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

Contents 1 Setting up a CACAO session 1.1 Background Info 2 Overview 2.1 Make user accounts & Setup user pages 2.2 Organize users into groups 2.3 Setup Top-most Category 2.4 Where to go for Help 3 CACAO Code 4 See Also

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

Background Info

First, a word about categories, users, and pages on GONUTS. MediaWiki, the software we use to run GONUTS, allows many different types of pages to exist on the same wiki; we'll be interested in four of them:

(1.) Main Namespace

Normal pages are exactly what you think - creatable, editable places for documentation or notes. On GONUTS you are allowed to make pages as you see fit. However, because of the scientific nature of GONUTS, we've created tools to facilitate making pages (specifically pages about genes and ontology terms.) These pages are in the Main namespace and do not need a prefix (like some other namespaces which we'll see later.)

(2.) User Namespace

User: pages are wiki pages associated with a particular user. Each user gets his/her own page. On GONUTS we use these to display a users' annotations and put them in groups. These pages require the User: prefix before the pagename. For example, if you wanted to view Fred Flintstone's page you might browse to:

User:Yabba Dabba Doo

(3.) Category Namesapce

Category: pages group similar wiki pages by topic. Category pages can include content, but their main purpose is an organizational one. Categories in MediaWiki are constructed in a bottom-up type of fashion. Instead of listing a category's members on it's page, each wiki page lists the category it is in. This is done by putting the following code within the source of a page: [[Category:category-name]].

For example, a page about College Station, TX might include the following wikitext:

[[Category:Cities in Texas]]
[[Category:American college towns]]
[[Category:Friendliest places on Earth]]

You can find more information about categories at: http://www.mediawiki.org/wiki/Help:Categories.

(4.) Template Namespace

Template: pages are like Category: pages, but they do not organize content. Instead they provide a way of abstracting content into one place that can be included on many different pages. You need not worry about the Template: namespace much, MediaWiki handles things transparently.

More information about namespaces can be found at http://www.mediawiki.org/wiki/Help:Namespaces.

Overview

Setting up a CACAO class can technically be done in any order, but over the years (and through lots of trial-and-error) we've found that some things are easier when done in a specific order. Before we get started, here's a quick overview of the steps we'll proceed through:

1. make user accounts & setup user pages
2. organize users into groups, fill in group pages
3. organize groups into a session, fill in the session page

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.

Make user accounts & Setup user pages

Each participant of CACAO needs to have an account. GONUTS operates on the "Vampire-Model" of account creation: any registered user can create new user accounts. If you don't already have an account email us at ecoliwiki@gmail.com to set one up for you. Once you have an account you can create new accounts one at a time by going to Special:UserLogin and clicking create account. Typically all that is required for an account is an email and a real-name. We suggest clicking the "by email" button - this means GONUTS will create a temporary password and email it to the new user.

Once you have created the accounts you can do one of two things:

1. have the participants setup their user pages themselves
2. set up their pages for them

Each user page for participants of CACAO should contain (at the minimum) two things:

1. a <cacao></cacao> tag
   • This tag will be where you specify which group and which class/session this user/student is in.
2. a team category
   • We are using categories to group the users. (The way we put a user (or a user-page) into a category is similar to using templates, but instead of double curly-brackets we use double square-brackets with a Category: prefix. )

For example, Daniel's page looks something like this:

==My Annotations==
<cacao>
group = Team Aggies
session = Texas A&M Sample CACAO 2011
</cacao>
[[Category:Team Aggies]]

This is a very simple user page. You can insert this wikitext into a user page by clicking the edit tab at the top of the page, entering text into the textbox and then clicking save page.

To be part of CACAO a user's page must include a single <cacao></cacao> set of tags with two parameters in-between them: group = group The group the user is in, with or without the Category: prefix. session = session The session/class the user is in, with or without the Category: prefix.

Organize users into groups

Some of the organization was done in the previous step. If you are not sure which students will be in which teams, you can defer this step until later. It is possible to edit any page at any time, and you can easily add a user to a category (a team) at a later date.

At this point in our tutorial the students have been arranged into teams, but the actual Category: pages for those teams do not have any content. You can edit each team's page by following links from users' pages (the containing categories are listed at the bottom of a page), or by browsing to them. For example, if you look at the example user-page above you will see Daniel is in Team Aggies. This means you will want to go to http://gowiki.tamu.edu/wiki/index.php/Category:Team Aggies.

Even though each user has a <cacao></cacao> table on their page it is sometimes useful to see an entire group's annotations. GONUTS is smart enough to show all annotations from all members of a group if you put a <cacao></cacao> tag on a category page. For example, Category:Team Aggies might look something like this:

Hello! We are TEAM AGGIES! Welcome to our team's page!

==Our Group's Annotations==
<cacao>
session = Texas A&M Sample CACAO 2011
</cacao>
 
==Our favorite links==
* http://tamu.edu 
* http://gowiki.tamu.edu

Each group must be put in the top-level category to be part of that Cacao. Just like we put the users into groups using categories, we will put the groups into a cacao using categories. In each group page add a Category: tag for the Cacao you would like to use. For example, we'll add our sample group to Texas A&M Sample CACAO 2011. The group's page would then look like this:

Hello! We are TEAM AGGIES! Welcome to our team's page!

==Our Group's Annotations==
<cacao>
session = Texas A&M Sample CACAO 2011
</cacao>

==Our favorite links==
* http://tamu.edu 
* http://gowiki.tamu.edu

[[Category:Texas A&M Sample CACAO 2011]]

This must be done for each group.

To be part of CACAO a groups page must include a single <cacao></cacao> set of tags with one parameter in-between them: session = session The session/class the user is in, with or without the Category: prefix.

Setup Top-most Category

This page is where most of the class information will be and will contain the scoreboard and all challenge information. The scoreboard tag looks very similar to the <cacao></cacao> tag.

<scoreboard />

In semester prior to Fall 2011, the <scoreboard /> tag was called the <cacaoScoreboard /> tag. The latter is still allowed for backwards-compatibility, but deprecated nonetheless.

Here is a sample Cacao session page:

=Class Information= 
Welcome to another exciting semester of biocuration using the Gene Ontology! 

=Schedule=
* Tuesdays 7-8:   curating!!!

=Scoreboard=
<scoreboard />

==See Also==
* [[Help:Gene Ontology]]

[[Category:CACAO]]

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.

CACAO Code

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 Daniel for more information.

See Also

• Help:Gene Ontology on GONUTS
• Help:Editing Tables on GONUTS
• http://ecoliwiki.net/colipedia/index.php/cacao