<?xml version="1.0" encoding="UTF-8"?>
<?xml-stylesheet type="text/xsl" href="FuGEFlowtoISATAB.xsl"?>
<!-- 
    ********************************************************************
    * FuGEFlow Experiment Annotation Example
    * **************************************
    * 
    * This document represents an example description of a flow cytometry 
    * experiment that is compliant with the Minimum Information about a 
    * Flow Cytometry Experiment (MIFlowCyt).
    * 
    * The purpose of this document is to validate FuGEFlow - a Flow Cytometry
    * specific extension of the FuGE model. Validation is understood in terms of
    * whether the FuGEFlow XML schema defines a language that allows to describe
    * flow cytometry experiments.
    *
    * This XML document is based on 
    * "MIFlowCyt Experiment Annotation Example" from February 20th, 2008
    * by Maura Gasparetto, Josef Spidlen, and Ryan R. Brinkman
    * 
    * License
    * The work may be used under the terms of the 
    * Creative Commons Attribution-ShareAlike 3.0 Unported license. 
    * You are free to share (copy, distribute and transmit), and adapt 
    * the work under the conditions specified at 
    * http://creativecommons.org/licenses/by-sa/3.0/legalcode
    * 
    * Acknowledgement
    * This work has been supported by NIH grant EB005034 from the 
    * National Institute of Biomedical Imaging And Bioengineering.
    * 
    * Disclaimer
    * The content is solely the responsibility of the authors and 
    * does not necessarily represent the official views of the 
    * National Institute of Biomedical Imaging And Bioengineering 
    * or the National Institutes of Health.
    *
    * Josef Spidlen, Ph.D., jspidlen@bccrc.ca, August 21, 2008
    * - with great contribution by Peter Wilkinson, University of Montreal
    ********************************************************************** 
-->
<fuge:FuGE Security_ref="Experiment_Description_Info" 
    xmlns:fuge="http://fuge.sourceforge.net/fuge/1.0" 
    xmlns:fcm="http://flowcyt.sourceforge.net/fugeflow/" 
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" 
    xmlns:xsd="http://www.w3.org/2001/XMLSchema"
    xmlns:obi="http://purl.obofoundry.org/obo/obi.owl"
    identifier="Donor_HSC_contribution_MGJSRB20080211" 
    name="Donor HSC Contribution" 
    xsi:schemaLocation="
        http://flowcyt.sourceforge.net/fugeflow/ ../../XSD/FuGEFlow.xsd
        http://fuge.sourceforge.net/fuge/1.0 ../../XSD/FuGEv1.xsd
    ">
    <!--
        The xsi:schemaLocation="http://fuge.sourceforge.net/fuge/1.0 ../XSD/FuGEv1.xsd"
        speeds up the validation agains FuGE XSD (locally). The following can be used to
        validate against FuGE XSD online at sourceforge.net: 
        xsi:schemaLocation="http://fuge.sourceforge.net/fuge/1.0 http://fuge.sourceforge.net/dev/V1Final/FuGEv1.xsd"
    -->
    
    <!-- 
        ********************************* 
        Materials
        *********************************
    -->
    
    <fuge:MaterialCollection>
    
        <!-- Fluorescent Reagents -->
        <!-- CD4 TxRed -->
        <fcm:FluorescentReagent identifier="CD4_TxRed_FluorescentReagent" name="CD4 TxRed Reagent" catalogNumber="553648">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="T-helper" />
            </fcm:_measuredCharacteristics> 
            <fcm:_reporter GenericMaterial_ref="TxRed_Reporter_Component" />
            <fcm:_detector AnalyteDetector_ref="ad_H129.19" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>
        <!-- CD8 TxRed -->
        <fcm:FluorescentReagent identifier="CD8_TxRed_FluorescentReagent" name="CD8 TxRed Reagent" catalogNumber="553028">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="T-Suppresor" />
            </fcm:_measuredCharacteristics>     
            <fcm:_reporter GenericMaterial_ref="TxRed_Reporter_Component_2" />     
            <fcm:_detector AnalyteDetector_ref="ad_53-6.7" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>
        <!-- CD45R APC -->
        <fcm:FluorescentReagent identifier="CD45R_APC_FluorescentReagent" name="CD45R APC Reagent" catalogNumber="553092">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="B cells" />
            </fcm:_measuredCharacteristics>
            <fcm:_reporter GenericMaterial_ref="APC_Reporter_Component" />
            <fcm:_detector AnalyteDetector_ref="ad_RA3-6B2" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>
        <!-- Gr1 PE -->
        <fcm:FluorescentReagent identifier="Gr1_PE_FluorescentReagent" name="Gr1 PE Reagent" catalogNumber="551461">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="Granulocytes" />
            </fcm:_measuredCharacteristics>
            <fcm:_reporter GenericMaterial_ref="PE_Reporter_Component" />
            <fcm:_detector AnalyteDetector_ref="ad_1A8" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>
        <!-- CD11b PE -->
        <fcm:FluorescentReagent identifier="CD11b_PE_FluorescentReagent" name="CD11b PE Reagent" catalogNumber="557397">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="Monocytes" />
            </fcm:_measuredCharacteristics>
            <fcm:_reporter GenericMaterial_ref="PE_Reporter_Component_2" />
            <fcm:_detector AnalyteDetector_ref="ad_M1-70" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>        
        <!-- CD45.1 FITC -->
        <fcm:FluorescentReagent identifier="CD45.1_FITC_FluorescentReagent" name="CD45.1 FITC Reagent" catalogNumber="553775">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="Donor leukocytes" />
            </fcm:_measuredCharacteristics>
            <fcm:_reporter GenericMaterial_ref="FITC_Reporter_Component" />      
            <fcm:_detector AnalyteDetector_ref="ad_A20" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>
        <!-- CD45.2 PerCP -->
        <fcm:FluorescentReagent identifier="CD45.2_PerCP_FluorescentReagent" name="CD45.2 PerCP Reagent" catalogNumber="552950">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="Recipient leukocytes" />
            </fcm:_measuredCharacteristics>
            <fcm:_reporter GenericMaterial_ref="PerCP_Reporter_Component" />
            <fcm:_detector AnalyteDetector_ref="ad_104" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>
        <!-- DAPI -->
        <fcm:FluorescentReagent identifier="DAPI_FluorescentReagent" name="DAPI Reagent" catalogNumber="7034">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_measuredCharacteristics>
                <fuge:Description text="Cell viability" />
            </fcm:_measuredCharacteristics> 
            <fcm:_reporter GenericMaterial_ref="DAPI_Reporter_Component" />     
            <fcm:_detector AnalyteDetector_ref="ad_DAPI" />
            <fcm:_otherInformation>
                <fuge:Description text="Reagent used in a cocktail" />
            </fcm:_otherInformation>
        </fcm:FluorescentReagent>
    
        <!-- Analyte Detectors -->
        <!-- anti-CD4 -->
        <fcm:AnalyteDetector identifier="ad_H129.19" name="anti-CD4" cloneNumber="H129.19">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="CD4" />
            <fcm:_otherInformation><fuge:Description text="anti-CD4" /></fcm:_otherInformation>
        </fcm:AnalyteDetector>
        <!-- anti-CD8 -->
        <fcm:AnalyteDetector identifier="ad_53-6.7" name="anti-CD8" cloneNumber="53-6.7">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="CD8" />
            <fcm:_otherInformation><fuge:Description text="anti-CD8" /></fcm:_otherInformation>
        </fcm:AnalyteDetector>
        <!-- anti-CD45R -->
        <fcm:AnalyteDetector identifier="ad_RA3-6B2" name="anti-CD45R" cloneNumber="RA3-6B2">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="CD45R" />
            <fcm:_otherInformation><fuge:Description text="anti-CD45R" /></fcm:_otherInformation>
        </fcm:AnalyteDetector>
        <!-- anti-Gr1 -->
        <fcm:AnalyteDetector identifier="ad_1A8" name="anti-Gr1" cloneNumber="1A8">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="Gr1" />
            <fcm:_otherInformation><fuge:Description text="anti-Gr1" /></fcm:_otherInformation>
        </fcm:AnalyteDetector>
        <!-- anti-CD11b -->
        <fcm:AnalyteDetector identifier="ad_M1-70" name="anti-CD11b" cloneNumber="M1-70">
            <fuge:_characteristics OntologyTerm_ref="anti-CD11b_OT" />
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="CD11b" />
            <fcm:_otherInformation><fuge:Description text="anti-CD11b" /></fcm:_otherInformation>
        </fcm:AnalyteDetector>
        <!-- anti-CD45.1 -->
        <fcm:AnalyteDetector identifier="ad_A20" name="anti-CD45.1" cloneNumber="A20">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="CD45.1" />
            <fcm:_otherInformation><fuge:Description text="anti-CD45.1" /></fcm:_otherInformation>
        </fcm:AnalyteDetector>
        <!-- anti-CD45.2 -->
        <fcm:AnalyteDetector identifier="ad_104" name="anti-CD45.2" cloneNumber="104">
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="CD45.2" />
            <fcm:_otherInformation><fuge:Description text="anti-CD45.2" /></fcm:_otherInformation>
        </fcm:AnalyteDetector>
        <!-- DAPI -->
        <fcm:AnalyteDetector identifier="ad_DAPI" name="DAPI">
            <fuge:_descriptions><fuge:Description text="DAPI" /></fuge:_descriptions>
            <fcm:_make OntologyTerm_ref="BD_OT" />
            <fcm:_analyte GenericMaterial_ref="DNA_of_Membrane-compromised_Cells" />
        </fcm:AnalyteDetector>     
        
        <!-- Analytes -->
        <!-- CD4 -->
        <fuge:GenericMaterial identifier="CD4"><fuge:_characteristics OntologyTerm_ref="CD4_OT" /></fuge:GenericMaterial>
        <!-- CD8 -->
        <fuge:GenericMaterial identifier="CD8"><fuge:_characteristics OntologyTerm_ref="CD8_OT" /></fuge:GenericMaterial>
        <!-- CD45R -->
        <fuge:GenericMaterial identifier="CD45R"><fuge:_characteristics OntologyTerm_ref="CD45R_OT" /></fuge:GenericMaterial>
        <!-- Gr1 -->
        <fuge:GenericMaterial identifier="Gr1">
            <fuge:_descriptions><fuge:Description text="See http://www.springerlink.com/content/w2422227v4577426/" /></fuge:_descriptions>
        </fuge:GenericMaterial>
        <!-- CD11b -->
        <fuge:GenericMaterial identifier="CD11b"><fuge:_characteristics OntologyTerm_ref="CD11b_OT" /></fuge:GenericMaterial>
        <!-- CD45.1 -->
        <fuge:GenericMaterial identifier="CD45.1" >
            <fuge:_descriptions>
                <fuge:Description 
                    text="CD45 is an essential regulator of leukocyte activation and development, and is now known to be a protein tyrosine phosphatase, 
                    e.g. CD45 is able to dephosphorylate the Src family of protein kinases. This activity is now known to be required for signal transduction 
                    induced by T and B cell antigen receptor engagement, cytokine signaling and Fc receptor stimulation. The functional state of CD45 also 
                    has a pronounced effect on lymphocyte development. CD45 exists in multiple forms, such as the restricted variants and as allelic forms 
                    CD45.1/Ly5.1 and CD45.2/Ly5.2. The former arises as a result of alternative splicing of different exons. The specificity of antibodies to 
                    CD45.1 and CD45.2 has been exploited in studies in which resolution of donor and recipient cells is essential, such as in gene therapy or 
                    bone marrow transplantation." />
            </fuge:_descriptions>
        </fuge:GenericMaterial>
        <!-- CD45.2 -->
        <fuge:GenericMaterial identifier="CD45.2">
            <fuge:_descriptions>
                <fuge:Description 
                    text="CD45 is an essential regulator of leukocyte activation and development, and is now known to be a protein tyrosine phosphatase, 
                    e.g. CD45 is able to dephosphorylate the Src family of protein kinases. This activity is now known to be required for signal transduction 
                    induced by T and B cell antigen receptor engagement, cytokine signaling and Fc receptor stimulation. The functional state of CD45 also 
                    has a pronounced effect on lymphocyte development. CD45 exists in multiple forms, such as the restricted variants and as allelic forms 
                    CD45.1/Ly5.1 and CD45.2/Ly5.2. The former arises as a result of alternative splicing of different exons. The specificity of antibodies to 
                    CD45.1 and CD45.2 has been exploited in studies in which resolution of donor and recipient cells is essential, such as in gene therapy or 
                    bone marrow transplantation." />
            </fuge:_descriptions>
        </fuge:GenericMaterial>
        <fuge:GenericMaterial identifier="DNA_of_Membrane-compromised_Cells">
            <fuge:_descriptions><fuge:Description text="Used for identification of viable cells." /></fuge:_descriptions>
        </fuge:GenericMaterial>
        
