kenwebb · September 9, 2024 18:59
diff --git a/xholonWorkbook.xml b/xholonWorkbook.xml
 <?xml version="1.0" encoding="UTF-8"?>
 <!--Xholon Workbook http://www.primordion.com/Xholon/gwt/ MIT License, Copyright (C) Ken Webb, Mon Sep 09 2024 14:59:24 GMT-0400 (Eastern Daylight Time)-->
 <XholonWorkbook>

 <Notes><![CDATA[
 Xholon
 ------
 Title: Fung Diabetes Code - 2 - Compartment Model
 Description: 
 Url: http://www.primordion.com/Xholon/gwt/
 InternalName: 6fe36475e9f6228a1343626c1ac850f2
 Keywords: 

 My Notes
 --------
 8 Sept 2024

 This workbook is a continuation of Fung Diabetes Code - 1.

 I will include the following from Dr. Fung's "Diabetes Code" book:
 - human/animal anatomy/physiology compartments that are included in the book (ex: Liver)
 - small molecules (glucose, insulin)
 - organize in some way (ex: active vs passive)
 - conditions (medical terminology) (ex: hyperinsulinemia, fatty liver)

 Notes:
 - maybe use a Petri Net approach; although this workbook is probably just about getting the terminology/vocabulary/ontology together
 - I can reuse this workbook in follow-up workbooks
 - make the subtrees easily reusable

 ### References
 (1) https://www.doctorjasonfung.com/the-diabetes-code

 (2) various
    - my copy of The Physiology Coloring Book
    - ideas from SBML structure

 (3) https://openstax.org/details/books/anatomy-and-physiology-2e
    Anatomy and Physiology 2e, ©2022 Rice University
    - I downloaded this book

 (4) https://openstax.org
    OPENSTAX
    OpenStax provides free, peer-reviewed, openly licensed textbooks for introductory college and Advanced
    Placement® courses and low-cost, personalized courseware that helps students learn. A nonprofit ed tech
    initiative based at Rice University, we’re committed to helping students access the tools they need to complete
    their courses and meet their educational goals.

 (5) google search: insulin resistance
    - some excelllent-looking diagrams are available
    
 (6) https://my.clevelandclinic.org/health/diseases/22206-insulin-resistance
    - extensive document; looks good

 (7) Obesity and type 2 diabetes mellitus: connections in epidemiology, pathogenesis, and treatments, Rexiata Ruze, et al, 2023, Frontiers in Endocrinology

 ]]></Notes>  

 <_-.XholonClass>
  <DiaCompartmentSystem/>
  
  <!-- compartments -->
  <Compartment>
    <!-- organs of a human/animal body -->
    <Liver><!-- The liver is the organ primarily responsible for detoxifying the blood before it travels throughout the body. AnatPhys2e p.96 hepatic --></Liver>
    <Pancreas/>
    <Intestines/>
    <Hypothalamus/>
    
    <Tissue>
      <AdiposeTissue/> <!-- There are two types of adipose tissue, white adipose tissue (WAT) and brown adipose tissue (BAT),
        which are also known as white and brown fat, respectively, and comprise two types of fat cells. wikipedia -->
    </Tissue>
    
    <Cell>
      <Adipocyte> <!-- Adipocytes, also known as lipocytes and fat cells, are the cells that primarily compose adipose tissue, specialized in storing energy as fat. wikipedia, ref[7] -->
        <WhiteAdipocyte/>
        <BrownAdipocyte/>
        <BeigeAdipocyte/>
      </Adipocyte>
    </Cell>
    
    <!-- Adipocyte components -->
    <LipidDroplet/>
    <Mitochondrion/>
    <Nucleus/> <!-- cell nucleus -->
    
  </Compartment>
  
  <!-- small molecules -->
  <SmallMolecule>
    
    <Carbohydrate>
      <Sugar>
        <Glucose/>
        <Fructose/>
        <Sucrose/>
      </Sugar>
    </Carbohydrate>
    
    <Triglyceride/> <!-- body fat, made from glucose and NOT from dietary fat, Fung p.109, AnatPhys2e p.65 -->
    <!-- an ester derived from glycerol and three fatty acids  wikipedia -->
    <Ester/>
    <Glycerol/>
    <FattyAcid/>
    
