Difference between revisions of "IGEM Wiki"

From SynBioCyc
Jump to: navigation, search
 
(17 intermediate revisions by one user not shown)
Line 4: Line 4:
 
=== Resources/Cheatsheets ===
 
=== Resources/Cheatsheets ===
  
* http://2018.igem.org/Resources/Wiki_Editing_Help
+
* [http://2018.igem.org/Resources/Wiki_Editing_Help iGEM Wiki Editing Help (has guidelines you must follow and a few tips) ]
* https://www.mediawiki.org/wiki/Help:Formatting
+
* [https://www.mediawiki.org/wiki/Help:Formatting Media Wiki Formatting (has everything you could ever want to do) ]
  
 
=== Creating a New Page ===
 
=== Creating a New Page ===
Line 16: Line 16:
  
 
<pre>
 
<pre>
[[CH391L/S14/YourPageName]]
+
[[Team:Austin_UTexas/PageName]]
[[CH391L/S14/YourPageName | Link text that you want to display rather than page name]]
+
[[Team:Austin_UTexas/PageName | Link text that you want to display rather than page name]]
 
</pre>
 
</pre>
  
Line 36: Line 36:
 
You can find more examples [https://www.mediawiki.org/wiki/Help:Links#External_links here].
 
You can find more examples [https://www.mediawiki.org/wiki/Help:Links#External_links here].
  
=== Adding Images and Files ===
+
=== Making Headers ===
 +
 
 +
There are two ways to make headers:
 +
 
 +
The first uses Wiki shorthand:
 +
<pre>
 +
= Heading 1 =
 +
== Heading 2 ==
 +
=== Heading 3 ===
 +
</pre>
 +
 
 +
The second uses HTML tags:
 +
<pre>
 +
<h1>Heading 1</h1>
 +
<h2>Heading 2</h2>
 +
<h3>Heading 3</h3>
 +
</pre>
 +
 
 +
Try these out. Notice a difference in how they are rendered? Which one should you use for the website?
 +
 
 +
Why do you want to use headings? This allows a table of contents to be created that will automatically be updated when you add or take away headers later. Very handy!!
 +
 
 +
=== Images and Files ===
  
 
#First click the "Upload files" link in the toolbar under "wiki tools" and upload your file or image.
 
#First click the "Upload files" link in the toolbar under "wiki tools" and upload your file or image.
Line 42: Line 64:
 
#* If you (or someone else!) uploads a file with the same name, it will overwrite the older version!
 
#* If you (or someone else!) uploads a file with the same name, it will overwrite the older version!
 
# Now edit the Wiki page where you want the file to be linked from or the image displayed.
 
# Now edit the Wiki page where you want the file to be linked from or the image displayed.
#*'''For images''', to display the image embedded in the page add a tag of the form:<pre>[[Image:T--OFFICIAL team name--File_name.xxx | frame | right | Short description of image]]</pre>If the image needs to be resized within your topic page, you can specify to use a thumbnail: <pre>[[Image:T--OFFICIAL team name--File_name.xxx| thumb | left | Short description of image]]</pre> Or a fixed number of pixels for the width: <pre>[[Image:T--OFFICIAL team name--File_name.xxx | thumb | right | 150 px | Short description of image]]</pre> You can can also specify some additional [http://www.mediawiki.org/wiki/Help:Images display options] for images, including adding a border.
+
#*'''For images''', to display the image embedded in the page add a tag of the form:<pre>[[Image:T--OFFICIAL team name--File_name.xxx | frame | right | Short description of image]]</pre>If the image needs to be resized within your topic page, you can specify to use a thumbnail: <pre>[[Image:T--OFFICIAL team name--File_name.xxx| thumb | left | Short description of image]]</pre> Or a fixed number of pixels for the width: <pre>[[Image:T--OFFICIAL team name--File_name.xxx | thumb | right | 150 px | Short description of image]]</pre>Or one that is inline rather than floating around your text: <pre>[[Image:T--OFFICIAL team name--File_name.xxx | none | Short description of image]]</pre>  You can can also specify some additional [http://www.mediawiki.org/wiki/Help:Images display options] for images, including adding a border.
 
