<!DOCTYPE MAGE-ML SYSTEM "MAGE-ML.dtd">
<MAGE-ML identifier="Protocol_test">
<Protocol_package>
	<Hardware_assnlist>
		<Hardware identifier="Hardware:PCR1"
			  name="PE TC 9700"
			  model="9700"
			  make="Perkin Elmer">
		</Hardware>
		<Hardware identifier="Hardware:OligoSynthesizer1"
			  name="Synthesizer"
			  make="Gene Machines">
		</Hardware>
		<Hardware identifier="Hardware:Scanner1"
			  name="Axon Scanner"
			  model="4000A"
			  make="Axon Instruments">
		</Hardware>
		<Hardware identifier="Hardware:Arrayer1"
			  name="DeRisi class arrayer"
			  model="version 1.0">
		</Hardware>
	</Hardware_assnlist>
	<Software_assnlist>
		<Software identifier="Software:GenePix3.0"
			  name="GenePix">
		</Software>
	</Software_assnlist>
	<Protocol_assnlist>
		<Protocol identifier="Protocol:OligoSynthesis"
			  name="Oligonucleotide Synthesis"
			  text="70mer oligos were synthesized">
			<Hardwares_assnreflist>
				<Hardware_ref identifier="Hardware:OligoSynthesizer1" />
			</Hardwares_assnreflist>
		</Protocol>
		<Protocol identifier="Protocol:PCRcDNA"
			  name="PCR of cDNA"
			  text="cDNAs were amplified using vector primers.">
			<ParameterTypes_assnlist>
				<Parameter identifier="ForwardPrimer" 
					name="Forward Primer"/>
				<Parameter identifier="ReversePrimer" 
					name="Reverse Primer"/>
			</ParameterTypes_assnlist>
			<Hardwares_assnreflist>
				<Hardware_ref identifier="Hardware:PCR1" />
			</Hardwares_assnreflist>
		</Protocol>
		<Protocol identifier="Protocol:ArrayPrinting"
			  name="Array Printing">
			<ParameterTypes_assnlist>
				<Parameter identifier="ParameterType:TipNumber" 
					name="Tip Number"/>
				<Parameter identifier="ParameterType:TipSpacing" 
						name="Tip Spacing"/>
				<Parameter identifier="ParameterType:SpotSpacing" 
						name="Spot Spacing"/>
				<Parameter identifier="ParameterType:ZoneColumns" 
						name="Zone Columns"/>
				<Parameter identifier="ParameterType:ZoneRows" 
						name="Zone Rows"/>
			</ParameterTypes_assnlist>
			<Hardwares_assnreflist>
				<Hardware_ref identifier="Hardware:Arrayer1" />
			</Hardwares_assnreflist>
		</Protocol>
		<Protocol identifier="Protocol:Hybridization"
			  name="Hybridization and wash">
			<ParameterTypes_assnlist>
				<Parameter identifier="ParameterType:HybridizationTime"
					   name="Hybridization Time" />
				<Parameter identifier="ParameterType:Wash1Time"
					   name="Wash 1 Time" />
				<Parameter identifier="ParameterType:Wash2Time"
					   name="Wash 2 Time" />
			</ParameterTypes_assnlist>
		</Protocol>
		<Protocol identifier="Protocol:Scan"
			  name="Scan">
			<ParameterTypes_assnlist>
			<Parameter identifier="ParameterType:PMT_voltage_635"
					   name="PMT Voltage" />
			<Parameter identifier="ParameterType:PMT_voltage_532"
					   name="PMT Voltage" />
			</ParameterTypes_assnlist>
			<Hardwares_assnreflist>
				<Hardware_ref identifier="Hardware:Scanner1" />
			</Hardwares_assnreflist>
			<Softwares_assnreflist>
				<Software_ref identifier="Software:GenePix3.0" />
			</Softwares_assnreflist>
		</Protocol>
		<Protocol identifier="Protocol:FeatureExtraction"
			  name="Feature Extraction">
			<ParameterTypes_assnlist>
			<Parameter identifier="ParameterType:FeatureSpacing" 
					name="Feature Spacing"/>
			<Parameter identifier="ParameterType:Featurepacing" 
					name="Spot Spacing"/>
			<Parameter identifier="ParameterType:FeatureDiameter" 
					name="Spot Diameter"/>
			</ParameterTypes_assnlist>
			<Softwares_assnreflist>
				<Software_ref identifier="Software:GenePix3.0" />
			</Softwares_assnreflist>
		</Protocol>
	</Protocol_assnlist>
	</Protocol_package>
</MAGE-ML>