        <!-- Reporters Dyes -->
        <!-- TxRed -->
        <fuge:GenericMaterial name="TxRed" identifier="TxRed_Reporter_Component">
            <fuge:_characteristics OntologyTerm_ref="TexasRed_OT" />
        </fuge:GenericMaterial> 
        <!-- Another TxRed -->
        <fuge:GenericMaterial name="TxRed" identifier="TxRed_Reporter_Component_2">
            <fuge:_characteristics OntologyTerm_ref="TexasRed_OT" />
        </fuge:GenericMaterial>
        <!-- APC -->
        <fuge:GenericMaterial name="APC" identifier="APC_Reporter_Component">
            <fuge:_characteristics OntologyTerm_ref="APC_OT" />
        </fuge:GenericMaterial>
        <!-- PE -->
        <fuge:GenericMaterial name="PE" identifier="PE_Reporter_Component">
            <fuge:_characteristics OntologyTerm_ref="PE_OT" />
        </fuge:GenericMaterial>
        <!-- Another PE -->
        <fuge:GenericMaterial name="PE" identifier="PE_Reporter_Component_2">
            <fuge:_characteristics OntologyTerm_ref="PE_OT" />
        </fuge:GenericMaterial>
        <!-- FITC -->
        <fuge:GenericMaterial name="FITC" identifier="FITC_Reporter_Component">
            <fuge:_characteristics OntologyTerm_ref="FITC_OT" />
        </fuge:GenericMaterial>
        <!-- PerCP -->
        <fuge:GenericMaterial name="PerCP" identifier="PerCP_Reporter_Component">
            <fuge:_characteristics OntologyTerm_ref="PerCP_OT" />
        </fuge:GenericMaterial>
        <!-- DAPI -->
        <fuge:GenericMaterial name="DAPI" identifier="DAPI_Reporter_Component">
            <fuge:_characteristics OntologyTerm_ref="DAPI_OT" />
        </fuge:GenericMaterial>
        
        <!-- 4 Donor mice -->
        <!-- Donor 1 -->
        <fcm:Organism identifier="Doner_Mouse_1">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />  
            <fcm:_phenotype OntologyTerm_ref="Black_Pep3b_mouse_phenotype" />
        </fcm:Organism>        
        <!-- Donor 2 -->
        <fcm:Organism identifier="Doner_Mouse_2">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="Black_Pep3b_mouse_phenotype" />
        </fcm:Organism>
        <!-- Donor 3 -->
        <fcm:Organism identifier="Doner_Mouse_3">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="Black_Pep3b_mouse_phenotype" />
        </fcm:Organism>
        <!-- Donor 4 -->
        <fcm:Organism identifier="Doner_Mouse_4">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="Ly-5_Congenic_C57BL-6_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="Black_Pep3b_mouse_phenotype" />
        </fcm:Organism>
        
        <!-- 12 Recipient Mice -->
        <!-- Recipient 1 -->
        <fcm:Organism identifier="Recipient_Mouse_1">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
         </fcm:Organism>
        <!-- Recipient 2 -->
        <fcm:Organism identifier="Recipient_Mouse_2">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 3 -->
        <fcm:Organism identifier="Recipient_Mouse_3">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 4 -->
        <fcm:Organism identifier="Recipient_Mouse_4"> 
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" /> 
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 5 -->
        <fcm:Organism identifier="Recipient_Mouse_5">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 6 -->
        <fcm:Organism identifier="Recipient_Mouse_6">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 7 -->
        <fcm:Organism identifier="Recipient_Mouse_7">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 8 -->
        <fcm:Organism identifier="Recipient_Mouse_8">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 9 -->
        <fcm:Organism identifier="Recipient_Mouse_9">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 10 -->
        <fcm:Organism identifier="Recipient_Mouse_10">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 11 -->
        <fcm:Organism identifier="Recipient_Mouse_11">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        <!-- Recipient 12 -->
        <fcm:Organism identifier="Recipient_Mouse_12">
            <fcm:_age><fuge:AtomicValue value="6"><fuge:_unit OntologyTerm_ref="Month_Unit_OT" /></fuge:AtomicValue></fcm:_age>
            <fcm:_otherInformation>
                <fuge:Description text="Animal located at the Animal Resource Centre (ARC) of the BC Cancer Research Centre (BCCRC)" />
            </fcm:_otherInformation>
            <fcm:_taxnomyNCBI OntologyTerm_ref="MusMusculus_C57BL-6J_Pep3b" />
            <fcm:_gender OntologyTerm_ref="male_OT" />
            <fcm:_genotype OntologyTerm_ref="C57BL/6J_W41/W41_mouse_genotype" />
            <fcm:_phenotype OntologyTerm_ref="White_W41_W41_mouse_phenotype" />
        </fcm:Organism>
        
        <!-- 12 unstained samples, 1 from each recepient -->
        <!-- Unstained Sample 1 -->
        <fcm:Sample name="Unstained Sample 1" identifier="Unstained_Sample_1">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_1" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 2 -->
        <fcm:Sample name="Unstained Sample 2" identifier="Unstained_Sample_2">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_2" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 3 -->
        <fcm:Sample name="Unstained Sample 3" identifier="Unstained_Sample_3">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_3" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 4 -->
        <fcm:Sample name="Unstained Sample 4" identifier="Unstained_Sample_4">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_4" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 5 -->
        <fcm:Sample name="Unstained Sample 5" identifier="Unstained_Sample_5">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_5" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 6 -->
        <fcm:Sample name="Unstained Sample 6" identifier="Unstained_Sample_6">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_6" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 7 -->
        <fcm:Sample name="Unstained Sample 7" identifier="Unstained_Sample_7">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_7" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 8 -->
        <fcm:Sample name="Unstained Sample 8" identifier="Unstained_Sample_8">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_8" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 9 -->
        <fcm:Sample name="Unstained Sample 9" identifier="Unstained_Sample_9">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_9" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 10 -->
        <fcm:Sample name="Unstained Sample 10" identifier="Unstained_Sample_10">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_10" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 11 -->
        <fcm:Sample name="Unstained Sample 11" identifier="Unstained_Sample_11">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_11" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Unstained Sample 12 -->
        <fcm:Sample name="Unstained Sample 12" identifier="Unstained_Sample_12">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_12" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, unstained stage, ready to be stained" /></fcm:_otherInformation>
        </fcm:Sample>
        
        <!-- 12 stained samples -->
        <!-- Stained sample 1 -->
        <fcm:Sample name="Sample 1" identifier="Sample_1">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_1" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 2 -->
        <fcm:Sample name="Sample 2" identifier="Sample_2">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_2" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 3 -->
        <fcm:Sample name="Sample 3" identifier="Sample_3">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_3" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 4 -->
        <fcm:Sample name="Sample 4" identifier="Sample_4">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_4" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 5 -->
        <fcm:Sample name="Sample 5" identifier="Sample_5">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_5" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 6 -->
        <fcm:Sample name="Sample 6" identifier="Sample_6">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_6" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained stage" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 7 -->
        <fcm:Sample name="Sample 7" identifier="Sample_7">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_7" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 8 -->
        <fcm:Sample name="Sample 8" identifier="Sample_8">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_8" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 9 -->
        <fcm:Sample name="Sample 9" identifier="Sample_9">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_9" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 10 -->
        <fcm:Sample name="Sample 10" identifier="Sample_10">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_10" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 11 -->
        <fcm:Sample name="Sample 11" identifier="Sample_11">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_11" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        <!-- Stained sample 12 -->
        <fcm:Sample name="Sample 12" identifier="Sample_12">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="OBI_0000112" />
            <fcm:_sourceOrganism Organism_ref="Recipient_Mouse_12" />
            <fcm:_otherInformation><fuge:Description text="Peripheral blood, stained" /></fcm:_otherInformation>
        </fcm:Sample>
        
        <!-- Single Stain Control Samples -->
        <fcm:Sample name="Single Stain Control 1" identifier="Single_Stain_Control_1">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="Single_Stain_Control_OT" />
            <fcm:_otherInformation><fuge:Description text="Compensation tube 1 (FL1): FITC+Ab" /></fcm:_otherInformation>
        </fcm:Sample>
        <fcm:Sample name="Single Stain Control 2" identifier="Single_Stain_Control_2">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="Single_Stain_Control_OT" />
            <fcm:_otherInformation><fuge:Description text="Compensation tube 2 (FL2): PE+Ab" /></fcm:_otherInformation>
        </fcm:Sample>
        <fcm:Sample name="Single Stain Control 3" identifier="Single_Stain_Control_3">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="Single_Stain_Control_OT" />
            <fcm:_otherInformation><fuge:Description text="Compensation tube 3 (FL3): TxRed+Ab" /></fcm:_otherInformation>
        </fcm:Sample>
        <fcm:Sample name="Single Stain Control 4" identifier="Single_Stain_Control_4">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="Single_Stain_Control_OT" />
            <fcm:_otherInformation><fuge:Description text="Compensation tube 4 (FL4): PerCP+Ab" /></fcm:_otherInformation>
        </fcm:Sample>
        <fcm:Sample name="Single Stain Control 5" identifier="Single_Stain_Control_5">
            <fuge:_materialType OntologyTerm_ref="PB_OT" />
            <fcm:_subType OntologyTerm_ref="Single_Stain_Control_OT" />
            <fcm:_otherInformation><fuge:Description text="Compensation tube 5 (FL6): APC+Ab" /></fcm:_otherInformation>
        </fcm:Sample>
        
        <!-- HSC from doners (to be transplanted to a recipient) -->
        <!-- HSC from donor 1 -->
        <fuge:GenericMaterial identifier="HSC_from_donor_1" name="HSC from donor 1">
            <fuge:_characteristics OntologyTerm_ref="HSC_OT" />
        </fuge:GenericMaterial>
        <!-- HSC from donor 2 -->
        <fuge:GenericMaterial identifier="HSC_from_donor_2" name="HSC from donor 2">
            <fuge:_characteristics OntologyTerm_ref="HSC_OT" />
        </fuge:GenericMaterial>
        <!-- HSC from donor 3 -->
        <fuge:GenericMaterial identifier="HSC_from_donor_3" name="HSC from donor 3">
            <fuge:_characteristics OntologyTerm_ref="HSC_OT" />
        </fuge:GenericMaterial>
        <!-- KSL HSC from donor 4 -->
        <fuge:GenericMaterial identifier="KSL_HSC_from_donor_4" name="KSL HSC from donor 4">
            <fuge:_characteristics OntologyTerm_ref="KSL_HSC_OT" />
        </fuge:GenericMaterial>
        
        <!-- Fluorescent Cocktail  -->
        <fcm:FluorescentReagentCocktail identifier="StainingCocktail_1" name="Staining Cocktail 1" /> 
    
    </fuge:MaterialCollection>
    
    
    <!-- 
        ********************************* 
        References
        *********************************
    -->
    
    <fuge:ReferenceableCollection>
        <!-- Description of the protocol used within this experiment -->
        <fuge:BibliographicReference 
            identifier="bibRef_1_Szilvassy_1990" name="Szilvassy et al., 1990" authors="Szilvassy, S.J.; Humphries, R.K.; Lansdorp, P.M.; Eaves, A.C.; Eaves, C.J." 
            title="Quantitative Assay for Totipotent Reconstituting Hematopoietic Stem Cells by a Competitive Repopulation Strategy" 
            publication="Proceedings of the National Academy of Sciences" year="1990" volume="87" pages="8736-8740" />
    </fuge:ReferenceableCollection>
    
    
    <!-- 
        ********************************* 
        Investigations and its components
        *********************************
    -->
    
    <fuge:InvestigationCollection>
        <!-- A single investigation having single flow cytometry component -->
        <fuge:Investigation identifier="DonHSCC2LMC 2006-07-28 MGCS" start="2006-07-08T00:00:00" end="2006-11-30T00:00:00" name="Donor hematopoietic stem cells contribution to lymphocytes and myeloid cells">
            <fuge:_descriptions>
                <fuge:Description text="The Competitive Repopulation Assay is used for the experiment. It is a quantitative 
                    assay for long-term repopulating stem cells with the potential for reconstituting all 
                    hematopoietic lineages. This assay has two key features. The first is the use of competitive 
                    repopulation conditions that ensure not only the detection of a very primitive class of 
                    hematopoietic stem cells but also the survival of lethally irradiated mice transplanted with 
                    very low numbers of such cells. The second is the use of a limiting-dilution experimental 
                    design to allow stem cell quantitation." />
            </fuge:_descriptions>
            
            <fuge:_bibliographicReferences BibliographicReference_ref="bibRef_1_Szilvassy_1990" />
            
            <!-- Investigation component for flow cytometry part of the study -->
            <fuge:InvestigationComponent identifier="IC_FCM">
                <fuge:_factors Factor_ref="fact_HSC" />
                <fuge:_factors Factor_ref="fact_KSLHSC" />
                
                <fuge:_qualityControlDescription>
                    <fuge:Description text="Decreasing numbers of donor HSC cells (5, 20, 100) were injected at day 0 into 3 groups respectively of recipient mice; 3 mice per group. (KSL) HSC cells (500) were injected into each mouse of the control group (3 mice in the control group). PB has been collected from positive as well as negative mice in order to provide a staining control. Mice from the 500 KSL group were consider as the positive controls; mice that are not reconstituted as the negative controls. Unstained controls have not been used as they are not critical for the evaluation of results because in each sample dull negative cells are being compared to bright positive populations." />
                </fuge:_qualityControlDescription>
                <fuge:_allProtocolApplications ProtocolApplication_ref="CreateStainingCocktail_1" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_1" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_2" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_3" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Collect_cells_from_doner_4" />
                
                <!-- 5 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_1" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_4" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_7" />
                <!-- 20 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_2" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_5" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_8" />
                <!-- 100 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_3" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_6" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_9" />
                <!-- 500 KSL HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_10" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_11" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Inject_cells_into_recipient_12" />
                
                <!-- 5 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_1" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_4" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_7" />
                  <!-- 20 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_2" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_5" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_8" />
                <!-- 100 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_3" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_6" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_9" />
                <!-- 500 KSL HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_10" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_11" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Sample_12" />
                
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Single_Stain_Control_1" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Single_Stain_Control_2" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Single_Stain_Control_3" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Single_Stain_Control_4" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Create_Single_Stain_Control_5" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Data_Acquisition_Protocol_Application_1" />
                
