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Delivering bioinformatics MapReduce applications in the cloud

Lukas Forer, Tomislav Lipic, Sebastian Schonherr, Hansi Weisensteiner, Davor Davidovic, Florian Kronenberg, Enis Afgan
2014 2014 37th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO)  
This paper presents integration of two existing systems: Cloudgene, a bioinformatics MapReduce workflow framework, and CloudMan, a cloud manager for delivering application execution environments.  ...  The ever-increasing data production and availability in the field of bioinformatics demands a paradigm shift towards the utilization of novel solutions for efficient data storage and processing, such as  ...  ACKNOWLEDGMENT This work was, in part, supported by the "Scalable Big Data Bioinformatics Analysis in the Cloud" grant from the Croatian Ministry of Science, Education, and Sport and the Austrian Federal  ... 
doi:10.1109/mipro.2014.6859593 dblp:conf/mipro/ForerLSWDKA14 fatcat:5f4jlfzqgjdrjmnegafbvdge44

CloudMan as a platform for tool, data, and analysis distribution

Enis Afgan, Brad Chapman, James Taylor
2012 BMC Bioinformatics  
Conclusions: With the enabled customization and sharing of instances, CloudMan can be used as a platform for collaboration.  ...  The presented solution improves accessibility of cloud resources, tools, and data to the level of an individual researcher and contributes toward reproducibility and transparency of research solutions.  ...  The Department specifically disclaims responsibility for any analyses, interpretations or conclusions.  ... 
doi:10.1186/1471-2105-13-315 pmid:23181507 pmcid:PMC3556322 fatcat:lma3lbbwyfg4nbcvmr7pye6uke

Building and provisioning bioinformatics environments on public and private Clouds

Enis Afgan, Konstantinos Krampis, Nuwan Goonasekera, Karolj Skala, James Taylor
2015 2015 38th International Convention on Information and Communication Technology, Electronics and Microelectronics (MIPRO)  
In this paper we describe one such framework, its compatibility with multiple Clouds and present an automated process for deploying the entire system so it can be made easily available on any Cloud.  ...  To take advantage of the scalability offered by the cloud, additional frameworks are required to create virtualized compute clusters and emulate the most common infrastructure found on institutional resources  ...  Additional funding is provided by Huck Institutes for the Life Sciences at Penn State and, in part, under a grant with the Pennsylvania Department of Health using Tobacco Settlement Funds.  ... 
doi:10.1109/mipro.2015.7160269 dblp:conf/mipro/AfganKGST15 fatcat:grslkqjyt5glhpbuefpefwdr7u

BioBlend: automating pipeline analyses within Galaxy and CloudMan

C. Sloggett, N. Goonasekera, E. Afgan
2013 Bioinformatics  
We present BioBlend, a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs.  ...  BioBlend makes it easy for bioinformaticians to automate endto-end large-data analysis, from scratch, in a way that is highly accessible to collaborators, by allowing them to both provision the required  ...  Funding: This work was, in part, supported by the Genomics Virtual Laboratory (GVL) grant from the National eResearch Collaboration Tools and Resources (NeCTAR). Conflict of interest: None declared.  ... 
doi:10.1093/bioinformatics/btt199 pmid:23630176 pmcid:PMC4288140 fatcat:wzs5buyyrjd57pr5txrx3pwa7i

CloudMan: A platform for portable cloud manufacturing services

Soheil Qanbari, Samira Mahdi Zadeh, Soroush Vedaei, Schahram Dustdar
2014 2014 IEEE International Conference on Big Data (Big Data)  
The proposed platform incorporates OASIS Topology and Orchestration Specification for cloud Applications (TOSCA) policies, plans and templates as a mechanism for dynamic configuration, portability and  ...  Having this rigorous analysis in mind, we present a holistic architecture for CloudMan, as it considers the manufacturing data, material and event flow from sensors and shop floors, through services to  ...  ACKNOWLEDGMENT The research leading to these results is sponsored by the Doctoral College of Adaptive Distributed Systems at the Vienna University of Technology as well as the Pacific Controls cloud Computing  ... 
doi:10.1109/bigdata.2014.7004334 dblp:conf/bigdataconf/QanbariZVD14 fatcat:fcsxruy2jvcw7kbt7yadh2kd7a

