kenwebb/xholonWorkbook.xml

## xholonWorkbook.xml
<?xml version="1.0" encoding="UTF-8"?>
<!--Xholon Workbook http://www.primordion.com/Xholon/gwt/ MIT License, Copyright (C) Ken Webb, Thu Oct 12 2023 09:25:29 GMT-0400 (Eastern Daylight Saving Time)-->
<XholonWorkbook>

<Notes><![CDATA[
Xholon
------
Title: Electronic Circuits
Description:
Url: http://www.primordion.com/Xholon/gwt/
InternalName: 3f359c0049ca003bf254f7fcd776acf0
Keywords:

My Notes
--------
7 Oct 2023

This workbook explores modeling electricity, electronics, electronic ciruits, and related topics, using Xholon.

### TODO
- take KiCad 6 course, and get related book
- look over my previus notes on this stuff
 - netlists
 - focus on regions of same voltage, as objects
 - electronic components are active objects (like enzymes?)
- I should be able to use ideas from my Cell models
 - compartments, enzymes
- Petri Nets
- focus on electrons

Each time step, each component can try to balance the voltages/nodes it's adjacent to.
Maybe just change zero or one unit per time step.
How to deal with batteries and sun/solar cells that are sources of new electrons?
 - an active object and a store of energy

- include an example of a netlist
- be able to parse a netlist, and create a Xholon model

### Example netlist (describes the SVG example I use) - confirm that this is correct
Circuit with battery and four resistors
v 1 0 dc 1.2
r 1 0 110
r 1 2 220
r 2 0 330
r 2 0 330

### Do biological cells have tiny electrical and magnetic fields?

ChatGPT

Yes, biological cells do generate tiny electrical and magnetic fields as a result of the various electrochemical processes occurring within them. These fields are a consequence of the movement of charged particles, such as ions (charged atoms or molecules), across the cell membrane and within the cell itself.

  * Electrical Fields: Biological cells maintain a difference in electrical charge across their cell membranes, known as the membrane potential. This is primarily achieved through the movement of ions like sodium (Na+), potassium (K+), calcium (Ca2+), and chloride (Cl-) across the cell membrane. The movement of these ions creates electrical gradients and generates electrical fields across the cell membrane.

  * Magnetic Fields: As electrical currents flow within cells, they generate magnetic fields according to Ampere's law and the principles of electromagnetism. These magnetic fields are extremely weak and localized, but they do exist. However, they are typically much weaker than the electrical fields generated by the same processes.

It's important to note that the electrical and magnetic fields generated by individual biological cells are generally very weak and not typically detectable with standard instruments used in biology or medicine. These fields are on the order of microvolts to millivolts for electrical fields and picoteslas for magnetic fields. They are mainly of interest in the field of electrophysiology, where researchers study the electrical activity of cells, such as neurons and cardiac cells, using specialized techniques like patch-clamp recordings and magnetoencephalography (MEG).

In summary, while biological cells do generate tiny electrical and magnetic fields due to the movement of charged particles, these fields are usually too weak to be detected without specialized equipment and are of more significance in research and clinical contexts than in everyday life.

### References

() see my notebook for:
    7 Oct 2023
    30 Dec 2021
      Sodtware, Electronics, Cell Biology, etc. (2 pages of ideas)
    11 Jan 2022
      Electricity - Electronics and Cell Biology
       - pools of electric voltage
      SPICE netlist
       - example, an diagramSVG
       - some good ideas
    29 Jan 2022
      Electricity - Pure Mathematical Object
    28 June 2022
      ngspice (on HP ZBook)
    2 July 2022
      KiCad + Xholon
    7 July 2022
      Electronic Building Blocks
    3 Oct 2022
      Biology, Electronics, General Structures
    17 Oct 2022
      Biological Photovoltaics
    4 Nov 2022
      Electrons - Physics, Chemistry, Biology
    11 Nov 2022
      Biology and Electronics

() http://www.netlogoweb.org/launch#http://www.netlogoweb.org/assets/modelslib/Curricular%20Models/NIELS/Series%20Circuit.nlogo
    - and other NetLogo NIELS models

() http://ccl.northwestern.edu/rp/niels/index.shtml

() https://en.wikipedia.org/wiki/Drude_model

() https://en.wikipedia.org/wiki/Free_electron_model

() https://en.wikipedia.org/wiki/SPICE

() https://en.wikipedia.org/wiki/Netlist
    In electronic design, a netlist is a description of the connectivity of an electronic circuit.
    In its simplest form, a netlist consists of a list of the electronic components in a circuit
    and a list of the nodes they are connected to.
    A network (net) is a collection of two or more interconnected components.