                <!-- 5 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data01.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data04.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data07.fcs" />
                <!-- 20 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data02.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data05.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data08.fcs" />
                <!-- 100 HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data03.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data06.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data09.fcs" />
                <!-- 500 KSL HSC -->
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data10.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data11.fcs" />
                <fuge:_allProtocolApplications ProtocolApplication_ref="Compensate_and_gate_data12.fcs" />
            </fuge:InvestigationComponent>
            
            
            <!-- Contacts, authors, etc. -->
            <fuge:ContactRole Contact_ref="Clayton_Smith">
                <fuge:_role OntologyTerm_ref="OBI_0000103" />
            </fuge:ContactRole>      
            <fuge:ContactRole Contact_ref="Maura_Gasparetto">
                <fuge:_role OntologyTerm_ref="OBI_0000357" />
            </fuge:ContactRole>     
            <fuge:ContactRole Contact_ref="TFL_BCCRC">
                <fuge:_role OntologyTerm_ref="OBI_0000184" />
            </fuge:ContactRole>
            
            <!-- All source materials -->
            <fuge:_sourceMaterials Material_ref="Doner_Mouse_1" />
            <fuge:_sourceMaterials Material_ref="Doner_Mouse_2" />
            <fuge:_sourceMaterials Material_ref="Doner_Mouse_3" />
            <fuge:_sourceMaterials Material_ref="Doner_Mouse_4" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_1" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_2" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_3" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_4" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_5" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_6" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_7" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_8" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_9" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_10" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_11" />
            <fuge:_sourceMaterials Material_ref="Recipient_Mouse_12" />
            <fuge:_sourceMaterials Material_ref="CD4_TxRed_FluorescentReagent" />
            <fuge:_sourceMaterials Material_ref="CD8_TxRed_FluorescentReagent" />
            <fuge:_sourceMaterials Material_ref="CD45R_APC_FluorescentReagent" />
            <fuge:_sourceMaterials Material_ref="Gr1_PE_FluorescentReagent" />
            <fuge:_sourceMaterials Material_ref="CD11b_PE_FluorescentReagent" />
            <fuge:_sourceMaterials Material_ref="CD45.1_FITC_FluorescentReagent" />
            <fuge:_sourceMaterials Material_ref="CD45.2_PerCP_FluorescentReagent" />
            <fuge:_sourceMaterials Material_ref="DAPI_FluorescentReagent" />
            
            <!-- Experiment driving hypothesis -->
            <fuge:_hypothesis>
                <fuge:Description text="The purpose of the experiment is to quantify donor hematopoietic stem cells (HSC) contribution 
                    to lymphocytes and myeloid cells by flow cytometric analysis of peripheral blood (PB) cells stained 
                    with appropriate combinations of donor specific marker and lineage specific antibodies. The hypothesis 
                    is that donor HSC contribute significantly to recipient’s lymphocytes and myeloid cells." />
            </fuge:_hypothesis>
            
            <!-- Conclusions of the experiment -->
            <fuge:_conclusion>
                <fuge:Description text="Mice are considered reconstituted (positive) if their PB contains at least one percent of donor derived 
                    myeloid and lymphoid cells at 4 months or later post transplantation. In this sense, 1 mouse out of 3 in the 
                    5 cell group was considered positive, 1 mouse out of 3 in the 20 cell group was considered positive, all 3 
                    mice in the 100 cell group were considered positive and all 3 mice in the 500 cell control group were 
                    considered positive. This indicates that higher number of transplanted HSC cells invokes donor derived 
                    myeloid and lymphoid cells in the recipient." />
            </fuge:_conclusion>
            
            <!-- Keywords -->
            <fuge:_investigationSummary OntologyTerm_ref="keyword_1_blood" />
            <fuge:_investigationSummary OntologyTerm_ref="keyword_2_transplant" />
            <fuge:_investigationSummary OntologyTerm_ref="keyword_3_donor" />
            <fuge:_investigationSummary OntologyTerm_ref="keyword_4_recipient" />
            <fuge:_investigationSummary OntologyTerm_ref="keyword_5_leukocyte" />
            <fuge:_investigationSummary OntologyTerm_ref="keyword_6_lymphocyte" />
            <fuge:_investigationSummary OntologyTerm_ref="keyword_7_monocyte" />
            <fuge:_investigationSummary OntologyTerm_ref="keyword_8_granulocyte" />
            
        </fuge:Investigation>
        
        <!-- Investigation factors, number of injected cells -->
        <!-- HSC -->
        <fuge:Factor identifier="fact_HSC">
            <fuge:_descriptions><fuge:Description text="HSC cells injected into a recipient mice" /></fuge:_descriptions>
            <fuge:FactorValue><fuge:AtomicValue value="0" /></fuge:FactorValue>
            <fuge:FactorValue><fuge:AtomicValue value="5" /></fuge:FactorValue>
            <fuge:FactorValue><fuge:AtomicValue value="20" /></fuge:FactorValue>
            <fuge:FactorValue><fuge:AtomicValue value="100" /></fuge:FactorValue>
        </fuge:Factor>
        <!-- KSL HSC -->
        <fuge:Factor identifier="fact_KSLHSC">
            <fuge:_descriptions><fuge:Description text="Kit+/sca-1+/Lineage- (KSL) HSC cells injected into a recipient mice" /></fuge:_descriptions>
            <fuge:FactorValue><fuge:AtomicValue value="0" /></fuge:FactorValue>
            <fuge:FactorValue><fuge:AtomicValue value="500" /></fuge:FactorValue>            
        </fuge:Factor>
        
    </fuge:InvestigationCollection>
    
    
    <!-- 
        ********************************* 
        Data
        *********************************
    -->
    
    <fuge:DataCollection>
        
        <!-- 12 list mode data files (FCS files), one file per recipient-->
        <!-- data01.fcs -->
        <fcm:ListModeDataFile location="file:///data01.fcs" identifier="data01.fcs" name="data01.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_1" />
        </fcm:ListModeDataFile>    
        <!-- data02.fcs -->
        <fcm:ListModeDataFile location="file:///data02.fcs" identifier="data02.fcs" name="data02.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_2" />
        </fcm:ListModeDataFile>
        <!-- data03.fcs -->
        <fcm:ListModeDataFile location="file:///data03.fcs" identifier="data03.fcs" name="data03.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_3" />
        </fcm:ListModeDataFile>
        <!-- data04.fcs -->
        <fcm:ListModeDataFile location="file:///data04.fcs" identifier="data04.fcs" name="data04.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_4" />
        </fcm:ListModeDataFile>
        <!-- data05.fcs -->
        <fcm:ListModeDataFile location="file:///data05.fcs" identifier="data05.fcs" name="data05.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_5" />
        </fcm:ListModeDataFile>
        <!-- data06.fcs -->
        <fcm:ListModeDataFile location="file:///data06.fcs" identifier="data06.fcs" name="data06.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_6" />
        </fcm:ListModeDataFile>
        <!-- data07.fcs -->
        <fcm:ListModeDataFile location="file:///data07.fcs" identifier="data07.fcs" name="data07.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_7" />
        </fcm:ListModeDataFile>
        <!-- data08.fcs -->
        <fcm:ListModeDataFile location="file:///data07.fcs" identifier="data07.fcs" name="data07.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_8" />
        </fcm:ListModeDataFile>
        <!-- data09.fcs -->
        <fcm:ListModeDataFile location="file:///data09.fcs" identifier="data09.fcs" name="data09.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_9" />
        </fcm:ListModeDataFile>
        <!-- data10.fcs -->
        <fcm:ListModeDataFile location="file:///data10.fcs" identifier="data10.fcs" name="data10.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_10" />
        </fcm:ListModeDataFile>
        <!-- data11.fcs -->
        <fcm:ListModeDataFile location="file:///data11.fcs" identifier="data11.fcs" name="data11.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_11" />
        </fcm:ListModeDataFile>
        <!-- data12.fcs -->
        <fcm:ListModeDataFile location="file:///data12.fcs" identifier="data12.fcs" name="data12.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Sample_12" />
        </fcm:ListModeDataFile>   
        
        <!-- 5 single stain control list mode data files (FCS files), one file per single stain control compensation tube -->
        <!-- compdata1.fcs -->
        <fcm:ListModeDataFile location="file:///compdata1.fcs" identifier="compdata1.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Single_Stain_Control_1" />
        </fcm:ListModeDataFile>
        <!-- compdata2.fcs -->
        <fcm:ListModeDataFile location="file:///compdata2.fcs" identifier="compdata2.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Single_Stain_Control_2" />
        </fcm:ListModeDataFile>
        <!-- compdata3.fcs -->
        <fcm:ListModeDataFile location="file:///compdata3.fcs" identifier="compdata3.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Single_Stain_Control_3" />
        </fcm:ListModeDataFile>
        <!-- compdata4.fcs -->
        <fcm:ListModeDataFile location="file:///compdata4.fcs" identifier="compdata4.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Single_Stain_Control_4" />
        </fcm:ListModeDataFile>
        <!-- compdata5.fcs -->
        <fcm:ListModeDataFile location="file:///compdata5.fcs" identifier="compdata5.fcs">
            <fuge:_externalFormatDocumentation>
                <fuge:URI location="http://www.isac-net.org/index.php?option=com_content&amp;task=view&amp;id=101&amp;Itemid=46" />
            </fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="OBI_0000021" />
            <fcm:_sample Sample_ref="Single_Stain_Control_5" />
        </fcm:ListModeDataFile>
        

        <!-- Fluorescence compensation matrix (wihtin the Gating-ML file) -->
        <fuge:ExternalData location="file:///Gating.xml#spillover_01" identifier="spillover_01" name="spillover_01">
            <fuge:_externalFormatDocumentation><fuge:URI location="http:///flowcyt.sourceforge.net/gating/latest.pdf" /></fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="Gating-ML_OT" />
        </fuge:ExternalData>
        
        <!-- Gating description in a Gating-ML file -->
        <fuge:ExternalData location="file:///Gating.xml" identifier="gating_file_01" name="Gating description file">
            <fuge:_externalFormatDocumentation><fuge:URI location="http://flowcyt.sourceforge.net/gating/latest.pdf" /></fuge:_externalFormatDocumentation>
            <fuge:_fileFormat OntologyTerm_ref="Gating-ML_OT" />
        </fuge:ExternalData>
        
