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The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

Enis Afgan, Dannon Baker, Marius van den Beek, Daniel Blankenberg, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Carl Eberhard, Björn Grüning, Aysam Guerler (+8 others)
2016 Nucleic Acids Research  
The Department specifically disclaims responsibility for any analyses, interpretations or conclusions.  ...  These include the members of the Galaxy user and developer communities and organizers of Galaxy Community Conferences. We are indebted to these helpful people.  ...  Finally, Galaxy provides collaborative and transparent analyses by enabling users to share and publish their analyses via the Web.  ... 
doi:10.1093/nar/gkw343 pmid:27137889 pmcid:PMC4987906 fatcat:i2mu7olb3zdtxd4sbzafkyqeku

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update

Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek, Dave Bouvier, Martin Čech, John Chilton, Dave Clements, Nate Coraor, Björn A Grüning, Aysam Guerler, Jennifer Hillman-Jackson (+8 others)
2018 Nucleic Acids Research  
Started in 2005, Galaxy continues to focus on three key challenges of data-driven biomedical science: making analyses accessible to all researchers, ensuring analyses are completely reproducible, and making  ...  Framework and user interface improvements now enable Galaxy to be used for analyzing tens of thousands of datasets, and >5500 tools are now available from the Galaxy ToolShed.  ...  regardless of their informatics expertise and tool developers seeking a wider audience and broad integration of their tools; (b) reproducible analyses regardless of the particular platform and (c) transparent  ... 
doi:10.1093/nar/gky379 pmid:29790989 pmcid:PMC6030816 fatcat:bfp64x6qizahzjj5yoybdkufku

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.  ...  We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.  ...  Acknowledgments The authors would like to thank our colleagues of the ATRAGENE, ISOFT, University Paris Diderot, INTS, CNRS, University Paris Sud, and INSERM for their precious advice on this paper.  ... 
doi:10.1155/2015/904541 pmid:26125026 pmcid:PMC4466500 fatcat:slexkxvpmvcfxfuc5gfrsrp6n4

deepTools2: a next generation web server for deep-sequencing data analysis

Fidel Ramírez, Devon P Ryan, Björn Grüning, Vivek Bhardwaj, Fabian Kilpert, Andreas S Richter, Steffen Heyne, Friederike Dündar, Thomas Manke
2016 Nucleic Acids Research  
We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data.  ...  A public and documented API for access to deepTools functionality is also available.  ...  ACKNOWLEDGEMENTS The authors would like to thank all users of deepTools for their constructive feedback and suggestions.  ... 
doi:10.1093/nar/gkw257 pmid:27079975 pmcid:PMC4987876 fatcat:ahu4m25edvhgjjysfdvtxnnekq

Cloud bursting galaxy: federated identity and access management

2019 Bioinformatics  
However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms.  ...  We have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms.  ...  We have implemented our approach in the Galaxy platform, which is used across the world for large-scale biomedical analyses.  ... 
doi:10.1093/bioinformatics/btz472 pmid:31197310 pmcid:PMC6956780 fatcat:3bfgqrd4efeq7bxbea45cmzitu

PhenoMeNal: Processing and analysis of Metabolomics data in the Cloud [article]

Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Tim Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich Guenther, Evangelos Handakas (+44 others)
2018 bioRxiv   pre-print
The deployed cloud environments can be dynamically scaled to enable large-scale analyses which are interfaced through standard data formats, versioned, and have been tested for reproducibility and interoperability  ...  It provides scientists with a ready-to-use, workflow-driven, reproducible and shareable data analysis platform harmonizing the software installation and configuration through user-friendly web interfaces  ...  Galaxy facilitates collaborative exchange, reproducibility and traceability of data analysis by enabling users to share entire workflows and analysis histories [19] .  ... 
doi:10.1101/409151 fatcat:ix5mbzcubvh7terrapsla3zeo4

Integration of EGA secure data access into Galaxy

Youri Hoogstrate, Chao Zhang, Alexander Senf, Jochem Bijlard, Saskia Hiltemann, David van Enckevort, Susanna Repo, Jaap Heringa, Guido Jenster, Remond J.A. Fijneman, Jan-Willem Boiten, Gerrit A. Meijer (+4 others)
2016 F1000Research  
High-throughput molecular profiling techniques are routinely generating vast amounts of data for translational medicine studies.  ...  Acknowledgements We would like to thank Justin Paschall and Serena Scollen for helpful suggestions and comments.  ...  Jochem Bijlard contributed his work mostly when he was working at the computer science department, Vrije Universiteit Amsterdam.  ... 
doi:10.12688/f1000research.10221.1 pmid:28232859 pmcid:PMC5302147 fatcat:eufkxb7tcrdwnajjdioxfwjlpy

Exchange of Clinical and Omics Data According to FAIR Principles: A Review of Open Source Solutions

