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GridR: An R-based tool for scientific data analysis in grid environments

Dennis Wegener, Thierry Sengstag, Stelios Sfakianakis, Stefan Rüping, Anthony Assi
2009 Future generations computer systems  
In this paper, we describe an analysis tool based on the statistical environment R, GridR, which allows using the collection of methodologies available as R packages in a grid environment.  ...  As a proof of the concept, an example of microarray-based analysis taken from the literature was reproduced using GridR.  ...  Acknowledgments The authors gratefully acknowledge the financial support of the European Commission for the Project ACGT, FP6/2004/IST-026996.  ... 
doi:10.1016/j.future.2008.09.004 fatcat:2ba72wlcmrb4bh25b2rndsyyo4

GridR: An R-Based Grid-Enabled Tool for Data Analysis in ACGT Clinico-Genomics Trials

Dennis Wegener, Thierry Sengstag, Stelios Sfakianakis, Stefan Ruping, Anthony Assi
2007 Third IEEE International Conference on e-Science and Grid Computing (e-Science 2007)  
GMLE is currently being applied to astroinformatics for determining the shape of star streams in the Milky Way galaxy, and to particle physics in a search for theory-predicted but yet unobserved sub-atomic  ...  We expect that scientific computing frameworks, such as GMLE, will help bridge the gap between scientists needing to analyze ever larger amounts of data and ever more complex distributed computing environments  ...  The GMLE package provides an easy to use tool for scientific researchers looking to harness the power of modern distributed computing environments, in addition to aiding research into concurrent maximum  ... 
doi:10.1109/e-science.2007.41 dblp:conf/eScience/WegenerSSRA07 fatcat:olblq5synrfqti4ensmpmvaire

Supporting Parallel R Code in Clinical Trials: A Grid-Based Approach

Dennis Wegener, Thierry Sengstag, Stelios Sfakianakis, Stefan Rüping
2008 2008 IEEE International Symposium on Parallel and Distributed Processing with Applications  
In this paper, we describe an extension to the ACGT GridR environment which allows the parallelization of loops in R scripts in view of their distributed execution on a computational grid.  ...  In ACGT, GridR scripts are executed in the framework of a specifically developed workflow environment, which is also briefly outlined in the present article.  ...  Acknowledgments The authors gratefully acknowledge the financial support of the European Commission for the Project ACGT, FP6/2004/IST-026996. References  ... 
doi:10.1109/ispa.2008.29 dblp:conf/ispa/WegenerSSR08 fatcat:a42ukhvvsvet7cyxr7levl54si

Building a System for Advancing Clinico-Genomic Trials on Cancer

Stelios Sfakianakis, Norbert M. Graf, Alexander Hoppe, Stefan Rüping, Dennis Wegener, Lefteris Koumakis, George Zacharioudakis
2009 Professional Practice in Artificial Intelligence  
In the project ACGT, a grid-based software system to support clinicians and bio-statisticians in their daily work is being developed.  ...  The analysis of clinico-genomic data poses complex computational problems.  ...  Acknowledgments: The authors wish to thank the ACGT consortium for their contributions and various ideas on which the ACGT project was developed.  ... 
dblp:conf/ifip12/SfakianakisGHRWKZ09 fatcat:akpvrowf65fq5juyzxtbnegpq4

ACGT: advancing clinico-genomic trials on cancer - four years of experience

Luis Martin, Alberto Anguita, Norbert Graf, Manolis Tsiknakis, Mathias Brochhausen, Stefan Rüping, Anca Bucur, Stelios Sfakianakis, Thierry Sengstag, Francesca Buffa, Holger Stenzhorn
2011 Studies in Health Technology and Informatics  
An urgent need exists to access data in a uniform manner, to share information among different clinical and research centers, and to store data in secure repositories assuring the privacy of patients.  ...  The challenges regarding seamless integration of distributed, heterogeneous and multilevel data arising in the context of contemporary, post-genomic clinical trials cannot be effectively addressed with  ...  The R language was adopted as the prime tool for carrying out statistical analysis of the data.  ... 
pmid:21893844 fatcat:m5qggzte4vhvjbdxo44ie3axwu

The ACGT project in retrospect: Lessons learned and future outlook

Anca Bucur, Stefan Ruping, Thierry Sengstag, Stelios Sfakianakis, Manolis Tsiknakis, Dennis Wegener
2011 Procedia Computer Science  
In this paper we describe the way the ACGT consortium has approached important challenges in the design and the execution of the clinical trials such as the issues of data integration, semantics based  ...  The objective of the ACGT (Advancing Clinico-Genomic Trials on Cancer: Open Grid Services for improving Medical Knowledge Discovery, project that has recently concluded successfully was  ...  Acknowledgements The authors gratefully acknowledge the financial support of the European Commission for the Project ACGT, FP6/2004/IST-026996.  ... 
doi:10.1016/j.procs.2011.04.119 fatcat:ls5emmpmrrfwnhnkscbpazorge

Towards an environment for data mining based analysis processes in bioinformatics and personalized medicine

