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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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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Hydronium and hydroxide ions are present both in pure water and in all aqueous solutions, and their concentrations are inversely proportional as determined by the ion product of water (Kw). The concentrations of these ions in a solution are often critical determinants of the solution’s properties and the chemical behaviors of its other solutes. Two different solutions can differ in their hydronium or hydroxide ion concentrations by a million, billion, or even trillion times. A common means of...
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Diploid organisms inherit genetic material through chromosomes from both parents. Copies of the same gene are known as alleles. In most cases, both alleles are simultaneously expressed and allow various cellular processes to function optimally. If one of the alleles is missing or mutated, the expression of the other allele can compensate; however, this is not true for all genes.
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Genome Size and the Evolution of New Genes03:21

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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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restfulSE: A semantically rich interface for cloud-scale genomics with Bioconductor.

Shweta Gopaulakrishnan1, Samuela Pollack1,2, B J Stubbs1

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Summary

Bioconductor's SummarizedExperiment data model now supports remote storage via the restfulSE package. This enables querying genomic data remotely using familiar tools, improving accessibility for cancer genomics applications.

Keywords:
BigQueryBioconductorBioinformaticsHDF5REST APIs

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Bioconductor's SummarizedExperiment class is a standard for matrix-like biological assay data.
  • It is widely adopted, used by over 200 Bioconductor packages.
  • Current limitations include challenges with remote data access and storage.

Purpose of the Study:

  • To introduce restfulSE, a package enabling remote storage for SummarizedExperiment objects.
  • To demonstrate querying genomic data stored remotely using familiar programmatic interfaces.
  • To facilitate the use of large-scale genomic datasets, particularly in cancer genomics.

Main Methods:

  • Deployment of the SummarizedExperiment data model for remote access.
  • Integration with remote back ends such as HDF5 and Google BigQuery.
  • Development of applications for cancer genomics utilizing remote data querying.

Main Results:

  • Successful implementation of restfulSE for remote SummarizedExperiment data access.
  • Demonstrated utility in cancer genomics applications with remote HDF5 and Google BigQuery back ends.
  • Abstracted remote interfaces, simplifying data access for users and developers.

Conclusions:

  • The restfulSE package extends Bioconductor's SummarizedExperiment class to support remote data storage.
  • This facilitates efficient querying of large genomic datasets, enhancing cancer genomics research.
  • It bridges the gap between local data handling and scalable remote data solutions.