GMOD

Site Guidelines

This page discusses editorial policies and best practices to follow when updating or creating content in the GMOD web site.

Contents

Introduction

The GMOD web site editorial policies and best practices are defined here. Consistent use of these policies and practices will hopefully lead to a consistent and readable web site.

This page first introduces meta-guidelines. These are guidelines about these guidelines and cover things like how to update the guidelines, and when you can ignore them. These are followed by the actual guidelines, describing how content should be created.

Meta-Guidelines

Or, Guidelines on Guidelines.

Ignoring

Q: Can I ignore these guidelines?

A: Yes.

We would much rather have a contribution that completely ignores these guidelines than not have the contribution at all.

This is for pragmatic and philosophical reasons. The whole goal of a wiki is to encourage people to contribute and maintain content. Site guidelines encourage a clean and well organized web site, but if the guidelines discourage people from contributing in the first place, then they have defeated the whole purpose.

It also takes some time to become proficient at MediaWiki (the wiki package behind this web site), and it can be a challenge to learn MediaWiki details and site policies at the same time.

However, once you get comfortable with MediaWiki, please think about writing your content so it does conform to these standards.

Updating

These guidelines are a work in progress and you are encouraged to suggest additions, deletions or revisions to them. The best way to do this is to send your comments to the GMOD Help Desk. Alternatively, you can post them to this page (or to this page’s discussion/talk page).

Enforcing

Q: Is there any enforcement of these guidelines?

A: Not really.

Beyond the usual wiki practices, there is no enforcement of these guidelines. This means that any non-conforming material you write won’t be deleted, but it might be modified to follow the guidelines if and when somebody notices.

Guidelines

This is a list of guidelines for creating content in the GMOD web site. Some guidelines are accompanied by discussion that explains them.

Guidelines are shown like this.

Discussion is shown as regular text.

Page Names

Capitalization

Use Generous Capitalization instead of Parsimonious capitalization.

For example, use “Site Guidelines” instead of “Site guidelines”.

It looks better.

Redirects

Use of MediaWiki redirects for page name synonyms is encouraged.

This means that if a user types “Generic Genome Browser” in the “Go/Search” box and you have a redirect defined for “GBrowse” then they will go directly to the GBrowse page, instead of the search results page.

To create a redirect page, enter the name of the redirect page in the Go/Search box and hit enter. Then click on the “create this page” link. In our example, you would enter/search for “Generic Genome Browser”.

This will display an empty page. Enter

#REDIRECT [[Page Name to Redirect to]]

In our example this would be:

#REDIRECT [[GBrowse]]

and then save the page.

A slight downside of this is that the Special:Allpages view now displays lots of pages that are only redirects to other pages. This turns into more of an index than a listing of all pages.

Minor vs Major Edits

If you do not want the page you are editing to be listed in the New & Revised Pages list on the GMOD home page, then mark your edit as minor.

When you update a page in this web site you can flag it as a minor edit. As of December 2007, the minor/major edit distinction is used in one place in the GMOD web site: Major edits (that is, edits that are not marked as minor) cause the page to be listed in the New & Revised Pages list on the GMOD home page. That list is a reverse chronological ordering of all recent non-minor edits

If your edit is small, such as a spelling or other typo correction, then mark it as a minor edit.

Tags / Categories

Tag any pages you edit with appropriate categories for that page.

Be generous in your tagging. If a particular category gets too many pages in it then the help desk will subdivide that category.

This web site makes extensive use of tags, called categories in MediaWiki, to flag pages as being related to different topics. To encourage the use of categories, an input field and tag cloud listing existing categories is shown at the bottom of every edit page. You can either type in the category name or click on the category in the tag cloud to add it to the current page.

As of January, 2008 we are still adding category tags to pages. Once that work is closer to complete, categories will be prominently featured in site navigation.

New Categories

If you think we need a new category then create it.

You can create a new category by typing the new category name in the Categories form on an edit page.

When creating a new category please:

Or, just send your new category suggestion to the GMOD Help Desk and we will add it.

Uploading Files

Destination Filenames

When uploading a file, please give the file a meaningful Destination filename.

The Destination filename is the name the file will have in the GMOD web site. Why does this matter? Filenames are displayed in Categories, but none of the text in the file is. Therefore the filename should describe the contents of the file.

For example, the file Gkl777.pdf is an article on ParameciumDB from Nucleic Acids Research, but if you look at the file’s listing in the Publications category all you see is “Gkl777.pdf”. You have to follow the link to find out what the file is about.

File Categories

When uploading a presentation or a paper, please add it to the Presentations or Publications categories. Also add the file to any other appropriate categories.

If the file is an image that is being linked to from a page then you don’t need to categorize it.

Diagrams and Cartoons

When uploading a diagram or cartoon that was created in a drawing program upload the exported image file (png, jpg, gif) and the original source file. Load both files with the same name, but different extensions.

This will allow others (and yourself) to modify the diagrams in the future rather than recreate them from scratch.

Format

Please Note:

  1. These guidelines were first developed for the GMOD Courses, where these were used to format the Tutorial pages.
  2. If this seems daunting, please see Meta-Guideline #1: Ignoring, and hopefully feel better.

Descriptions of what formatting is desired and how to achieve it. For each type of text, this shows a minimum desired formatting, and, in most cases, a better (but more work) formatting.

Many of these are the result of questions and suggestions from past participants.

Type of text Minimum Better
Files, Directories and Paths
Use fixed width font 
Check the thingy.conf file.

Check the thingy.conf file.

 

Check the <tt>thingy.conf</tt> file.

