Exploratory programming in the virtual laboratory
Eryk Ciepiela,Daniel Harezlak,J. Kocot,Tomasz Bartynski,Marek Kasztelnik,Piotr Nowakowski,Tomasz Gubała,Maciej Malawski,Marian Bubak +8 more
- 01 Oct 2010
- pp 621-628
TL;DR: An overview of the most important features of the Experiment Workbench, which is the main user interface of the Virtual laboratory, are presented, and a sample experiment from the computational chemistry domain is discussed.
read more
Abstract: GridSpace 2 is a novel virtual laboratory framework enabling researchers to conduct virtual experiments on Grid-based resources and other HPC infrastructures. GridSpace 2 facilitates exploratory development of experiments by means of scripts which can be written in a number of popular languages, including Ruby, Python and Perl. The framework supplies a repository of gems enabling scripts to interface low-level resources such as PBS queues, EGEE computing elements, scientific applications and other types of Grid resources. Moreover, GridSpace 2 provides a Web 2.0-based Experiment Workbench supporting development and execution of virtual experiments by groups of collaborating scientists. We present an overview of the most important features of the Experiment Workbench, which is the main user interface of the Virtual laboratory, and discuss a sample experiment from the computational chemistry domain.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Virtual Laboratory to Improve Students' Problem-Solving Skills on Electricity Concept
TL;DR: In this paper, the authors examined the effect of the use of virtual labs on problem-solving ability of students to the concept of electricity and found that the experimental class' students have a higher ability to plan and implement problems than those of the control class.
The Collage Authoring Environment
Piotr Nowakowski,Eryk Ciepiela,Daniel Harezlak,J. Kocot,Marek Kasztelnik,Tomasz Bartynski,Jan Meizner,Grzegorz Dyk,Maciej Malawski +8 more
- 01 Jan 2011
TL;DR: An environment which enables authors to seamlessly embed chunks of executable code (called assets) into scientific publications and allow repeated execution of such assets on underlying computing and data storage resources, as required by scientists who wish to build upon the presented results is proposed.
76
Virtual laboratory of electricity concept to improve prospective physics teachers creativity
TL;DR: In this paper, a virtual laboratory for electrical materials has been developed as an alternative laboratory due to the limited equipment of physics experiments and simultaneously assisting students in visualizing abstract concepts in physics.
A hybrid HPC/cloud distributed infrastructure
TL;DR: The results indicate that accommodating some parts of the multiscale computation on cloud resources can lead to low performance without a proper adjustment of CPUs power and workload, but by enforcing a load-balancing strategy one can benefit from the extra Cloud resources.
41
Component Approach to Computational Applications on Clouds
Maciej Malawski,Maciej Malawski,Jan Meizner,Marian Bubak,Marian Bubak,Pawel Gepner +5 more
- 01 Jan 2011
TL;DR: The measured performance of virtual machine startup time and virtualization overhead indicate promising prospects for exploiting such infrastructures along with the proposed component-based approach.
38
References
PACKMOL: a package for building initial configurations for molecular dynamics simulations.
TL;DR: This work has developed a code able to pack millions of atoms, grouped in arbitrarily complex molecules, inside a variety of three‐dimensional regions, which can be intersections of spheres, ellipses, cylinders, planes, or boxes.
cclib: A library for package‐independent computational chemistry algorithms
TL;DR: The cclib platform as discussed by the authors is a platform for the development of package-independent computational chemistry algorithms, which can automatically detect, parse, and convert the extracted information into a standard internal representation.
5.5K
Biopython: freely available Python tools for computational molecular biology and bioinformatics
Peter J. A. Cock,Tiago Antao,Jeffrey T. Chang,Brad Chapman,Cymon J. Cox,Andrew Dalke,Iddo Friedberg,Thomas Hamelryck,Frank Kauff,Bartosz Wilczyński,Michiel J. L. de Hoon +10 more
TL;DR: Biopython includes modules for reading and writing different sequence file formats and multiple sequence alignments, dealing with 3D macro molecular structures, interacting with common tools such as BLAST, ClustalW and EMBOSS, accessing key online databases, as well as providing numerical methods for statistical learning.
Scientific Workflow Management and the Kepler System
Bertram Ludäscher,Bertram Ludäscher,Ilkay Altintas,Chad Berkley,Dan Higgins,Efrat Jaeger,Matthew B. Jones,Edward A. Lee,Jing Tao,Yang Zhao +9 more
TL;DR: Kepler as mentioned in this paper is a scientific workflow system, which is currently under development across a number of scientific data management projects and is a community-driven, open source project, and always welcome related projects and new contributors to join.
Scientific workflow management and the Kepler system: Research Articles
Bertram Ludäscher,Ilkay Altintas,Chad Berkley,Dan Higgins,Efrat Jaeger,Matthew B. Jones,Edward A. Lee,Jing Tao,Yang Zhao +8 more
TL;DR: Characteristics of and requirements for scientific workflows as identified in a number of application projects are described, and some key features of Kepler and its underlying Ptolemy II system, planned extensions, and areas of future research are described.
1.2K