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added recipes (again) #62

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Dec 11, 2015
Merged

added recipes (again) #62

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Binary file added recipes/Tradis_adapter_primers.xlsx
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413 changes: 413 additions & 0 deletions recipes/Transposon12/Chemistry/Chemistry.xml
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7 changes: 7 additions & 0 deletions recipes/Transposon12/Exposures/Sony.xml
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<?xml version="1.0" encoding="utf-8" ?>
<Exposures>
<Exposure Name="A" Start="1037" Ramp="0" />
<Exposure Name="T" Start="500" Ramp="0" />
<Exposure Name="C" Start="1037" Ramp="0" />
<Exposure Name="G" Start="500" Ramp="0" />
</Exposures>
11 changes: 11 additions & 0 deletions recipes/Transposon12/Exposures/SonyV2.xml
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<?xml version="1.0" encoding="utf-8" ?>
<Exposures>
<Exposure Name="A" Start="260" IsIndexed="false" Ramp="5.2" />
<Exposure Name="A" Start="1037" IsIndexed="true" Ramp="0" />
<Exposure Name="T" Start="125" IsIndexed="false" Ramp="2.5" />
<Exposure Name="T" Start="500" IsIndexed="true" Ramp="0" />
<Exposure Name="C" Start="260" IsIndexed="false" Ramp="5.2" />
<Exposure Name="C" Start="1037" IsIndexed="true" Ramp="0" />
<Exposure Name="G" Start="125" IsIndexed="false" Ramp="2.5" />
<Exposure Name="G" Start="500" IsIndexed="true" Ramp="0" />
</Exposures>
26 changes: 26 additions & 0 deletions recipes/Transposon12/Protocol/1Read1Index.xml
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<?xml version="1.0"?>
<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
<ChemistryRef ChemistryName="OnBoardClusterGeneration" />
<ChemistryRef ChemistryName="FirstReadPreparation" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
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<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="EndDeblock" />
<ReadRef ReadName="FirstRead" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Index1Preparation" />
<ReadRef ReadName="IndexRead1" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="TemplateRinse" />
<ChemistryRef ChemistryName="End" />

