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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

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update

Vahid Jalili, Enis Afgan, Qiang Gu, Dave Clements, Daniel Blankenberg, Jeremy Goecks, James Taylor, Anton Nekrutenko
2020 Nucleic Acids Research  
Since 2005, the Galaxy project has fostered a global community focused on achieving accessible, reproducible, and collaborative research.  ...  and publishes analyses using Galaxy, leads bioinformatics workshops that introduce and use Galaxy, and develops interactive training materials for Galaxy.  ...  We are extremely grateful to the Texas Advanced Computing Center at the University of Texas for hosting the Public Galaxy site.  ... 
doi:10.1093/nar/gkaa434 pmid:32479607 pmcid:PMC7319590 fatcat:ykgnlubu7jhwlapfinzuxczkxq

Datasets2Tools, repository and search engine for bioinformatics datasets, tools and canned analyses

Denis Torre, Patrycja Krawczuk, Kathleen M. Jagodnik, Alexander Lachmann, Zichen Wang, Lily Wang, Maxim V. Kuleshov, Avi Ma'ayan
2018 Scientific Data  
Acknowledgements This work is partially supported by the National Institutes of Health (NIH) grants U54HL127624, U54CA189201, and OT3OD025467 to AM.  ...  In addition to this, platforms such as Galaxy 10 provide interfaces that allow users to easily create complex bioinformatics workflows and pipelines that can be collaboratively shared on the web.  ...  At the same time, published analyses from print publications are often difficult to find, access, and reproduce.  ... 
doi:10.1038/sdata.2018.23 pmid:29485625 pmcid:PMC5827688 fatcat:p5aac5qv3zcfdjc5xbhxjb4lsq

qPortal: A platform for data-driven biomedical research

Christopher Mohr, Andreas Friedrich, David Wojnar, Erhan Kenar, Aydin Can Polatkan, Marius Cosmin Codrea, Stefan Czemmel, Oliver Kohlbacher, Sven Nahnsen, Frederique Lisacek
2018 PLoS ONE  
Application of both systems to a small case study shows the differences between a data-driven approach (qPortal) and a workflow-driven approach (Galaxy). qPortal, a one-stop-shop solution for biomedical  ...  We compare our approach to Galaxy, one of the most widely used scientific workflow and analysis platforms in computational biology.  ...  The authors thank the openBIS Helpdesk for their fast and insightful answers regarding our questions.  ... 
doi:10.1371/journal.pone.0191603 pmid:29352322 pmcid:PMC5774839 fatcat:krsc5gog2be7nc4qxb7ddyld3u

Recommendations to enhance rigor and reproducibility in biomedical research

Jaqueline J Brito, Jun Li, Jason H Moore, Casey S Greene, Nicole A Nogoy, Lana X Garmire, Serghei Mangul
2020 GigaScience  
Biomedical research depends increasingly on computational tools, but mechanisms ensuring open data, open software, and reproducibility are variably enforced by academic institutions, funders, and publishers  ...  We provide 8 recommendations to improve reproducibility, transparency, and rigor in computational biology—precisely the values that should be emphasized in life science curricula.  ...  Lana Martin for helping with the design of Fig. 1 and constructive discussions and comments on the manuscript.  ... 
doi:10.1093/gigascience/giaa056 pmid:32479592 pmcid:PMC7263079 fatcat:pkaywcozivd6xirlx4nyyaznby

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

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

Kristian Peters, James Bradbury, Sven Bergmann, Marco Capuccini, Marta Cascante, Pedro de Atauri, Timothy M D Ebbels, Carles Foguet, Robert Glen, Alejandra Gonzalez-Beltran, Ulrich L Günther, Evangelos Handakas (+44 others)
2018 GigaScience  
The research field is dynamic and expanding with applications across biomedical, biotechnological, and many other applied biological domains.  ...  Its computationally intensive nature has driven requirements for open data formats, data repositories, and data analysis tools.  ...  Galaxy facilitates collaborative exchange, reproducibility, and traceability of data analysis by enabling users to share entire workflows and analysis histories [24] .  ... 
doi:10.1093/gigascience/giy149 pmid:30535405 pmcid:PMC6377398 fatcat:srtrsdrzd5bitjztymyqy4nypy

