AI - Biological Cell Entities

xholonWorkbook.xml

<?xml version="1.0" encoding="UTF-8"?>
<!--Xholon Workbook http://www.primordion.com/Xholon/gwt/ MIT License, Copyright (C) Ken Webb, Mon Jul 28 2025 14:43:50 GMT-0400 (Eastern Daylight Time)-->
<XholonWorkbook>

<Notes><![CDATA[
Xholon
------
Title: AI - Biological Cell Entities
Description: 
Url: http://www.primordion.com/Xholon/gwt/
InternalName: ec355ca8eda554d528341a0c7225ba3a
Keywords: 

My Notes
--------
28 July 2025

Using (local) AI to generate parts of a Xholon workbook.

]]></Notes>

<markdown><![CDATA[
% ollama run llama3

#### prompt
>>> Create a list of entities found inside a biological cell. Include all major parts and organelles.
Use the singular form for each Entity name, for example "Ribosome" rather than "Ribosomes".
Use camel case for the Entity name, for example "CellMembrane" rather than "Cell Membrane".
Do not include an abbreviation as part of the entity name.
Present the list in csv format.
Include a name and description for each entity, for example:
"Nucleus","The control center of the cell where DNA is stored and replicated."
Include a header line: "Entity","Description"

Here is the list of entities found inside a biological cell:

"Entity","Description"
"Nucleus","The control center of the cell where DNA is stored and replicated."
"Cytoplasm","The fluid-filled region of the cell where many metabolic processes take place."
"CellMembrane","A thin layer of lipid and protein molecules that separates the cell from its environment."
"Mitochondria","Energy-producing organelles found in the cytoplasm, responsible for generating most of the energy needed by the cell."
"Lysosome","A membrane-bound sac containing digestive enzymes that breaks down and recycles cellular waste and foreign substances."
"EndoplasmicReticulum","A network of flattened membranous tubules and sacs involved in protein synthesis, folding, and transport."
"GolgiApparatus","A complex organelle responsible for processing and modifying proteins and lipids synthesized by the cell."
"Cytoskeleton","An internal framework of fibers that provides structural support, shape, and movement to the cell."
"Ribosome","The site of protein synthesis in the cytoplasm, where mRNA is translated into amino acid chains."
"Chloroplast","Green organelles found in plant cells responsible for photosynthesis, converting light energy into chemical energy."
"Peroxisome","A small organelle involved in the breakdown of fatty acids and amino acids."
"Cilium","Tiny hair-like structures on the surface of some cells that aid in movement and sensing their environment."
"LipidDroplet","Small droplets of lipids found throughout the cytoplasm, storing energy and participating in cellular signaling."
"Centriole","A small organelle involved in the formation of cilia and flagella during cell division."
"Nucleolus","A region within the nucleus where ribosomal RNA synthesis occurs."
"SarcoplasmicReticulum","A type of smooth endoplasmic reticulum found in muscle cells that stores calcium ions."
"Chromatin","The complex of DNA, histone proteins, and other molecules that make up the chromosome structure."

Note: I've excluded some less well-known or specialized entities to keep the list manageable. Let me know if you'd like me to add any specific ones!

>>> Create a list of entities found inside a biological cell. Include all major parts and organelles, plus 30 additional less well-known entities.
Use the singular form for each Entity name, for example "Ribosome" rather than "Ribosomes".
Use camel case for the Entity name, for example "CellMembrane" rather than "Cell Membrane".
Do not include an abbreviation as part of the entity name.
Present the list in csv format.
Include a name and description for each entity, for example:
"Nucleus","The control center of the cell where DNA is stored and replicated."
Include a header line: "Entity","Description"

Here is the list of entities found inside a biological cell:

