CHR Notebooks are interactive objects that execute code and visualise data. We have partnered with CoCalc (https://cocalc.com) for cloud-based long-term hosting of Jupyter Notebooks associated with CHR articles.

CHR Notebooks allow authors to provide more than a static two-dimensional snapshot of the results of research presented in article figures. Authors can link to a CHR Notebook which hosts the underlying data and code and allows readers to interrogate and probe the data to explore alternative ideas and gain further insights.

How to interact with CHR Notebooks

CHR Notebooks are hosted on CoCalc (https://cocalc.com) and, when included with an article, will be linked to from the caption of article figures. This link takes a reader to the Jupyter Notebook file.

To view and interact with a CHR Notebook, a reader must launch it as their own project: click ‘Edit your own copy’, ‘Create a New Project’, then open the Jupyter Notebook file (*.ipynb) to launch the online CHR notebook. 

Further details and documentation on using CoCalc can be found on the CoCalc website.

How to prepare your CHR Notebook(s)

A CHR Notebook should contain the data and code used to generate a figure in a CHR article and it must be linked to from the figure caption. The output of the CHR Notebook should, therefore, be identical to the image used as the figure. 
You can prepare Jupyter Notebooks in your own environment or in CoCalc’s online notebooks. For submission, they must be uploaded to CoCalc. It is possible to use CoCalc for free with trial projects, but projects associated with a licence have higher performance and users do not need a CoCalc account to use them. CHR Notebooks will be associated with the Cambridge University Press (CUP) licence after submission (see ‘Submission instructions’ below).

Please take note of the following requirements when preparing your CHR Notebook:

• CHR Notebooks must be prepared using a Python library already installed by CoCalc (see the full list).
• You should create one CoCalc project for your article and create a top-level directory folder called ‘CHR-Notebooks’. Include a folder underneath this for each figure that has a CHR Notebook. 
• The figure folders should be named according to their running order (i.e., Figure 1, Figure 2, etc.).  
• The figure folders should contain the Jupyter Notebook files (*.ipynb) and any other output (e.g., HTML renderings) associated with that figure.
• Data can be included in the figure folders or in another folder if it is shared across figures. Please ensure the figure and data folders are all nested underneath the ‘CHR-Notebooks’ directory folder in the file hierarchy to ensure all necessary files are available when share links are created. 
• Share links for your CHR Notebooks are created by ‘publishing’ the top level CHR-Notebooks directory folder (choose “Published (unlisted) – only people with the link can view this”). You can find the share links for each file in the publish controls. For more details, see CoCalc instructions.
• Include links to the Jupyter Notebook file (*.ipynb) or any HTML renderings in the figure caption in your paper. 

Submission and production of CHR Notebooks

If you are interested in submitting an article to CHR with associated Jupyter Notebooks, please prepare them as outlined above and add links to the CHR Notebooks in the figure caption of the figure that it relates to (see ‘How to prepare your CHR Notebook(s)’ above). 

Please follow the steps below: 

1. Re-name your CoCalc project with the manuscript ID of your Submission (this will be in the format CHR-##-####) 
2. Make CUP a Collaborator. This can be done in the ‘users’ section by searching for ‘Cambridge University Press’ in the ‘Add new collaborators’ box (as per instructions).
3. Email CHRproduction@cambridge.org to confirm that CUP are a collaborator and the project is now named with the manuscript ID. CUP will then apply the CUP licence to your shared project.

During production, a new Cambridge controlled CoCalc project will be created, which you will not be a collaborator on. Your ‘CHR-Notebooks’ directory folder will be copied into this and updates made to the descriptive metadata linking it to the published version of record (you will be asked to provide key words and the manuscript authors).

Persistent cambridge.org redirects will be created for each ‘share’ link in the manuscript. The original ‘share’ links in your manuscript will be replaced with the persistent links as part of the typesetting process. You will be asked to provide a list of all ‘share’ links and the figure they relate to.

Publication of CHR Notebooks

CHR Notebooks will be made publicly available and will be discoverable by search engines as well as those with the links from the published version of record.