5,786 research outputs found
Autoplot: A browser for scientific data on the web
Autoplot is software developed for the Virtual Observatories in Heliophysics
to provide intelligent and automated plotting capabilities for many typical
data products that are stored in a variety of file formats or databases.
Autoplot has proven to be a flexible tool for exploring, accessing, and viewing
data resources as typically found on the web, usually in the form of a
directory containing data files with multiple parameters contained in each
file. Data from a data source is abstracted into a common internal data model
called QDataSet. Autoplot is built from individually useful components, and can
be extended and reused to create specialized data handling and analysis
applications and is being used in a variety of science visualization and
analysis applications. Although originally developed for viewing
heliophysics-related time series and spectrograms, its flexible and generic
data representation model makes it potentially useful for the Earth sciences.Comment: 16 page
Shingle 2.0: generalising self-consistent and automated domain discretisation for multi-scale geophysical models
The approaches taken to describe and develop spatial discretisations of the
domains required for geophysical simulation models are commonly ad hoc, model
or application specific and under-documented. This is particularly acute for
simulation models that are flexible in their use of multi-scale, anisotropic,
fully unstructured meshes where a relatively large number of heterogeneous
parameters are required to constrain their full description. As a consequence,
it can be difficult to reproduce simulations, ensure a provenance in model data
handling and initialisation, and a challenge to conduct model intercomparisons
rigorously. This paper takes a novel approach to spatial discretisation,
considering it much like a numerical simulation model problem of its own. It
introduces a generalised, extensible, self-documenting approach to carefully
describe, and necessarily fully, the constraints over the heterogeneous
parameter space that determine how a domain is spatially discretised. This
additionally provides a method to accurately record these constraints, using
high-level natural language based abstractions, that enables full accounts of
provenance, sharing and distribution. Together with this description, a
generalised consistent approach to unstructured mesh generation for geophysical
models is developed, that is automated, robust and repeatable, quick-to-draft,
rigorously verified and consistent to the source data throughout. This
interprets the description above to execute a self-consistent spatial
discretisation process, which is automatically validated to expected discrete
characteristics and metrics.Comment: 18 pages, 10 figures, 1 table. Submitted for publication and under
revie
KInNeSS: A Modular Framework for Computational Neuroscience
Making use of very detailed neurophysiological, anatomical, and behavioral data to build biological-realistic computational models of animal behavior is often a difficult task. Until recently, many software packages have tried to resolve this mismatched granularity with different approaches. This paper presents KInNeSS, the KDE Integrated NeuroSimulation Software environment, as an alternative solution to bridge the gap between data and model behavior. This open source neural simulation software package provides an expandable framework incorporating features such as ease of use, scalabiltiy, an XML based schema, and multiple levels of granularity within a modern object oriented programming design. KInNeSS is best suited to simulate networks of hundreds to thousands of branched multu-compartmental neurons with biophysical properties such as membrane potential, voltage-gated and ligand-gated channels, the presence of gap junctions of ionic diffusion, neuromodulation channel gating, the mechanism for habituative or depressive synapses, axonal delays, and synaptic plasticity. KInNeSS outputs include compartment membrane voltage, spikes, local-field potentials, and current source densities, as well as visualization of the behavior of a simulated agent. An explanation of the modeling philosophy and plug-in development is also presented. Further developement of KInNeSS is ongoing with the ultimate goal of creating a modular framework that will help researchers across different disciplines to effecitively collaborate using a modern neural simulation platform.Center for Excellence for Learning Education, Science, and Technology (SBE-0354378); Air Force Office of Scientific Research (F49620-01-1-0397); Office of Naval Research (N00014-01-1-0624
Improving the Representation and Conversion of Mathematical Formulae by Considering their Textual Context
Mathematical formulae represent complex semantic information in a concise
form. Especially in Science, Technology, Engineering, and Mathematics,
mathematical formulae are crucial to communicate information, e.g., in
scientific papers, and to perform computations using computer algebra systems.
Enabling computers to access the information encoded in mathematical formulae
requires machine-readable formats that can represent both the presentation and
content, i.e., the semantics, of formulae. Exchanging such information between
systems additionally requires conversion methods for mathematical
representation formats. We analyze how the semantic enrichment of formulae
improves the format conversion process and show that considering the textual
context of formulae reduces the error rate of such conversions. Our main
contributions are: (1) providing an openly available benchmark dataset for the
mathematical format conversion task consisting of a newly created test
collection, an extensive, manually curated gold standard and task-specific
evaluation metrics; (2) performing a quantitative evaluation of
state-of-the-art tools for mathematical format conversions; (3) presenting a
new approach that considers the textual context of formulae to reduce the error
rate for mathematical format conversions. Our benchmark dataset facilitates
future research on mathematical format conversions as well as research on many
problems in mathematical information retrieval. Because we annotated and linked
all components of formulae, e.g., identifiers, operators and other entities, to
Wikidata entries, the gold standard can, for instance, be used to train methods
for formula concept discovery and recognition. Such methods can then be applied
to improve mathematical information retrieval systems, e.g., for semantic
formula search, recommendation of mathematical content, or detection of
mathematical plagiarism.Comment: 10 pages, 4 figure
XML Matchers: approaches and challenges
Schema Matching, i.e. the process of discovering semantic correspondences
between concepts adopted in different data source schemas, has been a key topic
in Database and Artificial Intelligence research areas for many years. In the
past, it was largely investigated especially for classical database models
(e.g., E/R schemas, relational databases, etc.). However, in the latest years,
the widespread adoption of XML in the most disparate application fields pushed
a growing number of researchers to design XML-specific Schema Matching
approaches, called XML Matchers, aiming at finding semantic matchings between
concepts defined in DTDs and XSDs. XML Matchers do not just take well-known
techniques originally designed for other data models and apply them on
DTDs/XSDs, but they exploit specific XML features (e.g., the hierarchical
structure of a DTD/XSD) to improve the performance of the Schema Matching
process. The design of XML Matchers is currently a well-established research
area. The main goal of this paper is to provide a detailed description and
classification of XML Matchers. We first describe to what extent the
specificities of DTDs/XSDs impact on the Schema Matching task. Then we
introduce a template, called XML Matcher Template, that describes the main
components of an XML Matcher, their role and behavior. We illustrate how each
of these components has been implemented in some popular XML Matchers. We
consider our XML Matcher Template as the baseline for objectively comparing
approaches that, at first glance, might appear as unrelated. The introduction
of this template can be useful in the design of future XML Matchers. Finally,
we analyze commercial tools implementing XML Matchers and introduce two
challenging issues strictly related to this topic, namely XML source clustering
and uncertainty management in XML Matchers.Comment: 34 pages, 8 tables, 7 figure
Hyperbolic Browsers: From GUI to KUI
This paper studies the development of web browsers and describes a hyperbolic browser, a dynamic browser that organizes information visually
RGtk2: A Graphical User Interface Toolkit for R
Graphical user interfaces (GUIs) are growing in popularity as a complement or alternative to the traditional command line interfaces to R. RGtk2 is an R package for creating GUIs in R. The package provides programmatic access to GTK+ 2.0, an open-source GUI toolkit written in C. To construct a GUI, the R programmer calls RGtk2 functions that map to functions in the underlying GTK+ library. This paper introduces the basic concepts underlying GTK+ and explains how to use RGtk2 to construct GUIs from R. The tutorial is based on simple and pratical programming examples. We also provide more complex examples illustrating the advanced features of the package. The design of the RGtk2 API and the low-level interface from R to GTK+ are discussed at length. We compare RGtk2 to alternative GUI toolkits for R.
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