ENCORE evolution and evaluation. ENCORE evolved through different versions incorporating changes based on practical experiences, evaluations, and group discussions. This led to gradual improvements in the ENCORE approach and documentation, broader use for research projects, and Git/GitHub proficiency within our research group. In turn, this led to better and more transparent organization of projects and increased reproducibility. Further changes are expected in the future.

Research lifecycle. Most (biomedical) studies go through the stages of (1) study preparation, (2) data collection (involving sample collection and processing, and data generation), (3) computational approaches for data analyses, modelling and/or simulations, and (4) (open-access/open-source) publication & archiving. Published research findings will drive new studies. ENCORE focuses on computational reproducibility (stage 3).

The 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.