467 research outputs found
Human performance prediction in man-machine systems. Volume 1 - A technical review
Tests and test techniques for human performance prediction in man-machine systems task
Human performance prediction in man-machine systems. Part 2 - The test catalog
Human performance prediction in man machine systems - test catalog table
SCelVis: Powerful explorative single cell data analysis on the desktop and in the cloud
Background: Single cell omics technologies present unique opportunities for biomedical and life sciences from lab to clinic, but the high dimensional nature of such data poses challenges for computational analysis and interpretation. Furthermore, FAIR data management as well as data privacy and security become crucial when working with clinical data, especially in cross-institutional and translational settings. Existing solutions are either bound to the desktop of one researcher or come with dependencies on vendor-specific technology for cloud storage or user authentication. Results: To facilitate analysis and interpretation of single-cell data by users without bioinformatics expertise, we present SCelVis, a flexible, interactive and user-friendly app for web-based visualization of pre-processed single-cell data. Users can survey multiple interactive visualizations of their single cell expression data and cell annotation, and download raw or processed data for further offline analysis. SCelVis can be run both on the desktop and cloud systems, accepts input from local and various remote sources using standard and open protocols, and allows for hosting data in the cloud and locally. Methods: SCelVis is implemented in Python using Dash by Plotly. It is available as a standalone application as a Python package, via Conda/Bioconda and as a Docker image. All components are available as open source under the permissive MIT license and are based on open standards and interfaces, enabling further development and integration with third party pipelines and analysis components. The GitHub repository is https://github.com/bihealth/scelvis
SCelVis: exploratory single cell data analysis on the desktop and in the cloud
BACKGROUND: Single cell omics technologies present unique opportunities for biomedical and life sciences from lab to clinic, but the high dimensional nature of such data poses challenges for computational analysis and interpretation. Furthermore, FAIR data management as well as data privacy and security become crucial when working with clinical data, especially in cross-institutional and translational settings. Existing solutions are either bound to the desktop of one researcher or come with dependencies on vendor-specific technology for cloud storage or user authentication. RESULTS: To facilitate analysis and interpretation of single-cell data by users without bioinformatics expertise, we present SCelVis, a flexible, interactive and user-friendly app for web-based visualization of pre-processed single-cell data. Users can survey multiple interactive visualizations of their single cell expression data and cell annotation, define cell groups by filtering or manual selection and perform differential gene expression, and download raw or processed data for further offline analysis. SCelVis can be run both on the desktop and cloud systems, accepts input from local and various remote sources using standard and open protocols, and allows for hosting data in the cloud and locally. We test and validate our visualization using publicly available scRNA-seq data. METHODS: SCelVis is implemented in Python using Dash by Plotly. It is available as a standalone application as a Python package, via Conda/Bioconda and as a Docker image. All components are available as open source under the permissive MIT license and are based on open standards and interfaces, enabling further development and integration with third party pipelines and analysis components. The GitHub repository is https://github.com/bihealth/scelvis
Asymptotic Level Density of the Elastic Net Self-Organizing Feature Map
Whileas the Kohonen Self Organizing Map shows an asymptotic level density
following a power law with a magnification exponent 2/3, it would be desired to
have an exponent 1 in order to provide optimal mapping in the sense of
information theory. In this paper, we study analytically and numerically the
magnification behaviour of the Elastic Net algorithm as a model for
self-organizing feature maps. In contrast to the Kohonen map the Elastic Net
shows no power law, but for onedimensional maps nevertheless the density
follows an universal magnification law, i.e. depends on the local stimulus
density only and is independent on position and decouples from the stimulus
density at other positions.Comment: 8 pages, 10 figures. Link to publisher under
http://link.springer.de/link/service/series/0558/bibs/2415/24150939.ht
Cellular Structures for Computation in the Quantum Regime
We present a new cellular data processing scheme, a hybrid of existing
cellular automata (CA) and gate array architectures, which is optimized for
realization at the quantum scale. For conventional computing, the CA-like
external clocking avoids the time-scale problems associated with ground-state
relaxation schemes. For quantum computing, the architecture constitutes a novel
paradigm whereby the algorithm is embedded in spatial, as opposed to temporal,
structure. The architecture can be exploited to produce highly efficient
algorithms: for example, a list of length N can be searched in time of order
cube root N.Comment: 11 pages (LaTeX), 3 figure
Stress-Energy Tensor for the Massless Spin 1/2 Field in Static Black Hole Spacetimes
The stress-energy tensor for the massless spin 1/2 field is numerically
computed outside and on the event horizons of both charged and uncharged static
non-rotating black holes, corresponding to the Schwarzschild,
Reissner-Nordstrom and extreme Reissner-Nordstr\"om solutions of Einstein's
equations. The field is assumed to be in a thermal state at the black hole
temperature. Comparison is made between the numerical results and previous
analytic approximations for the stress-energy tensor in these spacetimes. For
the Schwarzschild (charge zero) solution, it is shown that the stress-energy
differs even in sign from the analytic approximation. For the
Reissner-Nordstrom and extreme Reissner-Nordstrom solutions, divergences
predicted by the analytic approximations are shown not to exist.Comment: 5 pages, 4 figures, additional discussio
Venn diagrams may indicate erroneous statistical reasoning in transcriptomics
A common application of differential expression analysis is finding genes that are differentially expressed upon treatment in only one out of several groups of samples. One of the approaches is to test for significant difference in expression between treatment and control separately in the two groups, and then select genes that show statistical significance in one group only. This approach is then often combined with a gene set enrichment analysis to find pathways and gene sets regulated by treatment in only this group. Here we show that this procedure is statistically incorrect and that the interaction between treatment and group should be tested instead. Moreover, we show that gene set enrichment analysis applied to such incorrectly defined genes group-specific genes may result in misleading artifacts. Due to the presence of false negatives, genes significant in one, but not the other group are enriched in gene sets which correspond to the overall effect of the treatment. Thus, the results appear related to the problem at hand, but do not reflect the group-specific effect of a treatment. A literature search revealed that more than a quarter of papers which used a Venn diagram to illustrate the results of separate differential analysis have also applied this incorrect reasoning
Conditional Quantum Dynamics and Logic Gates
Quantum logic gates provide fundamental examples of conditional quantum
dynamics. They could form the building blocks of general quantum information
processing systems which have recently been shown to have many interesting
non--classical properties. We describe a simple quantum logic gate, the quantum
controlled--NOT, and analyse some of its applications. We discuss two possible
physical realisations of the gate; one based on Ramsey atomic interferometry
and the other on the selective driving of optical resonances of two subsystems
undergoing a dipole--dipole interaction.Comment: 5 pages, RevTeX, two figures in a uuencoded, compressed fil
Tension Dynamics and Linear Viscoelastic Behavior of a Single Semiflexible Polymer Chain
We study the dynamical response of a single semiflexible polymer chain based
on the theory developed by Hallatschek et al. for the wormlike-chain model. The
linear viscoelastic response under oscillatory forces acting at the two chain
ends is derived analytically as a function of the oscillation frequency . We
shall show that the real part of the complex compliance in the low frequency
limit is consistent with the static result of Marko and Siggia whereas the
imaginary part exhibits the power-law dependence +1/2. On the other hand, these
compliances decrease as the power law -7/8 for the high frequency limit. These
are different from those of the Rouse dynamics. A scaling argument is developed
to understand these novel results.Comment: 23 pages, 6 figure
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