123,825 research outputs found
Global Grids and Software Toolkits: A Study of Four Grid Middleware Technologies
Grid is an infrastructure that involves the integrated and collaborative use
of computers, networks, databases and scientific instruments owned and managed
by multiple organizations. Grid applications often involve large amounts of
data and/or computing resources that require secure resource sharing across
organizational boundaries. This makes Grid application management and
deployment a complex undertaking. Grid middlewares provide users with seamless
computing ability and uniform access to resources in the heterogeneous Grid
environment. Several software toolkits and systems have been developed, most of
which are results of academic research projects, all over the world. This
chapter will focus on four of these middlewares--UNICORE, Globus, Legion and
Gridbus. It also presents our implementation of a resource broker for UNICORE
as this functionality was not supported in it. A comparison of these systems on
the basis of the architecture, implementation model and several other features
is included.Comment: 19 pages, 10 figure
Bioconductor: open software development for computational biology and bioinformatics.
The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples
Plyades: A Python Library for Space Mission Design
Plyades: A Python Library for Space Mission Design Designing a space mission
is a computation-heavy task. Software tools that conduct the necessary
numerical simulations and optimizations are therefore indispensable. The
usability of existing software, written in Fortran and MATLAB, suffers because
of high complexity, low levels of abstraction and out-dated programming
practices. We propose Python as a viable alternative for astrodynamics tools
and demonstrate the proof-of-concept library Plyades which combines powerful
features with Pythonic ease of use
Towards a service-oriented e-infrastructure for multidisciplinary environmental research
Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures
Knowledge-based Expressive Technologies within Cloud Computing Environments
Presented paper describes the development of comprehensive approach for
knowledge processing within e-Sceince tasks. Considering the task solving
within a simulation-driven approach a set of knowledge-based procedures for
task definition and composite application processing can be identified. This
procedures could be supported by the use of domain-specific knowledge being
formalized and used for automation purpose. Within this work the developed
conceptual and technological knowledge-based toolbox for complex
multidisciplinary task solv-ing support is proposed. Using CLAVIRE cloud
computing environment as a core platform a set of interconnected expressive
technologies were developed.Comment: Proceedings of the 8th International Conference on Intelligent
Systems and Knowledge Engineering (ISKE2013). 201
Object-oriented implementations of the MPDATA advection equation solver in C++, Python and Fortran
Three object-oriented implementations of a prototype solver of the advection
equation are introduced. The presented programs are based on Blitz++ (C++),
NumPy (Python), and Fortran's built-in array containers. The solvers include an
implementation of the Multidimensional Positive-Definite Advective Transport
Algorithm (MPDATA). The introduced codes exemplify how the application of
object-oriented programming (OOP) techniques allows to reproduce the
mathematical notation used in the literature within the program code. A
discussion on the tradeoffs of the programming language choice is presented.
The main angles of comparison are code brevity and syntax clarity (and hence
maintainability and auditability) as well as performance. In the case of
Python, a significant performance gain is observed when switching from the
standard interpreter (CPython) to the PyPy implementation of Python. Entire
source code of all three implementations is embedded in the text and is
licensed under the terms of the GNU GPL license
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