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Building a Science Gateway For Processing and Modeling Sequencing Data Via Apache Airavata.

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High-performance computing (HPC) resources can process large DNA sequencing datasets. A new web gateway simplifies using these powerful tools for genome biologists, making complex analysis accessible without specialized expertise.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Exponential growth in DNA sequencing data necessitates advanced computational resources.
  • Desktop platforms struggle with the scale of modern genomic data processing.
  • High-performance computing (HPC) offers solutions but requires specialized user expertise.

Purpose of the Study:

  • To develop a user-friendly web-based platform for genome biologists to access HPC resources.
  • To create a gateway for the dREG algorithm, facilitating analysis of mammalian genomes.
  • To enable biologists to perform compute-intensive tasks without needing HPC expertise.

Main Methods:

  • Customized the PHP Gateway for Airavata (PGA) framework to create a web computing platform.
  • Leveraged Extreme Science and Engineering Discovery Environment (XSEDE) for CPU, GPU, and storage resources.
  • Integrated the dREG algorithm into the platform for analyzing nascent RNA sequencing data.

Main Results:

  • Developed a web gateway (dREG gateway) for analyzing functional regions in mammalian genomes.
  • Provided biologists with free, user-friendly access to powerful GPU computing resources via XSEDE.
  • Circumvented the need for specialized knowledge in HPC installation, configuration, and execution.

Conclusions:

  • The dREG gateway democratizes access to advanced computational genomics tools for biologists.
  • Web gateways simplify the use of HPC resources, accelerating genomic data analysis.
  • This platform enhances research capabilities by providing accessible, powerful computing for genomic studies.