    
    <Hormone>
      <Insulin/> <!-- made in the pancreas -->
    </Hormone>
    
  </SmallMolecule>
  
  <!-- carbohydrate chains -->
  <Glycogen/>
  
  <!-- amino acid chains, polypeptides, proteins and enzymes -->
  <Protein>
    <Enzyme/>
  </Protein>
  
  <!-- medical and other conditions, disease -->
  <Condition>
    <Hyperinsulinemia/>
    <FattyLiver/>
    <Hypertriglyceridemia/>
    <NonAlcoholicFattyLiverDisease/> <!-- NAFLD Fung p.81 -->
    <Diabetes> <!-- = Diabetes Mellitus -->
      <DiabetesType1/>
      <DiabetesType2/>
    </Diabetes>
    <Prediabetes/>
  </Condition>
  
  <!-- processes -->
  <Process>
    <Metabolism/>
    <Catabolism/>
    <Anabolism/>
    <NutrientFlow/>
    <DeNovoLipogenesis/> <!-- DNL -->
    <StorageOfExcessGlucose>
      <!-- two forms of storage of excess glucose: (Fung p.109)
      1. glycogen - like storing it in the fridge
      2. triglycerides - like storing in the freezer
      -->
    </StorageOfExcessGlucose>
    <Fasting/>
    <RandleCycle/>
    <InsulinResistance/> <!-- Liver, hepatic cycle -->
    <BetaCellDysfunction/> <!-- Pancreas, pancreatic cycle -->
  </Process>
  
  <Compartments/>
  
  <SmallMolecules/>
  
  <Conditions/>
  
 </_-.XholonClass>

 <xholonClassDetails>
  
  <Liver><port name="pancreas" connector="../Pancreas" /></Liver>
  
  <AdiposeTissue/>
  <WhiteAdipocyte><Color>rgba(255, 255, 255, 1.0)</Color></WhiteAdipocyte>
  <BeigeAdipocyte><Color>rgba(245, 245, 220, 1.0)</Color></BeigeAdipocyte>
  <BrownAdipocyte><Color>rgba(210, 105, 30, 1.0)</Color></BrownAdipocyte>
  
  <LipidDroplet><Color>Yellow</Color></LipidDroplet>
  <Mitochondrion><Color>Brown</Color></Mitochondrion>
  <Nucleus><Color>Blue</Color></Nucleus>
  
 </xholonClassDetails>

 <DiaCompartmentSystem>
  
  <Compartments>
    <Intestines/>
    <Liver></Liver>
    <Pancreas/>
  </Compartments>
  
  <!-- an ester derived from glycerol and three fatty acids  wikipedia -->
  <Triglyceride>
    <Ester/>
    <FattyAcid multiplicity="3"/>
  </Triglyceride>
  
  <Sucrose>
    <Glucose multiplity="1"/>
    <Fructose multiplicity="1"/>
  </Sucrose>
  
  <AdiposeTissue> <!-- see wikipedia image -->
    <WhiteAdipocyte>
      <Nucleus multiplicity="1"/>
      <LipidDroplet multiplicity="1"/>
      <Mitochondrion multiplicity="1"/>
    </WhiteAdipocyte>
    <BeigeAdipocyte>
      <Nucleus multiplicity="1"/>
      <LipidDroplet multiplicity="5"/>
      <Mitochondrion multiplicity="3"/>
    </BeigeAdipocyte>
    <BrownAdipocyte>
      <Nucleus multiplicity="1"/>
      <LipidDroplet multiplicity="8"/>
      <Mitochondrion multiplicity="8"/>
    </BrownAdipocyte>
  </AdiposeTissue>
  
 </DiaCompartmentSystem>

 <SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
 <svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
  <g>
    <title>Block</title>
    <rect id="DiaCompartmentSystem/Compartments" fill="#98FB98" height="50" width="50" x="25" y="0"/>
    <g>
      <title>Height</title>
      <rect id="DiaCompartmentSystem/Compartments/Liver" fill="#6AB06A" height="50" width="10" x="80" y="0"/>
    </g>
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 </XholonWorkbook>
	<?xml version="1.0" encoding="UTF-8"?>
	<!--Xholon Workbook http://www.primordion.com/Xholon/gwt/ MIT License, Copyright (C) Ken Webb, Mon Sep 09 2024 14:59:24 GMT-0400 (Eastern Daylight Time)-->
	<XholonWorkbook>

	<Notes><![CDATA[
	Xholon
	------
	Title: Fung Diabetes Code - 2 - Compartment Model
	Description:
	Url: http://www.primordion.com/Xholon/gwt/
	InternalName: 6fe36475e9f6228a1343626c1ac850f2
	Keywords:

	My Notes
	--------
	8 Sept 2024

	This workbook is a continuation of Fung Diabetes Code - 1.

	I will include the following from Dr. Fung's "Diabetes Code" book:
	- human/animal anatomy/physiology compartments that are included in the book (ex: Liver)
	- small molecules (glucose, insulin)
	- organize in some way (ex: active vs passive)
	- conditions (medical terminology) (ex: hyperinsulinemia, fatty liver)

	Notes:
	- maybe use a Petri Net approach; although this workbook is probably just about getting the terminology/vocabulary/ontology together
	- I can reuse this workbook in follow-up workbooks
	- make the subtrees easily reusable

	### References
	(1) https://www.doctorjasonfung.com/the-diabetes-code

	(2) various
	- my copy of The Physiology Coloring Book
	- ideas from SBML structure

	(3) https://openstax.org/details/books/anatomy-and-physiology-2e
	Anatomy and Physiology 2e, ©2022 Rice University
	- I downloaded this book

	(4) https://openstax.org
	OPENSTAX
	OpenStax provides free, peer-reviewed, openly licensed textbooks for introductory college and Advanced
	Placement® courses and low-cost, personalized courseware that helps students learn. A nonprofit ed tech
	initiative based at Rice University, we’re committed to helping students access the tools they need to complete
	their courses and meet their educational goals.

	(5) google search: insulin resistance
	- some excelllent-looking diagrams are available

	(6) https://my.clevelandclinic.org/health/diseases/22206-insulin-resistance
	- extensive document; looks good

	(7) Obesity and type 2 diabetes mellitus: connections in epidemiology, pathogenesis, and treatments, Rexiata Ruze, et al, 2023, Frontiers in Endocrinology

	]]></Notes>

	<_-.XholonClass>
	<DiaCompartmentSystem/>

	<!-- compartments -->
	<Compartment>
	<!-- organs of a human/animal body -->
	<Liver><!-- The liver is the organ primarily responsible for detoxifying the blood before it travels throughout the body. AnatPhys2e p.96 hepatic --></Liver>
	<Pancreas/>
	<Intestines/>
	<Hypothalamus/>

	<Tissue>
	<AdiposeTissue/> <!-- There are two types of adipose tissue, white adipose tissue (WAT) and brown adipose tissue (BAT),
	which are also known as white and brown fat, respectively, and comprise two types of fat cells. wikipedia -->
	</Tissue>

	<Cell>
	<Adipocyte> <!-- Adipocytes, also known as lipocytes and fat cells, are the cells that primarily compose adipose tissue, specialized in storing energy as fat. wikipedia, ref[7] -->
	<WhiteAdipocyte/>
	<BrownAdipocyte/>
	<BeigeAdipocyte/>
	</Adipocyte>
	</Cell>

	<!-- Adipocyte components -->
	<LipidDroplet/>
	<Mitochondrion/>
	<Nucleus/> <!-- cell nucleus -->

	</Compartment>

	<!-- small molecules -->
	<SmallMolecule>

	<Carbohydrate>
	<Sugar>
	<Glucose/>
	<Fructose/>
	<Sucrose/>
	</Sugar>
	</Carbohydrate>

	<Triglyceride/> <!-- body fat, made from glucose and NOT from dietary fat, Fung p.109, AnatPhys2e p.65 -->
	<!-- an ester derived from glycerol and three fatty acids wikipedia -->
	<Ester/>
	<Glycerol/>
	<FattyAcid/>


