Cell atlas

Source for the "Atlas of Bacterial and Archaeal Cell Structure" by Catherine M. Oikonomou and Grant J. Jensen.

Table of contents

• Installation
• Usage
• Getting help
• Contributing
• License
• Authors and history

Installation

Install Pandoc Version >= 2.11 and Python Version >=3.

Usage

Run the build script using:

python3 _build.py
# or (depending on python configuration)
python _build.py

This will delete the site/ directory in the this script's working directory. Videos are will not be included in the site build and need to be moved to a videos directory in 'site' directory. Supplemental files (video preview images, narration, and pdb files) are required for the site to function completely and are available to download from CaltechDATA

Offline versions of the cell atlas are automatically generated in the cell_atlas_offline and cell_atlas_offline_lite directories, assuming you have "video", "videos-480p", "narration", and "stillimages" directories present. In order to zip up the offline version, navigate to cell_atlas_offline and cell_atlas_offline_lite directories and use the command zip -rX cell_atlas_offline_lite.zip *

You can optionally create .webp version of image files by installing cwebp and running python _webp.py stillimages. The site will always fall back to the .jpg images if the .webp versions are not available or not suported.

Getting help

Please submit an issue using the issue tracker in this repo

Contributing

You can submit change requests by submitting a pull request through GitHub.

License

Software produced by the Caltech Library is Copyright (C) 2023, Caltech. This software is freely distributed under a BSD/MIT type license. Please see the LICENSE file for more information.

The book text is (C) 2023, Caltech.

Authors and Acknowledgments

Catherine M. Oikonomou and Grant J. Jensen wrote "Atlas of Bacterial and Archaeal Cell Structure". See the full list of Acknowledgments in the book text.

Kian Badie, Tom Morrell, and Robert Doiel developed the software in this repository that automates book formatting and integrates videos from CaltechDATA.

Software Development was funded by the California Institute of Technology Library and the Jensen Lab.

"File" icon by Vectorstall from the Noun Project.

"Video" icon by i cons from the Noun Project.

"Image" by Dooder from the Noun Project.

"cycle" by ImageCatalog from the Noun Project.