#*'''For files''', you can link to the file using this Wiki markup:<pre>[[Media:T--OFFICIAL team name--File_name.xxx | Name of link to your file]]</pre>It will link to the page which gives details about the file (when it was uploaded, its size, etc.) instead of directly to the file, if you use this syntax:<pre>[[File:T--OFFICIAL team name--File_name.xxx | Name of link to your file]]</pre>
 
#*'''For files''', you can link to the file using this Wiki markup:<pre>[[Media:T--OFFICIAL team name--File_name.xxx | Name of link to your file]]</pre>It will link to the page which gives details about the file (when it was uploaded, its size, etc.) instead of directly to the file, if you use this syntax:<pre>[[File:T--OFFICIAL team name--File_name.xxx | Name of link to your file]]</pre>
 +
 +
=== References ===
 +
 +
There are some special tags that make adding references to a page much, much easier.
 +
 +
[https://helpwiki.evergreen.edu/wiki/index.php/References_-_Mediawiki Instructions Here]
 +
 +
Decide on a standard citation style to use for the iGEM pages now, so that there won't be a need for a lot of reformatting later.
 +
 +
Here is a nice clean style used by [https://academic.oup.com/nar/pages/Ms_Prep_Submission#preparation Nucleic Acids Research]:
 +
 +
Geng, P., Leonard, S. P., Mishler, D. M., Barrick, J. E. (2019) Synthetic genome defenses against selfish DNA elements stabilize engineered bacteria against evolutionary failure. ''ACS Synth. Biol.'' '''8''', 521-531.
  
 
=== Tutorial ===
 
=== Tutorial ===
Line 50: Line 84:
  
 
<pre>
 
<pre>
https://2019.igem.org/Team:Austin_UTexas/YourName
+
https://2019.igem.org/Team:Austin_UTexas/YourNameSandbox
 
</pre>
 
</pre>
  
 
The page shouldn't exist to click "edit page".
 
The page shouldn't exist to click "edit page".
  
2. Add a link to your neighbor's page (internal link)!
+
2. Add an internal link to your neighbor's page and another link to the main page (it's called "Team:Austin_UTexas").
  
3. Add a link to some other website (external link)!
+
3. Add an external link to some other website!
  
4. Add an image to your page (be sure it's appropriate and not copyrighted!)
+
4. Add some headers to your page.
 +
 
 +
5. Add an image to your page (be sure it's appropriate and not copyrighted!)
  
 
Name your image in this way to avoid any conflicts with other people's images.
 
Name your image in this way to avoid any conflicts with other people's images.
Line 70: Line 106:
 
[[Image:Austin_UTexas_logo.png| frame | none | Example image you can use]]
 
[[Image:Austin_UTexas_logo.png| frame | none | Example image you can use]]
  
5. Finally, discuss how you will keep page names and file names organized. I recommend making a directory on UT Box that contains all files uploaded to the Wiki.
+
6. Add the website template to your page. This will change the appearance of everything:
 +
 
 +
<pre>
 +
{{Austin_UTexas}}
 +
</pre>
 +
 
 +
7. Add a citation and a reference list to your page.
 +
 
 +
8. Finally, discuss as a group how you will keep page names and file names organized. I recommend making a directory on UT Box that contains all files uploaded to the Wiki.

Latest revision as of 08:52, 10 June 2019

Your team page: https://2019.igem.org/Team:Austin_UTexas

Resources/Cheatsheets

Creating a New Page

Your pages must be named in this format: Team:Austin_UTexas/PageName

You are allowed to categorize things by adding extra slashes to the name like this: Team:Austin_UTexas/CategoryName/PageName

The easiest way to create a new page is to create a link (on another page) and then click on that link to edit the new page. To do this, you can edit a page to contain a link in one of these two ways:

[[Team:Austin_UTexas/PageName]]
[[Team:Austin_UTexas/PageName | Link text that you want to display rather than page name]]

If you want the new page to show up in the menu, you need to edit the template.

