CAGI 2011 - Frequently asked questions on website issues

How can I keep up-to-date with CAGI news?
Will there be CAGI 2012?
What are the results of CAGI 2010
How do I participate in the CAGI experiment?
I already registered for CAGI 2010, do I need to register again?
What is the project deadline?
How do I submit predictions?
How do I create a CAGI group?
How do I add members to a CAGI group?
How do I manage member roles in a CAGI group?
How many CAGI groups can I belong to?
Now that I created a group, how do I submit predictions?
How many submissions can I submit?
How can I withdraw a submission?

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 Newsletter. It will contain announcements, status updates, and other useful information on the experiment. You can subscribe to the Newsletter by using the "Subscribe" link in the left bar of the CAGI website. Subscribing to the Newsletter 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.

Will there be CAGI 2012?

Yes, there would be a CAGI experiment during the year 2012 and the schedule will be announced shortly.

What are the results of CAGI 2010

The organizers and assessors are now finalizing the assessments of CAGI 2010. We are planning to write a manuscript describing the results. Presentation by Assessor Pauline Ng at the ISMB 2011 conference is available for download for registered users. In addition, a video presentation by Predictor Rachel Karchin and her group is available for registered users. Please go to the page CAGI 2010 Results.

How do I participate in the CAGI experiment?

To participate in the CAGI 2011 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 "Create new account" in the right menu.

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 CAGI 2010, do I need to register again?

If you registered for the CAGI 2010 experiment, we kindly ask you to register again for CAGI 2011 (you may use the same username if you wish).

What is the project deadline?

The CAGI prediction season will span summer 2011. Prediction submission deadline will be 31 August for the mouse exomes challenge. For the remaining challenges the submission deadlines start on 30 September and continue until 31 October. Please see the each individual challenge page for details, or the Key dates page.

The assessment season will occur during fall 2011 with the CAGI Conference in 9-10 December. For updated information, please see the Key dates page, or sign up for the CAGI Newsletter.

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?

Note that results from CAGI 2011 will be released, and predictions will be linked to group identities.

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 right-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 right-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 right-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 created a group, how do I submit predictions?

Go to your group home page by clicking your group name on the right side menu (to see your groups, please log in). To access the prediction submission forms, go to the "All submission forms" link on the right 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 two files:

  1. 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.
  2. 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.

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

For some of the challenges, the prediction submission form also includes keyword lists of the features, and the training methods you used to make your predictions. If the given keywords do not apply to your method, please use the "free text" field to define new keywords.

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 can I submit?

If you wish, your group may submit more than one submission per challenge, and up to 6 in total will be considered in the assessment of that challenge. It is technically possible to submit more than 6 submissions, but we will only consider the first 6 received submissions for the assessment.

How can I withdraw a submission?

If your group wishes to withdraw a submission, it may be done by the group PI (only) before the submission deadline of that challenge. In such case, the PI of the group will need to contact the CAGI organizers by email at cagi@genomeinterpretation.org. The following items must all be included into the withdrawal request:

  • the challenge name,
  • the group name,
  • the PI name,
  • the submission ID,
  • and the timestamp of the submission to be withdrawn.

Note that results from CAGI 2011 will be released, and predictions will be linked to group identities.