"Entity","Description"
"CellMembrane","The outermost layer of the cell that separates the cell from its environment and regulates what enters and leaves the cell."
"Nucleus","The control center of the cell where DNA is stored and replicated."
"Cytoplasm","The jelly-like substance inside the cell membrane where metabolic processes take place."
"Mitochondria","The powerhouses of the cell responsible for generating energy through cellular respiration."
"Lysosome","A membrane-bound organelle that contains digestive enzymes and is responsible for breaking down and recycling cellular waste and debris."
"GolgiApparatus","A complex network of flattened sacs and tubules involved in protein modification, sorting, and packaging."
"EndoplasmicReticulum","A network of membranous tubules and cisternae that plays a crucial role in protein synthesis and transport."
"Ribosome","A small organelle responsible for translating mRNA into proteins."
"Cytoskeleton","A network of protein filaments that provides structural support, shape, and movement to the cell."
"Nucleolus","A region within the nucleus where ribosomal RNA is synthesized."
"Peroxisome","A small organelle involved in the breakdown of fatty acids and amino acids."
"Centriole","A small structure involved in the formation of cilia, flagella, and the spindle fibers during cell division."
"Lamin","A protein that forms a network-like structure beneath the nuclear envelope."
"NuclearPoreComplex","A specialized structure that regulates the transport of molecules between the nucleus and the cytoplasm."
"Chloroplast","An organelle found in plant cells responsible for photosynthesis."
"Vacuole","A storage compartment within the cell used to store water, salts, and waste products."
"Cilium","A tiny hair-like structure involved in movement and sensing."
"Ficolin","A protein involved in the recognition of foreign substances and activation of the immune response."
"Histone","A small basic protein that compactly wraps around DNA in the nucleus."
"Telomere","The protective caps on the ends of chromosomes that prevent fusion with neighboring chromosomes."
"MagnesiumIonChannel","A type of ion channel that regulates magnesium levels within the cell."
"SodiumPotassiumPump","An enzyme complex responsible for maintaining proper sodium and potassium ion concentrations across the cell membrane."
"Polyribosome","A group of ribosomes attached to a single mRNA molecule."
"Exosome","A small vesicle involved in cellular waste removal and intercellular communication."
"Chaperone","A protein that assists the correct folding of other proteins."
"DyneinMotor","A molecular motor that moves along microtubules and helps to organize the cytoskeleton."
"Microfilament","One of the three main components of the cytoskeleton, responsible for cell shape and movement."
"IntermediateFilament","Another component of the cytoskeleton involved in cell structure and differentiation."
"Tubulin","A protein that forms microtubules, one of the key components of the cytoskeleton."
"MicrotubuleNucleationSite","The site where microtubules are formed and stabilized within the cell."
"Centromere","A specialized region on a chromosome where the kinetochore attaches during cell division."
"Mitin","A protein that helps to organize the spindle fibers during mitosis."
"Tropomyosin","A protein involved in muscle contraction and relaxation."
"Elastin","A protein that provides elasticity and flexibility to connective tissue."
"Actinin","A protein involved in actin filament formation and dynamics."

Note: This is not an exhaustive list, but it includes many of the major organelles and less well-known entities found inside a biological cell.

>>> Reformat the csv list as XML, for example: <Entities><Cilium><Anno>A tiny hair-like structure involved in movement and sensing.</Anno></Cilium></Entities>
Here is the reformatted list in XML format:

<Entities>
  <CellMembrane>
    <Name>Cell Membrane</Name>
    <Description>The outermost layer of the cell that separates the cell from its environment and regulates what enters and leaves the cell.</Description>
  </CellMembrane>
  <Nucleus>
    <Name>Nucleus</Name>
    <Description>The control center of the cell where DNA is stored and replicated.</Description>
  </Nucleus>
  <Cytoplasm>
    <Name>Cytoplasm</Name>
    <Description>The jelly-like substance inside the cell membrane where metabolic processes take place.</Description>
  </Cytoplasm>
  <Mitochondria>
    <Name>Mitochondria</Name>
    <Description>The powerhouses of the cell responsible for generating energy through cellular respiration.</Description>
  </Mitochondria>
  <Lysosome>
    <Name>Lysosome</Name>
    <Description>A membrane-bound organelle that contains digestive enzymes and is responsible for breaking down and recycling cellular waste and debris.</Description>
  </Lysosome>
  <GolgiApparatus>
    <Name>Golgi Apparatus</Name>
    <Description>A complex network of flattened sacs and tubules involved in protein modification, sorting, and packaging.</Description>
  </GolgiApparatus>
  <EndoplasmicReticulum>
    <Name>Endoplasmic Reticulum</Name>
    <Description>A network of membranous tubules and cisternae that plays a crucial role in protein synthesis and transport.</Description>
  </EndoplasmicReticulum>
  <Ribosome>
    <Name>Ribosome</Name>
    <Description>A small organelle responsible for translating mRNA into proteins.</Description>
  </Ribosome>
  <Cytoskeleton>
    <Name>Cytoskeleton</Name>
    <Description>A network of protein filaments that provides structural support, shape, and movement to the cell.</Description>
  </Cytoskeleton>
  <Nucleolus>
    <Name>Nucleolus</Name>
    <Description>A region within the nucleus where ribosomal RNA is synthesized.</Description>
  </Nucleolus>
  <Peroxisome>
    <Name>Peroxisome</Name>
    <Description>A small organelle involved in the breakdown of fatty acids and amino acids.</Description>
  </Peroxisome>
  <Centriole>
    <Name>Centriole</Name>
    <Description>A small structure involved in the formation of cilia, flagella, and the spindle fibers during cell division.</Description>
  </Centriole>
  <Lamin>
    <Name>Lamin</Name>
    <Description>A protein that forms a network-like structure beneath the nuclear envelope.</Description>
  </Lamin>
  <NuclearPoreComplex>
    <Name>Nuclear Pore Complex</Name>
    <Description>A specialized structure that regulates the transport of molecules between the nucleus and the cytoplasm.</Description>
  </NuclearPoreComplex>
  <Chloroplast>
    <Name>Chloroplast</Name>
    <Description>An organelle found in plant cells responsible for photosynthesis.</Description>
  </Chloroplast>
  <Vacuole>
    <Name>Vacuole</Name>
    <Description>A storage compartment within the cell used to store water, salts, and waste products.</Description>
  </Vacuole>
  <Cilium>
    <Name>Cilium</Name>
    <Description>A tiny hair-like structure involved in movement and sensing.</Description>
  </Cilium>
  <Ficolin>
    <Name>Ficolin</Name>
    <Description>A protein involved in the recognition of foreign substances and activation of the immune response.</Description>
  </Ficolin>
  <Histone>
    <Name>Histone</Name>
    <Description>A small basic protein that^C

>>> NO. Try again.
I apologize for the mistake. Here is the list reformatted in XML:

<Entities>
  <Entity>
    <Name>CellMembrane</Name>
    <Description>The outermost layer of the cell that separates the cell from its environment and regulates what enters and leaves the cell.</Description>
  </Entity>
  <Entity>
    <Name>Nucleus</Name>
    <Description>The control center of the cell where DNA is stored and replicated.</Description>
  </Entity>
  <Entity>
    <Name>Cytoplasm</Name>
    <Description>The jelly-like substance inside^C

>>> NO. Instead of <Entity><Name>CellMembrane</Name></Entity>
I want "<CellMembrane><Anno>The outermost layer of the cell that separates the cell from its environment and regulates what enters and leaves the cell.</Anno></CellMembrane>".

>>> NO.
... Instead of:
... "<CellMembrane><Name>CellMembrane</Name><Description>The outermost layer of the cell that separates the cell from its environment and regulates what enters and leaves the cell.</Description></CellMembrane>"
... I want
... "<CellMembrane><Anno>The outermost layer of the cell that separates the cell from its environment and regulates what enters and leaves the cell.</Anno></CellMembrane>".
I apologize for the mistake. Here is the reformatted list in XML:

OK

>>> Create a separate XML structure that includes just the name of each entity, for example: <Entity><CellMembrane/><Nucleus/></Entity>

Here is the XML structure with just the names of each entity:

OK

>>> Use only the following color names: AliceBlue,AntiqueWhite,Aqua,Aquamarine,Azure,Beige,Bisque,Black,BlanchedAlmond,Blue,BlueViolet,Brown,BurlyWood,CadetBlue,Chartreuse,Chocolate,Coral,CornflowerBlue,Cornsilk,Crimson,Cyan,DarkBlue,DarkCyan,DarkGoldenRod,DarkGray,DarkGreen,DarkKhaki,DarkMagenta,DarkOliveGreen,DarkOrange,DarkOrchid,DarkRed,DarkSalmon,DarkSeaGreen,DarkSlateBlue,DarkSlateGray,DarkTurquoise,DarkViolet,DeepPink,DeepSkyBlue,DimGray,DodgerBlue,FireBrick,FloralWhite,ForestGreen,Fuchsia,Gainsboro,GhostWhite,Gold,GoldenRod,Gray,Green,GreenYellow,HoneyDew,HotPink,IndianRed,Indigo,Ivory,Khaki,Lavender,LavenderBlush,LawnGreen,LemonChiffon,LightBlue,LightCoral,LightCyan,LightGoldenRodYellow,LightGray,LightGreen,LightPink,LightSalmon,LightSeaGreen,LightSkyBlue,LightSlateGray,LightSteelBlue,LightYellow,Lime,LimeGreen,Linen,Magenta,Maroon,MediumAquaMarine,MediumBlue,MediumOrchid,MediumPurple,MediumSeaGreen,MediumSlateBlue,MediumSpringGreen,MediumTurquoise,MediumVioletRed,MidnightBlue,MintCream,MistyRose,Moccasin,NavajoWhite,Navy,OldLace,Olive,OliveDrab,Orange,OrangeRed,Orchid,PaleGoldenRod,PaleGreen,PaleTurquoise,PaleVioletRed,PapayaWhip,PeachPuff,Peru,Pink,Plum,PowderBlue,Purple,RebeccaPurple,Red,RosyBrown,RoyalBlue,SaddleBrown,Salmon,SandyBrown,SeaGreen,SeaShell,Sienna,Silver,SkyBlue,SlateBlue,SlateGray,Snow,SpringGreen,SteelBlue,Tan,Teal,Thistle,Tomato,Turquoise,Violet,Wheat,White,WhiteSmoke,Yellow,YellowGreen

Here is the updated XML structure with a Color node for each entity:
... it refused to do more than about 10 of them

>>> Continue with the rest of the entities. You can do it!

Thank you for the encouragement!

Here is the completed XML structure with a Color node for each entity:
... again it refused

]]></markdown>

<params>
  <param name="TooltipUseAnno" value="true"/>
</params>

<_-.XholonClass>

  <PhysicalSystem/>
    
  <CellEntity>
    <CellMembrane/>
    <Nucleus/>
    <Cytoplasm/>
    <Mitochondria/>
    <Lysosome/>
    <GolgiApparatus/>
    <EndoplasmicReticulum/>
    <Ribosome/>
    <Cytoskeleton/>
    <Nucleolus/>
    <Peroxisome/>
    <Centriole/>
    <Lamin/>
    <NuclearPoreComplex/>
    <Chloroplast/>
    <Vacuole/>
    <Cilium/>
    <Ficolin/>
    <Histone/>
    <Telomere/>
    <MagnesiumIonChannel/>
    <SodiumPotassiumPump/>
    <Polyribosome/>
    <Exosome/>
    <Chaperone/>
    <DyneinMotor/>
    <Microfilament/>
    <IntermediateFilament/>
    <Tubulin/>
    <MicrotubuleNucleationSite/>
    <Centromere/>
    <Mitin/>
    <Tropomyosin/>
    <Elastin/>
    <Actinin/>
  </CellEntity>
  
