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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

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update

Galaxy Community
2022
Key Galaxy technical developments include an improved user interface for launching large-scale analyses with many files, interactive tools for exploratory data analysis, and a complete suite of machine  ...  Galaxy is a mature, browser accessible workbench for scientific computing. It enables scientists to share, analyze and visualize their own data, with minimal technical impediments.  ...  ACKNOWLEDGEMENTS The growth of the Galaxy project is made possible by a growing community of world-wide users, developers, system administrators, and educators.  ... 
doi:10.1093/nar/gkac247 pmid:35446428 fatcat:plesvbnagrfyhkgstrsvys3hw4

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols

Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen (+6 others)
2021 Nucleic Acids Research  
The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational  ...  resources, thereby promoting the reproducibility of complex bioinformatics analyses.  ...  Nextflow and galaxy support Recently, Dockstore has added support for the Nextflow (16) and Galaxy (17) workflow languages.  ... 
doi:10.1093/nar/gkab346 pmid:33978761 fatcat:zwvges37mva2hfc4aaa4w5dkyy

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

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

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service

Marco Antonio Tangaro, Pietro Mandreoli, Matteo Chiara, Giacinto Donvito, Marica Antonacci, Antonio Parisi, Angelica Bianco, Angelo Romano, Daniela Manila Bianchi, Davide Cangelosi, Paolo Uva, Ivan Molineris (+9 others)
2021 BMC Bioinformatics  
By facilitating the set-up and configuration of Galaxy web servers, Laniakea provides researchers with a powerful and highly customisable platform for executing complex bioinformatics analyses.  ...  In 2020 we introduced Laniakea, a software platform conceived to streamline the configuration and deployment of "on-demand" Galaxy instances over the cloud.  ...  Acknowledgements The authors thank ELIXIR-Italy and ReCaS-Bari for providing the computing and bioinformatics facilities.  ... 
doi:10.1186/s12859-021-04401-3 pmid:34749633 pmcid:PMC8574934 fatcat:jszcn3pt4zdxxddlhw7qm5d3su

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

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

EOSC-Life Report on the work of the initial demonstrators

Frauke Leitner, Jose Maria Carazo, Johanna Bischof, Natalie Haley, Pauline Audergon, Carlos Oscar Sorzano, Laura del Cano, Pablo Conesa, Cymon J. Cox, Gianluca De Moro, Corre Erwan, Katrina Exter (+32 others)
2021 Zenodo  
work done in EOSC-Life to build an open digital and collaborative space for biological and medical research.  ...  valuable resources (databases, workflows, web platform...), the actions undertaken within EOSC-Life to disseminate the demonstrator achievement and finally the results of the demonstrator survey to learn  ...  This project has received funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 824087.  ... 
doi:10.5281/zenodo.4817722 fatcat:r4rso6bxcrdfdon7iaznxaql6i

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

Life Science in EOSC: Summary of EOSC-Life impact and key results

Niklas Blomberg, Friederike Schmidt-Tremmel, Caitlin Ahern
2021 Zenodo  
Access to data and cloud services will be underpinned by a shared federated authentication and authorisation infrastructure (Life Science AAI) including step-up security for controlled data access.  ...  Existing solutions and requirements have been documented and form the basis of the continually developed "Sensitive data toolkit" for the LS RI and their users.  ...  EOSC-Life provides access and support to cloud resources for the life science community and offers deployable platforms for workflows.  ... 
doi:10.5281/zenodo.5179992 fatcat:dver6ogjanbaplihmhuzwdf6pe

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

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

EOSC-Life EOSC Cloud feasibility assessment for Demonstrators

Philip Gribbon, Helen Parkinson, Gesa Witt
2020 Zenodo  
EOSC-Life involves multiple complex cloud deployments of life sciences data, analyses and services for biomedical research users and infrastructures.  ...  A cloud deployment training event (with WP7) and a hackathon event to bring together the WP1 Data experts and Demonstrator teams was then organised to raise the overall technical capability and capacities  ...  Executive Summary EOSC-Life involves multiple complex cloud deployments of life sciences data, analyses and services for biomedical research users and infrastructures.  ... 
doi:10.5281/zenodo.4010371 fatcat:sa5fgbbhnje6xnk6txvn3jy44m

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

Marco Antonio Tangaro, Giacinto Donvito, Marica Antonacci, Matteo Chiara, Pietro Mandreoli, Graziano Pesole, Federico Zambelli
2020 GigaScience  
Finally, the implementation of Laniakea can be easily adapted and expanded to support different services and platforms beyond Galaxy.  ...  At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance and to the underlying virtual machine (VM  ...  Acknowledgements This work has been supported by the European Commission H2020 research and innovation program under grant agreements with ID 653549 and 857650. We  ... 
doi:10.1093/gigascience/giaa033 pmid:32252069 fatcat:jel5cyph2bbt7k7wogxtmopkum
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