Design and implementation of a hybrid cloud system for large-scale human genomic research

Nagasaki, Masao; Sekiya, Yayoi; Asakura, Akihiro; Teraoka, Ryo; Otokozawa, Ryoko; Hashimoto, H.; Kawaguchi, Takahisa; Fukazawa, Keiichiro; Inadomi, Yuichi; Murata, Ken T.; Ohkawa, Yasuyuki; Yamaguchi, Izumi; Mizuhara, Takamichi; Tokunaga, Katsushi; Sekiya, Yuji; Hanawa, Toshihiro; Yamada, Ryo; Matsuda, Fumihiko

doi:10.1038/s41439-023-00231-2

Cited by 5 publications

(2 citation statements)

References 33 publications

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“…The supercomputers allowed researchers to process vast amounts of genomic data quickly and accurately. They employed advanced algorithms and machine learning techniques to identify specific genetic variations that could impact the virus's transmissibility or virulence [49]. The findings provided valuable insights into the genetic diversity of SARS-CoV-2 and its potential implications for public health measures [50].…”

Section: Genome Sequencingmentioning

confidence: 99%

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

Mustafa,

Makhawi

2023

Preprint

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The COVID-19 pandemic has unveiled the critical role that supercomputers play in addressing global health crises. This perspective article explores the transformative impact of supercomputing in pandemic response, highlighting how these powerful machines have transitioned from crisis management tools to essential components of preparedness strategies. In this article, we examine the key contributions of supercomputers in combating the pandemic, including their ability to accelerate scientific research, facilitate data analysis, model complex scenarios, and optimize resource allocation. Furthermore, we delve into the role of supercomputing in strengthening public health infrastructure and preparedness. We analyze the lessons learned from the pandemic and emphasize the need for proactive investment in supercomputing capabilities, data infrastructure, and computational expertise as a crucial element of pandemic preparedness efforts. By harnessing the potential of supercomputers, countries can establish robust computational frameworks that enable real-time monitoring, early detection, and effective response to future outbreaks. Moreover, we address the challenges faced by supercomputing initiatives, including the need for enhanced international collaboration, equitable access to computing resources, and the ethical considerations associated with data privacy and security. We discuss potential strategies to overcome these challenges and foster a global network of interconnected supercomputing centers dedicated to pandemic preparedness and response. Finally, we highlight ongoing research and development efforts aimed at advancing supercomputing technologies, such as exascale computing and quantum computing, and their potential to revolutionize pandemic response. We emphasize the importance of sustained investment in research and development to ensure that supercomputing remains at the forefront of future pandemic preparedness strategies.

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Section: Genome Sequencingmentioning

confidence: 99%

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

Mustafa,

Makhawi

2023

Preprint

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“…These services provide researchers with access to a larger pool of compute resources that are available within many institution-based clusters, as well as storage and sharing capacity for large genomic datasets (Langmead & Nallore 2018). Cloud-based toolsets have now been developed for automating components of genomics data analysis and processing (Nagasaki et al 2023), single cell sequencing (Li et al 2020) and proteomics (Muth et al 2023), among many other bioinformatics tasks.…”

Section: Introductionmentioning

confidence: 99%

Maloja: simple and scalable Snakemake workflow orchestration in the cloud

Giustizia,

Hodgson,

Andress

et al. 2024

Preprint

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As sequencing technologies have matured, bioinformatics tasks have become more complex, computationally demanding, and data intensive. Workflow management software has been developed to aid in simplifying the replicable chaining of complex bioinformatics jobs, and cloud computing has emerged as a potential solution to the computational demands of this work. However, the capacity to effectively deploy these resources is limited by the expertise required to implement these solutions. Here, we develop Maloja, an easily deployed cloud workflow orchestrator. This tool interprets existing scientific workflows written in Snakemake and deploys them in appropriately scaled AWS cloud resources. We test the utility of this new toolset using previously published and custom built Snakemake workflows for ecological genomics tasks, revealing how this tool can facilitate the use of cloud resources without prior cloud architecture expertise.

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A comprehensive review and conceptual framework for cloud computing adoption in bioinformatics

Banimfreg

2023

Healthcare Analytics

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Design and implementation of a hybrid cloud system for large-scale human genomic research

Cited by 5 publications

References 33 publications

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

<strong></strong>Supercomputers at the Forefront: From Crisis to Preparedness in Pandemic Response

Maloja: simple and scalable Snakemake workflow orchestration in the cloud

A comprehensive review and conceptual framework for cloud computing adoption in bioinformatics

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