Frequently Asked Questions

How can I keep up-to-date with CAGI news?

If you are interested in keeping up-to-date with CAGI announcements, you can subscribe to the CAGI newsletters and/or follow @CAGInews on Twitter. The newsletters contain announcements, status updates, and other useful information on the experiment. Please note that subscribing to the Newsletter alone will not grant you access to the restricted datasets of CAGI, or allow you to submit predictions or participate in the meeting. If you are interested in a more active role within the CAGI experiment, please see below for instructions on how to create a user account and register.

Where can I find previous CAGIs details?

Please go to the page Previous CAGIs.

Where can I find the presentations of previous CAGIs?

Presentations are available for download for registered users at CAGI Presentations

How do I participate in the CAGI experiment?

To participate in the CAGI 2015 experiment you must have an account on the CAGI website at http://genomeinterpretation.org. Anybody can create an account by going to the website above and clicking on "Register for CAGI".

Upon registering, you will need to read and accept the CAGI data use agreement by signing with your initials. Your registration will be pending until approved by the CAGI organizers. When your application is accepted, you will receive an email with a one-time link to access your account, where you will be able to set your password. If you do not receive an email after submitting the registration application, please check your spam/junk folders. You can also contact the CAGI website administrator.

I already registered for a previous CAGI, do I need to register again?

If you registered for a previous CAGI experiment, you need not register again for CAGI 2015 (you may use the same username).

How do I submit predictions?

In CAGI, only groups may submit predictions (naturally, a group may be formed by a single user). To access the submission forms, please create a CAGI group as described below, and then read instructions in the section below: Now that I created a group, how do I submit predictions?

How do I create a CAGI group?

In order to create a group, the intended group administrator needs to be logged into the CAGI website. He or she creates a group through the "Create user group" link on the left-side menu. For the mandatory field "Title," please provide a short alphanumeric name for your group. You may also provide a longer name under "Group name," and a description for your group under "Description". Upon successfully creating a group, a link with the group title will appear on the left-side menu.

How do I add members to a CAGI group?

Once you have created a CAGI group, there will be a "Manage Group" link on the left-side panel. Click on this link and go to the "Add members" tab at the top. Then enter the desired usernames, separated by commas, in the "List of users" box. Only registered users may be added to a group.

How do I manage member roles in a CAGI group?

In CAGI groups, the user that creates a group becomes the group administrator. This role may not be changed. In addition, there are two other roles, the group PI (Principal Investigator) and the group corresponding member. By default, the group admin has also been assigned the roles of PI and corresponding member upon creation of the group. Every group must have one or more PI and corresponding member. The corresponding members will receive all emails about the submissions and their analysis. To assign the role of PI or corresponding member, please go to the "Manage Group" link on the left-side menu, and then select the "Configure roles" tab at the top.

How many CAGI groups can I belong to?

Users can belong to a maximum 5 CAGI user groups.

Now that I have created a group, how do I submit predictions?

Go to your group home page by clicking your group name on the left side menu (to see your groups, please log in). To access the prediction submission forms, go to the "All submission forms" link on the left side menu. From the "All submission forms" page, select the link to the submission form that you want to submit predictions for.

In order to submit predictions, you need to prepare the following files:

• Prediction file: This file is a tab-delimited text file. The CAGI organizers will provide a specific file template for each dataset, and predictions must be submitted using the template. In addition, a validation script for each dataset will be provided, and predictors must check the correctness of the format before submitting their predictions. Please make sure you follow the submission guidelines strictly.
• Methods description file: This file contains a detailed description of the method used to make the predictions (similar to the style of the Methods section in a scientific article). The allowed file formats are doc, txt, pdf, and zip.
• Anonymous method file: This file is required only for anonymous submissions. For anonymous submissions a regular method description file is still required as well, in case the prediction is announced as laid out in the anonymity policy guidelines.

In addition, you will need to specify the authors of your submission.

Once you submit the prediction, you should receive an email confirmation of the submission. In addition, the PI and the corresponding member of the group will receive an email notification.

How many submissions per challenge are allowed?

If you wish, your group may submit more than one submission per challenge, a maximum of 6 submissions are allowed per challenge. It is possible to edit or delete any of the (up to) 6 submissions from respective submission form or All submission for group link. The first submission made by the group from challenge submission form1 will be considered as the primary submission for assessment purposes. You can also choose to make an anonymous submission conforming to the CAGI Anonymity policy. Once a submission is chosen as anonymous, it is mandatory to provide the anonymous method for the prediction submission. An anonymous submission can be later changed/edited to public. However, a public submission cannot be changed to anonymous.

How can I withdraw a submission?

If your group wishes to withdraw a submission, it may be done by deleting the corresponding submission from the All submission for group link.

How can I revise authorship for submitted challenges?

If your group wishes to revise authorship for any challenge submission, it may be done by following the instructions given under Group editing FAQ link under "My groups" left side panel.

Last updated: November 30, 2020