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.
Filters
Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service
2021
BMC Bioinformatics
Preserved Fulltext
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. ...
The system can be accessed through a dedicated and user-friendly web interface that allows the Galaxy web server's initial configuration and deployment. ...
We are grateful to BIOGEN biobank-a member of the Telethon Network of Genetic Biobanks (Project No. GTB12001), funded by Telethon Italywhich provided the biological samples for Use Case 8. ...
doi:10.1186/s12859-021-04401-3
pmid:34749633
pmcid:PMC8574934
fatcat:jszcn3pt4zdxxddlhw7qm5d3su
Reproducible Data Analysis Pipelines for Precision Medicine
[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.
Technologies such as high-throughput sequencing enable cheaper data collection at higher speed, but rely on modern data analysis platforms to extract knowledge from these high dimensional datasets. ...
Precision medicine brings the promise of more precise diagnosis and individual-zed therapeutic strategies from analyzing a cancer's genomic signature. ...
Acknowledgements We would like to thank Daniel Del Balso for his work implementing the initial WGS analysis pipeline. ...
doi:10.1101/354811
fatcat:tvg7stc3lvd4fczdi77gveue24
Experiences building Globus Genomics: a next-generation sequencing analysis service using Galaxy, Globus, and Amazon Web Services
2014
Concurrency and Computation
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 2015; you can also visit the original URL.
The file type is application/pdf.
We describe Globus Genomics, a system that we have developed for rapid analysis of large quantities of next-generation sequencing (NGS) genomic data. ...
This system achieves a high degree of end-to-end automation that encompasses every stage of data analysis including initial data retrieval from remote sequencing centers or storage (via the Globus file ...
., for an award of Amazon Web Services time that facilitated early experiments. We thank Globus Genomics users for their invaluable contributions. ...
doi:10.1002/cpe.3274
pmid:25342933
pmcid:PMC4203657
fatcat:glcie6spdzdllakjibkyniqo5y
High-Performance Integrated Virtual Environment (HIVE) Tools and Applications for Big Data Analysis
2014
Genes
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 High-performance Integrated Virtual Environment (HIVE) is a high-throughput cloud-based infrastructure developed for the storage and analysis of genomic and associated biological data. ...
HIVE consists of a web-accessible interface for authorized users to deposit, retrieve, share, annotate, compute and visualize Next-generation Sequencing (NGS) data in a scalable and highly efficient fashion ...
Acknowledgements We would like to acknowledge the following people for providing feedback and HIVE support: ...
doi:10.3390/genes5040957
pmid:25271953
pmcid:PMC4276921
fatcat:fpkwi7qj6bhkxp6y3k2nxv2lre
Cloud Computing for Next-Generation Sequencing Data Analysis
[chapter]
2017
Cloud Computing - Architecture and Applications
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.
share the lessons we learned from the implementation of Rainbow, a cloud-based tool for large-scale genome sequencing data analysis. ...
High-throughput next-generation sequencing (NGS) technologies have evolved rapidly and are reshaping the scope of genomics research. ...
Galaxy Cloud [57] , a cloudbased Galaxy platform for the analysis of data at a large scale, is the most used platform for bioinformatics. ...
doi:10.5772/66732
fatcat:2ewdbtp2bjhx7j7tj4e3auwqke
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
2019
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 2020; you can also visit the original URL.
The file type is application/pdf.
The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. ...
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). ...
For post-genomic analyses, there is a workshop on the analysis, visualization and integration of multi-level -omics data, which introduces the web-based platform Omics-Fusion 17 . ...
doi:10.12688/f1000research.20244.1
pmid:33163154
pmcid:PMC7607484
fatcat:g4gztfjahrbkdepxw6rgkjfhjy
Selected Approaches and Frameworks to Carry out Genomic Data Analysis on the Cloud
2015
Scalable Computing : Practice and Experience
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 2015; you can also visit the original URL.
The file type is application/pdf.
While High Performance Computing clouds allow researchers to process large amounts of genomic data, complex resource and software configuration tasks must be carried out beforehand. ...
This paper examines commonly used cloud-based genomic analysis services, introduces the approach of exposing data as services and proposes two new solutions (HPCaaS and Uncinus) which aim to automate service ...
obtained from a IaaS cloud, and (iii) the Galaxy software application used as a web-based platform for exposing and accessing HPC application services. ...
doi:10.12694/scpe.v16i1.1058
fatcat:7snkmbj24ra27m5mhpgrbs4mzq
Will digital pathology be as disruptive as genomics?
2018
Journal of Pathology Informatics
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.
Acknowledgments The author would like to thank the Mayo Clinic Center for Individualized Medicine and Department of Laboratory Medicine and Pathology for funding this work. ...
Lessons Learned from GenomIcs that Inform dIGItaL PathoLoGy Growth There are at least five significant "lessons learned" during the growth of genomics that are well suited to be transferred to digital ...
