21,358 research outputs found
Iris: an Extensible Application for Building and Analyzing Spectral Energy Distributions
Iris is an extensible application that provides astronomers with a
user-friendly interface capable of ingesting broad-band data from many
different sources in order to build, explore, and model spectral energy
distributions (SEDs). Iris takes advantage of the standards defined by the
International Virtual Observatory Alliance, but hides the technicalities of
such standards by implementing different layers of abstraction on top of them.
Such intermediate layers provide hooks that users and developers can exploit in
order to extend the capabilities provided by Iris. For instance, custom Python
models can be combined in arbitrary ways with the Iris built-in models or with
other custom functions. As such, Iris offers a platform for the development and
integration of SED data, services, and applications, either from the user's
system or from the web. In this paper we describe the built-in features
provided by Iris for building and analyzing SEDs. We also explore in some
detail the Iris framework and software development kit, showing how astronomers
and software developers can plug their code into an integrated SED analysis
environment.Comment: 18 pages, 8 figures, accepted for publication in Astronomy &
Computin
ImageJ2: ImageJ for the next generation of scientific image data
ImageJ is an image analysis program extensively used in the biological
sciences and beyond. Due to its ease of use, recordable macro language, and
extensible plug-in architecture, ImageJ enjoys contributions from
non-programmers, amateur programmers, and professional developers alike.
Enabling such a diversity of contributors has resulted in a large community
that spans the biological and physical sciences. However, a rapidly growing
user base, diverging plugin suites, and technical limitations have revealed a
clear need for a concerted software engineering effort to support emerging
imaging paradigms, to ensure the software's ability to handle the requirements
of modern science. Due to these new and emerging challenges in scientific
imaging, ImageJ is at a critical development crossroads.
We present ImageJ2, a total redesign of ImageJ offering a host of new
functionality. It separates concerns, fully decoupling the data model from the
user interface. It emphasizes integration with external applications to
maximize interoperability. Its robust new plugin framework allows everything
from image formats, to scripting languages, to visualization to be extended by
the community. The redesigned data model supports arbitrarily large,
N-dimensional datasets, which are increasingly common in modern image
acquisition. Despite the scope of these changes, backwards compatibility is
maintained such that this new functionality can be seamlessly integrated with
the classic ImageJ interface, allowing users and developers to migrate to these
new methods at their own pace. ImageJ2 provides a framework engineered for
flexibility, intended to support these requirements as well as accommodate
future needs
The SUMO toolbox: a tool for automatic regression modeling and active learning
Many complex, real world phenomena are difficult to study directly using controlled experiments. Instead, the use of computer simulations has become commonplace as a feasible alternative. Due to the computational cost of these high fidelity simulations, surrogate models are often employed as a drop-in replacement for the original simulator, in order to reduce evaluation times. In this context, neural networks, kernel methods, and other modeling techniques have become indispensable. Surrogate models have proven to be very useful for tasks such as optimization, design space exploration, visualization, prototyping and sensitivity analysis. We present a fully automated machine learning tool for generating accurate surrogate models, using active learning techniques to minimize the number of simulations and to maximize efficiency
Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.
Modern computational neuroscience employs diverse software tools and multidisciplinary expertise to analyze heterogeneous brain data. The classical problems of gathering meaningful data, fitting specific models, and discovering appropriate analysis and visualization tools give way to a new class of computational challenges--management of large and incongruous data, integration and interoperability of computational resources, and data provenance. We designed, implemented and validated a new paradigm for addressing these challenges in the neuroimaging field. Our solution is based on the LONI Pipeline environment [3], [4], a graphical workflow environment for constructing and executing complex data processing protocols. We developed study-design, database and visual language programming functionalities within the LONI Pipeline that enable the construction of complete, elaborate and robust graphical workflows for analyzing neuroimaging and other data. These workflows facilitate open sharing and communication of data and metadata, concrete processing protocols, result validation, and study replication among different investigators and research groups. The LONI Pipeline features include distributed grid-enabled infrastructure, virtualized execution environment, efficient integration, data provenance, validation and distribution of new computational tools, automated data format conversion, and an intuitive graphical user interface. We demonstrate the new LONI Pipeline features using large scale neuroimaging studies based on data from the International Consortium for Brain Mapping [5] and the Alzheimer's Disease Neuroimaging Initiative [6]. User guides, forums, instructions and downloads of the LONI Pipeline environment are available at http://pipeline.loni.ucla.edu
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
Towards structured sharing of raw and derived neuroimaging data across existing resources
Data sharing efforts increasingly contribute to the acceleration of
scientific discovery. Neuroimaging data is accumulating in distributed
domain-specific databases and there is currently no integrated access mechanism
nor an accepted format for the critically important meta-data that is necessary
for making use of the combined, available neuroimaging data. In this
manuscript, we present work from the Derived Data Working Group, an open-access
group sponsored by the Biomedical Informatics Research Network (BIRN) and the
International Neuroimaging Coordinating Facility (INCF) focused on practical
tools for distributed access to neuroimaging data. The working group develops
