From NuGOwiki

http://www.textoloouc4tmo.com http://www.textboctroct.com Dear Editor,

Congratulations! You have been chosen to be one of NuGO’s metabolomic experts! We would appreciate it if you would give us your opinion about our new NuGOwiki metabolomics database. We are aware of the fact that time of an expert is very scarce and expensive, so we are offering you this digital camera if we get your response back within 10 days (details KODAK EasyShare C530).

Contents 1 The project 2 The status of the project 3 What we want you to do 4 Tips to get started 4.1 Introduction 4.2 Log into the NuGOwiki 4.3 Editing 4.4 Page History 4.5 Discussion

The project

As nutrition and metabolism are closely linked, metabolomics holds high promises for this area. However, the complexity of the interactions between nutrients and the metabolome and their effect on health is poorly understood and tools for the biological interpretation of metabolome changes are essentially lacking. Therefore, NuGO has decided to develop a public information database describing the biology of all metabolites relevant for nutrition and their relation to health & disease. Each compound will have a page, or a ‘wikicard’, and on each wikicard, there will be a ‘metabobox’ which will begin the article. For the realization of this project NuGO has teamed up with the Genome Canada initiative on the Human Metabolome Project, so that we can make use of the contents (about 1700 human metabolites) and data- and textmining tools of their Human Metabolite Database. We decided that the database should be in the form of a wiki (an example of a wiki is Wikipedia), which allows us to construct the database in a global effort. A wiki is a type of website that allows users to add, remove, or otherwise edit all content very quickly and easily, which makes a wiki an effective tool for collaborative writing. Data- and text-mining tools will partly provide the up-to-date biological metabolite information. Following that, expert NuGO curators will be appointed to scrutinise and complete the content of the wiki.

We envisage this database becoming the central resource for anyone seeking information on metabolic compounds and their biological function.

The status of the project

We have designed a preliminary template and filled this with the kind of biological information that in our opinion should be included. This Vitamin C wikicard can be seen on Ascorbic Acid. Furthermore, we decided that every metabolite should have different taxonomies (a biochemical-, functional-, and nutritional taxonomy), so that the metabolome can be categorized in several ways. Finally, the data- and text-mining tools will gather information for the 1700 metabolites to create stub articles (short and insufficient pages of information that require additions) and a metabobox for each compound..

What we want you to do

We created 10 wikicards of different metabolites and partially filled in the information that was gathered by the data- and text-mining tools. We want you to:

1. Fill in section one of the questionnaire.
2. Edit and complete 1 of these wikicards. As listed below, you are responsible for the editing of wikicard.(Please take care to note how long you spend on this step and the following one.)
3. There are eleven other wiki-cards under development at this phase of the project. Please select three that you feel you could contribute to and follow the links below to edit the material and any comments in the discussion page.
   • Ascorbic Acid (example page)
   • Beta-hydroxybutyrate (editor: Manuela Rist)
   • Arachidonic Acid (editor: Marjan van Erk)
   • Arginine (editor: Kaatje Lenaerts)
   • Methionine (editor: Udo Engelke)
   • Calcium (editor: Pilar Parra)
   • Trans-10 Cis-12 Conjugated Linoleic Acid (editor: Baukje de Roos)
   • Folic Acid (editor: Susan Duthie)
   • 1-Heptadecanoyl-Glycerol (editor: Arild Rustan)
   • 2-Oxo-Octanoic Acid (editor: Robert-Jan Lamers)
   • Carnitine (editor: Luisa Bonet)
   • N-benzoylglycine (editor: Marianne Walsh)
4. Fill in section two of the questionnaire when you have completed the above steps.

You may wonder how you were selected for this job: Easy: your name was the first hit on NuGOnet related to the search of the compound, or a related issue... Wikis are used by people all over the world with varying degrees of computer literacy so please don’t feel that you may not have enough IT experience to complete this task. We need to measure the usability of the tool so that other users, just like you, will feel comfortable the first time they go to approach the wiki.

Tips to get started

Introduction

A wiki is a set of web pages whereby anyone with permission can access the pages and edit them as they read them. Tim Berners Lee – who is credited with the invention of the World Wide Web – originally envisaged a system that facilitated annotation, a system where the reader never left a page without making a contribution. He encouraged browser developers from the very beginning to incorporate this feature into their applications. But it was one of the features of the World Wide Web that failed to flourish. Until the late nineties when blogs, wikis and other fully interactive tools became mainstream and all of a sudden, now everyone is an editor.

At the moment the NuGOwiki is password protected, which means that articles (or wikicards) can only be edited when you log into the database. Once you reply to this mail indicating an interest in the project, we will send your account details be email.

Log into the NuGOwiki

• From any page in the wiki
• On the top right corner you will find ‘log in/create account’, click this link
• Fill in your username and password (see your e-mail) and press ‘log in’
• You are ready to edit your page
• To navigate to your page, please enter the exact name of the compound in the search box on the left side of the page and click ‘Go’.

The tabs at the top of a wiki page are the most crucial element in learning how to use it:

Editing

Each page in a wiki has a number of views which you can use. These are represented as tags at the top of the page. Clicking on the ‘Edit’ tab brings up a view that allows the user to edit the content of the page. Simple formatting allows you to create headings, lists, tables etc, and to insert images.

Tip: One of the best ways to learn about these formatting rules is to browse a wiki and click on the edit view in all of the pages to see how other people have formatted their work. If you don’t know how to italicise a word, for example, you can click on the edit tab of a page where you see a word italicised, and you will immediately see the formatting used to achieve the desired effect.

Page History

When things are so easily edited, it is important to be able to keep track of these changes. The history tab displays the evolution of the page; the different versions and what has been added or taken away in each of them. Other details captured depend on the configuration of the wiki but usually the user can be identified, or their IP address, when the changes were made and a small summary of what was done.

Tip: Another way to track the changes within a wiki is to use the ‘Recent Changes’ button. In NuGOwiki, this is located on the left hand side of the page in the main navigation block. A quick look at this page will tell you what pages are being worked on at present and by whom.

Discussion

The discussion tab of a wiki page leads to a newly editable page where authors and contributors can thrash out any debate surrounding the content of the article. This keeps the content clean and focused and gives a forum for any contentious issues regarding the content.

Tip: When putting your name to any comments in the discussion view of a page, you can add four tildes (Ben 12:36, 7 June 2006 (IST)) as a logged in user to generate an automatic time stamp and signature.