Philipp Pugliese, Christian Knell, Jan Christoph
2020 Methods of Information in Medicine  
Due to the specialization of the research platforms and the fact that FAIR are only principles and not standards, the platforms have to be examined in individual cases to see whether and how they can be  ...  Background Due to the ongoing increase and importance of the sustainable reusability of data, the findable, accessible, interoperable, reusable or FAIR principles were developed which are also relevant  ...  The authors thank the contributors of the Base, Ensembl, Galaxy, GenePattern, ISA-Tools, LabKey Server, openBIS, SABIO-RK and SEEK platforms who answered our request for information.  ... 
doi:10.1055/s-0040-1712968 pmid:32620018 fatcat:o2acklthsbbzlclmfs7xyrpsg4

Connecting data, tools and people across Europe: ELIXIR's response to the COVID-19 pandemic

Niklas Blomberg, Katharina B. Lauer
2020 European Journal of Human Genetics  
Providing open tools, workflows and computational resources to drive reproducible and collaborative science.  ...  ELIXIR, the European research infrastructure for life science data, provides open access to data, tools and workflows in the response to the COVID-19 pandemic.  ...  The European Genome-phenome Archive (EGA) is a resource for the secure archival and access to all types of potentially identifiable genetic and phenotypic data resulting from biomedical research projects  ... 
doi:10.1038/s41431-020-0637-5 pmid:32415272 fatcat:46ymefukfnhtplzplvjuawrm2y

MAJIQ-SPEL: Web-Tool To Interrogate Classical And Complex Splicing Variations From RNA-Seq Data [article]

Christopher Green, Matthew R. Gazzara, Yoseph Barash
2017 bioRxiv   pre-print
Using a matching primer design algorithm it also suggests users possible primers for experimental validation by RT-PCR and displays those, along with the matching protein domains affected by the LSV, on  ...  UCSC Genome Browser for further downstream analysis.  ...  The galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update.  ... 
doi:10.1101/136077 fatcat:g6qymezotjfexlth4sg4trgzeq

Using to generate and annotate workbench tool descriptions

Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager
2017 F1000Research  
Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible  ...  The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description.  ...  interoperability and reproducibility.  ... 
doi:10.12688/f1000research.12974.1 pmid:29333231 pmcid:PMC5747335 fatcat:knz3bxbcbjf65haydr53vhz7di

Experiences in integrated data and research object publishing using GigaDB

Scott C Edmunds, Peter Li, Christopher I Hunter, Si Zhe Xiao, Robert L Davidson, Nicole Nogoy, Laurie Goodman
2016 International Journal on Digital Libraries  
Here data analyses can be reproduced and built upon by users without coding backgrounds or heavy computational infrastructure in a more democratized manner.  ...  In the era of computation and data-driven research, traditional methods of disseminating research are no longer fit-for-purpose.  ...  Acknowledgements The authors would like to thank BGI and China National Genebank for supporting GigaScience with seed funding and data, and the BBSRC and NERC for collaboration funding.  ... 
doi:10.1007/s00799-016-0174-6 fatcat:nnjugpp5tfeo3hdmrkq5tnkxuu

3. Reproducible Data Management and AnalysisUsing R [chapter]

Bjørn Fjukstad, Nikita Shvetsov, Therese H. Nøst, Hege Bøvelstad, Till Halbach, Einar Holsbø, Knut Hansen, Lars Ailo Bongo
2020 Advancing Systems Epidemiology in Cancer  
Standardizing and documenting computational analyses is necessary to ensure reproducible results.  ...  We describe an R-based implementation of data management and preprocessing that is well integrated with the analysis tools typically used for statistical analysis of omics data.  ...  ACKNOWLEDGEMENTS The NOWAC study was supported by a grant from the European Research Council (ERC-AdG 232997 TICE). Some of the data in this article are from the Cancer Registry of Norway. The  ... 
doi:10.18261/9788215041193-2020-03 fatcat:scby3z2xhzdjznwo6cfyf5zg7m

Cloud Based Metalearning System for Predictive Modeling of Biomedical Data

Milan Vukićević, Sandro Radovanović, Miloš Milovanović, Miroslav Minović
2014 The Scientific World Journal  
Rapid growth and storage of biomedical data enabled many opportunities for predictive modeling and improvement of healthcare processes.  ...  for analysis of biomedical data.  ...  Acknowledgment This research is partially funded by Grants from the Serbian Ministry of Science and Technological Development, Contract nos. III 41008 and TR 32013. The Scientific World Journal  ... 
doi:10.1155/2014/859279 pmid:24892101 pmcid:PMC4032768 fatcat:pv6bldhbgvakzdyximx5qt45de

Report On Existing Software Tools, Workflows And Analytical Pipelines Initially Supported In The Phenomenal Grid - D9.1

Peters Kristian, Schober Daniel, Neumann, Salek Reza, Moreno, Et Al.
2016 Zenodo  
This deliverable reports several Use Cases and the initially planned architecture to support running them on the PhenoMeNal e-Infrastructure.  ...  "Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences." Genome Biol 11.8 (2010): R86.  ...  Galaxy is a widely used workflow platform that has helped to transform genomics research by massively increasing the accessibility to powerful data analysis tools 1 .  ... 
doi:10.5281/zenodo.153902 fatcat:nams4pl545g5dhbt4sde7ywfcm
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