- Users should not be shy about editing the wiki, especially when adding information, correcting mistakes, and adding comments. When proposing a major change (such as altering a reaction mechanism), users can post comments on the "talk" pages that accompany every page in the wiki (click on the the discussion tab at the top of any page). A discussion can be held amongst users of the site, and a consensus can be reached before the change is made.
- Users should sign their name to comments that they make. This can easily be acheived by typing 4 tildes (~~~~). When the page is saved, the 4 tildes will be replaced with your username and the date and time. This makes it easier for people to know who made the comment, and when they made it.
- The best way to learn the syntax of the wiki, for editing existing pages or adding new pages in a manner consistent with the existing conventions and style of the wiki, is to click on "edit" and look at the coding behind the pages. You can copy and paste the code for a page, and use it as a template for a new page or section, changing the content as appropriate and keeping the style.
Page linking
- Link proteins names all the time. Every time a protein in the pathway is named, it should be bracketed by [[Imported:YPM/'s and |'s and ]]'s, even if a page for that protein does not yet exist.
- When applicable, multiple names for a protein, reaction, etc. should link to the same page. The way to do this is using redirects. For example, Ste4 and Ste18 both redirect to Ste4:Ste18 (because we're assuming that Ste4 and Ste18 are constitutively associated). So the contents of the Ste4 page is #REDIRECT [[Imported:YPM/Ste4:Ste18|Ste4:Ste18]], and thus clicking on a Ste4 link takes you directly to the Ste4:Ste18 page. This allows for easier referencing to Ste4 itself, or the Ste4:Ste18 dimer depending on context, but make both links lead to the same place.
Referencing
- Each fact given in the wiki is referenced to its source. This is done by including the author names, year of publication, and link to the paper on PubMed. To generate an automatic link to the article on pubmed, just type PMID 12345678, but replace 12345678 with the article's actual PubMed ID number.
Link to main page and categories
- Each wiki page in the model contains a link to the main model page, a link that includes that page in the Yeast Pheromone Response Model category, and a <hr> to put a bar across the screen. The link to the main model page Yeast pheromone response model makes navigation around the wiki easier. The link to the category places the page within that particular category. This serves to help organize the pages in the wiki, as well as ensure that the BNG model file can be correctly constructed (see modelExtension).
Here is an example the first four lines of all the model pages:
[[Imported:YPM/Category:Yeast Pheromone Response Model|Category:Yeast Pheromone Response Model]]
Back to [[Imported:YPM/Yeast pheromone response model|main model]] page<br>
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