Sharing datasets with collaborators

Once you have converted your data in the format used by chemiscope, you might want to share it with collaborators. There are multiple ways to do this, we’ll go over them in this section.

Online visualizer at chemiscope.org

Uploading datasets

The simplest way to share chemiscope dataset is to send the corresponding file (my-dataset.json or my-dataset.json.gz) to your collaborators.

They can then load this file from the main chemiscope website: https://chemiscope.org/. Here they can use the Load/Save menu to upload the dataset to the website.

Loading from an URL

You can also host your dataset in any publicly accessible web server such as your home page. Given a file hosted at https://university.edu/~myself/dataset.json, you can then load this file directly in chemiscope by going to https://chemiscope.org/?load=https://university.edu/~myself/dataset.json. This allow you to create links to directly open a given dataset in the main chemiscope website, loading such dataset from your own webpage.

In general, you can set the load GET parameter on https://chemiscope.org to any url-encoded URL, and chemiscope will try to load the dataset from this URL.

Saving visualization state

You can save the current visualization settings from the website using the Load/Save menu. This will allow you to download a JSON file, which you can use later to reset visualization state.

If you are loading a file from an URL by creating a link that looks like https://chemiscope.org/?load=https://university.edu/dataset.json.gz, you can use the settings GET parameter to specify the URL of saved settings: https://chemiscope.org/?load=https://university.edu/dataset.json.gz&settings=https://university.edu/settings.json

Standalone offline visualizer

There are some cases where you do not want to depend on an online tool when sharing your dataset, such as scientific article supplementation information. For these use cases, a standalone, offline visualizer exists that uses the same input file format as the default interface. You can download the latest version of the standalone viewer at https://chemiscope.org/chemiscope_standalone.html.

This file contains all the required HTML and JavaScript code for chemiscope. You can then add your own dataset by adding the corresponding JSON file at the end of the chemiscope_standalone.html file.

WARNING: Only JSON, not compressed JSON (.json.gz) files are supported with the standalone HTML visualizer.

cat chemiscope_standalone.html my-dataset.json > my-dataset.html

You can then share the my-dataset.html file with others, who can open it in any web browser.

To re-build the chemiscope_standalone.html file from sources, please follow the steps below:

git clone https://github.com/cosmo-epfl/chemiscope
cd chemiscope
npm install
npm run build
python3 ./utils/generate_standalone.py