AnnoJ.config = {

	tracks : [


		//Models
		{
			id   : 'genes',
			name : 'Gene Models',
			type : 'ModelsTrack',
			path : 'Annotation models',
			data : 'hs/fetchers/models/genes.php',
			height : 120,
			showControls : true
		},
		{
			id   : 'hs_ref',
			name : 'HG18 genome sequence',
			type : 'ReadsTrack',
			path : 'Annotation models',
			data : 'hs/fetchers/refs/hs_ref.php',
			height : 20
		},
		{
			id   : 'herv',
			name : 'HERVs',
			type : 'ModelsTrack',
			path : 'Annotation models',
			data : 'hs/fetchers/models/herv.php',
			height : 30,
			showControls : true
		},
		{
			id   : 'lines',
			name : 'LINEs',
			type : 'ModelsTrack',
			path : 'Annotation models',
			data : 'hs/fetchers/models/lines_hg18.php',
			height : 30,
			showControls : true
		},


		
		//Regions
		{
			id   : 'regions_i90_partial_mc',
			name : 'IMR90 PMDs',
			type : 'ReadsTrack',
			path : 'Differential Methylation',
			data : 'hs/fetchers/methylation/regions_i90_partial_mc.php',
			iconCls : 'salk_meth',
			height : 20
		},		
		{
			id   : 'regions_dmr',
			name : 'DMRs',
			type : 'ReadsTrack',
			path : 'Differential Methylation',
			data : 'hs/fetchers/methylation/regions_i90_h1_dmr.php',
			iconCls : 'salk_meth',
			height : 20
		},
		{
			id   : 'mc_h1_unique_5FDR',
			name : 'H1 > IMR90 mCs, 5% FDR',
			type : 'MethTrack',
			path : 'Differential Methylation',
			data : 'hs/fetchers/methylation/mc_h1_unique_5FDR.php',
			iconCls : 'salk_meth',
			height : 50
		},
		{
			id   : 'mc_i90_unique_5FDR',
			name : 'IMR90 > H1 mCs, 5% FDR',
			type : 'MethTrack',
			path : 'Differential Methylation',
			data : 'hs/fetchers/methylation/mc_i90_unique_5FDR.php',
			iconCls : 'salk_meth',
			height : 50
		},

							
		//DNA Methylation
		{
			id   : 'mc_h1',
			name : 'H1 mC',
			type : 'MethTrack',
			path : 'Methylcytosines',
			data : 'hs/fetchers/methylation/mc_h1.php',
			iconCls : 'salk_meth',
			height : 50
		},
		{
			id   : 'mc_i90',
			name : 'IMR90 mC',
			type : 'MethTrack',
			path : 'Methylcytosines',
			data : 'hs/fetchers/methylation/mc_i90.php',
			iconCls : 'salk_meth',
			height : 50
		},
		{
			id   : 'mc_h1_r1',
			name : 'H1 mC replicate 1',
			type : 'MethTrack',
			path : 'Methylcytosines',
			data : 'hs/fetchers/methylation/mc_h1_r1.php',
			iconCls : 'salk_meth',
			height : 50
		},
		{
			id   : 'mc_h1_r2',
			name : 'H1 mC replicate 2',
			type : 'MethTrack',
			path : 'Methylcytosines',
			data : 'hs/fetchers/methylation/mc_h1_r2.php',
			iconCls : 'salk_meth',
			height : 50
		},
		{
			id   : 'mc_i90_r1',
			name : 'IMR90 mC replicate 1',
			type : 'MethTrack',
			path : 'Methylcytosines',
			data : 'hs/fetchers/methylation/mc_i90_r1.php',
			iconCls : 'salk_meth',
			height : 50
		},
		{
			id   : 'mc_i90_r2',
			name : 'IMR90 mC replicate 2',
			type : 'MethTrack',
			path : 'Methylcytosines',
			data : 'hs/fetchers/methylation/mc_i90_r2.php',
			iconCls : 'salk_meth',
			height : 50
		},
		