  <Cell/>
  
</_-.XholonClass>

<xholonClassDetails>
  
  <!--<Entities>-->
  <CellMembrane>
    <Anno>The outermost layer of the cell that separates the cell from its environment and regulates what enters and leaves the cell.</Anno>
    <Color>Coral</Color>
  </CellMembrane>
  <Nucleus>
    <Anno>The control center of the cell where DNA is stored and replicated.</Anno>
    <Color>CornflowerBlue</Color>
  </Nucleus>
  <Cytoplasm>
    <Anno>The jelly-like substance inside the cell membrane where metabolic processes take place.</Anno>
    <Color>Lavender</Color>
  </Cytoplasm>
  <Mitochondria>
    <Anno>A type of organelle responsible for generating energy in the form of ATP.</Anno>
    <Color>GoldenRod</Color>
  </Mitochondria>
  <Lysosome>
    <Anno>A membrane-bound organelle that contains digestive enzymes and is responsible for breaking down and recycling cellular waste and debris.</Anno>
    <Color>BurlyWood</Color>
  </Lysosome>
  <GolgiApparatus>
    <Anno>A complex network of flattened sacs and tubules involved in protein modification, sorting, and packaging.</Anno>
    <Color>Chartreuse</Color>
  </GolgiApparatus>
  <EndoplasmicReticulum>
    <Anno>A network of membranous tubules and cisternae that plays a crucial role in protein synthesis and transport.</Anno>
    <Color>DeepSkyBlue</Color>
  </EndoplasmicReticulum>
  <Ribosome>
    <Anno>A small organelle responsible for translating mRNA into proteins.</Anno>
    <Color>Beige</Color>
  </Ribosome>
  <Cytoskeleton>
    <Anno>A network of protein filaments that provides structural support, shape, and movement to the cell.</Anno>
    <Color>Turquoise</Color>
  </Cytoskeleton>
  <Nucleolus>
    <Anno>A region within the nucleus where ribosomal RNA is synthesized.</Anno>
    <Color>SeaGreen</Color>
  </Nucleolus>
  <Peroxisome>
    <Anno>A small organelle involved in the breakdown of fatty acids and amino acids.</Anno>
    <Color>Brown</Color>
  </Peroxisome>
  <Centriole>
    <Anno>A small structure involved in the formation of cilia, flagella, and the spindle fibers during cell division.</Anno>
    <Color>Khaki</Color>
  </Centriole>
  <Lamin>
    <Anno>A protein that forms a network-like structure beneath the nuclear envelope.</Anno>
    <Color>OldLace</Color>
  </Lamin>
  <NuclearPoreComplex>
    <Anno>A specialized structure that regulates the transport of molecules between the nucleus and the cytoplasm.</Anno>
    <Color>Sienna</Color>
  </NuclearPoreComplex>
  <Chloroplast>
    <Anno>An organelle found in plant cells responsible for photosynthesis.</Anno>
    <Color>Chartreuse</Color>
  </Chloroplast>
  <Vacuole>
    <Anno>A storage compartment within the cell used to store water, salts, and waste products.</Anno>
    <Color>PaleTurquoise</Color>
  </Vacuole>
  <Cilium>
    <Anno>A tiny hair-like structure involved in movement and sensing.</Anno>
    <Color>SeaGreen</Color>
  </Cilium>
  <Microfilament>
    <Anno>A component of the cytoskeleton involved in cell movement, shape, and division.</Anno>
    <Color>Turquoise</Color>
  </Microfilament>
  <Tubulin>
    <Anno>A protein that forms microtubules, which are components of the cytoskeleton involved in cell movement and division.</Anno>
    <Color>SteelBlue</Color>
  </Tubulin>
  <IntermediateFilament>
    <Anno>A protein that forms intermediate filaments, which are components of the cytoskeleton involved in maintaining cell shape and providing mechanical support.</Anno>
    <Color>Khaki</Color>
  </IntermediateFilament>
  <Histone>
    <Anno>A small basic protein that compactly wraps around DNA in the nucleus.</Anno>
    <Color>RebeccaPurple</Color>
  </Histone>
  <!--</Entities>-->
  
  <Avatar><Color>red</Color></Avatar>
</xholonClassDetails>

<PhysicalSystem>
  
  <CellMembrane>
    <Nucleus/>
  </CellMembrane>
  
  <!-->>> Construct a new XML structure, that represents the composite structure of a single biological cell. Use only the entities that we have already defined.

Here is an example of an XML structure that represents the composite structure of a single biological cell:-->

<Cell>
  <CellMembrane/>
  <Cytoplasm>
    <Mitochondria/>
    <Lysosome/>
    <EndoplasmicReticulum/>
    <Ribosome/>
    <Cytoskeleton>
      <Microfilament/>
      <IntermediateFilament/>
      <Tubulin/>
    </Cytoskeleton>
  </Cytoplasm>
  <Nucleus>
    <Nucleolus/>
    <Histone/>
  </Nucleus>
  <Centriole/>
  <Chloroplast/>
  <Vacuole/>
  <Cilium/>
</Cell>

<!--This structure represents a single biological cell, with its various components such as the cell membrane, cytoplasm, nucleus, and organelles like mitochondria, lysosomes, 
endoplasmic reticulum, ribosomes, microfilaments, intermediate filaments, and tubulin.-->

</PhysicalSystem>

<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="PhysicalSystem/Cell" fill="#98FB98" height="50" width="50" x="25" y="0"/>
    <g>
      <title>Height</title>
      <rect id="PhysicalSystem/Cell/Cytoplasm" 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>

</XholonWorkbook>