</Protocol>
27 changes: 27 additions & 0 deletions recipes/Transposon12/Protocol/1Read2Index.xml
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<?xml version="1.0"?>
<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
<ChemistryRef ChemistryName="OnBoardClusterGeneration" />
<ChemistryRef ChemistryName="FirstReadPreparation" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="EndDeblock" />
<ReadRef ReadName="FirstRead" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Index1Preparation" />
<ReadRef ReadName="IndexRead1" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Index2Preparation" />
<ReadRef ReadName="IndexRead2" />
<ChemistryRef ChemistryName="TemplateRinse" />
<ChemistryRef ChemistryName="End" />
</Protocol>
30 changes: 30 additions & 0 deletions recipes/Transposon12/Protocol/2Read1Index.xml
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<?xml version="1.0"?>
<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
<ChemistryRef ChemistryName="OnBoardClusterGeneration" />
<ChemistryRef ChemistryName="FirstReadPreparation" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="EndDeblock" />
<ReadRef ReadName="FirstRead" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Index1Preparation" />
<ReadRef ReadName="IndexRead1" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Deprotection" />
<ChemistryRef ChemistryName="PairedEndTurnaround" />
<ChemistryRef ChemistryName="SecondReadPreparation" />
<ReadRef ReadName="SecondRead" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="TemplateRinse" />
<ChemistryRef ChemistryName="End" />
</Protocol>
33 changes: 33 additions & 0 deletions recipes/Transposon12/Protocol/2Read2Index.xml
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<?xml version="1.0"?>
<Protocol Version="Fraise 0.7.1 Amplicon v1.1">
<ChemistryRef ChemistryName="OnBoardClusterGeneration" />
<ChemistryRef ChemistryName="FirstReadPreparation" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
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<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="Index2CompleteCycleDark2" />
<ChemistryRef ChemistryName="EndDeblock" />
<ReadRef ReadName="FirstRead" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Index1Preparation" />
<ReadRef ReadName="IndexRead1" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Index2Preparation" />
<ReadRef ReadName="IndexRead2" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="Deprotection" />
<ChemistryRef ChemistryName="PairedEndTurnaround" />
<ChemistryRef ChemistryName="SecondReadPreparation" />
<ReadRef ReadName="SecondRead" />
<ChemistryRef ChemistryName="EndDeblock" />
<ChemistryRef ChemistryName="TemplateRinse" />
<ChemistryRef ChemistryName="End" />
</Protocol>
23 changes: 23 additions & 0 deletions recipes/Transposon12/Reads/Reads.xml
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<?xml version="1.0"?>
<ReadDefinitions Version="Fraise 0.7.1 Amplicon v1.1">
<ReadDefinition Name="FirstRead">
<FirstBase ChemistryName="FirstBase" Cycles="1" />
<Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
<End ChemistryName="EndRead" />
</ReadDefinition>
<ReadDefinition Name="IndexRead1" IsIndexed="True" >
<FirstBase ChemistryName="FirstBase" Cycles="1" />
<Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
<End ChemistryName="EndRead" />
</ReadDefinition>
<ReadDefinition Name="SecondRead" IsIndexed="false">
<FirstBase ChemistryName="FirstBase" Cycles="1" />
<Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
<End ChemistryName="EndRead" />
</ReadDefinition>
<ReadDefinition Name="IndexRead2" IsIndexed="true">
<FirstBase ChemistryName="FirstBase" Cycles="1" />
<Imaging ChemistryName="CompleteCycle" Cycles="NumCycles - 1" />
<End ChemistryName="EndRead" />
</ReadDefinition>
</ReadDefinitions>
25 changes: 25 additions & 0 deletions recipes/Transposon12/Reagents/MaintenanceWash.xml
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<?xml version="1.0" encoding="utf-8" ?>
<Reagents Name="Bolt Avocado Reagents" Version="Selector Valve Positions v2.2">
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="1" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="2" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="3" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="4" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="5" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="6" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="7" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="8" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="9" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="10" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="11" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="12" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="13" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="14" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="15" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="16" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="17" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="18" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="19" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="20" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="21" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="22" />
</Reagents>
25 changes: 25 additions & 0 deletions recipes/Transposon12/Reagents/PostRunWash.xml
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<?xml version="1.0" encoding="utf-8" ?>
<Reagents Name="Bolt Avocado Reagents" Version="Selector Valve Positions v2.2">
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="1" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="2" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="3" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="4" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="5" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="6" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="7" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="8" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="9" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="10" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="11" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="12" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="13" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="14" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="15" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="16" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="17" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="18" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="19" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="20" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="21" />
<Reagent Name="PW1" Description="PW1" SelectorValvePosition="22" />
</Reagents>
24 changes: 24 additions & 0 deletions recipes/Transposon12/Reagents/Sequencing.xml
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<?xml version="1.0" encoding="utf-8" ?>
<Reagents Name="Shock Reagents" Version="Selector Valve Positions v2.2">
<Reagent Name="IMS" Description="Incorporation Mix" SelectorValvePosition="1" />
<Reagent Name="SRE" Description="Scan Mix" SelectorValvePosition="2" />
<Reagent Name="PR2" Description="Incorporation Buffer" SelectorValvePosition="3" />
<Reagent Name="CMS" Description="Cleavage Mix" SelectorValvePosition="4" />
<Reagent Name="AMS1" Description="Amplification Mix 1" SelectorValvePosition="5" />
<Reagent Name="AMS2" Description="Amplification Mix 2" SelectorValvePosition="6" />
<Reagent Name="LPM" Description="Lin Pre Mix" SelectorValvePosition="7" />
<Reagent Name="LDR" Description="Formamide" SelectorValvePosition="8" />
<Reagent Name="LMX1" Description="Linearization Mix" SelectorValvePosition="9" />
<Reagent Name="LMX2" Description="R2 Lin Mix" SelectorValvePosition="10" />
<Reagent Name="RMF" Description="Resynthesis Mix" SelectorValvePosition="11" />
<Reagent Name="HP10" Description="R1 Primer Mix" SelectorValvePosition="12" />
<Reagent Name="HP12" Description="Index Primer Mix" SelectorValvePosition="13" />
<Reagent Name="HP11" Description="R2 Primer Mix" SelectorValvePosition="14" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="15" />
<Reagent Name="PW2" Description="Water" SelectorValvePosition="16" />
<Reagent Name="TMP" Description="Template" SelectorValvePosition="17" />
<Reagent Name="C1" Description="Custom 1 Primer Mix" SelectorValvePosition="18" />
<Reagent Name="C2" Description="Custom 2 Primer Mix" SelectorValvePosition="19" />
<Reagent Name="C3" Description="Custom 3 Primer Mix" SelectorValvePosition="20" />
<Reagent Name="PW3" Description="Water" SelectorValvePosition="21" />
</Reagents>
Binary file added recipes/Transposon12/Wash/130702_ImplementingCarryoverDecontamWash_v3.docx
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102 changes: 102 additions & 0 deletions recipes/Transposon12/Wash/LineWash.xml
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<?xml version="1.0"?>
<Recipe xmlns:xsd="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" Name="LineWash_v0.3">