						
		//Bisulfite sequencing
		{
			id   : 'h1_bs',
			name : 'H1 MethylC-Seq reads',
			type : 'ReadsTrack',
			path : 'Bisulfite sequencing reads',
			data : 'hs/fetchers/bisulfite/reads_h1.php',
			iconCls : 'salk_meth',
			height : 130
		},
		{
			id   : 'i90_bs',
			name : 'IMR90 MethylC-Seq reads',
			type : 'ReadsTrack',
			path : 'Bisulfite sequencing reads',
			data : 'hs/fetchers/bisulfite/reads_i90.php',
			iconCls : 'salk_meth',
			height : 130
		},
		{
			id   : 'h1_r1_bs',
			name : 'H1 replicate 1 MethylC-Seq reads',
			type : 'ReadsTrack',
			path : 'Bisulfite sequencing reads',
			data : 'hs/fetchers/bisulfite/reads_h1_r1.php',
			iconCls : 'salk_meth',
			height : 130
		},
		{
			id   : 'h1_r2_bs',
			name : 'H1 replicate 2 MethylC-Seq reads',
			type : 'ReadsTrack',
			path : 'Bisulfite sequencing reads',
			data : 'hs/fetchers/bisulfite/reads_h1_r2.php',
			iconCls : 'salk_meth',
			height : 130
		},
		{
			id   : 'i90_r1_bs',
			name : 'IMR90 repliate 1 MethylC-Seq reads',
			type : 'ReadsTrack',
			path : 'Bisulfite sequencing reads',
			data : 'hs/fetchers/bisulfite/reads_i90_r1.php',
			iconCls : 'salk_meth',
			height : 130
		},
		{
			id   : 'i90_r2_bs',
			name : 'IMR90 replicate 2 MethylC-Seq reads',
			type : 'ReadsTrack',
			path : 'Bisulfite sequencing reads',
			data : 'hs/fetchers/bisulfite/reads_i90_r2.php',
			iconCls : 'salk_meth',
			height : 130
		},
		
		
		
		//mRNA-seq
		{
			id   : 'mrna_h1',
			name : 'H1 mRNA',
			type : 'ReadsTrack',
			path : 'Messenger RNA',
			data : 'hs/fetchers/mrna/mrna_h1.php',
			iconCls : 'salk_mrna',
			height : 60
		},
		
		{
			id   : 'mrna_imr90',
			name : 'IMR90 mRNA',
			type : 'ReadsTrack',
			path : 'Messenger RNA',
			data : 'hs/fetchers/mrna/mrna_imr90.php',
			iconCls : 'salk_mrna',
			height : 60
		},
		
		
		
		//smRNA-seq
		{
			id   : 'reads_sm_h1_r1',
			name : 'H1 small RNA',
			type : 'ReadsTrack',
			path : 'Small RNA',
			data : 'hs/fetchers/smrna/reads_sm_h1_r1.php',
			iconCls : 'salk_smrna',
			height : 40
		},
		{
			id   : 'reads_sm_imr90_r1',
			name : 'IMR90 small RNA',
			type : 'ReadsTrack',
			path : 'Small RNA',
			data : 'hs/fetchers/smrna/reads_sm_imr90_r1.php',
			iconCls : 'salk_smrna',
			height : 40
		},
		
