AnnoJ.config = {

	tracks : [

		//Models
		{
			id   : 'tair7',
			name : 'Gene Models (TAIR7)',
			type : 'ModelsTrack',
			path : 'Annotation Models',
			data : 'fetchers/models/tair7.php',
			showControls : true,
			height : 100
		},{
			id   : 'tair8',
			name : 'Gene Models (TAIR8)',
			type : 'ModelsTrack',
			path : 'Annotation models',
			data : 'fetchers/models/tair8.php',
			height : 80,
			showControls : true
		},{
			id   : 'repeats',
			name : 'Repeats',
			type : 'MaskTrack',
			path : 'Annotation Models',
			data : 'fetchers/models/repeats.php',
			minHeight : 20,
			maxHeight : 60,
			height : 20,
			single : true
		},
		
		//Messenger RNA
		{
			id   : 'mrna_axtell',
			name : 'Axtell Degradome Data',
			type : 'ReadsTrack',
			path : 'Cleavage Libraries',
			data : 'fetchers/brian/mrna_clv_axtell.php',
			iconCls : 'salk_mrna',
			height : 80
		},{	
			id   : 'mrna_col0_green',
			name : 'PARE Col-0 (Green and Meyers Labs)',
			type : 'ReadsTrack',
			path : 'Cleavage Libraries',
			data : 'fetchers/brian/mrna_clv_col0_green.php',
			iconCls : 'salk_mrna',
			height : 80
		},{	
			id   : 'mrna_xrn4_green',
			name : 'PARE xrn4 (Green and Meyers Labs)',
			type : 'ReadsTrack',
			path : 'Cleavage Libraries',
			data : 'fetchers/brian/mrna_clv_xrn4_green.php',
			iconCls : 'salk_mrna',
			height : 80
		},{	
			id   : 'mrna_col0',
			name : 'GMUCT Col-0',
			type : 'ReadsTrack',
			path : 'Cleavage Libraries',
			data : 'fetchers/brian/mrna_clv_col0.php',
			iconCls : 'salk_mrna',
			height : 80
		},{
			id   : 'mrna_ein5',
			name : 'GMUCT <i>ein5</i>',
			type : 'ReadsTrack',
			path : 'Cleavage Libraries',
			data : 'fetchers/brian/mrna_clv_ein5.php',
			iconCls : 'salk_mrna',
			height : 80
		},{
			id   : 'mrna_array_col0_buds',
			name : 'mRNA Col-0 buds (Ecker Lab tiling array)',		
			type : 'MicroarrayTrack',
			path : 'Messenger RNA',
			data : 'fetchers/microarray/mrna_col0_buds.php',
			iconCls : 'salk_mrna',
			height : 60
		},{
			id   : 'mrna_array_abh1',
			name : 'mRNA <i>abh1-1</i> buds (Ecker Lab tiling array)',		
			type : 'MicroarrayTrack',
			path : 'Messenger RNA',
			data : 'fetchers/microarray/mrna_abh1.php',
			iconCls : 'salk_mrna',
			height : 60
		},{
			id   : 'mrna_array_ein5',
			name : 'mRNA <i>ein5-6</i> buds (Ecker Lab tiling array)',		
			type : 'MicroarrayTrack',
			path : 'Messenger RNA',
			data : 'fetchers/microarray/mrna_ein5.php',
			iconCls : 'salk_mrna',
			height : 60
		},{
			id   : 'mrna_array_ein5Xabh1',
			name : 'mRNA <i>ein5-6</i> <i>abh1-1</i> buds (Ecker Lab tiling array)',		
			type : 'MicroarrayTrack',
			path : 'Messenger RNA',
			data : 'fetchers/microarray/mrna_ein5Xabh1.php',
			iconCls : 'salk_mrna',
			height : 60
		},
		
		//smRNA
		{
			id   : 'smrna_col0',
			name : 'smRNA Col-0',
			type : 'ReadsTrack',
			path : 'Small RNA',
			data : 'fetchers/brian/smrna_col0.php',
			iconCls : 'salk_smrna',
			height : 80
		},		
		{
			id   : 'smrna_abh1',
			name : 'smRNA <i>abh1</i>',
			type : 'ReadsTrack',
			path : 'Small RNA',
			data : 'fetchers/brian/smrna_abh1.php',
			iconCls : 'salk_smrna',
			height : 80
		},		
		{
			id   : 'smrna_ein5',
			name : 'smRNA <i>ein5</i>',
			type : 'ReadsTrack',
			path : 'Small RNA',
			data : 'fetchers/brian/smrna_ein5.php',
			iconCls : 'salk_smrna',
			height : 80
		},		
		{
			id   : 'smrna_ein5Xabh1',
			name : 'smRNA <i>ein5</i>X<i>abh1</i>',
			type : 'ReadsTrack',
			path : 'Small RNA',
			data : 'fetchers/brian/smrna_ein5Xabh1.php',
			iconCls : 'salk_smrna',
			height : 80
		}				
	],
	
	active : [
		'tair7','tair8','repeats',
		'mrna_axtell','mrna_col0_green','mrna_xrn4_green','mrna_col0','mrna_ein5',
		'mrna_array_col0_buds','mrna_array_abh1','mrna_array_ein5','mrna_array_ein5Xabh1',
		'smrna_col0','smrna_abh1','smrna_ein5','smrna_ein5Xabh1'
	],
	
	genome    : 'fetchers/arabidopsis_thaliana.php',
	bookmarks : 'fetchers/arabidopsis_thaliana.php',
	stylesheets : [
		{
			id   : 'css1',
			name : 'Plugins CSS',
			href : 'css/plugins.css',
			active : true
		},{
			id   : 'css2',
			name : 'SALK CSS',
			href : 'css/salk.css',
			active : true
		}		
	],
	location : {
		assembly : '1',
		position : '1',
		bases    : 20,
		pixels   : 1
	},
	admin : {
		name  : 'Julian Tonti-Filippini',
		email : 'tontij01@student.uwa.edu.au',
		notes : 'Perth, Western Australia (UTC +8)'
	},
	citation : "<div style='text-align:left'>We kindly request that use of this resource or data in any publication be cited as follows:<br /><br />Gregory, B.D., OMalley, R.C., Lister, R., Urich, M.A., Tonti-Filippini, J., Chen, H., Millar, A.H., and Ecker, J.R. 2008. <b>A link between RNA metabolism and silencing affecting Arabidopsis development.</b> <a target='new' href='http://www.ncbi.nlm.nih.gov/pubmed/18486559'>Dev. Cell 14: 854-866.</a></div><hr />"
};