Check the thinigy.conf file.
Shell output
Use fixed width font
You can add a leading space on each line: 
 > "Pythium" for the default organism

Or use pre tags:

<pre>
Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Cell Ontology
[6] Plant Ontology
</pre>
> "Pythium" for the default organism

Or

Available ontologies:
[1] Relationship Ontology
[2] Sequence Ontology
[3] Gene Ontology
[4] Chado Feature Properties
[5] Cell Ontology
[6] Plant Ontology
 Same
Text to be entered by student
To distinguish it from surrounding text. Use fixed width font. 
 ~/work/galaxy-dist$ head tool_conf.xml
~/work/galaxy-dist$ head tool_conf.xml


~/work/galaxy-dist$ <span class="enter">head tool_conf.xml</span>

~/work/galaxy-dist$ head tool_conf.xml
Run a text editor
Just use gedit in any examples. It's confusing to novices to see vi, emacs. vim, xemacs and so on on different pages.


Edit the configuration file: gedit thingy.conf

Edit the configuration file:

gedit thingy.conf


Edit the configuration file: gedit thingy.conf TextEditorLink|gedit

Edit the configuration file:

gedit thingy.conf
A word on text editors such as gedit.
Shell Prompt?
Should we show the shell prompt in the wiki examples?
I dunno I dunno either
Code
Used fixed width font. Most programming languages can be color-coded in this wiki. 
<pre>
<tool id="get_flanks1" name="Get flanks">
  <description>
    returns flanking region/s for genes
  </description>
  <command interpreter="python">
    get_flanks.py $input ...
  </command>
...</pre>
<tool id="get_flanks1" name="Get flanks">
  <description>
    returns flanking region/s for genes
  </description>
  <command interpreter="python">
    get_flanks.py $input ...
  </command>
...
 
<syntaxhighlight lang="xml">
<tool id="get_flanks1" name="Get flanks">
  <description>
    returns flanking region/s for genes
  </description>
  <command interpreter="python">
    get_flanks.py $input ...
  </command>
...</syntaxhighlight>
<tool id="get_flanks1" name="Get flanks">
  <description>
    returns flanking region/s for genes
  </description>
  <command interpreter="python">
    get_flanks.py $input ...
  </command>
...
Instructions that are not to be performed during class
These can be negative examples or things were done to the VMware image before the course. 

<div class="dont">
Here's an example of what ''not'' to do:
 cd /;
 sudo rm -rf *
</div>

Here's an example of what not to do:

cd /
sudo rm -rf *
 Same
GUI Interaction
Looking for terseness and clarity


Now, to enable this theme, navigate to Administer, Site Building, Themes page and select the Pixture Reloaded radio button.

Now, to enable this theme, navigate to Administer, Site Building, Themes page and select the Pixture Reloaded radio button.


Now, to enable this theme, ''navigate'' to the '''Administer &rarr; Site Building &rarr; Themes''' page and ''select'' the '''Pixture Reloaded''' button.

Now, to enable this theme, navigate to the Administer → Site Building → Themes page and select the Pixture Reloaded button.

Embedding Media

The GMOD wiki uses Widgets to embed various types of file.

Flash

To embed Flash into a page, use the following syntax:

<oflash file="File:Movie.swf" caption="A cool flash movie that I made" width=500 height=900 />

More documentation on the OFlash MediaWiki page.

Writing Code

The GMOD wiki employs the extension Syntax Highlight GeSHi to produce code with highlighting. For coloured code, use the ` ` tag:

<syntaxhighlight lang="perl">
#!/usr/bin/perl
my $life = "over";
die("Goodbye, cruel world!");
</syntaxhighlight>

 #!/usr/bin/perl
 my $life = "over";
 die("Goodbye, cruel world!");

Languages supported include Javascript, Java, Perl, PHP, XML, CSS, and more. Full documentation can be found on the Syntax Highlight GeSHi MediaWiki page.

Adding References

If you wish to reference a paper with a PubMed ID or a digital object identifier (DOI), the full information can be automatically retrieved from PubMed or the CrossRef server for you. To create the reference, use the <ref /> tag:

<ref name=PMID:15752432 />

The name attribute can contain either a PubMed ID in the form PMID:00000000 or a DOI in the form DOI:10.1186/1471-2164-14-741.

Put the tag <references /> where you want the full references to appear on the page. The full details of each paper will magically appear in place of the <references /> tag.

Example

Wikitext

The 2013 paper by Leite ''et al.'' on the grooved shell carpet clam <ref name="DOI:10.1186/1471-2164-14-741" />
represents a first attempt to characterize ''Ruditapes decussatus'' transcriptome; it cites the classic Ficklin
''et al.'' Tripal paper <ref name="PMID:21959868" />.

<references />

Result

The 2013 paper by Leite et al. on the grooved shell carpet clam[1] represents a first attempt to characterize Ruditapes decussatus transcriptome; it cites the classic Ficklin et al. Tripal paper [2].

  1. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named DOI:10.1186.2F1471-2164-14-741
  2. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named PMID:21959868

Component Information Pages

The information pages about each component are generated by feeding the information on the tool_data page through a template. To edit what appears on the component page, you need to edit the corresponding tool_data page.

Tool data is stored in tag-value pairs in the format

 | tag = value

The value can be formatted wiki text or a wiki template, and may span numerous lines. For example:

| tag = value
| tag = '''value'''
| tag = [[Main Page|A link to a page]]

Some more wikitext here

[[Site Guidelines|A link to another page]]
| tag = Include A Template

The tool_data pages essentially act as a data store, and the page Template:ToolDisplay parses and formats the data to produce a standardized GMOD component page.

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