A reference model for deploying applications in virtualized environments

Enis Afgan, Dannon Baker, the Galaxy Team, Anton Nekrutenko, James Taylor
2011 Concurrency and Computation  
We provide a fully functional sample application deployment and implement a framework for managing the overall application deployment.  ...  and yields a set of higher-level services as a byproduct of the component organization and the underlying infrastructure.  ...  the Huck Institutes for the Life Sciences and the Institute for CyberScience at Penn State.  ... 
doi:10.1002/cpe.1836 pmid:33907528 pmcid:PMC8073171 fatcat:pxgaxwc4vjdfrji3burs6tz4na

Personalized cloud-based bioinformatics services for research and education: use cases and the elasticHPC package

Mohamed El-Kalioby, Mohamed Abouelhoda, Jan Krüger, Robert Giegerich, Alexander Sczyrba, Dennis P Wall, Peter Tonellato
2012 BMC Bioinformatics  
Acknowledgements We thank Shady Issa from Nile University for this help and support during the development of the elasticHPC. We thank the Amazon team for providing us with AWS compute hours.  ...  This article has been published as part of BMC Bioinformatics Volume 13 Supplement  ...  The usage of EMR framework within elasticHPC is generic to any tool as explained in the manual.  ... 
doi:10.1186/1471-2105-13-s17-s22 pmid:23281941 pmcid:PMC3521398 fatcat:jbyd47v4tff2fjesf5eaj5qlnm

Application Information Services for distributed computing environments

Enis Afgan, Purushotham Bangalore, Karolj Skala
2011 Future generations computer systems  
the Galaxy Team, "Dynamics of mitochondrial heteroplasmy in three families: A fully reproducible re-sequencing study",  ...  Galaxy CloudMan -design, portability, and efficiency study as well as implementation of autonomous webbased application for seamless use of cloud infrastructures.  ...  Title: "A Framework for Efficient Execution of Bioinformatics Applications across the Grid," MidSouth Computational Biology and Bioinformatics Society (MCBIOS), Starkville, MS, February 21, 2009.  ... 
doi:10.1016/j.future.2010.08.004 fatcat:bpdh6xgdozdlpig4bx37s7ept4

Harnessing cloud computing with Galaxy Cloud

Enis Afgan, Dannon Baker, Nate Coraor, Hiroki Goto, Ian M Paul, Kateryna D Makova, Anton Nekrutenko, James Taylor
2011 Nature Biotechnology  
A possible solution to this infrastructure challenge comes in the form of "cloud computing", a model where computation and storage exist as virtual resources, accessed via the Internet, which can be dynamically  ...  In general however, cloud resources are not provided in a form that can be immediately used by a researcher without informatics expertise.  ...  the samples and to volunteers for donating the samples.  ... 
doi:10.1038/nbt.2028 pmid:22068528 pmcid:PMC3868438 fatcat:bi254ehyubhzxgdat6sbuztt2e

Deploying Bioinformatics Workflows on Clouds with Galaxy and Globus Provision

Bo Liu, Borja Sotomayor, Ravi Madduri, Kyle Chard, Ian Foster
2012 2012 SC Companion: High Performance Computing, Networking Storage and Analysis  
This paper proposes a novel approach for deploying bioinformatics workflows in Cloud environments using Galaxy, a platform for scientific workflows, and Globus Provision, a tool for deploying distributed  ...  Cloud computing is attracting increasing attention as a means of providing users with fast provisioning of computational and storage resources, elastic scaling, and payas-you-go pricing.  ...  ACKNOWLEDGMENT We appreciate the help of CVRG community and Globus Online team. We also appreciate the Galaxy Team for their support and maintenance of Galaxy.  ... 
doi:10.1109/sc.companion.2012.131 dblp:conf/sc/LiuSMCF12 fatcat:yid45jeyg5adbbapfkrjgzywvq

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

Konstantinos Krampis, Tim Booth, Brad Chapman, Bela Tiwari, Mesude Bicak, Dawn Field, Karen E Nelson
2012 BMC Bioinformatics  
Conclusions: Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud.  ...  Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer.  ...  Acknowledgements We would like to thank all the Cloud BioLinux developers and community members that have volunteered their time on this project. Enis Afgan  ... 
doi:10.1186/1471-2105-13-42 pmid:22429538 pmcid:PMC3372431 fatcat:jt7b6p6wmja3hosaekuejm2e2a

Implementation of Cloud based Next Generation Sequencing data analysis in a clinical laboratory

Getiria Onsongo, Jesse Erdmann, Michael D Spears, John Chilton, Kenneth B Beckman, Adam Hauge, Sophia Yohe, Matthew Schomaker, Matthew Bower, Kevin A T Silverstein, Bharat Thyagarajan
2014 BMC Research Notes  
Findings: To address this challenge, our institution has developed a Galaxy-based data analysis pipeline which relies on a web-based, cloud-computing infrastructure to process NGS data and identify genetic  ...  One such difficulty includes the development of a robust bioinformatics pipeline that can handle the volume of data generated by high-throughput sequencing in a cost-effective manner.  ...  Anne-Francoise Lamblin, the Research Informatics Support Systems (RISS) program director and project lead for Galaxy Bioinformatics workbench, Shawn Houston, manager for Infrastructure Operations and User  ... 
doi:10.1186/1756-0500-7-314 pmid:24885806 pmcid:PMC4036707 fatcat:r5u75d22svf2tamsac7dqogg5q

Approaches for containerized scientific workflows in cloud environments with applications in life science

Ola Spjuth, Marco Capuccini, Matteo Carone, Anders Larsson, Wesley Schaal, Jon Ander Novella, Oliver Stein, Morgan Ekmefjord, Paolo Di Tommaso, Evan Floden, Cedric Notredame, Pablo Moreno (+5 others)
2021 F1000Research  
In this article, we review a number of approaches to using containers as implemented in the workflow tools Nextflow, Galaxy, Pachyderm, Argo, Kubeflow, Luigi and SciPipe, when deployed in cloud environments  ...  Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form  ...  Acknowledgements A previous version of this article is available from: https://doi.org/10.7287/peerj.preprints.27141v1.  ... 
doi:10.12688/f1000research.53698.1 fatcat:qy3gnqbsavcctctanch25ukgie

Selected Approaches and Frameworks to Carry out Genomic Data Analysis on the Cloud

Philip Church, Andrzej Goscinski
2015 Scalable Computing : Practice and Experience  
The current trend exposes applications and data as services, simplifying access to clouds.  ...  This paper examines commonly used cloud-based genomic analysis services, introduces the approach of exposing data as services and proposes two new solutions (HPCaaS and Uncinus) which aim to automate service  ...  and HPC application exposed as services to be executed in a Software as a Service (SaaS) cloud.  ... 
doi:10.12694/scpe.v16i1.1058 fatcat:7snkmbj24ra27m5mhpgrbs4mzq

CloudLaunch: Discover and Deploy Cloud Applications [article]

Enis Afgan, Andrew Lonie, James Taylor, Nuwan Goonasekera
2018 arXiv   pre-print
Here, we present the CloudLaunch application as a uniform platform for discovering and deploying applications for different cloud providers.  ...  Cloud computing is a common platform for delivering software to end users.  ...  A BasePluginComponent exists in the framework that can be used as a base class for providing much of the core functionality.  ... 
arXiv:1805.04005v2 fatcat:ny2oquchaffexlmt4zuedb4sqm
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