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BioBlend: automating pipeline analyses within Galaxy and CloudMan

C. Sloggett, N. Goonasekera, E. Afgan
2013 Bioinformatics  
infrastructure, and automate complex analyses over large data sets within the familiar Galaxy environment.  ...  We present BioBlend, a unified API in a high-level language (python) that wraps the functionality of Galaxy and CloudMan APIs.  ...  ACKNOWLEDGEMENTS Galaxy, CloudMan, and BioBlend have been developed by the Galaxy (http://wiki.galaxyproject.org/GalaxyTeam) and LSCC teams (http://www.vlsci.org.au/page/lscc).  ... 
doi:10.1093/bioinformatics/btt199 pmid:23630176 pmcid:PMC4288140 fatcat:wzs5buyyrjd57pr5txrx3pwa7i

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)  
Unlike newly developed web applications that can be designed from the ground up to utilize cloud APIs and run natively within cloud infrastructure, most complex bioinformatics pipelines that are in advanced  ...  states of development can only be encapsulated within VMs along with all their software and data dependencies.  ...  ACKNOWLEDGMENTS The efforts of the Galaxy Team (Dan Blankenberg, Dave Bouvier, Martin Cech, Dave Clements, Carl Eberhard, Jeremy Goecks, Nitesh Turaga, Sam Guerler, Jennifer Jackson and Anton Nekrutenko  ... 
doi:10.1109/mipro.2015.7160269 dblp:conf/mipro/AfganKGST15 fatcat:grslkqjyt5glhpbuefpefwdr7u

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  
Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses.  ...  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  ...  Within the last seven years Galaxy gained the ability to launch on AWS through the CloudMan Launcher Galaxy sub-project. 25 This initial setup followed a relative VM centric approach, which has natural  ... 
doi:10.12688/f1000research.53698.1 fatcat:qy3gnqbsavcctctanch25ukgie

Trends in IT Innovation to Build a Next Generation Bioinformatics Solution to Manage and Analyse Biological Big Data Produced by NGS Technologies

Alexandre G. de Brevern, Jean-Philippe Meyniel, Cécile Fairhead, Cécile Neuvéglise, Alain Malpertuy
2015 BioMed Research International  
In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats.  ...  This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools.  ...  Medical Research (INSERM, France) and labex GR-Ex to AdB, University Paris Sud and CNRS to CF, INRA, and AgroParisTech to CE, ISOFT to Jean-Philippe Meyniel, and ATRAGENE to Alain Malpertuy.  ... 
doi:10.1155/2015/904541 pmid:26125026 pmcid:PMC4466500 fatcat:slexkxvpmvcfxfuc5gfrsrp6n4

Referee report. For: Approaches for containerized scientific workflows in cloud environments with applications in life science [version 1; peer review: 2 not approved]

Roberto Vera Alvarez
2022
Scientific workflows are ideal for chaining containers into data analysis pipelines to aid in creating reproducible analyses.  ...  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  ...  Within the last seven years Galaxy gained the ability to launch on AWS through the CloudMan Launcher Galaxy sub-project. 25 his initial setup followed a relative VM centric approach, which has natural  ... 
doi:10.5256/f1000research.57113.r136766 fatcat:ko5yz6rlbbforlgclq25apbzle