A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Filters
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update
2018
Nucleic Acids Research
Preserved Fulltext
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
2020
Nucleic Acids Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
Scientific Data
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
PLoS ONE
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2018; you can also visit the original URL.
The file type is application/pdf.
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
2020
GigaScience
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
GigaScience
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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
2018
PLoS Computational Biology
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2018
bioRxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
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
2018
Scientific Reports
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2020; you can also visit the original URL.
The file type is application/pdf.
; (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]
2018
biorxiv/medrxiv
pre-print
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
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]
2020
Advancing Systems Epidemiology in Cancer
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
2021
F1000Research
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2022; you can also visit the original URL.
The file type is application/pdf.
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
2020
JAMIA Journal of the American Medical Informatics Association
Preserved Fulltext
A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2021; you can also visit the original URL.
The file type is application/pdf.
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
« Previous
Showing results 1 — 15 out of 254 results