        <!-- Results summary -->
        <!-- Results for Sample 1 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_1" name="Results for Sample 1">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="1" />
                <fuge:NameValueType name="Cells" value="5" />
                <fuge:NameValueType name="Doner" value="1" />
                <fuge:NameValueType name="Result" value="Negative" />
                <fuge:NameValueType name="Leukocytes" value="58.8" />
                <fuge:NameValueType name="Viable Leukocytes" value="92.1" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="0.2" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 58.8% of the total number of cells
                Viable Leukocytes (FSC-FL8): 92.1% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 0.2% of Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>   
        <!-- Results for Sample 2 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_2" name="Results for Sample 2">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="2" />
                <fuge:NameValueType name="Cells" value="20" />
                <fuge:NameValueType name="Doner" value="1" />
                <fuge:NameValueType name="Result" value="Negative" />
                <fuge:NameValueType name="Leukocytes" value="57.1" />
                <fuge:NameValueType name="Viable Leukocytes" value="94.5" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="0.8" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 57.1% of the total number of cells
                Viable Leukocytes (FSC-FL8): 94.5% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 0.8% of Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 3 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_3" name="Results for Sample 3">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="3" />
                <fuge:NameValueType name="Cells" value="100" />
                <fuge:NameValueType name="Doner" value="1" />
                <fuge:NameValueType name="Result" value="Positive" />
                <fuge:NameValueType name="Leukocytes" value="55.6" />
                <fuge:NameValueType name="Viable Leukocytes" value="93.1" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="43.1" />
                <fuge:NameValueType name="Doner-derived B-cells" value="30.9" />
                <fuge:NameValueType name="Doner-derived T-cells" value="30.4" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="38.8" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 55.6% of the total number of cells
                Viable Leukocytes (FSC-FL8): 93.1% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 43.1% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 30.9% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 30.4% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 38.8% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 4 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_4" name="Results for Sample 4">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="4" />
                <fuge:NameValueType name="Cells" value="5" />
                <fuge:NameValueType name="Doner" value="2" />
                <fuge:NameValueType name="Result" value="Negative" />
                <fuge:NameValueType name="Leukocytes" value="54.8" />
                <fuge:NameValueType name="Viable Leukocytes" value="97.2" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="0.1%" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 54.8% of the total number of cells
                Viable Leukocytes (FSC-FL8): 97.2% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 0.1% of Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 5 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_5" name="Results for Sample 5">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="5" />
                <fuge:NameValueType name="Cells" value="20" />
                <fuge:NameValueType name="Doner" value="2" />
                <fuge:NameValueType name="Result" value="Positive" />
                <fuge:NameValueType name="Leukocytes" value="53.6" />
                <fuge:NameValueType name="Viable Leukocytes" value="92.5" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="10.8" />
                <fuge:NameValueType name="Doner-derived B-cells" value="29.0" />
                <fuge:NameValueType name="Doner-derived T-cells" value="31.5" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="39.5" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 53.6% of the total number of cells
                Viable Leukocytes (FSC-FL8): 92.5% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 10.8% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 29.0% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 31.5% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 39.5% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 6 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_6" name="Results for Sample 6">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="6" />
                <fuge:NameValueType name="Cells" value="100" />
                <fuge:NameValueType name="Doner" value="2" />
                <fuge:NameValueType name="Result" value="Positive" />
                <fuge:NameValueType name="Leukocytes" value="56.6" />
                <fuge:NameValueType name="Viable Leukocytes" value="92.5" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="45.8" />
                <fuge:NameValueType name="Doner-derived B-cells" value="29.5" />
                <fuge:NameValueType name="Doner-derived T-cells" value="31.0" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="39.5" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 56.6% of the total number of cells
                Viable Leukocytes (FSC-FL8): 92.5% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 45.8% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 29.5% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 31.0% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 39.5% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 7 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_7" name="Results for Sample 7">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="7" />
                <fuge:NameValueType name="Cells" value="5" />
                <fuge:NameValueType name="Doner" value="3" />
                <fuge:NameValueType name="Result" value="Positive" />
                <fuge:NameValueType name="Leukocytes" value="48.8" />
                <fuge:NameValueType name="Viable Leukocytes" value="95.4" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="3.8" />
                <fuge:NameValueType name="Doner-derived B-cells" value="33.6" />
                <fuge:NameValueType name="Doner-derived T-cells" value="35.0" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="31.4" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 48.8% of the total number of cells
                Viable Leukocytes (FSC-FL8): 95.4% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 3.8% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 33.6% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 35.0% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 31.4% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 8 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_8" name="Results for Sample 8">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="8" />
                <fuge:NameValueType name="Cells" value="20" />
                <fuge:NameValueType name="Doner" value="3" />
                <fuge:NameValueType name="Result" value="Negative" />
                <fuge:NameValueType name="Leukocytes" value="55.8" />
                <fuge:NameValueType name="Viable Leukocytes" value="97.0" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="0.8%" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 55.8% of the total number of cells
                Viable Leukocytes (FSC-FL8): 97.0% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 0.8% of Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 9 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_9" name="Results for Sample 9">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="9" />
                <fuge:NameValueType name="Cells" value="100" />
                <fuge:NameValueType name="Doner" value="3" />
                <fuge:NameValueType name="Result" value="Positive" />
                <fuge:NameValueType name="Leukocytes" value="48.7" />
                <fuge:NameValueType name="Viable Leukocytes" value="92.4" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="35.8" />
                <fuge:NameValueType name="Doner-derived B-cells" value="29.6" />
                <fuge:NameValueType name="Doner-derived T-cells" value="28.0" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="42.4" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 48.7% of the total number of cells
                Viable Leukocytes (FSC-FL8): 92.4% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4):  35.8% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 29.6% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 28.0% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 42.4% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 10 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_10" name="Results for Sample 10">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="10" />
                <fuge:NameValueType name="Cells" value="500" />
                <fuge:NameValueType name="Doner" value="4" />
                <fuge:NameValueType name="Result" value="Positive" />       
                <fuge:NameValueType name="Leukocytes" value="55.8" />
                <fuge:NameValueType name="Viable Leukocytes" value="93.5" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="55.4" />
                <fuge:NameValueType name="Doner-derived B-cells" value="31.1" />
                <fuge:NameValueType name="Doner-derived T-cells" value="32.1" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="66.8" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 55.8% of the total number of cells
                Viable Leukocytes (FSC-FL8): 93.5% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 55.4% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 31.1% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 32.1% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 66.8% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 11 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_11" name="Results for Sample 11">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="11" />
                <fuge:NameValueType name="Cells" value="500" />
                <fuge:NameValueType name="Doner" value="4" />
                <fuge:NameValueType name="Result" value="Positive" /> 
                <fuge:NameValueType name="Leukocytes" value="56.8" />
                <fuge:NameValueType name="Viable Leukocytes" value="93.7" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="52.6" />
                <fuge:NameValueType name="Doner-derived B-cells" value="32.5" />
                <fuge:NameValueType name="Doner-derived T-cells" value="32.0" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="65.5" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 56.8% of the total number of cells
                Viable Leukocytes (FSC-FL8): 93.7% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 52.6% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 32.5% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 32.0% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 66.5% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        <!-- Results for Sample 12 -->
        <fuge:GenericInternalData identifier="Results_for_Sample_12" name="Results for Sample 12">
            <fuge:_propertySets>
                <fuge:NameValueType name="Sample" value="12" />
                <fuge:NameValueType name="Cells" value="500" />
                <fuge:NameValueType name="Doner" value="4" />
                <fuge:NameValueType name="Result" value="Positive" />
                <fuge:NameValueType name="Leukocytes" value="52.9" />
                <fuge:NameValueType name="Viable Leukocytes" value="91.7" />
                <fuge:NameValueType name="Donor-derived Viable Leukocytes" value="49.8" />
                <fuge:NameValueType name="Doner-derived B-cells" value="30.1" />
                <fuge:NameValueType name="Doner-derived T-cells" value="31.3" />
                <fuge:NameValueType name="Doner-derived Myeloid cells" value="68.6" />
            </fuge:_propertySets>
            <fuge:storage>
                Leukocytes (FSC-SSC): 52.9% of the total number of cells
                Viable Leukocytes (FSC-FL8): 91.7% of Leukocytes
                Donor-derived Viable Leukocytes (FL1-FL4): 49.8% of Viable Leukocytes
                Doner-derived B cells (FL2-FL6): 30.1% of Donor-derived Viable Leukocytes
                Doner-derived T cells (FL3-FL6): 31.3% of Donor-derived Viable Leukocytes
                Doner-derived Myeloid cells (FL2-FL6): 68.6% of Donor-derived Viable Leukocytes
            </fuge:storage>
        </fuge:GenericInternalData>
        
    </fuge:DataCollection>
    
    
    <!-- 
        ********************************* 
        Contact Details
        *********************************
    -->
    
    <fuge:AuditCollection>
        
        <!-- When was the experiment created and who are the owners of the description -->
        <fuge:Security identifier="Experiment_Description_Info">
            <fuge:_propertySets>
                <fuge:NameValueType name="version" type="string" value="1.0" />
                <fuge:NameValueType name="date of experiment description" type="xsd:dateTime" value="2008-07-30T16:02:00-08:00" />
            </fuge:_propertySets>
            <fuge:_owners Contact_ref="Clayton_Smith" />
            <fuge:_owners Contact_ref="Maura_Gasparetto" />
            <fuge:_owners Contact_ref="Josef_Spidlen" />
            <fuge:_owners Contact_ref="Peter_Wilkinson"/>
        </fuge:Security>
        
        <fuge:Person identifier="Clayton_Smith" name="Clayton Smith" address="BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada" email="clsmith@bccancer.bc.ca" phone="+1-813-903-6870" fax="+1-604-877-0712" lastName="Smith" firstName="Clayton" midInitials="A" />
        <fuge:Person identifier="Maura_Gasparetto" name="Maura Gasparetto" address="Terry Fox Laboratory, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada" email="mgaspare@bccrc.ca" lastName="Gasparetto" firstName="Maura" />
        <fuge:Person identifier="Josef_Spidlen" name="Josef Spidlen" address="Terry Fox Laboratory, BC Cancer Research Centre, 675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada" phone="+1 (604) 675-8000 x 7755" email="jspidlen@bccrc.ca" lastName="Spidlen" firstName="Josef" />
        <fuge:Person identifier="Peter_Wilkinson" name="Peter Wilkinson" email="pwilkinson@videotron.ca" firstName="Peter" lastName="Wilkinson" />
                
        <fuge:Organization identifier="TFL_BCCRC" name="Terry Fox Laboratory, BC Cancer Research Centre" address="675 West 10th Avenue, Vancouver, BC, V5Z 1L3, Canada" />
    
    </fuge:AuditCollection>
        
    
    <!-- 
        ********************************* 
        Protocols
        *********************************
    -->
    
    <fuge:ProtocolCollection>
                
        <!-- Create Staining Cocktail -->
        <fcm:CreateCocktailProtocol identifier="CreateStainingCocktail" name="Create Staining Cocktail">
            <fcm:BioTransformationAction identifier="CreateStainingCocktaiAction" actionOrdinal="1" />
        </fcm:CreateCocktailProtocol>
            
        <!-- Protocol for collection of donor HSC -->
        <fuge:GenericProtocol identifier="Donor_Cells_Collection_Protocol" protocolText="Collect donor hematopoietic stem cells and inject them into recipient mouse" >
            <fuge:GenericAction identifier="Collection" actionOrdinal="1" actionText="Collect hematopoietic stem cells from a donor mouse" />
        </fuge:GenericProtocol>
        
        <!-- Protocol for injection of donor HSC into recipient mouse -->
        <fuge:GenericProtocol identifier="Donor_Cells_Injection_Protocol">
            <fuge:GenericAction identifier="Irradiation" actionOrdinal="1" actionText="Irradiation of the recepient mouse">
                <fuge:GenericParameter identifier="dose" isInputParam="true">
                    <fuge:AtomicValue value="360"><fuge:_unit OntologyTerm_ref="Rad_Radiation_Unit_OT" /></fuge:AtomicValue>
                </fuge:GenericParameter>
            </fuge:GenericAction>
            <fuge:GenericAction identifier="Injection" actionOrdinal="2" actionText="Inject cells into recipient mouse" />
        </fuge:GenericProtocol>
        
        <!-- Staining (only) Protocol, used within the Treatment and staining protocol -->
        <fcm:StainSampleProtocol identifier="Staining_Protocol" name="Staining Protocol">
            <fcm:BioTransformationAction identifier="Staining_Protocol_Action" actionOrdinal="1" />
        </fcm:StainSampleProtocol>
        
        <!-- Treatment and staining protocol -->
        <fuge:GenericProtocol identifier="Treatment_And_Staining_Protocol" protocolText="Collect peripheral blood and stain with fluorescent reagents">
            <fuge:GenericAction identifier="Adjust_Concentration_Action" actionOrdinal="1" 
                actionText="Single cell suspensions are prepared and the cell concentrations are adjusted to 10^7/ml.">
                <fuge:GenericParameter identifier="cell concentration" isInputParam="true">
                    <fuge:AtomicValue value="10^7"><fuge:_unit OntologyTerm_ref="CellsPerML_Unit_OT" /></fuge:AtomicValue>
                </fuge:GenericParameter>
            </fuge:GenericAction>
            <fuge:GenericAction identifier="Block_Immunoglobulin_Fc_Receptors_Action" actionOrdinal="2" 
                actionText="Block Immunoglobulin Fc Receptors: In the mouse system, purified antibodies directed against mouse 
                    FcGamaI/III (Mouse BD FcBlock™, CD16/CD32, catalogue no. 553141 and 553142) have been used to block nonspecific 
                    staining due to FcR. To block FcR with BD FcBlock reagents, the cells are preincubated with 10 µg/ml of BD FcBlock 
                    antibody per 2x10^7 cells for 15–20 min at 4°C. The cells are not washed before the first staining step." />
            <fuge:GenericAction identifier="Staining_Action" actionOrdinal="3"
                actionText="Cells have been incubated for 40 minutes at 4°C in a staining buffer (approx. 10^6 cells in 100µl of 
                    staining buffer). The staining buffer contained a pre-titrated, optimal concentration (≤ 1µg) of a fluorescent 
                    monoclonal antibody specific for a receptor or with an immunoglobulin (Ig) isotype-matched control respectively." />
            <fuge:GenericAction identifier="Washing_Action" actionOrdinal="4" 
                actionText="After the incubation, cells have been washed 1x with 2ml of staining buffer and pelleted by 
                    centrifugation (250 X g for 5 min); supernatant has been removed." />
            <fuge:GenericAction identifier="Resuspend_in_PBSFCS_Action" actionOrdinal="5" 
                actionText="Finally, cells have been resuspended in PBS/2%FCS (Phosphate Buffered Solution, Fetal Calf Serum) 
                    for flow cytometric analysis." />
        </fuge:GenericProtocol>
        
        <!-- Data_Acquisition_Protocol -->
        <fcm:AcquisitionProtocol identifier="Data_Acquisition_Protocol" name="Data Acquisition Protocol">
            <fuge:_descriptions > 
                <fuge:Description text="Run samples through the cytometer and collect FCS data files." />
            </fuge:_descriptions>
            <fcm:BioTransformationAction identifier="InstrumentSetupAction" actionOrdinal="1" name="Instrument setup action">
                <fuge:_descriptions>
                    <fuge:Description text="Setting up the instrumentation" />
                </fuge:_descriptions>
            </fcm:BioTransformationAction>
            <fcm:BioTransformationAction identifier="SampleRunningAction" actionOrdinal="2" name="Load and run the sample">
                <fuge:_descriptions>
                    <fuge:Description text="Run the sample through the cytometer and get list mode data file." />
                </fuge:_descriptions>
            </fcm:BioTransformationAction>
            <fcm:_cytometrySoftware GenericSoftware_ref="BD_Facs_Diva" />
            <fcm:_cytometerEquipment Cytometer_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" />
        </fcm:AcquisitionProtocol>
        
        <!-- Data analysis protocol - created as a combination of compensation and gating -->
        <fuge:GenericProtocol identifier="CompensateAndGateProtocol">
            <fuge:GenericAction identifier="compensationAction" Protocol_ref="CompPr" actionOrdinal="1" actionText="Compensate the data file" />
            <fuge:GenericAction identifier="gatingAction" Protocol_ref="GatingPr" actionOrdinal="2" actionText="Gate the data file" />
        </fuge:GenericProtocol>
        
        <!-- Compensation Protocol - appears as the first action in the CompensateAndGateProtocol -->
        <fcm:CompensationProtocol identifier="CompPr" name="Compensation Protocol">
            <fuge:_types OntologyTerm_ref="SW_Compensation_OT" />
            <fcm:DataTransformationAction identifier="Compensation Action" actionOrdinal="1" name="Compensation">
                <fuge:_descriptions><fuge:Description text="Compensating a data file using a spillover matrix" /></fuge:_descriptions>
                <fcm:_executable GenericSoftware_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" />
                <fcm:_operatingSystem GenericSoftware_ref="Windows_XP" />
            </fcm:DataTransformationAction>
        </fcm:CompensationProtocol>
        
