The project wiki is part of the SimTk wiki farm and it is intended to facilitate collaborative development of scientific content. In this page, the team members can find brief instructions to facilitate their use of the wiki within the context of project requirements. Members of the project have full permissions to read, write, revert and delete pages. Appropriate links are provided for more detailed help on this specific wiki installation, which is based on MoinMoin.

DON'T BE SHY! Start editing. It is IMPORTANT for team members to use the wiki, because

• wikis are unstructured and collaborative not constrained by other communication means, e.g. e-mail;
• all editing is under version control:
• accessible history of individual and overall progress,
• no need to be afraid of making mistakes; one can always return back to a previous version;
• scientific contributions of individual team members and the whole project are clear and accessible by all team members and potentially by everyone:
• accurate acknowledgment of activities,
• facilitated dissemination;
• fully searchable.

# Wiki Organization

## Page Layout

Page Header. Displays the title of the page on the left. Clicking on the title lists other wiki pages linking to the current page. On the right, links to the main SimTk wiki area and the front page of the project can be found.

Navigation Bar. This region provides links to the front page of the project, recent activities in the wiki, search page, and wiki help in that order. The last tab on right is the current page, whereas all the other links remain the same, regardless the visited wiki page.

Actions Toolbar. This toolbar is page-specific and provides links to:

• Edit (Text): for text base editing of the current page.
• Edit (GUI): for editing of the current page using a graphical user interface.
• Info: to access revision history of the current page.
• Subscribe: to subscribe to the current page for notification of future edits.
• Attachments: to list files attached to the current page and to upload new attachments.
• More Actions: for more advanced activities that can be performed on the current page.

Page Contents. The contents of the wiki page follows the actions toolbar.

Search Box. Provides keyword search on the wiki constrained to wiki page titles (Titles) or full content (Text).

## Content Organization

Wiki is a dynamic and collaborative content generation platform. While there are not any rigid rules on the organization of content, a few guidelines may help team members to start creating pages related to their role and activities in the project:

• Create a subproject page, provide
• a description of the project,
• list of team members involved,
• milestones, and
• an approximate timeline for completion.
• Provide links to the subproject page at the FrontPage or from other project pages.

• Add other pages relevant to the subproject, these may include
• documentation (manuscripts, presentations, manuals, etc.),
• modeling and simulation related pages (specifications, discussions, simulation results, etc.), and
• experimentation related pages (data collection procedures, setup specifications, etc.).
• Attach files, images relevant to the page.
• Ensure that there are appropriate linking between relevant pages and source code (see InstructionsForSourceCodeRepository).

• Review and edit other pages lead by other team members.
• As wiki pages get mature, consider making them public (if they started as private), and add links in 'Documents' and 'Downloads' sections of the main project site for dissemination (see InstructionsForProjectSite).

It is advised to routinely search the wiki for content and track activities on individual pages as well as the whole wiki (see sections below).

There is no right or wrong way to organize the contents. Just do it! If someone does not like it, they can change.

# Searching the Wiki

The wiki provides a powerful search mechanism to find pages of interest. Before you create a new page, it will be wise to search for similar pages to see if the informations is already in the wiki. Searches on the whole wiki site can be conducted using the following mechanisms:

• Search Box: This is located at the top right corner of the wiki page and it is accessible from all pages. Type in your keyword(s) and click on the button labeled i) 'Title' to list pages which have the keyword(s) in their title or ii) 'Text' to list pages which have the keyword(s) in their full content.
• FindPage: This is the wiki page that provides similar search functionality. It can also be accessed through the link at the navigation bar.

For explanation of search functions, please refer to HelpOnSearching.

# Tracking Wiki Activities

## Overall Wiki Activity

RecentChanges page lists recent editing activities in the wiki in a chronological order (most recent first). This page is a good starting point for a summary of the evolution of the wiki site and contributions to individual pages by all team members. Items in the list include the name of the edited page (with relevant link to it), the team member who changed the page and brief comments. RecentChanges can be accessed through the link at the navigation toolbar.

## Page Activity

Editing activity on individual pages can be accessed through the 'Info' link at the actions toolbar. The list provides the revision history, including the time stamp of the update, the editor, comments, and various action links, e.g. view, to access a desired revision. The 'Diff' button permits side-to-side comparison of different versions.

It is advised that all team members subscribe all wiki pages to receive e-mail notifications whenever a member changes the wiki. Subscriptions will facilitate awareness to project progress and member contributions. This can be accomplished by:

• Subscribing to RecentChanges: Go to the RecentChanges page and follow the 'Subscribe' link at the actions toolbar. As a member updates any wiki page, the RecentChanges page is automatically updated and subscribers will receive an e-mail notification. Or,

• Subscribing to all pages: While at the wiki site, the 'Preferences' link at the top right corner opens UserPreferences page. In the 'Subscribed wiki pages', typing '.*' (without quotes) and saving preferences will subscribe the team member to all wiki pages.