Many of the lessons learned from genomics can, therefore, be applied.
the cost of data The significant expense can be invested to generate digital data from genomics and digital pathology. ...
doi:10.4103/jpi.jpi_25_18
pmid:30167342
pmcid:PMC6106127
fatcat:n2jzal2vvvdapbcpzlz6c4t3jm
Experiences with workflows for automating data-intensive bioinformatics
2015
Biology Direct
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 2017; you can also visit the original URL.
The file type is application/pdf.
High-throughput technologies, such as next-generation sequencing, have turned molecular biology into a data-intensive discipline, requiring bioinformaticians to use high-performance computing resources ...
Based on our experiences we define a set of recommendations for future systems to enable efficient yet simple bioinformatics workflow construction and execution. ...
MK and OK were supported by National Science Fund of Bulgaria within the "Methods for Data Analysis and Knowledge Discovery in Big Sequencing Dataset" project under contract DFNI02/7 of 12.12.2014. ...
doi:10.1186/s13062-015-0071-8
pmid:26282399
pmcid:PMC4539931
fatcat:cxotvdjwrndblm7gvu5myegsrq
Bioexcel Deliverable 2.1 – State Of The Art And Gap Analysis
2016
Zenodo
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.
Based o [...] ...
Finally, we realized that a high number of users would be interested in using remote tools, although several concerns have been raised about this, namely data privacy, reliability, and lack of control. ...
Galaxy Galaxy is an open, web-based platform for data intensive biomedical research. Galaxy can be accessed on a free public server http://usegalaxy.org/, or installed locally in the lab. ...
doi:10.5281/zenodo.263963
fatcat:o2v7ogjmnbauhn7txp2buz3pem
The de.NBI / ELIXIR-DE training platform - Bioinformatics training in Germany and across Europe within ELIXIR
2020
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 2020; you can also visit the original URL.
The file type is application/pdf.
The network provides a high-quality, coherent, timely, and impactful training program across its eight service centers. ...
The German Network for Bioinformatics Infrastructure (de.NBI) is a national and academic infrastructure funded by the German Federal Ministry of Education and Research (BMBF). ...
For post-genomic analyses, there is a workshop on the analysis, visualization and integration of multi-level -omics data, which introduces the web-based platform Omics-Fusion 20 . ...
doi:10.12688/f1000research.20244.2
fatcat:io4rgsengvddhlhwjgpqv5livu
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
2019
Genome 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.
We review recent data challenges with innovative approaches to model reproducibility and data sharing, and outline key lessons for improving quantitative biomedical data analysis through crowd-sourced ...
Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. ...
Solutions that involve a single lab distributing a package of tools and documentation for running on a single dataset or running a low throughput web server will not scale. ...
doi:10.1186/s13059-019-1794-0
pmid:31506093
pmcid:PMC6737594
fatcat:njzmseerufcghihkoiskuqq6km
Reproducible biomedical benchmarking in the cloud: lessons from crowd-sourced data challenges
2019
Genome 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 2021; you can also visit the original URL.
The file type is application/pdf.
We review recent data challenges with innovative approaches to model reproducibility and data sharing, and outline key lessons for improving quantitative biomedical data analysis through crowdsourced benchmarking ...
Challenges are achieving broad acceptance for addressing many biomedical questions and enabling tool assessment. ...
Solutions that involve a single lab distributing a package of tools and documentation for running on a single dataset or running a low throughput web server will not scale. ...
doi:10.18154/rwth-conv-241869
fatcat:hjaabhhqvfel7denahvnxab75i
Deliverable JIP1-2.8 - Status report on OH Knowledge Base - NGS
2021
Zenodo
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.
The web platform uses Galaxy as its workflow engine, and thus uses Galaxy for managing pipelines and sequencing tools. ...
These were the INNUENDO and the IRIDA systems, which seemed to be functional, active, up-to-date platforms which could manage and analyze high throughput microbial genomics data combined with visualization ...
A continuous analysis and comparison of the human-food isolates were done and the genome sequences from food/animas were send to SSI for analysis. ...
doi:10.5281/zenodo.5062329
fatcat:mca5ix3ojzewzd5gyyq7g6gm5a
Incorporating computational resources in a cancer research program
2014
Human Genetics
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.
Here, we discuss the lessons learned in our laboratory and share several recommendations to make this transition effectively. ...
However, a significant effort is required to adapt a molecular biology-based research program to take advantage of these datasets. ...
Acknowledgments Work in the Monteiro Lab is funded by NIH awards U19 CA148112 (GAME-ON consortium), U01 CA116167, R21 CA184996 (to N.W.) and by awards from the Moffitt Foundation. ...
doi:10.1007/s00439-014-1496-3
pmid:25324189
pmcid:PMC4401625
fatcat:gkrgo3kbsnag3hadp67q3pzqcq
« Previous
Showing results 1 — 15 out of 143 results