() https://en.wikipedia.org/wiki/Node_(circuits)
    In electrical engineering, a node is any region on a circuit between two circuit elements.
    see svg diagram "Each color in the circuit represents one node."

() https://unlcms.unl.edu/cas/physics/tsymbal/teaching/SSP-927/Section%2008_Electron_Transport.pdf
    Physics 927, E.Y.Tsymbal
    Section 8: Electronic Transport
    Drude model

() https://www.kicad.org/
    KiCad 7.0.8 Release
    Sat, Sep 30, 2023

() https://www.kicad.org/help/learning-resources/

() https://app.techexplorations.com/courses/kicad-like-a-pro-3e-ebook/
    KiCad Like a Pro, 3rd edition
    A book and video course for the world's favourite open source printed circuit board design software.
    By purchasing this edition of KiCad Like a Pro 3rd edition, you contribute to the ongoing development of this amazing tool.
    Tech Explorations will donate 50% of the profits from all sales of this Special Fundraising edition to the KiCad Project.
    EBOOK and video course are now UPDATED FOR KICAD 7
    I have updated this book for KiCad 7. For this update, I have checked all projects in this book and ensured that they work in KiCad 7.
    In the eBook, I have updated most screenshots to reflect the KiCad 7 user interface,
    and any content that mentions or uses functionality that does not apply in KiCad 7.
    I have also introduced Part 14 with 13 new chapters in which I explain the new features in KiCad 7.
    In the video course, I have replaced lectures in sections 1 and 3, and,
    and have introduced new lectures in a new section (15) dedicated to the new and updated features of KiCad 7.
    Please see the video course curriculum and eBook table of contents for more details.

() https://www.primordion.com/Xholon/gwt/Xholon.html?app=Cell&gui=clsc
    my Cell Model
    TransportProtein
    VoltageGatedChannel
      VoltageGatedCaChannel
    VoltageGatedKChannel
    VoltageGatedNaChannel
    etc.

() https://www.allaboutcircuits.com/textbook/reference/chpt-7/example-circuits-and-netlists/
    Example Circuits and Netlists
    The following circuits are pre-tested netlists for SPICE 2g6, complete with short descriptions when necessary.
    (See Chapter 2’s Computer Simulation of Electric Circuits for more information on netlists in SPICE.)
    numerous examples

() Becker, Reece, Poenie, The World of the Cell, third edition, 1996
    chapter 8, Transport across Membranes: Overcoming the permeability barrier, pp. 197-228
    passive and active transport, etc.

() https://biospice.sourceforge.net/
    Bio-SPICE
    Biological Simulation Program for Intra- and Inter-Cellular Evaluation

    Bio-SPICE, an open source framework and software toolset for Systems Biology,
    is intended to assist biological researchers in the modeling and simulation of spatio-temporal processes in living cells.
    In addition, our goal is to develop and serve a user community committed to using, extending,
    and exploiting these tools to further our knowledge of biological processes.

    KSW - it uses SBML; no mention of any connection with electronics SPICE

 ) https://biospice.sourceforge.net/documentation/Getting_Started_with_BioSpice_Tutorial.pdf
    37 page document

() https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5546598/
    PLoS One. 2017; 12(8): e0182385.
    Published online 2017 Aug 7. doi: 10.1371/journal.pone.0182385
    PMCID: PMC5546598' PMID: 28787027
    Modeling and simulation of biological systems using SPICE language
    Morgan Madec, Conceptualization, Investigation, Methodology, Software, Validation, Writing – original draft,¤*
    Christophe Lallement, Conceptualization, Supervision, Writing – review & editing,¤ and
    Jacques Haiech, Conceptualization, Supervision, Writing – review & editing¤