        <!-- Gating Protocol - appears as the second action in the CompensateAndGateProtocol -->
        <fcm:DataFilteringProtocol identifier="GatingPr" name="Gating Protocol">
            <fcm:DataTransformationAction identifier="Gating Action" actionOrdinal="1" name='Gating"'>
                <fuge:_descriptions><fuge:Description text="Gating of a data file" /></fuge:_descriptions>
                <fcm:_executable GenericSoftware_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" />
                <fcm:_operatingSystem GenericSoftware_ref="Windows_XP" />
            </fcm:DataTransformationAction> 
        </fcm:DataFilteringProtocol>
        
        <!-- Software -->
        
        <!-- Software BD Diva -->
        <fuge:GenericSoftware identifier="BD_Facs_Diva" version="5" name="BD Facs Diva">
            <fuge:_uri><fuge:URI location="www.bd.com" /></fuge:_uri>
            <fuge:_types OntologyTerm_ref="FCM_Analysis_SW_OT" />
        </fuge:GenericSoftware>
        
        <!-- Software used to create this XML file -->
        <fuge:GenericSoftware identifier="oXygen" version="8.1" name="oXygen XML Editor">
            <fuge:_uri><fuge:URI location="http://www.oxygenxml.com/" /></fuge:_uri>
            <fuge:_types OntologyTerm_ref="XML_Editor_OT" />
        </fuge:GenericSoftware>
        
        <!-- Software used for compensation and gating -->
        <fuge:GenericSoftware identifier="FlowJo_6_4_7_on_MacOSX_10_2_3" name="FlowJo" version="6.4.7">
            <fuge:_uri><fuge:URI location="http://www.flowjo.com/" /></fuge:_uri>
            <fuge:_types OntologyTerm_ref="FCM_Analysis_SW_OT" />
            <fuge:_types OntologyTerm_ref="Macintosh_OSX_10_2_3_OT" />
        </fuge:GenericSoftware>  
        
        <!-- Software Windows XP -->
        <fuge:GenericSoftware identifier="Windows_XP" version="XP" name="Microsoft Windows XP">
            <fuge:_uri><fuge:URI location="http://www.microsoft.com/" /></fuge:_uri>
            <fuge:_types OntologyTerm_ref="Operating_System_OT" />
        </fuge:GenericSoftware>
        

        <!-- ProtocolApplications -->

        <!-- Create Staining Cocktail 1 -->
        <fcm:CreateCocktailProtocolApplication CreateCocktailProtocol_ref="CreateStainingCocktail" identifier="CreateStainingCocktail_1"
            name="Create Staining Cocktail 1" activityDate="2006-11-19T20:00:00-08:00">            
            <fcm:_outputFluorescentReagentCocktail FluorescentReagentCocktail_ref="StainingCocktail_1" />
            <fcm:_inputCompleteFluorescentReagent FluorescentReagent_ref="CD4_TxRed_FluorescentReagent" />
            <fcm:_inputCompleteFluorescentReagent FluorescentReagent_ref="CD8_TxRed_FluorescentReagent" />
            <fcm:_inputCompleteFluorescentReagent FluorescentReagent_ref="CD45R_APC_FluorescentReagent" />
            <fcm:_inputCompleteFluorescentReagent FluorescentReagent_ref="CD11b_PE_FluorescentReagent" />
            <fcm:_inputCompleteFluorescentReagent FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent" />
            <fcm:_inputCompleteFluorescentReagent FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent" />
            <fcm:_inputCompleteFluorescentReagent FluorescentReagent_ref="DAPI_FluorescentReagent" />
        </fcm:CreateCocktailProtocolApplication>
        
        <!-- Get HSC from doners -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" 
            identifier="Collect_cells_from_doner_1" activityDate="2006-07-28T12:00:00-08:00">
            <fuge:_outputMaterials Material_ref="HSC_from_donor_1" />
            <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_1" />
        </fuge:GenericProtocolApplication>
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" 
            identifier="Collect_cells_from_doner_2" activityDate="2006-07-28T12:00:00-08:00">
            <fuge:_outputMaterials Material_ref="HSC_from_donor_2" />
            <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_2" />
        </fuge:GenericProtocolApplication>
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" 
            identifier="Collect_cells_from_doner_3" activityDate="2006-07-28T12:00:00-08:00">
            <fuge:_outputMaterials Material_ref="HSC_from_donor_3" />
            <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_3" />
        </fuge:GenericProtocolApplication>
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Collection_Protocol" 
            identifier="Collect_cells_from_doner_4" activityDate="2006-07-28T12:00:00-08:00">
            <fuge:_outputMaterials Material_ref="KSL_HSC_from_donor_4" />
            <fuge:_inputCompleteMaterials Material_ref="Doner_Mouse_4" />
        </fuge:GenericProtocolApplication>
        
        <!-- Inject HSC into recipient mice -->
        <!-- Inject HSC into recipient mouse 1 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_1" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_1" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_1" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_1">
                <fuge:AtomicValue value="5"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_1" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 2 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_2" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_2" />            
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_2" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_1">
                <fuge:AtomicValue value="20"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_2" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 3 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_3" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_3" />            
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_3" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_3" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 4 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_4" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_4" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_4" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_2">
                <fuge:AtomicValue value="5"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_4" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 5 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_5" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_5" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_5" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_2">
                <fuge:AtomicValue value="20"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_5" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 6 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_6" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_6" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_6" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_2">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_6" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 7 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol"
            identifier="Inject_cells_into_recipient_7" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_7" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_7" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_3">
                <fuge:AtomicValue value="5"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_7" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 8 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_8" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_8" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_8" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_3">
                <fuge:AtomicValue value="20"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_8" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 9 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_9" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_9" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_9" />
            <fuge:GenericMaterialMeasurement Material_ref="HSC_from_donor_3">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_9" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 10 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_10" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_10" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_10" />
            <fuge:GenericMaterialMeasurement Material_ref="KSL_HSC_from_donor_4">
                <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_10" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 11 -->
        <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
            identifier="Inject_cells_into_recipient_11" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_11" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_11" />
            <fuge:GenericMaterialMeasurement Material_ref="KSL_HSC_from_donor_4">
                <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_11" />
        </fuge:GenericProtocolApplication>
        <!-- Inject HSC into recipient mouse 12 -->
            <fuge:GenericProtocolApplication Protocol_ref="Donor_Cells_Injection_Protocol" 
                identifier="Inject_cells_into_recipient_12" activityDate="2006-07-28T15:00:00-08:00">
            <fuge:ActionApplication Action_ref="Irradiation" identifier="Irradiation_of_recipient_12" />
            <fuge:ActionApplication Action_ref="Injection" identifier="Injection_into_recipient_12" />
            <fuge:GenericMaterialMeasurement Material_ref="KSL_HSC_from_donor_4">
                <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="Cell_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Recipient_Mouse_12" />
        </fuge:GenericProtocolApplication>
        
        <!-- StainSampleProtocolApplications to be used in the Threatment and staining protocol application -->
        <!-- Stain Sample 1 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_1" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 2 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_2" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 3 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_3" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 4 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_4" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 5 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_5" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 6 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_6" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 7 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_7" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 8 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_8" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 9 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_9" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 10 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_10" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 11 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_11" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Sample 12 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Staining_Protocol_Application_12" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentCocktailMeasurement FluorescentReagentCocktail_ref="StainingCocktail_1">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentCocktailMeasurement>
        </fcm:StainSampleProtocolApplication>
        
        <!-- Single Stains -->
        <!-- Stain Control Sample 1 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Single_Staining_Protocol_Application_1" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentMeasurement FluorescentReagent_ref="CD45.1_FITC_FluorescentReagent">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Control Sample 2 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Single_Staining_Protocol_Application_2" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentMeasurement FluorescentReagent_ref="CD11b_PE_FluorescentReagent">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Control Sample 3 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Single_Staining_Protocol_Application_3" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentMeasurement FluorescentReagent_ref="CD4_TxRed_FluorescentReagent">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Control Sample 4 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Single_Staining_Protocol_Application_4" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentMeasurement FluorescentReagent_ref="CD45.2_PerCP_FluorescentReagent">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentMeasurement>
        </fcm:StainSampleProtocolApplication>
        <!-- Stain Control Sample 5 -->
        <fcm:StainSampleProtocolApplication StainSampleProtocol_ref="Staining_Protocol" identifier="Single_Staining_Protocol_Application_5" activityDate="2006-11-20T14:00:02-08:00">
            <fcm:FluorescentReagentMeasurement FluorescentReagent_ref="CD45R_APC_FluorescentReagent">
                <fuge:AtomicValue value="100"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fcm:FluorescentReagentMeasurement>
        </fcm:StainSampleProtocolApplication>
        
        <!-- Treatment and staining (creating samples), the Stain Sample xx protocol applications are being referenced from here  -->
        <!-- Create Sample 1 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_1" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS1_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS1_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS1_3" ProtocolApplication_ref="Staining_Protocol_Application_1" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS1_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS1_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_1">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_1" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 2 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_2" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS2_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS2_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS2_3" ProtocolApplication_ref="Staining_Protocol_Application_2" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS2_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS2_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_2">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_2" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 3 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_3" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS3_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS3_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS3_3" ProtocolApplication_ref="Staining_Protocol_Application_3" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS3_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS3_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_3">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_3" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 4 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_4" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS4_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS4_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS4_3" ProtocolApplication_ref="Staining_Protocol_Application_4" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS4_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS4_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_4">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_4" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 5 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_5" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS5_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS5_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS5_3" ProtocolApplication_ref="Staining_Protocol_Application_5" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS5_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS5_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_5">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_5" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 6 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_6" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS6_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS6_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS6_3" ProtocolApplication_ref="Staining_Protocol_Application_6" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS6_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS6_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_6">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_6" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 7 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_7" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS7_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS7_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS7_3" ProtocolApplication_ref="Staining_Protocol_Application_7" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS7_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS7_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_7">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_7" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 8 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_8" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS8_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS8_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS8_3" ProtocolApplication_ref="Staining_Protocol_Application_8" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS8_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS8_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_8">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_8" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 9 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_9" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS9_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS9_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS9_3" ProtocolApplication_ref="Staining_Protocol_Application_9" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS9_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS9_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_9">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_9" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 10 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_10" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS10_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS10_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS10_3" ProtocolApplication_ref="Staining_Protocol_Application_10" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS10_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS10_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_10">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_10" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 11 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_11" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS11_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS11_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS11_3" ProtocolApplication_ref="Staining_Protocol_Application_11" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS11_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS11_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_11">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_11" />
        </fuge:GenericProtocolApplication>
        <!-- Create Sample 12 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Sample_12" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="CS12_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="CS12_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="CS12_3" ProtocolApplication_ref="Staining_Protocol_Application_12" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="CS12_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="CS12_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_12">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Sample_12" />
        </fuge:GenericProtocolApplication>
        
        <!-- Creating Single Stain Control Samples -->
        <!-- Create Single Stain Control Sample 1 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Single_Stain_Control_1" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="SCS1_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="SCS1_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="SCS1_3" ProtocolApplication_ref="Single_Staining_Protocol_Application_1" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="SCS1_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="SCS1_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_1">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Single_Stain_Control_1" />
        </fuge:GenericProtocolApplication>
        <!-- Create Single Stain Control Sample 2 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Single_Stain_Control_2" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="SCS2_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="SCS2_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="SCS2_3" ProtocolApplication_ref="Single_Staining_Protocol_Application_2" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="SCS2_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="SCS2_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_1">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Single_Stain_Control_2" />
        </fuge:GenericProtocolApplication>
        <!-- Create Single Stain Control Sample 3 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Single_Stain_Control_3" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="SCS3_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="SCS3_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="SCS3_3" ProtocolApplication_ref="Single_Staining_Protocol_Application_3" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="SCS3_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="SCS3_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_1">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Single_Stain_Control_3" />
        </fuge:GenericProtocolApplication>
        <!-- Create Single Stain Control Sample 4 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Single_Stain_Control_4" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="SCS4_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="SCS4_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="SCS4_3" ProtocolApplication_ref="Single_Staining_Protocol_Application_4" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="SCS4_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="SCS4_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_1">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Single_Stain_Control_4" />
        </fuge:GenericProtocolApplication>
        <!-- Create Single Stain Control Sample 5 -->
        <fuge:GenericProtocolApplication Protocol_ref="Treatment_And_Staining_Protocol" identifier="Create_Single_Stain_Control_5" activityDate="2006-11-20T14:00:00-08:00">
            <fuge:ActionApplication Action_ref="Adjust_Concentration_Action" identifier="SCS5_1" />
            <fuge:ActionApplication Action_ref="Block_Immunoglobulin_Fc_Receptors_Action" identifier="SCS5_2" />
            <fuge:ActionApplication Action_ref="Staining_Action" identifier="SCS5_3" ProtocolApplication_ref="Single_Staining_Protocol_Application_5" />
            <fuge:ActionApplication Action_ref="Washing_Action" identifier="SCS5_4" />
            <fuge:ActionApplication Action_ref="Resuspend_in_PBSFCS_Action" identifier="SCS5_5" />
            <fuge:GenericMaterialMeasurement Material_ref="Unstained_Sample_1">
                <fuge:AtomicValue value="60"><fuge:_unit OntologyTerm_ref="Micro_Liter_Unit_OT" /></fuge:AtomicValue>
            </fuge:GenericMaterialMeasurement>
            <fuge:_outputMaterials Material_ref="Single_Stain_Control_5" />
        </fuge:GenericProtocolApplication>
       
        <!-- Data acquisition protocol applications -->
        <!-- Create all data files -->
        <fcm:AcquisitionProtocolApplication AcquisitionProtocol_ref="Data_Acquisition_Protocol"  identifier="Data_Acquisition_Protocol_Application_1" 
            activityDate="2006-11-21T15:00:00-08:00" name="Data Acquisition Protocol">
            <fuge:ActionApplication Action_ref="InstrumentSetupAction" identifier="DAPAA01.1" />
            <fuge:ActionApplication Action_ref="SampleRunningAction" identifier="DAPAA01.2" />
            
            <!-- Setup detector voltages -->
            <fcm:OpticalDetectorApplication Equipment_ref="FSC" identifier="FSC_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="FSC_Voltage">
                        <fuge:AtomicValue value="220"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            <fcm:OpticalDetectorApplication Equipment_ref="SSC" identifier="SSC_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="SSC_Voltage">
                        <fuge:AtomicValue value="330"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            <fcm:OpticalDetectorApplication Equipment_ref="FL1" identifier="FL1_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="FL1_Voltage">
                        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            <fcm:OpticalDetectorApplication Equipment_ref="FL2" identifier="FL2_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="FL2_Voltage">
                        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            <fcm:OpticalDetectorApplication Equipment_ref="FL3" identifier="FL3_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="FL3_Voltage">
                        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            <fcm:OpticalDetectorApplication Equipment_ref="FL4" identifier="FL4_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="FL4_Voltage">
                        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            <fcm:OpticalDetectorApplication Equipment_ref="FL6" identifier="FL6_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="FL6_Voltage">
                        <fuge:AtomicValue value="500"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            <fcm:OpticalDetectorApplication Equipment_ref="FL8" identifier="FL8_DA">
                <fcm:_voltageValue>
                    <fuge:ParameterValue Parameter_ref="FL8_Voltage">
                        <fuge:AtomicValue value="550"><fuge:_unit OntologyTerm_ref="V_Unit_OT" /></fuge:AtomicValue>
                    </fuge:ParameterValue>
                </fcm:_voltageValue>
            </fcm:OpticalDetectorApplication>
            
            <!-- BD FACS Aria  -->
            <fcm:CytometerApplication Equipment_ref="BD_FACSAria_Flow_Cytometer_SN_P0143" identifier="BD_FACSAria_CytometerApplication" />
            
            <fcm:_inputSampleSets>
                <!-- 5 Single stain controls samples -->
                <fcm:SampleSet identifier="Control_Sample_Set_1">
                    <fcm:_sample Sample_ref="Single_Stain_Control_1" />
                    <fcm:_sample Sample_ref="Single_Stain_Control_2" />
                    <fcm:_sample Sample_ref="Single_Stain_Control_3" />
                    <fcm:_sample Sample_ref="Single_Stain_Control_4" />
                    <fcm:_sample Sample_ref="Single_Stain_Control_5" />
                </fcm:SampleSet>
                <!-- 12 samples on the input of the instrument -->
                <fcm:SampleSet identifier="Sample_Set_1">
                    <fcm:_sample Sample_ref="Sample_1"/>
                    <fcm:_sample Sample_ref="Sample_2"/>
                    <fcm:_sample Sample_ref="Sample_3"/>
                    <fcm:_sample Sample_ref="Sample_4"/>
                    <fcm:_sample Sample_ref="Sample_5"/>
                    <fcm:_sample Sample_ref="Sample_6"/>
                    <fcm:_sample Sample_ref="Sample_7"/>
                    <fcm:_sample Sample_ref="Sample_8"/>
                    <fcm:_sample Sample_ref="Sample_9"/>
                    <fcm:_sample Sample_ref="Sample_10"/>
                    <fcm:_sample Sample_ref="Sample_11"/>
                    <fcm:_sample Sample_ref="Sample_12"/>
                </fcm:SampleSet>
            </fcm:_inputSampleSets>
            <fcm:_inputDataSets>
                <!-- 5 Control List Mode data files (single stain controls) -->
                <fcm:DataSet identifier="Control_Data_Set_1">
                    <fcm:_LMData ListModeDataFile_ref="compdata1.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="compdata2.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="compdata3.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="compdata4.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="compdata5.fcs"/>
                </fcm:DataSet>
                <!-- 12 List mode data file produced; each having a link the its particular sample -->
                <fcm:DataSet identifier="Data_Set_1">
                    <fcm:_LMData ListModeDataFile_ref="data01.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data02.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data03.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data04.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data05.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data06.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data07.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data08.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data09.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data10.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data11.fcs"/>
                    <fcm:_LMData ListModeDataFile_ref="data12.fcs"/>
                </fcm:DataSet>
            </fcm:_inputDataSets>
        </fcm:AcquisitionProtocolApplication>
        
        <!-- Compensation and Gating Protocol Application -->

        <!-- Compensate and gate data01.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data01.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data01.fcs" ProtocolApplication_ref="CompPr_App01" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data01.fcs" ProtocolApplication_ref="GatingPr_App01" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample01" />
            <fuge:_inputData Data_ref="data01.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_1" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App01">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App01">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data02.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data02.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data02.fcs" ProtocolApplication_ref="CompPr_App02" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data02.fcs" ProtocolApplication_ref="GatingPr_App02" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample02" />
            <fuge:_inputData Data_ref="data02.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_2" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App02">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App02">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data03.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data03.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data03.fcs" ProtocolApplication_ref="CompPr_App03" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data03.fcs" ProtocolApplication_ref="GatingPr_App03" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample03" />
            <fuge:_inputData Data_ref="data03.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_3" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App03">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App03">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data04.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data04.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data04.fcs" ProtocolApplication_ref="CompPr_App04" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data04.fcs" ProtocolApplication_ref="GatingPr_App04" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample04" />
            <fuge:_inputData Data_ref="data04.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_4" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App04">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App04">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data05.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data05.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data05.fcs" ProtocolApplication_ref="CompPr_App05" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data05.fcs" ProtocolApplication_ref="GatingPr_App05" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample05" />
            <fuge:_inputData Data_ref="data05.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_5" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App05">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App05">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data06.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data06.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data06.fcs" ProtocolApplication_ref="CompPr_App06" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data06.fcs" ProtocolApplication_ref="GatingPr_App06" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample06" />
            <fuge:_inputData Data_ref="data06.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_6" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App06">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App06">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data07.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data07.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data07.fcs" ProtocolApplication_ref="CompPr_App07" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data07.fcs" ProtocolApplication_ref="GatingPr_App07" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample07" />
            <fuge:_inputData Data_ref="data07.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_7" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App07">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App07">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data08.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data08.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data08.fcs" ProtocolApplication_ref="CompPr_App08" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data08.fcs" ProtocolApplication_ref="GatingPr_App08" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample08" />
            <fuge:_inputData Data_ref="data08.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_8" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App08">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App08">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data09.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data09.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data09.fcs" ProtocolApplication_ref="CompPr_App09" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data09.fcs" ProtocolApplication_ref="GatingPr_App09" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample09" />
            <fuge:_inputData Data_ref="data09.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_9" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App09">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App09">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data10.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data10.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data10.fcs" ProtocolApplication_ref="CompPr_App10" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data10.fcs" ProtocolApplication_ref="GatingPr_App10" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample10" />
            <fuge:_inputData Data_ref="data10.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_10" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App10">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App10">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data11.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data11.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data11.fcs" ProtocolApplication_ref="CompPr_App11" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data11.fcs" ProtocolApplication_ref="GatingPr_App11" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample11" />
            <fuge:_inputData Data_ref="data11.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_11" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App11">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App11">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>
        
        <!-- Compensate and gate data12.fcs -->
        <fuge:GenericProtocolApplication Protocol_ref="CompensateAndGateProtocol" identifier="Compensate_and_gate_data12.fcs" activityDate="2006-11-22T13:00:00-08:00">
            <fuge:ActionApplication Action_ref="compensationAction" identifier="Compensate_data12.fcs" ProtocolApplication_ref="CompPr_App12" />
            <fuge:ActionApplication Action_ref="gatingAction" identifier="Gate_data12.fcs" ProtocolApplication_ref="GatingPr_App12" />
            <fuge:SoftwareApplication Software_ref="FlowJo_6_4_7_on_MacOSX_10_2_3" identifier="FlowJoSample12" />
            <fuge:_inputData Data_ref="data12.fcs" />
            <fuge:_outputData Data_ref="Results_for_Sample_12" />
        </fuge:GenericProtocolApplication>
        <fcm:CompensationProtocolApplication CompensationProtocol_ref="CompPr" identifier="CompPr_App12">
            <fcm:_spilloverMatrix ExternalData_ref="spillover_01" />
        </fcm:CompensationProtocolApplication>
        <fcm:DataFilteringProtocolApplication  DataFilteringProtocol_ref="GatingPr" identifier="GatingPr_App12">
            <fcm:_outputGate ExternalData_ref="gating_file_01" /> 
        </fcm:DataFilteringProtocolApplication>

        <!-- Instrumentation description -->
        <fcm:Cytometer identifier="BD_FACSAria_Flow_Cytometer_SN_P0143" name="BD FACSAria at 11th floor SN P0143">
            <!--
                *************************************************************************************************** 
                Please note that MIFlowCyt only requires the make, model# and user-altered and configured parts.
                Here, we are trying to describe the whole instrument just to test that the model and the XSD allows
                for such a description!
                ***************************************************************************************************
            -->
            <fuge:_make OntologyTerm_ref="BD_OT" />
            <fuge:_model OntologyTerm_ref="OBI_0400040" />
            
            <!-- 1 Flow Cell  -->
            <fcm:FlowCell identifier="Cuvette_flow_cell">
                <fuge:_types OntologyTerm_ref="Cuvette_OT" />
                <fcm:_otherInformation>
                    <fuge:Description text="Quartz Cuvette Flow Cell, 160-um x 250-um, 15-mm long" />
                </fcm:_otherInformation>
            </fcm:FlowCell>
            
            <!-- 10 Optical Paths -->
            <!--  FSC Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-FSC" name="FSC Optical Path">
                <fcm:_opticalDetector OpticalDetector_ref="FSC" />
                <fcm:_lightSource LightSource_ref="Laser_488nm" />
            </fcm:OpticalPath>
            <!-- SSC Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-SSC" name="SSC Optical Path">
                <fcm:_opticalFilter OpticalFilter_ref="BP488_10o" />
                <fcm:_opticalDetector OpticalDetector_ref="SSC" />
                <fcm:_lightSource LightSource_ref="Laser_488nm" />
            </fcm:OpticalPath>
            <!-- FL1 Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-FL1" name="FL1 Optical Path">
                <fcm:_opticalFilter OpticalFilter_ref="LP502o" />
                <fcm:_opticalFilter OpticalFilter_ref="BP530_30o" />
                <fcm:_opticalDetector OpticalDetector_ref="FL1" />
                <fcm:_lightSource LightSource_ref="Laser_488nm" />
            </fcm:OpticalPath>
            <!-- FL2 Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-FL2" name="FL2 Optical Path">
                <fcm:_opticalFilter OpticalFilter_ref="LP556o" />
                <fcm:_opticalFilter OpticalFilter_ref="BP575_26o" />
                <fcm:_opticalDetector OpticalDetector_ref="FL2" />
                <fcm:_lightSource LightSource_ref="Laser_488nm" />
            </fcm:OpticalPath>
            <!-- FL3 Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-FL3" name="FL3 Optical Path">
                <fcm:_opticalFilter OpticalFilter_ref="LP595o" />
                <fcm:_opticalFilter OpticalFilter_ref="BP610_20o" />
                <fcm:_opticalDetector OpticalDetector_ref="FL3" />
                <fcm:_lightSource LightSource_ref="Laser_488nm" />
            </fcm:OpticalPath>
            <!-- FL4 Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-FL4" name="FL4 Optical Path">
                <fcm:_opticalFilter OpticalFilter_ref="LP655o" />
                <fcm:_opticalFilter OpticalFilter_ref="BP675_20o" />
                <fcm:_opticalDetector OpticalDetector_ref="FL4" />
                <fcm:_lightSource LightSource_ref="Laser_488nm" />
            </fcm:OpticalPath>
            <!-- FL6 Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-FL6" name="FL6 Optical Path">
                <fcm:_opticalFilter OpticalFilter_ref="BP660_20t1" />
                <fcm:_opticalDetector OpticalDetector_ref="FL6" />
                <fcm:_lightSource LightSource_ref="Laser_633nm" />
            </fcm:OpticalPath>
            <!-- FL8 Optical Path -->
            <fcm:OpticalPath identifier="OpticalPath-FL8" name="FL8 Optical Path">
                <fcm:_opticalFilter OpticalFilter_ref="LP502t2" />
                <fcm:_opticalFilter OpticalFilter_ref="BP530_30t2" />
                <fcm:_opticalDetector OpticalDetector_ref="FL8" />
                <fcm:_lightSource LightSource_ref="Laser_407nm" />
            </fcm:OpticalPath>
            
            <!-- 3 Light Sources -->
            <!-- Laser 488nm -->
            <fcm:LightSource identifier="Laser_488nm" name="Laser 488nm">
                <fuge:_types OntologyTerm_ref="OBI_0400096" /> 
                <fcm:_otherInformation>
                    <fuge:Description text="Coherent Sapphire, Class IIIb." />
                    <fuge:Description text="Elliptical Shape, Beam height is 9 +/- 3um and beam width is 65 +/- 7um." />
                </fcm:_otherInformation>
                <fcm:_polarization><fuge:AtomicValue value="none" /></fcm:_polarization>
                <fcm:WavelengthPeak>
                    <fcm:_wavelength><fuge:AtomicValue value="488"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:AtomicValue></fcm:_wavelength>
                    <fcm:_power><fuge:AtomicValue value="15.0"><fuge:_unit OntologyTerm_ref="mW_Unit_OT" /></fuge:AtomicValue></fcm:_power>   
                </fcm:WavelengthPeak>
                <fcm:BeamGeometry>
                    <fcm:_geometry><fuge:AtomicValue value="Elliptical" /></fcm:_geometry> 
                    <fcm:_xaxis>
                        <fuge:Range lowerLimit="58" upperLimit="72">
                            <fuge:_descriptions>
                                <fuge:Description text="+/- 7" />         
                            </fuge:_descriptions>
                            <fuge:_unit OntologyTerm_ref="um_Unit_OT" />
                        </fuge:Range>     
                    </fcm:_xaxis>
                    <fcm:_yaxis>
                        <fuge:Range lowerLimit="6" upperLimit="12 ">
                            <fuge:_descriptions>
                                <fuge:Description text="+/- 3" />         
                            </fuge:_descriptions>
                            <fuge:_unit OntologyTerm_ref="um_Unit_OT" />
                        </fuge:Range>
                    </fcm:_yaxis>
                </fcm:BeamGeometry>       
            </fcm:LightSource>
            <!-- Laser 633nm -->
            <fcm:LightSource identifier="Laser_633nm" name="Laser 633nm">
                <fuge:_types OntologyTerm_ref="OBI_0400053" />
                <fcm:_otherInformation>
                    <fuge:Description text="JDS UniphaseTM HeNe air-cooled, Class IIIb." />
                    <fuge:Description text="Elliptical Shape, Beam height is 9 +/- 3um and beam width is 65 +/- 7um" />
                </fcm:_otherInformation>
                <fcm:_polarization><fuge:AtomicValue value="none" /></fcm:_polarization>       
                <fcm:WavelengthPeak>
                    <fcm:_wavelength><fuge:AtomicValue value="633"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:AtomicValue></fcm:_wavelength>
                    <fcm:_power><fuge:AtomicValue value="15.0"><fuge:_unit OntologyTerm_ref="mW_Unit_OT" /></fuge:AtomicValue></fcm:_power>
                </fcm:WavelengthPeak>
                <fcm:BeamGeometry>
                    <fcm:_geometry><fuge:AtomicValue value="Elliptical" /></fcm:_geometry>
                    <fcm:_xaxis>
                        <fuge:Range lowerLimit="58" upperLimit="72">
                            <fuge:_descriptions>
                                <fuge:Description text="+/- 7" />         
                            </fuge:_descriptions>
                            <fuge:_unit OntologyTerm_ref="um_Unit_OT" />
                        </fuge:Range>
                    </fcm:_xaxis>
                    <fcm:_yaxis>
                        <fuge:Range lowerLimit="6" upperLimit="12">
                            <fuge:_descriptions>
                                <fuge:Description text="+/- 3" />         
                            </fuge:_descriptions>
                            <fuge:_unit OntologyTerm_ref="um_Unit_OT" />
                            <fuge:_dataType OntologyTerm_ref="Integer_OT" />
                        </fuge:Range>
                    </fcm:_yaxis>
                </fcm:BeamGeometry>
            </fcm:LightSource>
            <!-- Laser 407nm -->
            <fcm:LightSource identifier="Laser_407nm" name="Laser 407nm">
                <fuge:_types OntologyTerm_ref="OBI_0400096" />
                <fcm:_otherInformation>
                    <fuge:Description text="Point Source Violet solid state, Class IIIb." />
                    <fuge:Description text="Elliptical Shape, Beam height is 9 +/- 3um and beam width is 65 +/- 7um" />
                </fcm:_otherInformation>
                <fcm:_polarization><fuge:AtomicValue value="none" /></fcm:_polarization>
                <fcm:WavelengthPeak>
                    <fcm:_wavelength><fuge:AtomicValue value="407"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:AtomicValue></fcm:_wavelength>
                    <fcm:_power><fuge:AtomicValue value="15.0"><fuge:_unit OntologyTerm_ref="mW_Unit_OT" /></fuge:AtomicValue></fcm:_power> 
                </fcm:WavelengthPeak>
                <fcm:BeamGeometry>
                    <fcm:_geometry><fuge:AtomicValue value="Elliptical"></fuge:AtomicValue></fcm:_geometry>
                    <fcm:_xaxis>
                        <fuge:Range lowerLimit="58" upperLimit="72 ">
                            <fuge:_descriptions>
                                <fuge:Description text="+/- 7" />         
                            </fuge:_descriptions>
                            <fuge:_unit OntologyTerm_ref="um_Unit_OT" />
                        </fuge:Range>
                    </fcm:_xaxis>
                    <fcm:_yaxis>
                        <fuge:Range lowerLimit="6" upperLimit="12">
                            <fuge:_descriptions>
                                <fuge:Description text="+/- 3" />         
                            </fuge:_descriptions>
                            <fuge:_unit OntologyTerm_ref="um_Unit_OT" />
                        </fuge:Range>
                    </fcm:_yaxis>   
                </fcm:BeamGeometry>
            </fcm:LightSource>  
            
            <!-- 17 Optical Filters -->
            <!-- LP 735 -->
            <fcm:OpticalFilter identifier="LP735o" name="LP 735" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400067" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_LP735_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-A; Octagon (488nm laser), intended dye: PECy-7" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="735" upperLimit="N/A"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
                
            </fcm:OpticalFilter>
            <!-- BP 780/60 -->
            <fcm:OpticalFilter identifier="BP780_60o" name="BP 780/60" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP780_60_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-A; Octagon (488nm laser), intended dye: PECy-7" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="750" upperLimit="810"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>   
            </fcm:OpticalFilter>
            <!-- LP 655 -->
            <fcm:OpticalFilter identifier="LP655o" name="LP 655" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400067" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_LP655_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-B (FL4); Octagon (488nm laser), intended dye: PerCP" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="655" upperLimit="N/A"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- BP 675/20 -->
            <fcm:OpticalFilter identifier="BP675_20o" name="BP 675/20" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP675_20_OT" /> 
                <fcm:_otherInformation><fuge:Description text="Before PMT-B (FL4); Octagon (488nm laser), intended dye: PerCP" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="665" upperLimit="685"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- LP 595 -->
            <fcm:OpticalFilter identifier="LP595o" name="LP 595" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400067" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_LP595_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-C (FL3); Octagon (488nm laser), intended dye: PE-TxRed" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="595" upperLimit="N/A"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- BP 610/20 -->
            <fcm:OpticalFilter identifier="BP610_20o" name="BP 610/20" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP610_20_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-C (FL3); Octagon (488nm laser), intended dye: PE-TxRed" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="600" upperLimit="620"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- LP 556 -->
            <fcm:OpticalFilter identifier="LP556o" name="LP 556" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400067" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_LP556_OT" /> 
                <fcm:_otherInformation><fuge:Description text="Before PMT-D (FL2); Octagon (488nm laser), intended dye: PE or PI" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="556" upperLimit="N/A"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- BP 575/26 -->
            <fcm:OpticalFilter identifier="BP575_26o" name="BP 575/26" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP575_26_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-D (FL2); Octagon (488nm laser), intended dye: PE or PI" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="562" upperLimit="588"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- LP 502 -->
            <fcm:OpticalFilter identifier="LP502o" name="LP 502" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400067" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_LP502_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-E (FL1); Octagon (488nm laser), intended dye: FITC" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="502" upperLimit="N/A"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- BP 530/30 -->
            <fcm:OpticalFilter identifier="BP530_30o" name="BP 530/30" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP530_30_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-E (FL1); Octagon (488nm laser), intended dye: FITC" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="515" upperLimit="545"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>  
            </fcm:OpticalFilter>
            <!-- BP 488/10 -->
            <fcm:OpticalFilter identifier="BP488_10o" name="BP 488/10" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP488_10_OT" />     
                <fcm:_otherInformation><fuge:Description text="Before PMT-F; Octagon (488nm laser), SSC" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="483" upperLimit="493"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>     
            </fcm:OpticalFilter>
            <!-- LP 765 -->
            <fcm:OpticalFilter identifier="LP735t1" name="LP 765" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400067" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_LP735_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-A; Trigon 1 (633nm laser), intended dye: APC-Cy7" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="735" upperLimit="N/A"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- BP 780/60 -->
            <fcm:OpticalFilter identifier="BP780_60t1" name="BP 780/60" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP780_60_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-A; Trigon 1 (633nm laser), intended dye: APC-Cy7" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="750" upperLimit="810"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>    
            </fcm:OpticalFilter>
            <!-- BP 660/20 -->
            <fcm:OpticalFilter identifier="BP660_20t1" name="BP 660/20" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP660_20_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-B (FL6); Trigon 1 (633nm laser), intended dye: APC" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="650" upperLimit="670"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- LP 502 -->
            <fcm:OpticalFilter identifier="LP502t2" name="LP 502" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400067" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_LP502_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-A (FL8); Trigon 2 (407nm laser), intended dye: DAPI" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="502" upperLimit="N/A"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- BP 530/30 -->
            <fcm:OpticalFilter identifier="BP530_30t2" name="BP 530/30" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP530_30_OT" />
                <fcm:_otherInformation><fuge:Description text="Before PMT-A (FL8); Trigon 2 (407nm laser), intended dye: DAPI" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="515" upperLimit="545"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            <!-- BP 450/40 -->
            <fcm:OpticalFilter identifier="BP450_40t2" name="BP 450/40" installationDate="2006-02-15T00:00:00">
                <fuge:_types OntologyTerm_ref="OBI_0400013" />
                <fuge:_make OntologyTerm_ref="BD_OT" />
                <fuge:_model OntologyTerm_ref="BD_BP450_40_OT" />     
                <fcm:_otherInformation><fuge:Description text="Before PMT-B; Trigon 2 (407nm laser), intended dye: Pacific Blue, Cascade Blue, Alexa Fluor 405" /></fcm:_otherInformation>
                <fcm:_transmittedWavelength>
                    <fuge:Range lowerLimit="430" upperLimit="470"><fuge:_unit OntologyTerm_ref="nm_Unit_OT" /></fuge:Range>
                </fcm:_transmittedWavelength>
            </fcm:OpticalFilter>
            
            <!-- 6 Optical Detectors -->
            <!-- FSC -->
            <fcm:OpticalDetector identifier="FSC" name="Forward Scatter">
                <fuge:_types OntologyTerm_ref="OBI_0400083" />
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="FSC_voltage" name="FCS Voltage" />
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="FSC_amplification_type"><fuge:AtomicValue value="linear" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter>   
            </fcm:OpticalDetector>
            <!-- SSC -->
            <fcm:OpticalDetector identifier="SSC" name="Side Scatter">
                <fuge:_types OntologyTerm_ref="OBI_0400084" />
                <fcm:_otherInformation><fuge:Description text="PMT-F; Octagon (488nm laser)" /></fcm:_otherInformation>
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="SSC_voltage" name="SSC voltage" />
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="SSC_amplification_type"><fuge:AtomicValue value="linear" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter>
            </fcm:OpticalDetector>
            <!-- FL1 -->
            <fcm:OpticalDetector identifier="FL1" name="FL1">
                <fuge:_types OntologyTerm_ref="OBI_0400084" />
                <fcm:_otherInformation><fuge:Description text="PMT-E; Octagon (488nm laser)" /></fcm:_otherInformation>
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="FL1_voltage" name="FL1 voltage" />
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="FL1_amplification_type"><fuge:AtomicValue value="log" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter> 
            </fcm:OpticalDetector>
            <!-- FL2 -->
            <fcm:OpticalDetector identifier="FL2" name="FL2">
                <fuge:_types OntologyTerm_ref="OBI_0400084" />
                <fcm:_otherInformation><fuge:Description text="PMT-D; Octagon (488nm laser)" /></fcm:_otherInformation>
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="FL2_voltage" name="FL2 voltage" />
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="FL2_amplification_type"><fuge:AtomicValue value="log" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter>    
            </fcm:OpticalDetector>
            <!-- FL3 -->
            <fcm:OpticalDetector identifier="FL3" name="FL3">
                <fuge:_types OntologyTerm_ref="OBI_0400084" />
                <fcm:_otherInformation><fuge:Description text="PMT-C; Octagon (488nm laser)" /></fcm:_otherInformation>
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="FL3_voltage" name="FL3 voltage"/>
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="FL3_amplification_type"><fuge:AtomicValue value="log" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter>    
            </fcm:OpticalDetector>
            <!-- FL4 -->
            <fcm:OpticalDetector identifier="FL4" name="FL4">
                <fuge:_types OntologyTerm_ref="OBI_0400084" />
                <fcm:_otherInformation><fuge:Description text="PMT-B; Octagon (488nm laser)" /></fcm:_otherInformation>
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="FL4_voltage" name="FL4 voltage"/>
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="FL4_amplification_type"><fuge:AtomicValue value="log" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter>    
            </fcm:OpticalDetector>
            <!-- FL6 -->
            <fcm:OpticalDetector identifier="FL6" name="FL6">
                <fuge:_types OntologyTerm_ref="OBI_0400084" />
                <fcm:_otherInformation><fuge:Description text="PMT-B; Trigon 1 (633nm laser)" /></fcm:_otherInformation>
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="FL6_voltage" name="FL6 voltage"/>
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="FL6_amplification_type"><fuge:AtomicValue value="log" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter>    
            </fcm:OpticalDetector>
            <!-- FL8 -->
            <fcm:OpticalDetector identifier="FL8" name="FL8">
                <fuge:_types OntologyTerm_ref="OBI_0400084" />
                <fcm:_otherInformation><fuge:Description text="PMT-A; Trigon 2 (407nm laser)" /></fcm:_otherInformation>
                <fcm:_voltageParameter>
                    <fuge:GenericParameter identifier="FL8_voltage" name="FL8 voltage"/>
                </fcm:_voltageParameter>
                <fcm:_amplificationTypeParameter>
                    <fuge:GenericParameter identifier="FL8_amplification_type"><fuge:AtomicValue value="log" /></fuge:GenericParameter>
                </fcm:_amplificationTypeParameter>    
            </fcm:OpticalDetector>

