedented scale. Modern networks involve not only computers but also a wide variety of other interconnected devices ranging from mobile phones to other household items fitted with sensors. This vision of the "Internet of Things" (IoT) implies an inherent difficulty in modeling problems. Purpose: It is practically impossible to implement and test all scenarios for large-scale and complex adaptive communication networks as part of Complex Adaptive Communication Networks and Environments (CACOONS). The goal of this study is to explore the use of Agent-based Modeling as part of the Cognitive Agent-based Computing (CABC) framework to model a Complex communication network problem. Method: We use Exploratory Agent-based Modeling (EABM), as part of the CABC framework, to develop an autonomous multi-agent architecture for managing carbon footprint in a corporate network. To evaluate the application of complexity in practical scenarios, we have also introduced a company-defined computer usage policy. Results: The conducted experiments demonstrated two important results: Primarily CABC-based modeling approach such as using Agent-based Modeling can be an effective approach to modeling complex problems in the domain of IoT. Secondly, the specific problem of managing the Carbon footprint can be solved using a multiagent system approach.
Data from: Quantitative comparison of commercial and non-commercial metal artifact reduction techniques in computed tomography
Objectives: Typical streak artifacts known as metal artifacts occur in the presence of strongly attenuating materials in computed tomography (CT). Recently, vendors have started offering metal artifact reduction (MAR) techniques. In addition, a MAR technique called the metal deletion technique (MDT) is freely available and able to reduce metal artifacts using reconstructed images. Although a comparison of the MDT to other MAR techniques exists, a comparison of commercially available MAR techniques is lacking. The aim of this study was therefore to quantify the difference in effectiveness of the currently available MAR techniques of different scanners and the MDT technique. Materials and Methods: Three vendors were asked to use their preferential CT scanner for applying their MAR techniques. The scans were performed on a Philips Brilliance ICT 256 (S1), a GE Discovery CT 750 HD (S2) and a Siemens Somatom Definition AS Open (S3). The scans were made using an anthropomorphic head and neck phantom (Kyoto Kagaku, Japan). Three amalgam dental implants were constructed and inserted between the phantom's teeth. The average absolute error (AAE) was calculated for all reconstructions in the proximity of the amalgam implants. Results: The commercial techniques reduced the AAE by 22.0±1.6%, 16.2±2.6% and 3.3±0.7% for S1 to S3 respectively. After applying the MDT to uncorrected scans of each scanner the AAE was reduced by 26.1±2.3%, 27.9±1.0% and 28.8±0.5% respectively. The difference in efficiency between the commercial techniques and the MDT was statistically significant for S2 (p=0.004) and S3 (p<0.001), but not for S1 (p=0.63). Conclusions: The effectiveness of MAR differs between vendors. S1 performed slightly better than S2 and both performed better than S3. Furthermore, for our phantom and outcome measure the MDT was more effective than the commercial MAR technique on all scanners.
Data from: Calculating competitive intransitivity: computational challenges
Intransitive, or 'rock-paper-scissors' competition is compelling because it promotes species coexistence and because recent work suggests it may be common in natural systems. One class of intransitivity indices works by considering s, the minimum number of competitive reversals to convert a given competitive community (i.e., a 'tournament') to a hierarchy. The most straightforward example of such 'reversal-based' indices is Petraitis' index, t = 1 - s/M, where M is the maximum s across all possible n-species tournaments. Using exhaustive searches, we prove that Petraitis' formula for M (and, therefore, t) does not hold for n ≥ 7. Furthermore, the determination of s for even moderate values of n may prove difficult, as the equivalent graph-theoretical problem is NP-hard; there is no known computationally feasible way to compute an exact answer for anything but small values of n, let alone a closed-form solution. Petraitis' t is a valuable index of intransitivity; however, at present its use is limited to relatively species-poor systems. More broadly, reversal-based indices, while intuitive, may be problematic because of this computability issue.
Data from: Effect of arsenate substitution on phosphate repository of cell: a computational study
The structural analogy with phosphate derives arsenate into various metabolic processes associated with phosphate inside the organisms. But it is difficult to evaluate the effect of arsenate substitution on the stability of individual biological phosphate species, which span from a simpler monoester form like pyrophosphate to a more complex phosphodiester variant like DNA. In this study, we have classified the physiological phosphate esters into three different classes on the basis of their structural differences.This classification has helped us to present a concise theoretical study on the kinetic stability of phosphate analogue species of arsenate against hydrolysis. All the calculations have been carried out using QM/MM methods of our Own N-layer Integrated molecular Orbital molecular Mechanics. For quantum mechanical region we have used M06-2X density functional with 6-31+G(2d,2p) basis set and for molecular mechanics region AMBER force field. The calculated rate constants for hydrolysis show that none of the phosphate analogue species of arsenate has a reasonable stability against hydrolysis.
Data from: Use of anisotropy, 3D segmented atlas, and computational analysis to identify gray matter subcortical lesions common to concussive injury from different sites on the cortex
Traumatic brain injury (TBI) can occur anywhere along the cortical mantel. While the cortical contusions may be random and disparate in their locations, the clinical outcomes are often similar and difficult to explain. Thus a question that arises is, do concussions at different sites on the cortex affect similar subcortical brain regions? To address this question we used a fluid percussion model to concuss the right caudal or rostral cortices in rats. Five days later, diffusion tensor MRI data were acquired for indices of anisotropy (IA) for use in a novel method of analysis to detect changes in gray matter microarchitecture. IA values from over 20,000 voxels were registered into a 3D segmented, annotated rat atlas covering 150 brain areas. Comparisons between left and right hemispheres revealed a small population of subcortical sites with altered IA values. Rostral and caudal concussions were of striking similarity in the impacted subcortical locations, particularly the central nucleus of the amygdala, laterodorsal thalamus, and hippocampal complex. Subsequent immunohistochemical analysis of these sites showed significant neuroinflammation. This study presents three significant findings that advance our understanding and evaluation of TBI: 1) the introduction of a new method to identify highly localized disturbances in discrete gray matter, subcortical brain nuclei without postmortem histology, 2) the use of this method to demonstrate that separate injuries to the rostral and caudal cortex produce the same subcortical, disturbances, and 3) the central nucleus of the amygdala, critical in the regulation of emotion, is vulnerable to concussion.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.