Practical Implementation
Making a lab wiki requires wiki software and usually a database. The
author’s lab wiki site is hosted locally. To host your own website,
Apache HTTP software installed on a Mac mini or Linux machine is a
common method. To easily point lab members to a website, a domain name
should also be purchased or obtained from the Information Technology
(IT) department. The author uses MediaWiki16 and MySQL
database,17 both of which are freeware. Nowadays,
there are many options for wiki software, supported by different
database types18,19 with even LaTeX compatibility.
Besides MediaWiki, common free wiki software is also available through
TikiWiki20 and DokuWiki21, which
doesn’t require a database. Some companies will host your wiki for a
monthly fee, such as SiteGround, TMD hosting, A2 hosting, cloudways and
greengeeks. As well, Learning Management Software such as Blackboard and
Moodle have wiki creation tools. A class centered on research would need
to be created and then propagated every semester. These wikis are not as
versatile as one managed on your own, but it also requires less
administrative knowledge. Syntax and formatting examples given here are
specific to MediaWiki and analogous options are available through other
wiki software.
In MediaWiki, the LocalSettings.php file contains the configuration
settings for the wiki site, including how it interacts with the
internet. To set up your wiki, customize variables such as the
$wgSitename and database settings.
## Set the ScriptPath to where people should go to find your wiki
(https://your_website/labwiki)
$wgSitename = ”Set_to_Name_of_Wiki”;
$wgScriptPath = ”/labwiki”;
## The protocol and server name to use in fully-qualified URLs
$wgServer = ”https://set_to_your_website_address”;
## Database settings
$wgDBtype = ”mysql”;
$wgDBserver = ”localhost”;
$wgDBname = ”dbname_here”;
$wgDBuser = ”admin”;
$wgDBpassword = ”set_to_admin_password_for_database”;
To make the wiki password protected, edit the $wgGroupPermissions.
Different groups can be created with different permissions. For example,
the wikireader group has read-only access but the research group can
make new pages and edit material. After a username is made, it can be
assigned to a preexisting group, logged in as an administrator, under
Special Pages and User Rights Management.
#// Block everyone from creating an account, including reading and
editing
$wgGroupPermissions[’*’][’createaccount’] = false;
$wgGroupPermissions[’*’][’edit’] = false;
$wgGroupPermissions[’*’][’read’] = false;
#// Read-only accounts
$wgGroupPermissions[’wikireader’ ][’move’] = true;
$wgGroupPermissions[’wikireader’ ][’read’] = true;
$wgGroupPermissions[’wikireader’ ][’edit’] = false;
$wgGroupPermissions[’wikireader’ ][’createpage’] = false;
$wgGroupPermissions[’wikireader’ ][’createtalk’] = false;
$wgGroupPermissions[’wikireader’ ][’upload’] = false;
$wgGroupPermissions[’wikireader’ ][’reupload’] = false;
$wgGroupPermissions[’wikireader’ ][’reupload-shared’] = false;
$wgGroupPermissions[’wikireader’ ][’minoredit’] = false;
#// Editing accounts
##$wgGroupPermissions[’research’ ][’move’] = true;
##$wgGroupPermissions[’research’ ][’read’] = true;
##$wgGroupPermissions[’research’ ][’edit’] = true;
#$wgGroupPermissions[’research’ ][’createpage’] = true;
#$wgGroupPermissions[’research’ ][’createtalk’] = true;
#$wgGroupPermissions[’research’ ][’upload’] = true;
#$wgGroupPermissions[’research’ ][’reupload’] = true;
#$wgGroupPermissions[’research’ ][’reupload-shared’] = true;
#$wgGroupPermissions[’research’ ][’minoredit’] = true;
To make a new Topic Heading use the syntax of putting two equal signs on
both sides of the header. To make a new wiki page under each topic,
place double brackets around the title of each new page. A ‘*’ inserts a
bullet point and to nest a bullet point under another one, use ‘**’. The
syntax below is used to making the Main Page Contents (Figure 1).
