37,515 research outputs found
MOLNs: A cloud platform for interactive, reproducible and scalable spatial stochastic computational experiments in systems biology using PyURDME
Computational experiments using spatial stochastic simulations have led to
important new biological insights, but they require specialized tools, a
complex software stack, as well as large and scalable compute and data analysis
resources due to the large computational cost associated with Monte Carlo
computational workflows. The complexity of setting up and managing a
large-scale distributed computation environment to support productive and
reproducible modeling can be prohibitive for practitioners in systems biology.
This results in a barrier to the adoption of spatial stochastic simulation
tools, effectively limiting the type of biological questions addressed by
quantitative modeling. In this paper, we present PyURDME, a new, user-friendly
spatial modeling and simulation package, and MOLNs, a cloud computing appliance
for distributed simulation of stochastic reaction-diffusion models. MOLNs is
based on IPython and provides an interactive programming platform for
development of sharable and reproducible distributed parallel computational
experiments
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
Development of Grid e-Infrastructure in South-Eastern Europe
Over the period of 6 years and three phases, the SEE-GRID programme has
established a strong regional human network in the area of distributed
scientific computing and has set up a powerful regional Grid infrastructure. It
attracted a number of user communities and applications from diverse fields
from countries throughout the South-Eastern Europe. From the infrastructure
point view, the first project phase has established a pilot Grid infrastructure
with more than 20 resource centers in 11 countries. During the subsequent two
phases of the project, the infrastructure has grown to currently 55 resource
centers with more than 6600 CPUs and 750 TBs of disk storage, distributed in 16
participating countries. Inclusion of new resource centers to the existing
infrastructure, as well as a support to new user communities, has demanded
setup of regionally distributed core services, development of new monitoring
and operational tools, and close collaboration of all partner institution in
managing such a complex infrastructure. In this paper we give an overview of
the development and current status of SEE-GRID regional infrastructure and
describe its transition to the NGI-based Grid model in EGI, with the strong SEE
regional collaboration.Comment: 22 pages, 12 figures, 4 table
A Taxonomy of Workflow Management Systems for Grid Computing
With the advent of Grid and application technologies, scientists and
engineers are building more and more complex applications to manage and process
large data sets, and execute scientific experiments on distributed resources.
Such application scenarios require means for composing and executing complex
workflows. Therefore, many efforts have been made towards the development of
workflow management systems for Grid computing. In this paper, we propose a
taxonomy that characterizes and classifies various approaches for building and
executing workflows on Grids. We also survey several representative Grid
workflow systems developed by various projects world-wide to demonstrate the
comprehensiveness of the taxonomy. The taxonomy not only highlights the design
and engineering similarities and differences of state-of-the-art in Grid
workflow systems, but also identifies the areas that need further research.Comment: 29 pages, 15 figure
Quantum ESPRESSO: a modular and open-source software project for quantum simulations of materials
Quantum ESPRESSO is an integrated suite of computer codes for
electronic-structure calculations and materials modeling, based on
density-functional theory, plane waves, and pseudopotentials (norm-conserving,
ultrasoft, and projector-augmented wave). Quantum ESPRESSO stands for "opEn
Source Package for Research in Electronic Structure, Simulation, and
Optimization". It is freely available to researchers around the world under the
terms of the GNU General Public License. Quantum ESPRESSO builds upon
newly-restructured electronic-structure codes that have been developed and
tested by some of the original authors of novel electronic-structure algorithms
and applied in the last twenty years by some of the leading materials modeling
groups worldwide. Innovation and efficiency are still its main focus, with
special attention paid to massively-parallel architectures, and a great effort
being devoted to user friendliness. Quantum ESPRESSO is evolving towards a
distribution of independent and inter-operable codes in the spirit of an
open-source project, where researchers active in the field of
electronic-structure calculations are encouraged to participate in the project
by contributing their own codes or by implementing their own ideas into
existing codes.Comment: 36 pages, 5 figures, resubmitted to J.Phys.: Condens. Matte
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