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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq
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A toolbox for developing bioinformatics software.

Kristian Rother1, Wojciech Potrzebowski, Tomasz Puton

  • 1Laboratory of Structural Bioinformatics, Institute of Molecular Biology and Biotechnology, Collegium Biologicum, Adam Mickiewicz University, ul. Umultowska 89, 61-614 Poznan, Poland. krother@genesilico.pl

Briefings in Bioinformatics
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Summary
This summary is machine-generated.

This study presents 12 practical software engineering techniques for academic bioinformatics projects. These methods improve project planning, collaboration, and the quality and maintainability of scientific software.

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Area of Science:

  • Bioinformatics
  • Scientific Software Development
  • Computer Science

Background:

  • Academic software development, particularly in bioinformatics, often lacks systematic methodologies, leading to maintenance and availability issues.
  • Existing software engineering practices are difficult to adopt in academic settings, and specific technical improvements for bioinformatics programming are not widely documented.

Purpose of the Study:

  • To identify and describe a set of practical software development practices for academic environments.
  • To provide a toolbox of 12 techniques to facilitate the adoption of software engineering principles in bioinformatics projects.
  • To improve the quality, maintainability, and long-term availability of scientific software developed by researchers.

Main Methods:

  • Examination of 22 academic software projects to identify common development practices.
  • Development and description of 12 specific software engineering techniques.
  • Detailed case studies of 3 selected projects to illustrate the application of these techniques.

Main Results:

  • Identification of a set of useful practices for planning academic software projects.
  • Demonstration of how these practices support expert involvement (e.g., from experimentalists).
  • Evidence that the techniques promote higher quality and better maintainability of resulting programs.

Conclusions:

  • The proposed toolbox of 12 techniques offers a practical approach to enhance software engineering in academic bioinformatics.
  • These practices are expected to benefit a wide range of bioinformatics programming projects and aid in training scientific programmers.
  • Adoption of these systematic methods can address common challenges in academic software development, ensuring greater utility and longevity.