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Editing WiLiKi

Table of Contents of this page


Preliminaries

Wiki is a class of web-based softwares which allow you to view and edit web pages through a web browser. There are a number of wiki systems around (called Wiki clones) written in many different programming languages. The particular clone we use here is WiLiKi (see WiLiKi:WiLiKi) written in an implementation of the Scheme programming language (a major dialect of Lisp) called Gauche.

This page contains almost everything about how to write wiki pages using WiLiKi.

The following is a list of things to note when using this system:

  1. No HTML tags can be used. Wiki allows you to edit web pages with ease at the cost of limited capabilities.
  2. Images can be displayed only if they are located at www.pdbj.org or *.protein.osaka-u.ac.jp domains.
  3. If you find any problems, contact Akira Kinjo.
  4. There are a few known bugs in this wiki system. But it should be OK for most situations.

Link to other wiki page

A link to another wiki page is made by enclosing the page name by [[ and ]]. The page name of wiki pages are traditionally called WikiName.

A link to a usual URL can be made by just writing the URL. If you want to make a link to that URL with a different link name, enclose the URL (followed by the name you want) by "[" and "]" (square brackets).

Example:

[[Introduction to Proteins]]

http://www.pdbj.org/

[http://www.pdbj.org/ PDBj Home]

Output:

Introduction to Proteins

http://www.pdbj.org/

PDBj Home

Creating a new wiki page

Let "XXX" be the name of the new page. To create it, just make a link to that page, i.e., write

[[[XXX]]

then you will find something like this: XXX?. Note the quation mark (?) after the page name. By clicking "?", you enter the editing mode of that page.

Comments and line continuation

  • Lines starting with ";;" are treated as comments and are not output as HTML.
  • Lines starting with "~" are treated as continued from the previous line (except for comments).

Examples:

;; this is a comment.
A normal line.
~ a continued line.
;; even if comments are placed, they are simply ignored.
~ more continued lines....

Output:

A normal line. a continued line. more continued lines....

Paragraphs, line breaks, <hr> (horizontal line)

Contiguous lines are treated as one paragraph. An empty line separates two paragraphs.

If you want to force a line break (<br> in HTML), write "
" at the end of line.

Lines containing only our minuses "----" are horizontal lines (<hr> in HTML).

Example:

First paragraph.
Still in the first paragraph.

Second paragraph. line break -> ~% a line after the line break.
----

Output:

First paragraph. Still in the first paragraph.

Second paragraph. line break ->
a line after the line break.


Section heading

Lines starting with an asterisk "*" are headings. With increasing number of "*", "**", "***", ... , headings become smaller.

Example:

* head1
** head2
*** head3
**** head4
***** head5

Output:

head1

head2

head3

head4
head5

Inline decorations

When you enclose something by a pair of two single quotes ('), it is emphasized (<em> in HTML). By enclosing it by a pair of three single quotes, it is even more emphasized (<strong> in HTML). These are not applied over multiple lines automatically. If that's what you want, use line continuation using (~).

When you want to display special character sequences, you can use empty decorations (e.g., 6 single quotes).

Example:

''emphasized (<em>)'' word and '''even more emphasized (<strong>)''' word.

''emphasizing across
~lines''

Using empty modification to display a special character sequence ~''''''% as is.

Output: emphasized (<em>) word and even more emphasized (<strong>) word.

emphasizing across lines

Using empty decoration to display a special character sequence ~% as is.

Listing

Lines starting with "-" are unordered lists (<ul> in HTML), those starting with "#" are ordered lists (<ol> in HTML). By increasing the number of "-" or "#" like "--", "---", ... or "##", "###", ..., the depth of the lists increases. "-" and "#" can be mixed at different levels.

Definition lists (<dl> in HTML) can be made with lines starting with ":". Basic usage is ":heading:explanation". In this example, the explanation part can be on the next line. However, if the explanation part contains ":"'s, it must be on the next line. (It is OK for a heading to contain ":".)

Example.

- introduction
## part 1
--- part 1.1
--- part 1.2
## part 2
--- part 2.1
--- part 2.2
--- part 2.3
- conclusion

:FORTRAN: FORmula TRANslation
:LISP: 
LISt Processor / Lots of Irritating, Silly Parentheses
:Perl: Practical Extraction and Report Language /
Pathologically Eclectic Rubbish Lister

Output:

  • introduction
    1. part 1
      • part 1.1
      • part 1.2
    2. part 2
      • part 2.1
      • part 2.2
      • part 2.3
  • conclusion
FORTRAN

FORmula TRANslation

LISP

LISt Processor / Lots of Irritating, Silly Parentheses

Perl

Practical Extraction and Report Language / Pathologically Eclectic Rubbish Lister

Formatted text, verbatim blocks

If a line starts with a space, that line is displayed as an already formatted text (<pre> in HTML). If such lines continue, they are placed in one <pre> block. WiKiNames, URLs and inline modifications are processed.

