public static void main(String[] args) {
		String reactomeDir = Gpr.HOME + "/snpEff/db/reactome/txt/";
		String geneIdsFile = Gpr.HOME + "/snpEff/db/reactome/gene_ids/biomart_query_uniq.txt";
		String gtexDir = Gpr.HOME + "/snpEff/db/GTEx";
		String gtexSamples = gtexDir + "/GTEx_Analysis_Annotations_Sample_DS__Pilot_2013_01_31.txt";
		String gtexData = gtexDir + "/gtex_norm.10.txt";

		// Load reactome data
		Timer.showStdErr("Loading reactome data");
		Reactome reactome = new Reactome();
		reactome.setVerbose(true);
		reactome.load(reactomeDir, geneIdsFile);

		// Load GTEX data
		Timer.showStdErr("Loading GTEx data");
		Gtex gtex = new Gtex();
		gtex.setVerbose(true);
		gtex.load(gtexSamples, gtexData);

		reactome.simplifyEntities();

		// Simulate
		Timer.showStdErr("Running");
		reactome.run(gtex, null);

		// Save results
		String file = Gpr.HOME + "/circuit.txt";
		Timer.showStdErr("Saving results to '" + file + "'");
		if (reactome.monitor != null) reactome.monitor.save(file);
		if (reactome.monitorTrace != null) reactome.monitorTrace.save(file);
	}