Anno-J Instances

An Anno-J 'instance' is a website that you can visit to use the application. For example, the Salk Epigenome site is an 'instance'. Using an instance of Anno-J is simple; just visit the website using a W3C compliant web browser such as Safari or Firefox.

Creating an instance is a little more involved and requires website administration skills plus access to a web server (Mac OS X users: you already have access to the Apache web server). If you don't feel confident at this stage, then contact your local website administrator for advice.

1. Gain access to a web server
2. Configure a reverse proxy (not always required)
3. Create an instance
4. Configure the instance
5. Style the instance
6. Common problems

Configure the Instance Page

Having created the instance page, now comes the more involved task of configuring your AJ instance. Your configuration file can be a separate .js file that is linked to from the instance page, or the code can be included directly. Your choice.

Once you get the hang of configuration files, they are easy to make, but the first time around you will need to read the documentation for the various plugins to learn their configuration options. It's probably also a good idea to read up on services.

Here is an example of a typical configuration file. Copy and paste it into a file of your own and then change it to suit your needs. Note the difference between pointing to local and remote services.

	
		//The Anno-J configuration object
		AnnoJ.config = {
		
			//List of configurations for all tracks in the Anno-J instance
			tracks : [
		
				//Example config for a ModelsTrack
				{
					id   : 'models',
					name : 'Gene Models',
					type : 'ModelsTrack',
					path : 'Annotation models',

					//Pointing to a local service
					data : 'fetchers/models.php',
					height : 80,
					showControls : true
				},
				
				//Example config for a MethTrack
				{
					id   : 'meth',
					name : '5-methyl cytosine sites',
					type : 'MethTrack',
					path : 'DNA methylation',
					
					//Pointing to a remote service, the server must be configured as a reverse proxy
					data : 'proxy/http://some.remote.site/methylation.php',
					iconCls : 'salk_meth',
					height : 40
				},
				
				//Example config for a ReadsTrack
				{
					id   : 'reads',
					name : 'Deep sequencing',
					type : 'ReadsTrack',
					path : 'Reads',
					data : 'fetchers/bisulfite.php',
					iconCls : 'salk_meth',
					height : 70
				}, 	
				
				//Example config for a MicroarrayTrack
				{
					id   : 'wgta',
					name : 'Whole genome tiling array',
					type : 'MicroarrayTrack',
					path : 'Messenger RNA',
					data : 'fetchers/microarray.php',
					iconCls : 'salk_mrna',
					height : 60
				},
				
				//Example config for a SmallReadsTrack
				{
					id   : 'smrna_col0',
					name : 'smRNA Col-0',
					type : 'SmallReadsTrack',
					path : 'Small RNA',
					data : 'fetchers/smrna.php',
					iconCls : 'salk_smrna',
					height : 40
				}
			],
			
			//A list of tracks that will be active by default (use the ID of the track)
			active : [
				'models','meth','reads'
			],
			
			//Address of service that provides information about this genome
			genome    : 'fetchers/arabidopsis_thaliana.php',
			
			//Address of service that stores / loads user bookmarks
			bookmarks : 'fetchers/arabidopsis_thaliana.php',
		
			//A list of stylesheets that a user can select between (optional)
			stylesheets : [
				{
					id   : 'css1',
					name : 'Plugins CSS',
					href : 'css/plugins.css',
					active : true
				},{
					id   : 'css2',
					name : 'SALK CSS',
					href : 'css/salk.css',
					active : true
				}		
			],
			
			//The default 'view'. In this example, chr1, position 1, zoom ratio 20:1.
			location : {
				assembly : '1',
				position : 1,
				bases    : 20,
				pixels   : 1
			},
			
			//Site administrator contact details (optional)
			admin : {
				name  : 'Julian Tonti-Filippini',
				email : 'tontij01@student.uwa.edu.au',
				notes : 'Perth, Western Australia (UTC +8)'
			}
		};