ENCORE. A practical implementation to improve reproducibility and transparency of computational research

Reproducibility of computational research is often challenging despite established guidelines and best practices. Translating these guidelines into practical applications remains difficult. Over the past few years we have developed ENCORE as a practical approach to enhance transparency and reproducibility of computational research. ENCORE guides researchers in structuring and documenting a computational project.

ENCORE builds on previous efforts in computational reproducibility and integrates all project components into a standardized file system structure. It utilizes pre-defined files as documentation templates, leverages GitHub for software versioning, and includes an HTML-based navigator.

ENCORE is designed to be agnostic to the type of computational project, data, programming language, and ICT infrastructure, and does not rely on specific software tools.

Reference

  • van Kampen, A., Mahamune, U., Jongejan, A., van Schaik, B., Balashova, D., Lashgari, D., Pras-Raves, M., Wever, E., Dane, A., Valiente, R.G., and Moerland, P. (2024) ENCORE: a practical implementation to improve reproducibility and transparency of computational research. Nat Commun 15, 8117. https://doi.org/10.1038/s41467-024-52446-8. [pdf][Supplement]

See also Behind the paper

How to get started?

The ENCORE Wiki provides a good place to start. It contains a general description of the approach and links to further documentation.

If you want to start directly with your first ENCORE project, then clone the ENCORE template to your desktop PC or laptop, and open the Step by Step guide (pdf) that you will find in the root directory.


Need help or want to become involved?

The development of ENCORE is an ongoing process. Moreover, we would like to test and evaluate the approach with other scientific groups and disciplines. Do you want to get involved? Go to the Discussions and leave your thoughts, or drop an email to Antoine van Kampen: a.h.vankampen@amsterdamumc.nl.


The standardized File System Structure (sFSS) and its environment. The green box denotes the Project Compendium (sFSS) with part of the directory structure shown. The sFSS is the central point of entry for a project and is initially cloned from the ENCORE template GitHub repository when starting a new project. The project team is responsible for the organization and documentation of the project. Only the code and code documentation within the project compendium are synchronized to a project specific GitHub repository. An sFSS project compendium can be shared with a compendium recipient. The compendium recipient starts exploring the project by opening Navigate.html in a web browser.


ENCORE WIKI

ENCORE Discussions

ENCORE template:

Compendium Navigator:

Automation scripts

ENCORE Supplement: