Outline for Linux Workshop

January 26, 2005 & January 25, 2006 & January 30, 2008

Using the Wiki web tools

Introduction

• What is a Wiki (see http://en.wikipedia.org/wiki/Wiki)
  Wiki: revision control, variables, plugins, attachments, no database
  • Collaboration (anyone can edit)
  • Easy to edit (`wiki wiki` is Hawaiian for `quick`)
  • Own Formatting and Macros, plus HTML and JavaScript
  • Pages are topics created through WikiWords like your user name
    • Since the URL string is rather long, shorten it to http://biostat.mc.vanderbilt.edu/TopicName for outside use

Viewing the content

• View any page that isn't protected
• Basic navigation and page layout
  • topbar, sidebar, bottombar
  • Tangled Webs (WebHome, TWiki, Sandbox, Restricted, Trash)
  • page hierarchy - parents and children
  • Now where did I find that?

Finding content

• Jump - easiest, first choice
  • TWikiBrowserPlugins - Jump feature for Firefox
• Search - when topic name won't help
• WebTopicList and WebIndex ( long load time) - listing of all pages, for the curious
• Quick tour
  • DeptOps - list of department operations
    • FacultyOps
    • StaffOps
    • DeptNews
  • FacultyStaff - our department with links to personal pages
  • Projects - list of long-term projects with links to project information
  • Seminars - weekly topics, plus links to other seminars, like RClinic
  • StatComp - information about statistical computing
    • RS - R and S-Plus
  • HowToPagesList - useful list of various "how to" pages.
  • BioPhones - list of department phone numbers
  • EmailLists - list of addresses on each email list

Adding new content or changing existing content

• you must register to do this (UserRegistration)
• Use edit link at the top or bottom of topic
• the (edit) mode page
  • Formatting and Style
    • Create clear, but unique page names. Avoid anything cryptic like CE, UFad or QC.
    • Discussions - add signature (-- ColeBeck - 24 Jan 2005)
    • Examples
      • New paragraph - insert a blank line
      • Headings - three dashes followed by plus signs
        ---+++ Level 3 Heading
        • Table of contents - if you use headings, you may wish to create a table of contents at the top of the page with the %TOC% variable
      • Bold text - enclose text with asterisks
        *Bold*
      • Lists - three spaces followed by asterisk
           * List item
      • Table - columns and cells are created with vertical bars, each line is a row
        | Cell 1,1 | Cell 1,2 | Cell 1,3 |
        | Cell 2,1 | Cell 2,2 | Cell 2,3 |
      • Outside links - enclose link within brackets, link text within brackets, then nest both within brackets
        [[http://www.vanderbilt.edu][Vanderbilt]]
      • Interwiki links (see InterWikis) - link to external sites
        Google:TWiki
      • Prevent link - Prepend text with <nop> or !
        <nop>PageLink
    • Install the Firefox Extension to help edit pages - FirefoxExtensionTwiki
      • Other Twiki Firefox Extensions
    • Syntax help (see TextFormattingRules)
      • If you have text that you don't want rendered by TWiki, surround it with <vebatim> tags
    • You can enter HTML code or JavaScript
      • If you want to use JavaScript, surround it with <pre> tags and HTML comments
  • Preview, Save, QuietSave, Checkpoint, etc.
    • Save: Save topic and return to normal view
    • QuietSave: Save but will not trigger email notifaction to people monitoring the page (checks the "Minor changes" checkbox)
    • Checkpoint: Save, and re-edit immediately
    • Preview: Do not save yet, but show what the topic would look if saved
    • Cancel: Discard changes and return to view mode, release lock
  • Release edit lock & Minor changes checkboxes
    • Edit lock prevents simulataneous page edits
    • Minor changes are not emailed under notification rules
• Moving/renaming pages
  • More topic options (bottombar)
  • Move topic to Trash web to delete
  • Remember to check links on pages that refer to moved topic
• Attaching files (bottombar)
  • Linking to documents: Create reference to attachment
  • Displaying images: Use HTML in order to apply attribrutes
  • Examples

Here is my file:
%ATTACHURL%/name_of_attachment.txt
Here is my picture:
<img src="%ATTACHURLPATH%/name_of_image.gif" alt="my picture" height="200" width="300">

User Preferences

• user home page (see WikiUsers, on sidebar)
• preference variables
  • Set personal preferences on your user page through twiki variables (see Macros)
  • Example
    * Set RELEASEEDITLOCKCHECKBOX = checked="checked"
  • Hide preferences by enclosing them within HTML comment tags: <!-- and -->
• secure a page by user/group (see AccessControl and WikiGroups)
  • Use twiki variables: ALLOWTOPICCHANGE, ALLOWTOPICVIEW
  • Set VARIABLE=UserName, GroupName
• modifying the sidebar
  • Jump to guestLeftBar and edit or click the create link on sidebar

Plug-ins

• plug-ins add extra functionality to the twiki (see InstalledPlugins)
• Examples
  • DirectedGraphPlugin allows you to draw directed graphs
  • EFetchPlugin allows you to cite journals from pubmed
  • EditTablePlugin adds extra functionality to tables
  • LatexModePlugin allows you include mathematics through latex
  • NotificationPluginListTemplate allows you to be notified about topic changes
  • SourceHighlightingPlugin allows you to highlight R source code
  • SpreadSheetPlugin allows you to do basic spreadsheet commands on a table
• request a new one through DalePlummer or ColeBeck