ArticlePloS one2015
Genomics Virtual Laboratory: A Practical Bioinformatics Workbench for the Cloud.
Article in PloS one, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
67 citing papers in PubMed.
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- Producing high-quantity and high-quality recombinant adeno-associated virus by low-cis triple transfection.Molecular therapy. Methods & clinical development · 2024Article
- The venom and telopodal defence systems of the centipede Lithobius forficatus are functionally convergent serial homologues.BMC biology · 2024Article
- BTR: a bioinformatics tool recommendation system.Bioinformatics (Oxford, England) · 2024Article
- Short-wavelength-sensitive 1 (Ecology and evolution · 2024Article
- Automated management of AWS instances for training.GigaByte (Hong Kong, China) · 2024Article
- Sex-biased gene and microRNA expression in the developing mouse brain is associated with neurodevelopmental functions and neurological phenotypes.Biology of sex differences · 2023Article
- The Molecular Mechanisms Employed by the ParasiteInternational journal of molecular sciences · 2023Article
- Article
- Long-wavelength-sensitive (lws) opsin gene expression, foraging and visual communication in coral reef fishes.Molecular ecology · 2023Article
- The blood vasculature instructs lymphatic patterning in a SOX7-dependent manner.The EMBO journal · 2023Article
- An in vivo gene amplification system for high level expression in Saccharomyces cerevisiae.Nature communications · 2022Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnalyzing high throughput genomics data is a complex and compute intensive task, generally requiring numerous software tools and large reference data sets, tied together in successive stages of data transformation and visualisation. A computational platform enabling best practice genomics analysis ideally meets a number of requirements, including: a wide range of analysis and visualisation tools, closely linked to large user and reference data sets; workflow platform(s) enabling accessible, reproducible, portable analyses, through a flexible set of interfaces; highly available, scalable computational resources; and flexibility and versatility in the use of these resources to meet demands and expertise of a variety of users. Access to an appropriate computational platform can be a significant barrier to researchers, as establishing such a platform requires a large upfront investment in hardware, experience, and expertise.
resultsWe designed and implemented the Genomics Virtual Laboratory (GVL) as a middleware layer of machine images, cloud management tools, and online services that enable researchers to build arbitrarily sized compute clusters on demand, pre-populated with fully configured bioinformatics tools, reference datasets and workflow and visualisation options. The platform is flexible in that users can conduct analyses through web-based (Galaxy, RStudio, IPython Notebook) or command-line interfaces, and add/remove compute nodes and data resources as required. Best-practice tutorials and protocols provide a path from introductory training to practice. The GVL is available on the OpenStack-based Australian Research Cloud (http://nectar.org.au) and the Amazon Web Services cloud. The principles, implementation and build process are designed to be cloud-agnostic.
conclusionsThis paper provides a blueprint for the design and implementation of a cloud-based Genomics Virtual Laboratory. We discuss scope, design considerations and technical and logistical constraints, and explore the value added to the research community through the suite of services and resources provided by our implementation.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.