Cloud computing applications for biomedical science: A perspective

Vivek Navale, Philip E. Bourne, Francis Ouellette
2018 PLoS Computational Biology  
Cloud computing offers users pay-as-you-go access to services such as hardware infrastructure, platforms, and software for solving common biomedical computational problems.  ...  As such, cloud services are engineered to address big data problems and enhance the likelihood of data and analytics sharing, reproducibility, and reuse.  ...  Andrea Norris, Director, Center for Information Technology; and Dr. Vivien Bonazzi, Office of Director, National Institutes of Health.  ... 
doi:10.1371/journal.pcbi.1006144 pmid:29902176 pmcid:PMC6002019 fatcat:wfvdmkpytnbfbih27knmldrcyy

Cloud Bursting Galaxy: Federated Identity and Access Management [article]

Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks
2018 bioRxiv   pre-print
However, one challenge for large-scale biomedical data on the cloud is providing secure access, especially when datasets are distributed across platforms.  ...  have developed a generic and extensible approach for securely accessing biomedical datasets distributed across cloud computing platforms.  ...  Funding This work was supported by the National Institutes of Health [HG006620 and CA231877], the National Science Foundation [DBI 1661497]; and Oregon Health and Science University.  ... 
doi:10.1101/506238 fatcat:mxq6ie4flfambferdv223757ty

DNAp: A Pipeline for DNA-seq Data Analysis

Jason L. Causey, Cody Ashby, Karl Walker, Zhiping Paul Wang, Mary Yang, Yuanfang Guan, Jason H. Moore, Xiuzhen Huang
2018 Scientific Reports  
; (ii) it needs access to High-performance computing resources; (iii) the analysis needs to be consistent and be able to reproduce the results to facilitate comparisons as well as downstream analysis.  ...  It is also open, and can be easily customized with user intervention points, such as for updating reference files and different software or versions.  ...  However the information contained herein represents the position of the authors and not necessarily that of the FDA.  ... 
doi:10.1038/s41598-018-25022-6 pmid:29717215 pmcid:PMC5931599 fatcat:dxtmztlnefdbjbqznmvwj74cgi

Laniakea: an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures [article]

Marco Antonio Tangaro, Giacinto Donvito, Marica Antonacci, Matteo Chiara, Pietro Mandreoli, Graziano Pesole, Federico Zambelli
2018 biorxiv/medrxiv   pre-print
at the same time improving reproducibility and facilitating teamwork and data sharing among researchers.  ...  a "Galaxy on demand" Platform as a Service (PaaS).  ...  Acknowledgements 12 This work has been supported by the European Commission H2020 research and innovation program under grant 13 agreement RIA 653549. 14  ... 
doi:10.1101/472464 fatcat:7bwcxd23lveatajvdw46wkkmeu

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

BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference

Nomi L. Harris, Peter J. A. Cock, Christopher J. Fields, Karsten Hokamp, Jessica Maia, Monica Munoz-Torres, Malvika Sharan, Jason Williams
2021 F1000Research  
In 2020, BOSC partnered with the Galaxy Community Conference to form the Bioinformatics Community Conference (BCC2020); that was the first BOSC to be held online.  ...  The 22nd annual Bioinformatics Open Source Conference (BOSC 2021, open-bio.org/events/bosc-2021/) was held online as a track of the 2021 Intelligent Systems for Molecular Biology / European Conference  ...  Acknowledgements We are grateful to all those who helped make BOSC 2021 a success: the organizers, reviewers, volunteers, presenters, attendees, and the generous sponsors who enabled us to offset some  ... 
doi:10.12688/f1000research.74074.1 pmid:34721839 pmcid:PMC8524300 fatcat:metqcponazbl7cauyupds5t5yy

Can reproducibility be improved in clinical natural language processing? A study of 7 clinical NLP suites

William Digan, Aurélie Névéol, Antoine Neuraz, Maxime Wack, David Baudoin, Anita Burgun, Bastien Rance
2020 JAMIA Journal of the American Medical Informatics Association  
NLP frameworks could benefit from lessons learned from the bioinformatics field (eg, public repositories of curated tools and workflows or use of containers for shareability) to enhance the reproducibility  ...  To evaluate if WMS and other bioinformatics practices could impact the reproducibility of clinical NLP frameworks.  ...  GATE Teamware is a web-based collaborative annotation platform. GATE Mimir and GATE Cloud are designed to perform scalable and parallel analysis.  ... 
doi:10.1093/jamia/ocaa261 pmid:33319904 pmcid:PMC7936396 fatcat:63l3hlzuvnar5nbhdeqowck6t4
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