() https://www.youtube.com/watch?v=jlb7CSq3qvg
    July 3: Modeling Languages: Carlos Lopez and Morgan Madec, 2019
    Center for Reproducible Biomedical Modeling

() https://osf.io/8d269/
    BBSPICE - Modeling and simulation of biological systems using SPICE language
    Contributors: Morgan Madec
    Date created: 2017-07-07 04:28 AM | Last Updated: 2022-02-17 11:37 AM
    Identifier: DOI 10.17605/OSF.IO/8D269
    This repository contains the supplementary information associated to the paper "Modeling and simulation of biological systems using SPICE language",
    published in PLOS one in August, 2017 (https://doi.org/10.1371/journal.pone.0182385). It is composed of 5 folders.
    The folder Python Source Scripts contains 5 Python scripts:

() https://sbml.org/
    SBML

() https://antimony.sourceforge.net/
 ) https://antimony.sourceforge.net/Tutorial.pdf
 ) https://academic.oup.com/bioinformatics/article/25/18/2452/196238
    Antimony: a modular model definition language
    Bioinformatics, Volume 25, Issue 18, September 2009, Pages 2452–2454, https://doi.org/10.1093/bioinformatics/btp401
    Published: 03 July 2009
    Abstract

    Motivation:
    Model exchange in systems and synthetic biology has been standardized for computers with the Systems Biology Markup Language (SBML) and CellML,
    but specialized software is needed for the generation of models in these formats.
    Text-based model definition languages allow researchers to create models simply, and then export them to a common exchange format.
    Modular languages allow researchers to create and combine complex models more easily.
    We saw a use for a modular text-based language, together with a translation library to allow other programs to read the models as well.

    Summary:
    The Antimony language provides a way for a researcher to use simple text statements to create, import, and combine biological models,
    allowing complex models to be built from simpler models, and provides a special syntax for the creation of modular genetic networks.
    The libAntimony library allows other software packages to import these models and convert them either to SBML or their own internal format.

    Availability:
    The Antimony language specification and the libAntimony library are available under a BSD license from http://antimony.sourceforge.net/

() https://arxiv.org/pdf/2309.03344.pdf
    MakeSBML: A tool for converting between Antimony and SBML.
    Bartholomew E Jardine,Lucian P Smith,Herbert M Sauro
    • MakeSBML web application makes editing System Biology Markup Language (SBML) models easy with its
      use of Antimony modeling language.
    • MakeSBML speeds up development of system biology models by simplifying the reuse and expansion of existing
      SBML models.
    • Since MakeSBML is a client-side, web based application it can be hosted almost anywhere with minimal server-
      side resources.

() https://forum.kicad.info/t/exporting-layout-as-svg-browser-destination/33148/10
    - a kicad pc can be exported as SVG
    - I could make some of the components in the SVG clickable, in a Xholon app
      - for example a switch
    -

() Cytomorphic Electronic Systems: A reviewe and perspective, Douglas Raymond Beahm, 2021

() A compiler for Biological netowrks on silicon chips, J. Kyle Medley, et al, 2020

() Electrical output of bryophyte microbial fuel cell systems is sufficient to power a radio or an environmental sensor, Paolo Bombelli, et al, 2016

]]></Notes>

<_-.XholonClass>
  <ElectronicSystem/>

  <ElectronicCircuit/>

  <!-- Electronic Circuit Node as described in wikipedia Node_(circuits) -->
  <ECNode/>

  <!-- electronic components -->
  <Battery/>
  <Resistor/>

  <!-- battery components; source: ChatGPT
    TODO
    - These three should be subclasses of Script.
    - They are behaviors that operate on their parent Battery.
  -->
  <Anode superClass="Script"/>
  <Cathode superClass="Script"/>
  <Electrolyte/>


</_-.XholonClass>

<xholonClassDetails>
  <ECNode xhType="XhtypePurePassiveObject"/>
  <Battery xhType="XhtypeBehFgsxxx">
    <Color>BurlyWood</Color>
    <port name="port" index="0" connector="../ECNode[2]"/>
    <port name="port" index="1" connector="../ECNode[1]"/>
    <Anno>A battery is a device that converts chemical energy into electrical energy and provides a source of electric power for various electronic devices and systems. Batteries consist of one or more electrochemical cells, each of which is made up of several key components, including an anode, a cathode, and an electrolyte. The basic working principle of a battery involves a chemical reaction that results in the flow of electrons from the anode to the cathode through an external circuit, creating an electric current.</Anno>
  </Battery>

  <Resistor xhType="XhtypePureActiveObject">
    <Color>PaleGoldenRod</Color>
    <port name="port" index="0" connector="#xpointer(.[@roleName='r1']/../ECNode[2])"/>
    <port name="port" index="1" connector="#xpointer(.[@roleName='r1']/../ECNode[1])"/>

    <port name="port" index="0" connector="#xpointer(.[@roleName='r2']/../ECNode[2])"/>
    <port name="port" index="1" connector="#xpointer(.[@roleName='r2']/../ECNode[3])"/>

    <port name="port" index="0" connector="#xpointer(.[@roleName='r3']/../ECNode[3])"/>
    <port name="port" index="1" connector="#xpointer(.[@roleName='r3']/../ECNode[1])"/>

    <port name="port" index="0" connector="#xpointer(.[@roleName='r4']/../ECNode[3])"/>
    <port name="port" index="1" connector="#xpointer(.[@roleName='r4']/../ECNode[1])"/>
  </Resistor>

  <Anode><Anno>The anode is the negative terminal of the battery and is typically made of a material that can undergo an oxidation reaction. During this reaction, atoms at the anode lose electrons, producing positively charged ions and releasing electrons into the external circuit.</Anno>
  <DefaultContent><![CDATA[
var me, source, target, beh = {
  postConfigure: function() {
    me = this.cnode;
    source = me.xpath("../Electrolyte");
    target = me.parent().port(0);
  },
  act: function() {
    me.println(me.name() + " " + source.name() + " " + source.val() + " " + target.name() + " " + target.val());
    //source.val(source.val() - 1);
    //target.val(target.val() + 1);
    source.dec(1);
    target.inc(1);
  }
}
//# sourceURL=Anode.js
]]></DefaultContent>
  </Anode>

  <Cathode><Anno>The cathode is the positive terminal of the battery and is made of a material that can undergo a reduction reaction. In this reaction, positively charged ions from the anode combine with electrons from the external circuit to form neutral atoms or compounds.</Anno>
  <DefaultContent><![CDATA[
var me, source, target, beh = {
  postConfigure: function() {
    me = this.cnode;
    source = me.parent().port(1);
    target = me.xpath("../Electrolyte");
  },
  act: function() {
    me.println(me.name() + " " + source.name() + " " + source.val() + " " + target.name() + " " + target.val());
    if (source.val() > 0) {
      //source.val(source.val() - 1);
      //target.val(target.val() + 1);
      source.dec(1);
      target.inc(1);
    }
  }
}
//# sourceURL=Cathode.js
]]></DefaultContent>
  </Cathode>

  <Electrolyte xhType="XhtypePurePassiveObject"><Anno>The electrolyte is a substance that separates the anode and the cathode while allowing ions to move between them. It plays a crucial role in facilitating the chemical reactions by conducting ions. In some batteries, the electrolyte is a liquid, while in others, it may be a solid or a gel.</Anno></Electrolyte>

</xholonClassDetails>

<ElectronicSystem>

  <!-- the electronic circuit described in the SVG included with this workbook, and in the netlist -->
  <ElectronicCircuit>
    <ECNode roleName="0" val="1"><attribute name="val" value="0.0"/><Color>red</Color></ECNode>
    <ECNode roleName="1" val="2"><attribute name="val" value="0.0"/><Color>limegreen</Color></ECNode>
    <ECNode roleName="2" val="3"><attribute name="val" value="0.0"/><Color>blue</Color></ECNode>
    <Battery voltage="dc,1.2">
      <Cathode/>
      <Electrolyte><attribute name="val" value="1000.0"/></Electrolyte>
      <Anode/>
      <!-- TODO Cathode and Anode should have/be behaviors that deal with electrons -->
    </Battery>
    <Resistor roleName="r1" Ω="110"><Anno>This is a 110 Ohm resister.</Anno></Resistor>
    <Resistor roleName="r2" Ω="220"/>
    <Resistor roleName="r3" