sFSS Navigator - EDS-Bioinformatics-Laboratory/ENCORE GitHub Wiki

At later stages of a project, the sFSS may contain a large amount of information, potentially making it difficult for the compendium recipient to determine the best point of entry. Therefore, we developed the sFSS Navigator to provide a first overview of the project. It also provides a convenient tool to, for example, browse and show results while the project is still active.

The project team uses the 0_GETTINGSTARTED file to provide the compendium recipient with pointers to directories and files that contain the most relevant information such as the main results and the data and code that were used to generate these. The sFSS Navigator itself was developed following the ENCORE approach, and the project compendium can be found in Zenodo (Van Kampen et al., 2023).

The Navigator is a Python program, which scans the sFSS and generates a web page (Navigate.html) that can be opened in any web browser. The generated web page consists of four panels (Figure). The content of the panels is configured by the project owner to guide peers to the important parts of the project. A configuration file (Navigation.conf) allows to specify which subdirectories and files to show expandable directory tree (Figure).

Navigator panels

In addition to the Python code (Navigate.py), executables for Windows, macOS (for both Intel- and silicon-based chips) and shell scripts for Linux/Unix using Python v3 are provided to ensure the Navigator can be used if the Python interpreter is not installed. The executables are distributed with ENCORE releases, and are available from the Navigator repository releases. The Python script and compilation instructions are found on the GitHub repository of the sFSS Navigator. To execute the Navigate.py script you may need to setup Python environment that contains the required Python packages. See https://github.com/EDS-Bioinformatics-Laboratory/FSS-Navigator/tree/main/0_SoftwareEnvironment

VERSIONS

  • Version 1.0 (9 May 2023) - Compatible with ENCORE Template Version 3.x
  • Version 1.5 (23 May 2023) - Compatible with ENCORE Template Version 3.x and 4.x
  • Version 1.5.1 (30 July 2024) - Compatible with ENCORE Template Version 3.x and 4.x

Note: updates of the sFSS navigator can be obtained from the https://github.com/EDS-Bioinformatics-Laboratory/FSS-Navigator/releases