Quickstart Guide: IGVF protocols.io Workspace
Submitting to protocols.io is mandatory
All IGVF experimental labs are required to submit their experimental protocols to protocols.io. All measurement-sets can be linked to a protocols page using the property protocols. (See: https://data.igvf.org/profiles/measurement_set/schema/properties/?property=protocols)
Update your profile information
After creating an account on the site, please update your profile with your institution and affiliation with IGVF. This is required so that workspace administrators can verify your request to join the IGVF workspace, which is only open to IGVF Consortium members.
Click on your user icon in the upper right corner and select “Profile” to access your profile settings.
Click “Edit profile” in the sidebar to edit your information. Please add your institution(s) and your lab and/or grant center to your profile. You may also add a profile image and other information.
Accessing the Workspace
The IGVF protocols.io workspace is located at the following link:
https://protocols.io/workspaces/igvf
The workspace is private and accessible by invitation only. An administrator will check your profile to confirm that you are a member of IGVF before accepting the request. Please make sure your user profile includes your institution and affiliation information before joining. Otherwise, your request to join may be delayed.
Please contact your data wrangler to obtain an invitation link to the IGVF workspace.
The workspace is administered via the Stanford DACC protocols.io premium account. Please reach out to igvf-support@gowustl.onmicrosoft.com if you have any difficulties with accessing the site.
Workspace organization
To view the workspace folders, click on the IGVF icon in the sidebar and then click on “Workspace folder”:
Screenshot of sidebar displaying the options for the IGVF workspace.
All users have access to 2 main folders: “IGVF” and a personal folder with your name on it:
Two folders appear in the sidebar of the IGVF workspace. The IGVF folder is visible and accessible to all members of the workspace, whereas your personal folder is visible and accessible only to yourself.
This personal folder is completely private and not visible to other users or admins. Protocols created in this folder will be hidden to all other members by default unless intentionally shared with other users at your discretion.
Click the “NEW” button at the top of the page to create a new protocol or folder within your private folder. The same button also appears in the shared IGVF folder with the same functionality.
A guide on creating a protocol is available through the protocols.io help documentation. Once satisfied with the protocol, you may also move it into the main IGVF folder, where it will be accessible to all IGVF members.
Right clicking on a protocol in the directory opens a menu with several options. “Move to…” allows users to move the protocol into a different directory, such as a folder in the shared IGVF folder. “Share” allows users to grant access to other protocols.io users.
The IGVF folder contains multiple sub-folders for each grant. Please make sure to create or move protocols to the folder for your affiliated center. Note that all IGVF Consortium members have access to all folders in this list and can edit and comment on any protocols.
The IGVF folder is subdivided by grant. Please make sure to place protocols in the folder corresponding to your lab, but feel free to peruse and comment on protocols shared by other labs in any folder.