models and tools facilitating the structured interchange of neuroimaging
meta-data and is making progress towards a unified set of tools for such data
and meta-data exchange. We report on the key components required for integrated
access to raw and derived neuroimaging data as well as associated meta-data and
provenance across neuroimaging resources. The components include (1) a
structured terminology that provides semantic context to data, (2) a formal
data model for neuroimaging with robust tracking of data provenance, (3) a web
service-based application programming interface (API) that provides a
consistent mechanism to access and query the data model, and (4) a provenance
library that can be used for the extraction of provenance data by image
analysts and imaging software developers. We believe that the framework and set
of tools outlined in this manuscript have great potential for solving many of
the issues the neuroimaging community faces when sharing raw and derived
neuroimaging data across the various existing database systems for the purpose
of accelerating scientific discovery
SAMP, the Simple Application Messaging Protocol: Letting applications talk to each other
SAMP, the Simple Application Messaging Protocol, is a hub-based communication
standard for the exchange of data and control between participating client
applications. It has been developed within the context of the Virtual
Observatory with the aim of enabling specialised data analysis tools to
cooperate as a loosely integrated suite, and is now in use by many and varied
desktop and web-based applications dealing with astronomical data. This paper
reviews the requirements and design principles that led to SAMP's
specification, provides a high-level description of the protocol, and discusses
some of its common and possible future usage patterns, with particular
attention to those factors that have aided its success in practice.Comment: 12 pages, 3 figures. Accepted for Virtual Observatory special issue
of Astronomy and Computin
Data Management and Mining in Astrophysical Databases
We analyse the issues involved in the management and mining of astrophysical
data. The traditional approach to data management in the astrophysical field is
not able to keep up with the increasing size of the data gathered by modern
detectors. An essential role in the astrophysical research will be assumed by
automatic tools for information extraction from large datasets, i.e. data
mining techniques, such as clustering and classification algorithms. This asks
for an approach to data management based on data warehousing, emphasizing the
efficiency and simplicity of data access; efficiency is obtained using
multidimensional access methods and simplicity is achieved by properly handling
metadata. Clustering and classification techniques, on large datasets, pose
additional requirements: computational and memory scalability with respect to
the data size, interpretability and objectivity of clustering or classification
results. In this study we address some possible solutions.Comment: 10 pages, Late
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Arcadia, a software development environment research project
The research objectives of the Arcadia project are two-fold: discovery and development of environment architecture principles and creation of novel software development tools, particularly powerful analysis tools, which will function within an environment built upon these architectural principles.Work in the architecture area is concerned with providing the framework to support integration while also supporting the often conflicting goal of extensibility. Thus, this area of research is directed toward achieving external integration by providing a consistent, uniform user interface, while still admitting customization and addition of new tools and interface functions. In an effort to also attain internal integration, research is aimed at developing mechanisms for structuring and managing the tools and data objects that populate a software development environment, while facilitating the insertion of new kinds of tools and new classes of objects.The unifying theme of work in the tools area is support for effective analysis at every stage of a software development project. Research is directed toward tools suitable for analyzing pre-implementation descriptions of software, software itself, and towards the production of testing and debugging tools. In many cases, these tools are specifically tailored for applicability to concurrent, distributed, or real-time software systems.The initial focus of Arcadia research is on creating a prototype environment, embodying the architectural principles, which supports Ada1 software development. This prototype environment is itself being developed in Ada.Arcadia is being developed by a consortium of researchers from the University of California at Irvine, the University of Colorado at Boulder, the University of Massachusetts at Amherst, TRW, Incremental Systems Corporation, and The Aerospace Corporation. This paper delineates the research objectives and describes the approaches being taken, the organization of the research endeavor, and current status of the work
A Language and Hardware Independent Approach to Quantum-Classical Computing
Heterogeneous high-performance computing (HPC) systems offer novel
architectures which accelerate specific workloads through judicious use of
specialized coprocessors. A promising architectural approach for future
scientific computations is provided by heterogeneous HPC systems integrating
quantum processing units (QPUs). To this end, we present XACC (eXtreme-scale
ACCelerator) --- a programming model and software framework that enables
quantum acceleration within standard or HPC software workflows. XACC follows a
coprocessor machine model that is independent of the underlying quantum
computing hardware, thereby enabling quantum programs to be defined and
executed on a variety of QPUs types through a unified application programming
interface. Moreover, XACC defines a polymorphic low-level intermediate
representation, and an extensible compiler frontend that enables language
independent quantum programming, thus promoting integration and
interoperability across the quantum programming landscape. In this work we
define the software architecture enabling our hardware and language independent
approach, and demonstrate its usefulness across a range of quantum computing
models through illustrative examples involving the compilation and execution of
gate and annealing-based quantum programs
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