Text parts enclosed by a line containing only '{{{' and another line with only '}}}' are also treated as already formatted texts. In this case, WikiNames, etc. are not processed.

Example:

 lines starting with a space (<pre> block)
 ''emphasis'' or [[Topics]] (WikiName) or http://www.pdbj.org/
 are processed.
 This one also: [http://www.pdbj.org/ PDBj Home].
 {{{
 lines enclosed by {{{ and }}} are also  treated as verbatim block.
 ''emphasis'' or [[Topics]] (WikiName) or http://www.pdbj.org/ or 
 [http://www.pdbj.org/ PDBj Home] 
 are NOT processed.
 Note
 the text
 appears 
 as is. No automatic line continuations...
 }}}

Output:

 lines starting with a space (<pre> block)
 emphasis or Topics (WikiName) or http://www.pdbj.org/
 are processed.
 This one also: PDBj Home
lines enclosed by {{{ and }}} are also  treated as verbatim block.
''emphasis'' or [[Topics]] (WikiName) or http://www.pdbj.org/ or 
[http://www.pdbj.org/ PDBj Home] 
are NOT processed.
 Note
 the text
 appears 
 as is. No automatic line continuations...

Quotes

Parts enclosed by a line with only "<<<" and another line with only ">>>" are processed as quotes (<blockquote> in HTML). Quotes can be nested.

Example:

<<<
Also sprach Zarathustra:
<<<
ALSO also Also!
>>>
period.
>>>

Output:

Also sprach Zarathustra:

ALSO also Also!

period.

Putting images

URL of images must be www.pdbj.org/* or *.protein.osaka-u.ac.jp/*, otherwise images will not appear as such but becomes a link to that image.

[[$$image http://www.pdbj.org/pdb_images/8abp_y.jpg]]

Specifying the image size

You can write like this [[$$image http://www.pdbj.org/pdb_images/8abp_y.jpg width=100]] and 
[[$$image http://www.pdbj.org/pdb_images/135l_x.jpg width=30]] and so on.

You can write like this and and so on.

If the image is not on the allowed domain such as

[[$$image http://fuji-maru.sakura.ne.jp/jpg/805-31_240x320.jpg]]

It will appear like this: [image]

Tables

If there are "||" at the beginning and end of a line, the line is a row of a table (table line). Contiguous table lines make a table.

|| Col1 || Col2 || Col3 ||
|| 1 || 2 || 3||
||[[$$image http://www.pdbj.org/pdb_images/8abp_x.jpg width=100]]
~||[[$$image http://www.pdbj.org/pdb_images/8abp_y.jpg width=100]]
~||[[$$image http://www.pdbj.org/pdb_images/8abp.jpg width=100]]||
Col1 Col2 Col3
1 2 3

Making links to PDBj services

We use InterWikiName facility.

- [[xPSSS:1GOF]]
- [[jV3:1GOF]]
- [[eF-site:1GOF]]

Some useful macros

Automatically writing the primary citation for a given PDB ID.

If you write the following

[[$pdbj_citation 1gof]]

and commit, the primary citation for PDB ID 1gof will be expanded as follows:

Ito, N. Phillips, S.E. Stevens, C. Ogel, Z.B. McPherson, M.J. Keen, J.N. Yadav, K.D. Knowles, P.F.; "Novel thioether bond revealed by a 1.7 A crystal structure of galactose oxidase."; Nature; (1991) 350:87-90 PubMed:2002850.

Note there's only one "$" in the macro.

Automatically writing the EC (Enzyme Code) number for a given PDB ID.

Write

[[$pdbj_ec_number 1gof]]

and commit it, the EC number of 1gof will be displayed as

Enzyme:1.1.3.9

This links to http://www.expasy.org/enzyme/ If there is not EC number for the given PDB ID, nothing will be displayed.

[[$pdbj_ec_number 1j00]]

-> Enzyme:3.1.2.- Enzyme:3.1.1.5

Some other macros

Date/time

To display the date (and time) when the current page is committed, use the '$date' macro. Note, unlike other macros, there is only one dollar mark ($).

Example:

[[$date]] is the time when this page was committed.

Output: 2007/01/18 16:40:42 JST is the time when this page was committed.

Table of Contents

Table of contents of a Wiki Page is display by typing

TOC of [[Topics]]:
[[$$toc Topics]]

TOC of the current page:
[[$$toc]]

Output:

TOC of Topics:

    TOC of the current page:

    Index

    To make a list of pages that start with "xPSSS", write

    [[$$index xPSSS]]
    

      Compact Index

      Compact index can be made by

      [[$$cindex xPSSS /]] 
      ;; "/" is used as a separator. you can use other characters too!