		
		//Histones
		{
			id   : 'reads_H3K4me1_H1',
			name : 'H1 H3K4me1',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K4me1.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K4me2_H1',
			name : 'H1 H3K4me2',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K4me2.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K4me3_H1',
			name : 'H1 H3K4me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K4me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K36me3_H1',
			name : 'H1 H3K36me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K36me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K27me3_H1',
			name : 'H1 H3K27me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K27me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K9me3_H1',
			name : 'H1 H3K9me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K9me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K9ac_H1',
			name : 'H1 H3K9ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K9ac.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K18ac_H1',
			name : 'H1 H3K18ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K18ac.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K27ac_H1',
			name : 'H1 H3K27ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H3K27ac.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H4K5ac_H1',
			name : 'H1 H4K5ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H4K5ac.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H2BK5ac_H1',
			name : 'H1 H2BK5ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_H2BK5ac.php',
			iconCls : 'salk_dna',
			height : 40
		},		
		{
			id   : 'reads_input_H1',
			name : 'H1 Input',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_H1_Input.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K4me1_IMR90',
			name : 'IMR90 H3K4me1',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K4me1.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K4me2_IMR90',
			name : 'IMR90 H3K4me2',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K4me2.php',
			iconCls : 'salk_dna',
			height : 40
		},	
		{
			id   : 'reads_H3K4me3_IMR90',
			name : 'IMR90 H3K4me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K4me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K36me3_IMR90',
			name : 'IMR90 H3K36me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K36me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K27me3_IMR90',
			name : 'IMR90 H3K27me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K27me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K9me3_IMR90',
			name : 'IMR90 H3K9me3',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K9me3.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K9ac_IMR90',
			name : 'IMR90 H3K9ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K9ac.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K18ac_IMR90',
			name : 'IMR90 H3K18ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K18ac.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H3K27ac_IMR90',
			name : 'IMR90 H3K27ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H3K27ac.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'reads_H4K5ac_IMR90',
			name : 'IMR90 H4K5ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H4K5ac.php',
			iconCls : 'salk_dna',
			height : 40
		},		{
			id   : 'reads_H2BK5ac_IMR90',
			name : 'IMR90 H2BK5ac',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_H2BK5ac.php',
			iconCls : 'salk_dna',
			height : 40
		},		
		{
			id   : 'reads_input_IMR90',
			name : 'IMR90 Input',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/reads_IMR90_Input.php',
			iconCls : 'salk_dna',
			height : 40
		},
		{
			id   : 'domains_H3K4me3_H1',
			name : 'H1 H3K4me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_H1_H3K4me3.php',
			iconCls : 'salk_dna',
			height : 20
		},
		{
			id   : 'domains_H3K36me3_H1',
			name : 'H1 H3K36me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_H1_H3K36me3.php',
			iconCls : 'salk_dna',
			height : 20
		},		
		{
			id   : 'domains_H3K9me3_H1',
			name : 'H1 H3K9me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_H1_H3K9me3.php',
			iconCls : 'salk_dna',
			height : 20
		},
		{
			id   : 'domains_H3K27me3_H1',
			name : 'H1 H3K27me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_H1_H3K27me3.php',
			iconCls : 'salk_dna',
			height : 20
		},			
		{
			id   : 'domains_H3K4me3_IMR90',
			name : 'IMR90 H3K4me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_IMR90_H3K4me3.php',
			iconCls : 'salk_dna',
			height : 20
		},
		{
			id   : 'domains_H3K36me3_IMR90',
			name : 'IMR90 H3K36me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_IMR90_H3K36me3.php',
			iconCls : 'salk_dna',
			height : 20
		},		
		{
			id   : 'domains_H3K9me3_IMR90',
			name : 'IMR90 H3K9me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_IMR90_H3K9me3.php',
			iconCls : 'salk_dna',
			height : 20
		},
		{
			id   : 'domains_H3K27me3_IMR90',
			name : 'IMR90 H3K27me3 domains',
			type : 'ReadsTrack',
			path : 'Histone modifications',
			data : 'hs/fetchers/histones/domains_IMR90_H3K27me3.php',
			iconCls : 'salk_dna',
			height : 20
		}		
	],	
	
	active : [
		'genes', 'lines', 'herv', 'mrna_h1','mrna_imr90','mc_h1','mc_i90', 'reads_sm_h1_r1', 'reads_sm_imr90_r1','reads_H3K4me3_H1','reads_H3K36me3_H1','reads_H3K27me3_H1','reads_H3K4me3_IMR90','reads_H3K36me3_IMR90','reads_H3K27me3_IMR90'
	],
	
	genome    : 'hs/fetchers/homo_sapiens.php',
	bookmarks : 'hs/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 : '6',
		position : '31240092',
		bases    : 100,
		pixels   : 1
	},
	admin : {
		name  : 'Ryan Lister',
		email : 'lister@salk.edu',
		notes : 'The Salk Institute, La Jolla, CA, USA'
	},
};