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A Semantic-Based Approach to Attain Reproducibility of Computational Environments in Scientific Workflows: A Case Study [chapter]

Idafen Santana-Perez, Rafael Ferreira da Silva, Mats Rynge, Ewa Deelman, María S. Pérez-Hernández, Oscar Corcho
2014 Lecture Notes in Computer Science  
In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment.  ...  Results show that our approach can reproduce an equivalent execution environment of a predefined virtual machine image on both computing platforms. Fig. 2.  ...  Acknowledgements This material is based upon work supported in part by the National Science Foundation under Grant No. 0910812 to Indiana University for "FutureGrid: An Experimental, High-Performance Grid  ... 
doi:10.1007/978-3-319-14325-5_39 fatcat:z6hcnjrnxvhcbdpkmyeb2trehy

Towards Reproducibility in Scientific Workflows: An Infrastructure-Based Approach

Idafen Santana-Perez, María S. Pérez-Hernández
2015 Scientific Programming  
From the original workflow, we document its execution environment, by means of a set of semantic models and a catalogue of resources, and generate an equivalent infrastructure for reexecuting it.  ...  This work focuses on the equipment of a computational experiment, that is, the set of software and hardware components that are involved in the execution of a scientific workflow.  ...  (Formacion de Profesorado Universitario) from the Spanish Science and Innovation Ministry (MICINN).  ... 
doi:10.1155/2015/243180 fatcat:ymhjddscjfgdnnv5pideumdasa

OUP accepted manuscript

2017 Briefings in Bioinformatics  
Rezaul Karim is a PhD researcher at Semantics in eHealth and Life Sciences with expertise in the development of computational resources for the analysis and visualization of ribosome profiling (RiboSeq  ...  In this article, we will analyze the existing DWFS with regard to their capabilities toward public open data use as well as large-scale computational and human interface requirements.  ...  and João Bosco Jares for helping them in drawing the Figure 2 .  ... 
doi:10.1093/bib/bbx039 pmid:28419324 pmcid:PMC6169675 fatcat:xsdfepwqmnb7pgkmnep2ifn2wi

Cloud computing in e-Science: research challenges and opportunities

Xiaoyu Yang, David Wallom, Simon Waddington, Jianwu Wang, Arif Shaon, Brian Matthews, Michael Wilson, Yike Guo, Li Guo, Jon D. Blower, Athanasios V. Vasilakos, Kecheng Liu (+1 others)
2014 Journal of Supercomputing  
SOA (Service Oriented Architecture), workflow, the Semantic Web, and Grid computing are key enabling information technologies in the development of increasingly sophisticated e-Science infrastructures  ...  Such challenges demonstrate the need for a comprehensive analysis on using the above mentioned informatics techniques to develop appropriate e-Science infrastructure and platforms in the context of Cloud  ...  Acknowledgements We thank the anonymous reviewers for their constructive and insightful suggestions.  ... 
doi:10.1007/s11227-014-1251-5 fatcat:ribdemcam5coxmwoloszbc54ne

Reproducibility of Computational Experiments on Kubernetes-Managed Container Clouds with HyperFlow [chapter]

Michał Orzechowski, Bartosz Baliś, Renata G. Słota, Jacek Kitowski
2020 Lecture Notes in Computer Science  
Our solution addresses conservation of the scientific procedure, scientific data, execution environment and experiment deployment, while using standard tools in order to avoid maintainability issues that  ...  We propose a comprehensive solution for reproducibility of scientific workflows. We focus particularly on Kubernetes-managed container clouds, increasingly important in scientific computing.  ...  The research presented in this paper has been partially supported by the funds of Polish Ministry of Science and Higher Education assigned to the AGH University of Science and Technology.  ... 
doi:10.1007/978-3-030-50371-0_16 fatcat:eflcvgxm6zbfnc5gjyupy42tce

Linked Open Science-Communicating, Sharing and Evaluating Data, Methods and Results for Executable Papers

Tomi Kauppinen, Giovana Mira de Espindola
2011 Procedia Computer Science  
executing, validating and exploring research, 3) Cloud Computing for efficient and distributed computing, and 4) Creative Commons for the legal infrastructure.  ...  Linked Open Science is an approach to solve challenges of an executable paper.  ...  Acknowledgments This research has been partially funded by the International Research Training Group on Semantic Integration of Geospatial Information (DFG GRK 1498, see  ... 
doi:10.1016/j.procs.2011.04.076 fatcat:xti7vy3cmjh33ohbbgjustg2qu

Data Life Cycle Management and Analytics Code Execution Strategies for the Breath Gas Analysis Domain

Ibrahim Elsayed, Thomas Ludescher, Alexander Wöhrer, Thomas Feilhauer, Peter Brezany
2012 Procedia Computer Science  
The first is based on our previous work, in particular the e-Science Life Cycle Ontology, which traces semantics about procedures a researcher is conducting during the execution of a scientific study.  ...  The work discussed in this paper is mainly consolidated of two independently targeted frameworks: a data life cycle management framework for e-Science applications and a code execution framework handling  ...  The entire research team contributed to the discussions that led this paper and provided the environment in which the ideas could be implemented and evaluated.  ... 
doi:10.1016/j.procs.2012.04.017 fatcat:x7e3niybznfmhbcrcbtyxwp57e