	<Hormone>
	<Insulin/> <!-- made in the pancreas -->
	</Hormone>

	</SmallMolecule>

	<!-- carbohydrate chains -->
	<Glycogen/>

	<!-- amino acid chains, polypeptides, proteins and enzymes -->
	<Protein>
	<Enzyme/>
	</Protein>

	<!-- medical and other conditions, disease -->
	<Condition>
	<Hyperinsulinemia/>
	<FattyLiver/>
	<Hypertriglyceridemia/>
	<NonAlcoholicFattyLiverDisease/> <!-- NAFLD Fung p.81 -->
	<Diabetes> <!-- = Diabetes Mellitus -->
	<DiabetesType1/>
	<DiabetesType2/>
	</Diabetes>
	<Prediabetes/>
	</Condition>

	<!-- processes -->
	<Process>
	<Metabolism/>
	<Catabolism/>
	<Anabolism/>
	<NutrientFlow/>
	<DeNovoLipogenesis/> <!-- DNL -->
	<StorageOfExcessGlucose>
	<!-- two forms of storage of excess glucose: (Fung p.109)
	1. glycogen - like storing it in the fridge
	2. triglycerides - like storing in the freezer
	-->
	</StorageOfExcessGlucose>
	<Fasting/>
	<RandleCycle/>
	<InsulinResistance/> <!-- Liver, hepatic cycle -->
	<BetaCellDysfunction/> <!-- Pancreas, pancreatic cycle -->
	</Process>

	<Compartments/>

	<SmallMolecules/>

	<Conditions/>

	</_-.XholonClass>

	<xholonClassDetails>

	<Liver><port name="pancreas" connector="../Pancreas" /></Liver>

	<AdiposeTissue/>
	<WhiteAdipocyte><Color>rgba(255, 255, 255, 1.0)</Color></WhiteAdipocyte>
	<BeigeAdipocyte><Color>rgba(245, 245, 220, 1.0)</Color></BeigeAdipocyte>
	<BrownAdipocyte><Color>rgba(210, 105, 30, 1.0)</Color></BrownAdipocyte>

	<LipidDroplet><Color>Yellow</Color></LipidDroplet>
	<Mitochondrion><Color>Brown</Color></Mitochondrion>
	<Nucleus><Color>Blue</Color></Nucleus>

	</xholonClassDetails>

	<DiaCompartmentSystem>

	<Compartments>
	<Intestines/>
	<Liver></Liver>
	<Pancreas/>
	</Compartments>

	<!-- an ester derived from glycerol and three fatty acids wikipedia -->
	<Triglyceride>
	<Ester/>
	<FattyAcid multiplicity="3"/>
	</Triglyceride>

	<Sucrose>
	<Glucose multiplity="1"/>
	<Fructose multiplicity="1"/>
	</Sucrose>

	<AdiposeTissue> <!-- see wikipedia image -->
	<WhiteAdipocyte>
	<Nucleus multiplicity="1"/>
	<LipidDroplet multiplicity="1"/>
	<Mitochondrion multiplicity="1"/>
	</WhiteAdipocyte>
	<BeigeAdipocyte>
	<Nucleus multiplicity="1"/>
	<LipidDroplet multiplicity="5"/>
	<Mitochondrion multiplicity="3"/>
	</BeigeAdipocyte>
	<BrownAdipocyte>
	<Nucleus multiplicity="1"/>
	<LipidDroplet multiplicity="8"/>
	<Mitochondrion multiplicity="8"/>
	</BrownAdipocyte>
	</AdiposeTissue>

	</DiaCompartmentSystem>

	<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,
	<svg width="100" height="50" xmlns="http://www.w3.org/2000/svg">
	<g>
	<title>Block</title>
	<rect id="DiaCompartmentSystem/Compartments" fill="#98FB98" height="50" width="50" x="25" y="0"/>
	<g>
	<title>Height</title>
	<rect id="DiaCompartmentSystem/Compartments/Liver" fill="#6AB06A" height="50" width="10" x="80" y="0"/>
	</g>
	</g>
	</svg>
	]]></Attribute_String><Attribute_String roleName="setup">${MODELNAME_DEFAULT},${SVGURI_DEFAULT}</Attribute_String></SvgClient>

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