Dennis Wegener, Simona Rossi, Francesca Buffa, Mauro Delorenzi, Stefan Rüping
2013 Network Modeling Analysis in Health Informatics and Bioinformatics  
In this paper, we present the challenges for data mining based analysis in bio-and medical informatics and our approach towards a data mining environment addressing these requirements in the p-medicine  ...  To serve these new and diverse needs, bioinformatics and data mining are teaming up to generate tools and procedures for prediction of disease recurrence and progression, response to treatment, as well  ...  The GridR service (Bucur et al. 2011 ) allows for reusing R script-based data mining components.  ... 
doi:10.1007/s13721-013-0022-1 dblp:journals/netmahib/WegenerRBDR13 fatcat:xnr6jsiko5ff5px2mxbk7ckwfy

xgrid and R: Parallel Distributed Processing Using Heterogeneous Groups of Apple Computers

Sarah,C. Anoke, Yuting Zhao, Rafael Jaeger, Nicholas,J. Horton
2012 The R Journal  
Use of the grid for "embarassingly parallel" independent jobs has the potential for major speedups in time to completion.  ...  We describe the xgrid package which facilitates access to this system to undertake independent simulations or other long-running jobs that can be divided into replicate runs within R.  ...  Acknowledgements Thanks to Tony Caldanaro and Randall Pruim for technical assistance, as well as Molly Johnson, two anonymous reviewers and the associate editor for comments and useful suggestions on an  ... 
doi:10.32614/rj-2012-006 fatcat:axd6xkikifczlejut6czbywdty

GigaSOM.jl: High-performance clustering and visualization of huge cytometry datasets

Miroslav Kratochvíl, Oliver Hunewald, Laurent Heirendt, Vasco Verissimo, Jiří Vondrášek, Venkata P Satagopam, Reinhard Schneider, Christophe Trefois, Markus Ollert
2020 GigaScience  
The analysis of that amount of high-dimensional data becomes demanding in both hardware and software of high-performance computational resources.  ...  The implementation of GigaSOM.jl in the high-level and high-performance programming language Julia makes it accessible to the scientific community and allows for efficient handling and processing of datasets  ...  FlowSOM is currently available as an R package that has become an essential part of many workflows, analysis pipelines, and software suites, including FlowJo and Cytobank R [13] .  ... 
doi:10.1093/gigascience/giaa127 pmid:33205814 pmcid:PMC7672468 fatcat:dxbbboqj2jerxacuczpao37boy

Hybrid Ant Colony System and Genetic Algorithm Approach for Scheduling of Jobs in Computational Grid

Mustafa Muwafak Alobaedy, Ku Ruhana Ku-Mahamud
2015 Research Journal of Applied Sciences Engineering and Technology  
This study proposes a high level hybrid approach between ant colony system and genetic algorithm for job scheduling in grid computing. The proposed approach is based on a high level hybridization.  ...  Metaheuristic algorithms have been used to solve scheduling problems in grid computing. However, stand-alone metaheuristic algorithms do not always show good performance in every problem instance.  ...  Malaysia, Kedah, for the administration of this study.  ... 
doi:10.19026/rjaset.11.2044 fatcat:upbmbhm2vfczngtaiutl3t5uqi

Agama reference documentation [article]

Eugene Vasiliev
2019 arXiv   pre-print
Agama (Action-based Galaxy Modelling Architecture) is a software library intended for a broad range of tasks within the field of stellar dynamics.  ...  First of all, this is a detailed reference for the library itself. Second, it describes various mathematical and numerical methods that could be applicable in a broader context.  ...  , z plane (for an axisymmetric model) or 3d grid in R, z, φ (in general).  ... 
arXiv:1802.08255v2 fatcat:nytqg2wnzjhqneqhgkg2omo6di

Computational modeling of urban wind flow and natural ventilation potential of buildings [article]

R Rubina Ramponi, BJE Bert Blocken, L Livio Mazzarella, A Adriana Angelotti
Based on this analysis, grid C was used for the simulations.  ...  Based on these small differences, the basic grid was retained for further analysis and the grids for the other cases were prepared with a similar grid resolution.  ...  The differences among the three locations are more remarkable for higher PAD values.  ... 
doi:10.6100/ir762656 fatcat:wwx5lthrxrgmtcegdaagz54z6q

Object detection with MicrosoftHoloLens 2. A comparison between image and point cloud based algorithms

Sophie Herrmann, Ioannis Giannopoulos, Markus Kattenbeck
Due to the availability of both a 2D and 3D measurement device and ease of use, head mounted Augmented Reality glasses are used for data acquisition.  ...  This is an issue as a number of modern applications operate in the three dimensional world, therefore also require accurate 3D information.  ...  view-based)o ra3 Dr egular grid( voxel-grid-based). Anyo ft hose transformations leadst oal oss of information.  ... 
doi:10.34726/hss.2021.90361 fatcat:c3komdeidrbubckifkynp2dpg4

From cookstoves to smart homes: examining the social dynamics of household energy behaviour

Dylan Daniel Furszyfer Del Rio, Karen Makuch, Benjamin Sovacool, Consejo Nacional De Ciencia Y Tecnología
First, through an extensive literature review analysis from 2013 to 2017, it overviews the current knowledge to identify what behaviour change techniques are the most successful for the uptake and maintained  ...  Second, based on an original dataset involving expert interviews, site visits to retailers, and a comprehensive review of the literature, this PhD examines the promises and perils of smart home technologies  ...  She takes Ovia Health as an example, since this app has become a powerful tool for employers and health insurers to collect data about their workers' lives.  ... 
doi:10.25560/82180 fatcat:dnblppizcfbadg6uh46navum4m