MULTI-X, a State-of-the-Art Cloud-Based Ecosystem for Biomedical Research

Milton Hoz de Vila, Rahman Attar, Marco Pereanez, Alejandro F. Frangi
2018 2018 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
In this paper, we present MULTI-X, a cross-domain research-oriented platform, designed for collaborative and reproducible science.  ...  This cloud-based framework simplifies the logistical challenges of implementing data analytics and AI solutions by providing pre-configured environments with ad-hoc scalable computing resources and secure  ...  Locally, in series or parallel, or distributed, using load-balanced dynamically generated computing clusters. Reproducibility. Full execution environments can be saved, shared and reproduced.  ... 
doi:10.1109/bibm.2018.8621317 dblp:conf/bibm/VilaAPF18 fatcat:x3wewucqjfbkvfzp3gfuzv426q

DARE Platform: Enabling Easy Data-Intensive Workflow Composition and Deployment

2019 Zenodo  
DAREs technology translates scientists methods to concrete scientific workflows that can be portable and reproducible on different computing environments without making any (or little) changes.  ...  This work presents the DARE platform and working environment for enabling easy data-intensive workflow composition and deployment on clouds systems.  ...  In both execution environments, CWL was in charge to execute and connect each part of the RA application.  ... 
doi:10.5281/zenodo.3357805 fatcat:exlz3cby2vg5xncjxbwn4dl3le

ABA-Cloud: support for collaborative breath research

Ibrahim Elsayed, Thomas Ludescher, Julian King, Clemens Ager, Michael Trosin, Uygar Senocak, Peter Brezany, Thomas Feilhauer, Anton Amann
2013 Journal of Breath Research  
They build the basis for the development of an ontology (a concept from computer science used for communication between machines and/or humans and representation and reuse of knowledge) dedicated to breath  ...  reproducibility.  ...  We greatly appreciate the generous support of the government of Vorarlberg and its governor Landeshauptmann Dr Herbert Sausgruber.  ... 
doi:10.1088/1752-7155/7/2/026007 pmid:23619467 pmcid:PMC4913868 fatcat:mnc7v23fs5ehtbajruja3xujqa

Using Cloud-Aware Provenance to Reproduce Scientific Workflow Execution on Cloud

Khawar Hasham, Kamran Munir, Richard McClatchey
2015 Proceedings of the 5th International Conference on Cloud Computing and Services Science  
This paper also attempts to present a model that is used in the proposed design to achieve workflow reproducibility in the Cloud environment.  ...  the similar resources on the Cloud and re-executing the workflow on them and (c) by comparing the outputs of workflows.  ...  This project aims to assist the neuro-scientific community in analysing brain scans using workflows and distributed infrastructure (Grid and Cloud) to identify biomarkers that can help in diagnosing the  ... 
doi:10.5220/0005452800490059 dblp:conf/closer/HashamMM15 fatcat:mx7k3dqbdzdabeuwwdpnh2x35a

A Cloud-Based Platform for Democratizing and Socializing the Benchmarking Process

Fuad Bajaber, Amin Shafaat, Omar Batarfi, Radwa Elshawi, Abdulrahman Altalhi, Ahmed Barnawi, Sherif Sakr
2016 International Journal of Advanced Computer Science and Applications  
Performances evaluation, benchmarking and reproducibility represent significant aspects for evaluating the practical impact of scientific research outcomes in the Computer Science field.  ...  In this article, we present the design and the implementation details of the Liquid Benchmarking platform as a social and cloud-based platform for democratizing and socializing the software benchmarking  ...  ACKNOWLEDGEMENT This project was funded by the National Plan for Science, Technology and Innovation (MAARIFAH) -King Abdulaziz City for Science and Technology -the Kingdom of Saudi Arabia -award number  ... 
doi:10.14569/ijacsa.2016.070268 fatcat:qnevpnu3fjh6lph5vbadj2zv7u

D5.6: Evaluation report of service pilots [article]

Giuseppe La Rocca
2019 Zenodo  
Summarise the activities undertaken, and the available solutions and services that have been used by the Science Demonstrators to implement the pilot services. b.  ...  Drive and prioritise the integration of solutions and/or services to meet the functional and non-functional requirements requested by the Science Demonstrators.  ...  Additionally, initial engagement with the other Science Demonstrators (e.g. TEXTCROWD and DPHEP) was established to investigate a further development of the solution in different domains.  ... 
doi:10.5281/zenodo.5094777 fatcat:za4cewo57vea5lvlmz646usafy

The Systematic Study of Scientific Workflows in Distributed and Cloud Environments: A Review of Privacy Issues in Workflow Provenance, Challenges and Opportunities

Shridevi Erayya
2018 International Journal of Computer Applications  
At the end the paper discusses about the challenging task related to increasing number of workflows in the cloud environment is that managing various workflows, VMs & workflow execution on VM instances  ...  Resolving workflow execution is very important because workflow and cloud became most popular in cyber infrastructure projects.  ...  WFaaS also utilizes other cloud computing services such as IaaS, DaaS to get proper data, software packages and VM for its execution. Architecture for WFaaS in the Cloud.  ... 
doi:10.5120/ijca2018916696 fatcat:7ctw576kvvfjlilhmk5loxsg5q

A Secure Framework for Authentication of Documents in Cloud

Mr.Srikanth Ganta
2018 Helix  
It is explained how the documents can be processed using cloud computing environment where the application is integrated with Hadoop installed on Amazon EC2 web service.  ...  In order to overcome the setbacks, it is proposed a methodology with the stored data processing of encoding and decoding at cloud environment taking the support of cryptographic hash values.  ...  Peng [7] in his paper explained about "Reproducible research in computational science," .He explained that in the case where there is no possibility of full independent replication of a study, this reproducibility  ... 
doi:10.29042/2018-3406-3412 fatcat:cx7flk45wrb5vju4jus4i3qsve
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