<Protocol Version="LineWash">
<ChemistryRef ChemistryName="LineWash" Repeat="1" />
</Protocol>

<ChemistryDefinitions Version="LineWash_v0.3">
<ChemistryDefinition Name="CleanSyringe">
<ChemistryStep Description="CleanSyringe" Repeat="1"> <!--run water through syringe to reduce carryover since about to backflush-->
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="1000" />
<Wait Duration="10000" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="500" DispenseRate="1000" Volume="500" />
<Wait Duration="10000" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="500" />
</ChemistryStep>
</ChemistryDefinition>
<ChemistryDefinition Name="Oscillate">
<ChemistryStep Description="Oscillate" Repeat="1">
<!--add airbubble, fill syringe, and slowly pump back and forth increasing pressure-->
<PumpToFlowcell Solution="23" AspirationRate="1000" DispenseRate="2500" Volume="15" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
</ChemistryStep>
<ChemistryStep Description="OscillateSubStep" Repeat="49">
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="5"/>
<Wait Duration="1000" />
<Aspirate ReagentName="PW1" AspirationRate="2000" Volume="5" />
<Wait Duration="1000" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="10"/>
<Wait Duration="1000" />
<Aspirate ReagentName="PW1" AspirationRate="2000" Volume="5" />
<Wait Duration="6000" />
</ChemistryStep>
</ChemistryDefinition>
<ChemistryDefinition Name="Reprime">
<ChemistryStep Description="Reprime" Repeat="1"> <!--prime line with 500uL-->
<PumpToFlowcell ReagentName="PW1" AspirationRate="2000" DispenseRate="2500" Volume="500" />
</ChemistryStep>
</ChemistryDefinition>
<ChemistryDefinition Name="Flush">
<ChemistryStep Description="Flush" Repeat="1"> <!--empty tube and refill from bypass-->
<PumpToFlowcell ReagentName="PW1" AspirationRate="5000" DispenseRate="5000" Volume="3000" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
<AspirateFromBypass ReagentName="PW1" AspirationRate="2000" Volume="250" />
<DispenseToFlowcell ReagentName="PW1" DispenseRate="2000" Volume="250" />
</ChemistryStep>
</ChemistryDefinition>
<ChemistryDefinition Name="Wait180000">
<ChemistryStep Description="Wait180000" Repeat="1">
<Wait Duration="180000" />
</ChemistryStep>
</ChemistryDefinition>
</ChemistryDefinitions>

- <Reagents Name="ClogWashReagents" Version="Selector Valve Positions v2.2">
<Reagent Name="PW1" Description="Water" SelectorValvePosition="1" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="2" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="3" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="4" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="5" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="6" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="7" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="8" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="9" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="10" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="11" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="12" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="13" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="14" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="15" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="16" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="17" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="18" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="19" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="20" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="21" />
<Reagent Name="PW1" Description="Water" SelectorValvePosition="22" />
</Reagents>

<Name>LineWash_v0.3</Name>
</Recipe>
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