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Updated: Jul 12, 2025

Author Spotlight: Streamlining Visual Dynamics to Simplify Molecular Dynamics Simulations Using Gromacs
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Hypermedia-based software architecture enables Test-Driven Development.

Andrew R Post1,2, Nancy Ho1, Erik Rasmussen1

  • 1Huntsman Cancer Institute, University of Utah, Salt Lake City, UT 84112, United States.

JAMIA Open
|October 20, 2023
PubMed
Summary
This summary is machine-generated.

This study introduces the Comprehensive Oncology Research Environment (CORE) Browser, an open-source tool for managing cancer sequencing data in the cloud. Its hypermedia architecture and Test-Driven Development (TDD) approach achieved 78% code coverage, enhancing reliable data management.

Keywords:
cloud computingdata managementhigh-throughput nucleotide sequencingsoftware

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Area of Science:

  • Bioinformatics
  • Software Engineering
  • Cloud Computing

Background:

  • Bioinformatic data management is crucial for cancer research.
  • Existing tools often lack user-friendly, reliable cloud-based solutions.
  • Integrating agile software development practices can improve informatics tools.

Purpose of the Study:

  • To develop and evaluate an architecture for self-service bioinformatic data management in the cloud.
  • To create a user-friendly and reliable system for cancer researchers.
  • To leverage agile methodologies for efficient software development and testing.

Main Methods:

  • Developed the Comprehensive Oncology Research Environment (CORE) Browser, an open-source web application.
  • Utilized a microservices and hypermedia-based architecture.
  • Integrated Test-Driven Development (TDD) with parameterized test templates for hypermedia architectures.

Main Results:

  • The CORE Browser backend achieved 78% code coverage.
  • 121 test templates and 875 custom tests were executed 3031 times.
  • Hypermedia architecture facilitated test reuse and efficient development.

Conclusions:

  • A hypermedia approach to architecture significantly enhances testing efficiency and code coverage.
  • Integrating software engineering practices like TDD is vital for successful informatics projects.
  • The CORE Browser offers a stable data management solution, enabling faster advancements in analysis methods.