A team member may subscribe to only desired pages by going to the page and following the 'Subscribe' link at the actions toolbar.

# Creating Pages

The most natural way to create a page seems to be:

1. In an already existing page, create a link to the new page.
2. Follow that link to select from variety of page templates or to create a new empty page.

Use concise but specific page names. It is advised to name new pages in camel case, without any spaces (all initials of the words uppercase, the remainder lower). With this convention, when the page is typed in a wiki page, it will automatically be linked. For example, typing

ThisIsMyNewPage

while editing an existing page will create the link

When the page does not exist, the link will be shown in gray. Following this link will give the message:

This page does not exist yet. You can create a new empty page, or use one of the page templates.

Some useful templates, in terms of security, include the following, from most restrictive to most permissive:

1. OnlyProjectMembersTemplate -- Only team members can view and edit this page. It may be wise to use this as default.

2. SimtkReadTemplate -- Any Simtk.org registered user can read the wiki page. Only team members can edit the page.

3. PublicReadTemplate -- Anyone can read the wiki page. Only team members can edit the page.

4. PublicWriteTemplate -- Anyone can edit this page. Deletes and reverts are limited to team members.

If a new page name not conforming to camel case convention is desired, the link can be established as:

["This is my new page"]

For other ways to create a new page, please consult HelpOnPageCreation.

# Editing Pages

Pages can be edited by selecting the 'Edit (Text)' or 'Edit (GUI)' links in the actions toolbar. While 'Edit (GUI)' provides an easy to understand user interface for formatting, 'Edit (Text)' seems to be faster, with the disadvantage of the requirement to learn wiki markup language. This section will mostly focus on the text based editing mode. MoinMoin also provides comprehensive documentation for editing wiki pages, which can be accessed through:

Team members are encouraged to consult these sections and practice various editing features in the WikiSandBox.

## Formatting

Text formatting is conducted through a variety of buttons in the graphical user interface ('Edit (GUI)'). In text mode ('Edit (Text)'), one can find a short guide immediately under the edit box, in a shaded area. This guide is also provided in here:

Emphasis
''italics''; '''bold'''; '''''bold italics''''';
''mixed '''bold''' and italics''; ---- horizontal rule.
= Title 1 =; == Title 2 ==; === Title 3 ===;
==== Title 4 ====; ===== Title 5 =====.
Lists
space and one of: * bullets; 1., a., A., i., I. numbered items;
1.#n start numbering at n; space alone indents.
JoinCapitalizedWords; ["brackets and double quotes"]; url; [url]; [url label].
Tables
|| cell text |||| cell text spanning 2 columns ||
no trailing white space allowed after tables or titles.

For more detailed instructions, see HelpOnFormatting.

A wiki page can be linked directly by typing its name, if its name follows the camel case convention (initials uppercase, no spaces), e.g.

WikiPageLink

Otherwise, the page name should be within double quotes inside square brackets:

["wiki page link"]

https://simtk.org

## Attachments

The most natural way to attach a file to a page seems to be:

1. Create a link to the attachment.

To establish a link to an attachment in a page, type:

attachment:filename.ext

If the file has not already been uploaded, it will provide the link in the page as:

Following the link will open the 'Attachments' section of the wiki page where the file can be selected and uploaded. The file will be automatically renamed to that given while providing the link.

The 'Attachments' link in the action toolbar of the wiki page can be followed directly to attach files to the page. It should be noted that a link to those attachments will not appear on the wiki page and still need to be created by the editor.

## Images

Inserting images into a wiki page is the same as attachments. For example, a link to the image, given as

attachment:openknee-logo.png

will allow you to upload an image. Once uploaded, the wiki will show the image directly on the page (rather than as a link provided for attached files):

The wiki supports images of the format .gif, .jpg, and .png.

To have more control on the way image is displayed, one can use the ImageLink macro, e.g.,

[[ImageLink(openknee-logo.png, width=50, alt=Open Knee Logo)]]

## Equations

This wiki installation supports typesetting of equations using latex(\LaTeX).

For standalone equations, use latex(\LaTeX) commands as:

{ { {#!latex
Insert Equation Here
} } }

Remove spaces between { { { and } } }!

For example, typing

{ { {#!latex
\begin{displaymath}
\mathbf{X} =
\left( \begin{array}{ccc}
x_{11} & x_{12} & \ldots \\
x_{21} & x_{22} & \ldots \\
\vdots & \vdots & \ddots
\end{array} \right)
\end{displaymath}
} } }

Remove spaces between { { { and } } }!

while editing the page, inserts the equation to the page as:

If an equation is desired in line with text, type latex(\LaTeX) commands in the parenthesis

[[latex(Insert Equation Here)]]

[[latex($E=mc^2$)]]

produces latex($E=mc^2$).

For more details of latex(\LaTeX) support in MoinMoin, refer to http://johannes.sipsolutions.net/Projects/new-moinmoin-latex. Information on latex(\LaTeX) can be found at latex-introduction.pdf.