If you "lose" a page and can't find it via a link by know the name, just type a URL of this form in your browser:

https://2019.igem.org/Team:Austin_UTexas/PageName

External Links

There is a different format for linking to pages outside of the Wiki:

[https://mediawiki.org MediaWiki]

You can find more examples here.

Making Headers

There are two ways to make headers:

The first uses Wiki shorthand:

= Heading 1 =
== Heading 2 ==
=== Heading 3 ===

The second uses HTML tags:

<h1>Heading 1</h1>
<h2>Heading 2</h2>
<h3>Heading 3</h3>

Try these out. Notice a difference in how they are rendered? Which one should you use for the website?

Why do you want to use headings? This allows a table of contents to be created that will automatically be updated when you add or take away headers later. Very handy!!

Images and Files

  1. First click the "Upload files" link in the toolbar under "wiki tools" and upload your file or image.
    • important! Your images and files must have a "Destination filename" of the form T--OFFICIAL team name--File_name.xxx.
    • If you (or someone else!) uploads a file with the same name, it will overwrite the older version!
  2. Now edit the Wiki page where you want the file to be linked from or the image displayed.
    • For images, to display the image embedded in the page add a tag of the form:
      [[Image:T--OFFICIAL team name--File_name.xxx | frame | right | Short description of image]]
      If the image needs to be resized within your topic page, you can specify to use a thumbnail:
      [[Image:T--OFFICIAL team name--File_name.xxx| thumb | left | Short description of image]]
      Or a fixed number of pixels for the width:
      [[Image:T--OFFICIAL team name--File_name.xxx | thumb | right | 150 px | Short description of image]]
      Or one that is inline rather than floating around your text:
      [[Image:T--OFFICIAL team name--File_name.xxx | none | Short description of image]]
      You can can also specify some additional display options for images, including adding a border.
    • For files, you can link to the file using this Wiki markup:
      [[Media:T--OFFICIAL team name--File_name.xxx | Name of link to your file]]
      It will link to the page which gives details about the file (when it was uploaded, its size, etc.) instead of directly to the file, if you use this syntax:
      [[File:T--OFFICIAL team name--File_name.xxx | Name of link to your file]]

References

There are some special tags that make adding references to a page much, much easier.

Instructions Here

Decide on a standard citation style to use for the iGEM pages now, so that there won't be a need for a lot of reformatting later.

Here is a nice clean style used by Nucleic Acids Research:

Geng, P., Leonard, S. P., Mishler, D. M., Barrick, J. E. (2019) Synthetic genome defenses against selfish DNA elements stabilize engineered bacteria against evolutionary failure. ACS Synth. Biol. 8, 521-531.

Tutorial

1. Create a new "sandbox" page based on your name. We won't link it anywhere, so just type this in your browser:

https://2019.igem.org/Team:Austin_UTexas/YourNameSandbox

The page shouldn't exist to click "edit page".

2. Add an internal link to your neighbor's page and another link to the main page (it's called "Team:Austin_UTexas").

3. Add an external link to some other website!

4. Add some headers to your page.

5. Add an image to your page (be sure it's appropriate and not copyrighted!)

Name your image in this way to avoid any conflicts with other people's images.

T--Austin_UTexas--YourName_FileName

If you don't have your own image, use this one (right click to download it to your computer first):

Example image you can use

6. Add the website template to your page. This will change the appearance of everything:

{{Austin_UTexas}}

7. Add a citation and a reference list to your page.

8. Finally, discuss as a group how you will keep page names and file names organized. I recommend making a directory on UT Box that contains all files uploaded to the Wiki.