<?xml version="1.0"?>
<MAGE-ML identifier="Protocol_test">
	<Protocol_package>
		<Hardware_assnlist>
			<Hardware identifier="Hardware:PCR1" name="PE TC 9700" model="9700" make="Perkin Elmer"/>
			<Hardware identifier="Hardware:OligoSynthesizer1" name="Synthesizer" make="Gene Machines"/>
			<Hardware identifier="Hardware:Scanner1" name="Axon Scanner" model="4000A" make="Axon Instruments"/>
			<Hardware identifier="Hardware:Arrayer1" name="DeRisi class arrayer" model="version 1.0"/>
		</Hardware_assnlist>
		<Software_assnlist>
			<Software identifier="Software:GenePix3.0" name="GenePix"/>
		</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>

