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Guiding Policy for Developers and Contributors

Last Updated: 05-26-2022

The Aladdin Purpose

  • The purpose of Aladdin is to democratize bioinformatics and thereby make bioinformatics accessible to the widest number of labs, users, and institutions by lowering the cost, complexity, and skill level required to run routine bioinformatics workflows
  • All Aladdin software should not require the end-user to know the command line or know how to write code

How We Work Together

  • We commit all code to a revision control system (GitHub) to track changes and contributions
  • We use a versioning scheme of “major.minor.revision” for the platform, pipelines, and any associated modules
  • We will follow a code of conduct when working together

Open Source

  • Aladdin public pipelines are encouraged to be open source, though some customized pipelines may not be public or open source
  • We will welcome contributions from users and members of the community, and, contributions may be reviewed for code quality and testing to ensure reproducibility

Coding Standards

  • For each pipeline, we follow a set of standards for consistency and compatibility (document on GitHub with the details)

Bioinformatics Standards

  • The field of bioinformatics changes rapidly – we will leverage community support and committees of experts to constantly update our tools to be state-of-the-art
  • Each pipeline shall allow download of intermediates and unfiltered data files so that a researcher can pick up the results and do their own analysis at key stages if desired
  • We will produce publication-quality figures from our pipelines
  • Developers can contribute a single module to a pipeline or contribute entire pipelines regardless of pre-existing pipelines (we allow multiple modules or pipelines for the same purpose)