GONUTS has been updated to MW1.29.2. Most things seem to be working but be sure to report problems.

It is now the 3rd OPEN Period for CACAO Phage Hunters S2018! It will end on Friday July 20, 2018 at 05:59 pm CDT
This is your chance to make annotations OR challenge other team's annotations. You may also DEFEND or suggest improvements to your own annotations IF they have been challenged. Please note, although we ENCOURAGE challenges, an excess of identical challenges that do not appear to be applicable to the annotation or well thought out will be considered spam and ignored.

Have any questions? Please email us at ecoliwiki@gmail.com


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This page is intended to be a reference for setting up a new session for CACAO on GONUTS FOR INSTRUCTORS.

Things you'll need

A class roster or list of participants
Each student needs to have a username (either chosen or assigned) and a valid email address.
A (tentative) schedule of your class
You can set up CACAO in a variety of ways, see the discussion below for more information.
Topic(s) for annotation
CACAO can operate using any scientific literature, but it sometimes easier to focus upon a particular area

Setting up a CACAO session

Some definitions:

  • Session: We define a CACAO session as a group of annotation activities. These are typically a semester long, but can be of any arbitrary length.
  • Inning: A session is divided into one or more innings. An inning is divided into one or more parts based on the allowed activities
    • Annotation - Participants make annotations. Challenges are blocked
    • Challenge - Participants challenge annotations made by members of other teams. New annotations are blocked
    • Open - Both annotations and challenges are allowed.

A CACAO session involves several different kinds of pages on GONUTS.

Session scoreboard pages

Each CACAO session has a main scoreboard page with a name like Category:CACAO_Spring_2017. This organizes the teams in a CACAO session and is a central hub for the scoreboards and assessments. The schedule of innings is also set from the Session page.

The Session page name must start with a "Category:" prefix to place it in the Category namespace (this is required for various features like assigning teams to a Session)

Making an new session page

To create a new CACAO session,

  • make an empty page with an appropriate page name. Double click on replace_session_name and replace it with the name of your session. The form will automatically place the new page in the Category namespace.

  • Put {{subst:CACAO page}} in the content and save it. The first time you save it the Scheduling table won't show up.
  • Click Edit and save it again.
  • Edit the schedule table to set up the innings.
  • Go to the Talk page and put {{subst:CACAO talk page}} in the content and save it.

Players and teams

While it is possible to set up players and teams manually, it is much easier to send us the information in a tab-delimited text file so we can use a script on the server to set everything up automatically.

If you don't know which users are going to be in which groups, don't worry - this is a wiki, it's quite flexible.

Picking team names

We try to have all team names start with the word Team, which distinguishes CACAO teams from other Mediawiki category pages. A list of previously used team names can be found at Special:Cacao_Teams (you can see that we haven't always been good at enforcing the use of Team in the name).

Send us your roster

We can automate the creation of users and teams from a tab-delimited text file you send us. The format should be one user per row. Any row that starts with a # character is treated as a comment and is ignored. Example

#Team                 username            user_real_name         user_email
Team Groot            IamGroot            Groot                  groot@iplant.org	
Team Groot            Rocket              Rocket Racoon          guardian@timely.com	
Team Star Lord        PQuill              Peter Quill            quill@ravagers.org	
Team Star Lord        KPryde              Kitty Pryde            shadowcat@xavierschool.edu	
Team Infinity         Gamora              Bambi Long             gamora@daughtersofthanos.org
Team Infinity         AdamW               Adam Warlock           Adam@tribumal.com

Note that the username can be anything but the first letter must be uppercase. The real name should be in First Last.

Using this text file, we can automatically create accounts and user and group pages for the competition. This assumes we also know the name of CACAO session the players are participating in. You can view what these look like by going to one of the older CACAO competitions and looking at the Team and User links from the scoreboard.

When the accounts are created, the participants will receive an email telling them to claim their account. If they don't get the email, they should check their spam filters. The account has to be activated within 7 days or the account activation will expire. We can fix these manually, but it's easier to have people confirm their accounts as soon as possible.

Where to go for Help

If you have any questions or none of this makes any sense to you, then please email us at ecoliwiki@gmail.com. Someone from our team would love to help you get started using GONUTS. We can also set up some training via phone-conference on everything from using GONUTS to "what is the Gene Ontology." Please don't hesitate to contact us.


The code for CACAO is written as an extension to Mediawiki. It is written in object-oriented PHP and is free for download. Please email us for more information.

See Also