            <!-- To demonstrate the free text option of _opticalPathDescription -->
            <fcm:_opticalPathDescription>
                <fuge:Description text="See the OpticalPath element for structured information" />
            </fcm:_opticalPathDescription>
            
            <!-- To demonstrate the _otherInformation -->
            <fcm:_otherInformation><fuge:Description text="Located on 11th floor, room 1123" /></fcm:_otherInformation>
            
            <fcm:_excitationOpticsConfiguration>
                <fuge:Description text="The optical configuration was set by a BD technician on 2005-05-28" />
            </fcm:_excitationOpticsConfiguration>
            
        </fcm:Cytometer>
        
    </fuge:ProtocolCollection>
    
    
    <!-- 
        ********************************* 
        Ontology Terms
        *********************************
    -->
    <fuge:OntologyCollection>
        
        <!-- The manufacturers, e.g., BD, are supposed to be in the OBI ontology in the future. -->
        <fuge:OntologyIndividual term="Becton Dickinson" termAccession="N/A" identifier="BD_OT" />
        
        <!-- Instrumentation terms, some from OBI -->
        <fuge:OntologyIndividual term="FACSAria" termAccession="http://purl.obofoundry.org/obo/OBI_0400040" identifier="OBI_0400040" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        <fuge:OntologyIndividual term="Cuvette" termAccession="N/A" identifier="Cuvette_OT" />
        <fuge:OntologyIndividual term="Band pass filter" termAccession="http://purl.obofoundry.org/obo/OBI_0400013" identifier="OBI_0400013" name="Band pass filter" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        <fuge:OntologyIndividual term="Long pass filter" termAccession="http://purl.obofoundry.org/obo/OBI_0400067" identifier="OBI_0400067" name="Long pass filter" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        <fuge:OntologyIndividual term="Photodiode" termAccession="http://purl.obofoundry.org/obo/OBI_0400083" identifier="OBI_0400083" name="Photodiode" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        <fuge:OntologyIndividual term="Photomultiplier tube" termAccession="http://purl.obofoundry.org/obo/OBI_0400084" identifier="OBI_0400084" name="Photomultiplier tube" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        <fuge:OntologyIndividual term="Solid state laser" termAccession="http://purl.obofoundry.org/obo/OBI_0400096" identifier="OBI_0400096" name="Solid state laser" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        <fuge:OntologyIndividual term="HeNe laser" termAccession="http://purl.obofoundry.org/obo/OBI_0400053" identifier="OBI_0400053" name="HeNe laser" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        
        <!-- Instrumentation individuals (filters) - make/models -->
        <!-- LP filters from BD (filter models) -->
        <fuge:OntologyIndividual term="BD LP 502 filter" termAccession="N/A" identifier="BD_LP502_OT" />
        <fuge:OntologyIndividual term="BD LP 556 filter" termAccession="N/A" identifier="BD_LP556_OT" />
        <fuge:OntologyIndividual term="BD LP 595 filter" termAccession="N/A" identifier="BD_LP595_OT" />
        <fuge:OntologyIndividual term="BD LP 655 filter" termAccession="N/A" identifier="BD_LP655_OT" />
        <fuge:OntologyIndividual term="BD LP 735 filter" termAccession="N/A" identifier="BD_LP735_OT" />
        <!-- BP filters from BD (filter models) -->
        <fuge:OntologyIndividual term="BD BP 450/40 filter" termAccession="N/A" identifier="BD_BP450_40_OT" />
        <fuge:OntologyIndividual term="BD BP 488/10 filter" termAccession="N/A" identifier="BD_BP488_10_OT" />
        <fuge:OntologyIndividual term="BD BP 530/30 filter" termAccession="N/A" identifier="BD_BP530_30_OT" />
        <fuge:OntologyIndividual term="BD BP 575/26 filter" termAccession="N/A" identifier="BD_BP575_26_OT" />
        <fuge:OntologyIndividual term="BD BP 610/20 filter" termAccession="N/A" identifier="BD_BP610_20_OT" />
        <fuge:OntologyIndividual term="BD BP 660/20 filter" termAccession="N/A" identifier="BD_BP660_20_OT" />
        <fuge:OntologyIndividual term="BD BP 675/20 filter" termAccession="N/A" identifier="BD_BP675_20_OT" />
        <fuge:OntologyIndividual term="BD BP 780/60 filter" termAccession="N/A" identifier="BD_BP780_60_OT" />
        
        <!-- Analytes -->
        <fuge:OntologyIndividual identifier="CD4_OT" term="CD4" name="CD4" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD4" OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD4" />
        <fuge:OntologyIndividual identifier="CD8_OT" term="CD8" name="CD8" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD8" OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD8" />
        <fuge:OntologyIndividual identifier="CD45_OT" term="CD45" name="CD45" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD45" OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD45" />
        <fuge:OntologyIndividual identifier="CD11b_OT" termAccession="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD11b" term="CD11b" name="CD11b" OntologySource_ref="http://www.genecards.org/cgi-bin/carddisp.pl?gene=CD11b" />
        
        <!-- Dyes -->
        <fuge:OntologyIndividual term="Texas Red" name="Texas Red" OntologySource_ref="http://www.drmr.com/abcon/trfspec.html" termAccession="N/A" identifier="TexasRed_OT" />
        <fuge:OntologyIndividual term="Allophycocyanin (APC)" name="Allophycocyanin (APC)" OntologySource_ref="http://www.drmr.com/abcoN/APCfspec.html" termAccession="N/A" identifier="APC_OT" />
        <fuge:OntologyIndividual term="Phycoerythrin (PE)" name="Phycoerythrin (PE)" OntologySource_ref="http://www.drmr.com/abcon/PEfspec.html" termAccession="N/A" identifier="PE_OT" />
        <fuge:OntologyIndividual term="Fluorescein (FITC)" name="Fluorescein (FITC)" OntologySource_ref="http://www.drmr.com/abcon/Ffspec.html" termAccession="N/A" identifier="FITC_OT" />
        <fuge:OntologyIndividual term="Peridinin-chlorophyll-protein (PerCP)" name="Peridinin-chlorophyll-protein (PerCP)" termAccession="N/A" identifier="PerCP_OT" />
        <fuge:OntologyIndividual term="4,6-diamidino-2-phenylindole (DAPI)" name="4,6-diamidino-2-phenylindole (DAPI)" termAccession="N/A" identifier="DAPI_OT" />
        
        <!-- Phenotypes and genotypes of the mice -->
        <fuge:OntologyIndividual term="Black Pep3b Mouse" termAccession="N/A" identifier="Black_Pep3b_mouse_phenotype" />
        <fuge:OntologyIndividual term="White W41/W41 Mouse" termAccession="N/A" identifier="White_W41_W41_mouse_phenotype" />
        <fuge:OntologyIndividual term="Ly-5 Congenic C57BL-6 Mouse" termAccession="N/A" identifier="Ly-5_Congenic_C57BL-6_mouse_genotype" />
        <fuge:OntologyIndividual term="C57BL/6J W41/W41 Mouse" termAccession="N/A" identifier="C57BL/6J_W41/W41_mouse_genotype" />
        
        <!-- Organism details -->
        <fuge:OntologyIndividual term="male" name="male" identifier="male_OT" termAccession="PATO:0000384" OntologySource_ref="http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=PATO" />
        <fuge:OntologyIndividual term="Mus Musculus, C57BL/6J:Pep3b" name="Mus Musculus, C57BL/6J:Pep3b" identifier="MusMusculus_C57BL-6J_Pep3b" termAccession="http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&amp;id=10090&amp;lvl=3&amp;keep=1&amp;srchmode=1&amp;unlock&amp;mod=1#modif" OntologySource_ref="http://www.ncbi.nlm.nih.gov/Taxonomy/" /> 

         <!-- Likely from a cell ontology? -->
        <fuge:OntologyIndividual term="Human Stem Cell" termAccession="N/A" identifier="HSC_OT" />
        <fuge:OntologyIndividual term="KSL Human Stem Cell" termAccession="N/A" identifier="KSL_HSC_OT" />
        
        <!-- Units -->
        <fuge:OntologyIndividual term="radiation unit" termAccession="UO:0000127" identifier="Rad_Radiation_Unit_OT" OntologySource_ref="http://obo.cvs.sourceforge.net/obo/obo/ontology/phenotype/unit.obo" />
        <fuge:OntologyIndividual term="cells" termAccession="N/A" identifier="Cell_Unit_OT" />
        <fuge:OntologyIndividual term="month" termAccession="N/A" identifier="Month_Unit_OT" />
        <fuge:OntologyIndividual term="cells per ml" termAccession="N/A" identifier="CellsPerML_Unit_OT" />
        <fuge:OntologyIndividual term="µl" name="µl" termAccession="N/A" identifier="Micro_Liter_Unit_OT" />
        <fuge:OntologyIndividual term="nm" name="nm" termAccession="N/A" identifier="nm_Unit_OT" />
        <fuge:OntologyIndividual term="µm" name="µm" termAccession="N/A" identifier="um_Unit_OT" />
        <fuge:OntologyIndividual term="Volts" termAccession="N/A" identifier="V_Unit_OT" />
        <fuge:OntologyIndividual term="mW" termAccession="N/A" identifier="mW_Unit_OT" />
                
        <!-- IT stuff -->
        <fuge:OntologyIndividual term="Flow Cytometry Analysis Software" termAccession="N/A" identifier="FCM_Analysis_SW_OT" />
        <fuge:OntologyIndividual term="compensation computationally post acquisition" termAccession="N/A" identifier="SW_Compensation_OT" />
        <fuge:OntologyIndividual term="Extensible Markup Language (XML) Editor" termAccession="N/A" identifier="XML_Editor_OT" />
        <fuge:OntologyIndividual term="Macintosh OSX 10.2.3" termAccession="N/A" identifier="Macintosh_OSX_10_2_3_OT" />
        <fuge:OntologyIndividual term="Windows XP" termAccession="N/A" identifier="Windows_XP_OT" />
        <fuge:OntologyIndividual term="Operating System" termAccession="N/A" identifier="Operating_System_OT" />
        <fuge:OntologyIndividual term="Statistics Software" termAccession="N/A" identifier="Statistics_SW_OT" />
        <fuge:OntologyIndividual term="List-mode data file" termAccession="http://purl.obofoundry.org/obo/OBI_0000021" identifier="OBI_0000021" name="List-mode data file" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" />
        <fuge:OntologyIndividual term="Gating-ML File Format" termAccession="N/A" identifier="Gating-ML_OT" name="Gating-ML File Format" />
        
        <!-- Keywords, trying MeSH -->
        <fuge:OntologyIndividual term="Blood" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" termAccession="MeSH:Q000097" identifier="keyword_1_blood" />
        <fuge:OntologyIndividual term="Transplants" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" termAccession="MeSH:D019737" identifier="keyword_2_transplant" />
        <fuge:OntologyIndividual term="Donor" termAccession="N/A" identifier="keyword_3_donor" />
        <fuge:OntologyIndividual term="Recipient" termAccession="N/A" identifier="keyword_4_recipient" />
        <fuge:OntologyIndividual term="Leukocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" termAccession="MeSH:D007962" identifier="keyword_5_leukocyte" />
        <fuge:OntologyIndividual term="Lymphocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" termAccession="MeSH:D008214" identifier="keyword_6_lymphocyte" />
        <fuge:OntologyIndividual term="Monocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" termAccession="MeSH:D009000" identifier="keyword_7_monocyte" />
        <fuge:OntologyIndividual term="Granulocytes" OntologySource_ref="http://www.nlm.nih.gov/mesh/meshhome.html" termAccession="MeSH:D006098" identifier="keyword_8_granulocyte" />
        
        <!-- Roles from OBI -->
        <fuge:OntologyIndividual term="principal investigator role" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" termAccession="http://purl.obofoundry.org/obo/OBI_0000103" identifier="OBI_0000103" />
        <fuge:OntologyIndividual term="laboratory role" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" termAccession="http://purl.obofoundry.org/obo/OBI_0000184" identifier="OBI_0000184" />
        <fuge:OntologyIndividual term="author role" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" termAccession="http://purl.obofoundry.org/obo/OBI_0000357" identifier="OBI_0000357" />
        <fuge:OntologyIndividual term="biological specimen role" OntologySource_ref="http://purl.obofoundry.org/obo/obi.owl" termAccession="http://purl.obofoundry.org/obo/OBI_0000112" identifier="OBI_0000112"  />
        
        <fuge:OntologyIndividual term="single stain control role" termAccession="N/A" identifier="Single_Stain_Control_OT"  />
                
    </fuge:OntologyCollection>
    
    <!-- Additional administrative info about creation of this file. See also the Experiment_Description_Info Security -->
    <fuge:Provider identifier="Josef_Spidlen" name="Josef Spidlen (XML created in oXygen)" Software_ref="oXygen">
        <fuge:_propertySets>
            <fuge:NameValueType name="DateCreated" type="xsd:dateTime" value="2008-07-30T16:30:00"/>
            <fuge:NameValueType name="Version" type="Sring" value="1.0"/>
        </fuge:_propertySets>
        <fuge:ContactRole Contact_ref="Josef_Spidlen">
            <fuge:_role OntologyTerm_ref="OBI_0000357"/>
        </fuge:ContactRole>
    </fuge:Provider>
 
</fuge:FuGE>