==<big>”’Welcome to the Nagan Lab
Wiki”’</big>==
This is the Nagan group’s lab wiki. It contains information to carry out
Dr. Nagan’s computational research. All Nagan group members can view/add
content to the lab wiki. If you need an account, email Dr. Nagan
(maria.nagan@stonybrook.edu).
==New Nagan Group Member Assignments==
*[[Checklist for New Nagan Group Members]]
*[[Download a PDB from the PDB Databank and Learn VMD]]
*[[Learn vi and Unix]]
==Intro to Computers==
* [[Unix]]
* [[Vi Text Editor]]
* [[File Path]]
* [[Working from Home - ssh]]
==Introduction to Biomolecules==
* [[Central Dogma of Molecular Biology]]
* [[Nucleic Acid Structure]]
** [[2D and 3D RNA Structure]]
** [[RNA Structure Parameters]]
* [[Amino Acids and Protein Structure]]
* [[RNA Recognition]]
==Visualization==
*[[VMD]]
*[[Chimera]]
Numbered lists can also be made by using a “#” instead of a “*” in
the example above. To edit the newly created pages, select the new page
and choose to edit the page. Basic formatting such as bold and italics
can be found in the GUI formatting bar in edit mode (Figure 5). There
are also tools to insert internal links or new pages, external links,
new topics, pictures and media.
Both links to internal pages on the lab wiki and external links to
websites are useful tools to direct readers to more information. To
insert a link to an internal page, put double brackets around the page
name. If the page name is piped to a set of words, then insert a
“|” between the lab wiki page name and the words to display.
Surround the whole internal link with double brackets.
==Additional Help==
*For more information about the specifics of the pdb file, see [[pdb
file| What is a pdb file?]]
*For a tutorial on how to use VMD, see [[VMD]].
Linking to an external page requires placement of single brackets around
the web page address. By default, the web address link becomes a number.
If the actual web address should be displayed or link text, then include
a space between the link and the link text.
==Manuals==
The most current Amber manual can be found at [https://ambermd.org
https://ambermd.org]
Files can be uploaded to the wiki and then referred to in links;
although the types of files extensions may need to be expanded. The
allowed filetypes can be customized to include for example word
processing files, image files, presentation files and spreadsheets.
ImageMagick22 is common freeware that can edit images
but also make thumbnails for the wiki. To turn it on, set the variable
to $wgUseImageMagick = true and set the $wgImageMagickConvertCommand
to the correct path.
## To enable image uploads, make sure the ’uploads’ directory
## is writable, then set this to true:
$wgUploadPath = ”$wgScriptPath/uploads”;
$wgUploadDirectory = ”$IP/uploads”;
$wgEnableUploads = true;
$wgUseImageMagick = true;
$wgImageMagickConvertCommand = ”/usr/bin/convert”;
#Override the default with a bundle of filetypes:
$wgFileExtensions = array( ’png’, ’gif’, ’jpg’, ’jpeg’, ’ogg’, ’zip’,
’tar’, ’gz’, ’doc’,
’ppt’, ’txt’, ’csh’, ’xls’, ’pdf’, ’pdb’, ’xyz’, ’top’, ’crd’, ’frcmod’,
’lib’,
’scr’, ’perl’, ’awk’, ’in’, ’out’, ’com’, ’xlsx’, ’docx’, ’pptx’, ’ai’,
’psd’
);
The maximum file size limit may also need to be increased beyond the 500
KB default and enough disk space on the web hosting machine should be
ensured. To change the maximum file size, edit /etc/php.ini and change
the upload_max_filesize value to the desired value. Then restart
apache.
Links to images, media and files can be accomplished through the word
image, file or media followed by a colon and the name of the uploaded
file. Media displays a link to the actual file name. For images,
formatting options such as centering or resizing specifications can be
incorporated after a “|”, all surrounded by double brackets.
The Amber19 Tools Manual: [[media:Amber19_and_Tools.pdf]]
[[image:dna_rna.jpeg|center]]
Wiki management capabilities can be found under Special Pages. Here,
user accounts can be created, blocked and assigned to groups. As well,
there is a list of all pages and maintenance reports. Pages with broken
links and uploaded file lists can also be seen here.