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Related Concept Videos

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Genomics

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Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...
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The issues and trends in healthcare delivery are constantly changing. The COVID-19 pandemic is one recent issue that wreaked havoc on healthcare systems, causing a shortage of healthcare workers, high demand for medicines and supplies, and increased medical expenditure due to a lack of insurance. Other issues include rising healthcare costs and care fragmentation.
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Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...
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Bionimbus: a cloud for managing, analyzing and sharing large genomics datasets.

Allison P Heath1, Matthew Greenway1, Raymond Powell1

  • 1Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA.

Journal of the American Medical Informatics Association : JAMIA
|January 28, 2014
PubMed
Summary
This summary is machine-generated.

Bionimbus, a cloud platform, simplifies access to large genomics datasets for researchers. It provides essential tools and computational resources for managing and analyzing complex biological data, enhancing research accessibility.

Keywords:
biomedical cloudscloud computinggenomic clouds

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Increasingly large genomics and phenotypic datasets pose challenges for researchers in terms of access, management, and analysis.
  • Cloud-based computing platforms offer a potential solution by providing centralized data and analytical tools.

Purpose of the Study:

  • To introduce Bionimbus as an open-source cloud-computing platform designed to address the challenges of managing and analyzing large-scale genomics data.
  • To demonstrate the utility of Bionimbus for research projects requiring significant computational resources.

Main Methods:

  • Bionimbus utilizes OpenStack for on-demand virtual machines and GlusterFS for high-performance clustered file systems.
  • The platform incorporates Tukey for a unified portal with single sign-on access and Yates for automated infrastructure management.

Main Results:

  • Bionimbus supports various projects, including an acute myeloid leukemia resequencing project, by processing genomics and phenotypic data.
  • Specific computational pipelines for quality control, alignment, variant calling, and annotation are utilized.
  • Data analysis involves substantial computational resources, with alignment steps requiring eight CPUs for approximately 12 hours per sample, generating large BAM files.

Conclusions:

  • Researchers face difficulties in downloading and managing large genomics datasets due to storage and computational limitations.
  • Cloud computing platforms like Bionimbus, equipped with data commons, are a viable option for democratizing access to genomics research data.