How to submit your sessions

Prepare a folder

You need to prepare a folder that contains all the information to build a session. We highly recommend using underscore whenever space is used. You can view the current session list at https://github.com/nucleome/sessions/tree/main/4DN. Each submitter has a folder named by his/her GitHub id. All his/her sessions folder is in this folder. A folder with the name of an existing folder in the submitter's folder will overwrite (i.e., update) the existing session.

Prepare session data

Inside this folder, you need to prepare four files.

• The first file is a meta.json file representing the meta-information of this session. The details of the meta.json file are shown below.

{
    "Title":"4DN portal put DCIC visualization tool side-by-side",
    "Caption":"A custom webpage window is opened on the right. In this example, we open the DCIC visualization tool in this panel. Users can then compare the Nucleome Browser view side-by-side with the HiGlass view on the right. ",
    "Version":"version 1.0",
    "Author": "Yang Zhang (CMU)",
    "Required servers": "/d/portal,http://genome-dev.compbio.cs.cmu.edu:9007" 
}

A JSON file is a collection of keys and values. This example shows that at least five keys are required for a valid meta.json file. These keys are case-sensitive. Title is a short sentence describing the session. Caption is the caption that explains the details of this session. It may include details of data, regions of interest, etc. Version is the latest version of this session. Author is the contributor and affiliation of this session. Finally, Required servers is the data servers that this session depends on. For example, the session shown here is constructed using data from /d/portal (the default data server contains public 4DN data from the DCIC web portal). http://genome-dev.compbio.cs.cmu.edu:9007 is a custom data server. Note that for custom data, Nucleome Browser currently only supports HTTP rather than HTTPS.

• The second file is a session.json file representing the session file you downloaded from the Nucleome Browser. The documentation of sharing and saving session is here.
• The third file is a screenshot.jpg file which shows the screenshot of the session. Both JPG and PNG formats are supported.
• The fourth file is a thumbnail.jpg which is the thumbnail of the screenshot. You can use online tools such as this one or convert command (Linux system) to resize a figure. We recommend keeping the width of the thumbnail as 480px. For the convert command, you can use the following script to resize the screenshot to a 480px wide thumbnail.

# create a thumbnail with a width of 480px from an original picture screenshot.jpg
convert -thumbnail x480 screenshot.jpg thumbnail.jpg

Structure of a typical user folder

All users who have submitted sessions to this GitHub repo will have a folder named by GitHub id. Sessions folders from a user will be stored in his or her folder. An index.txt file indicates how many sessions (session folder name) a user has submitted. The structure of a user will like this.

<github id>
----index.txt
----<sesion 2 folder>
--------<meta.json>
--------<screenshot.jpg>
--------<thumbnail.jpg>
--------<session.json>
----<sesion 2 folder>
--------<meta.json>
--------<screenshot.jpg>
--------<thumbnail.jpg>
--------<session.json>

Prepare for a pull-request

Once you have prepared or the required files/folder, you can submit a pull request. After we process and test your session, your sessions will be shown up in https://gallery.nucleome.org