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Related Concept Videos

Genomics02:02

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 brain processes sensory information rapidly due to parallel processing, which involves sending data across multiple neural pathways at the same time. This method allows the brain to manage various sensory qualities, such as shapes, colors, movements, and locations, all concurrently. For instance, when observing a forest landscape, the brain simultaneously processes the movement of leaves, the shapes of trees, the depth between them, and the various shades of green. This enables a quick and...
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Evolutionary Relationships through Genome Comparisons02:54

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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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The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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Teaching computational genomics and bioinformatics on a high performance computing cluster-a primer.

Arun Sethuraman1

  • 1Department of Biology, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182, USA.

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|December 23, 2022
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Summary
This summary is machine-generated.

This course successfully trained students in computational genomics using high-performance computing (HPC) resources. The curriculum covered essential bioinformatics analyses, making advanced genomics accessible for educational purposes.

Keywords:
HPCbioinformaticscurriculumgenomics

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Area of Science:

  • Genomics and Bioinformatics
  • Computational Biology
  • Educational Technology

Background:

  • Genomics applications in medicine, agriculture, and conservation face high computational costs.
  • University classroom settings often lack access to necessary high-performance computing (HPC) resources for genomics training.
  • Increasing availability of cloud-based HPC resources presents opportunities for accessible genomics education.

Purpose of the Study:

  • To describe the successful implementation of a computational genomics and bioinformatics course.
  • To train upper-division undergraduate and graduate students in HPC-based genomics data analysis.
  • To provide accessible, hands-on experience with advanced bioinformatics tools and techniques.

Main Methods:

  • A 16-week upper-division undergraduate/graduate course in Computational Genomics and Bioinformatics was taught.
  • Students utilized dedicated 6-CPU NSF XSEDE Jetstream virtual machines for analyses.
  • The curriculum included theoretical and practical training in various genomics analyses.

Main Results:

  • Students gained hands-on experience in genomic data quality control, assembly, annotation, and variant calling.
  • Training encompassed phylogenomic analyses, population genomics, and genome-wide association studies.
  • Differential gene expression analysis using RNAseq data was also covered.

Conclusions:

  • The course successfully demonstrated the utility of HPC resources for genomics education.
  • Students acquired practical skills in a wide range of computational genomics analyses.
  • All course materials, including code and tutorials, are publicly available for broader educational use.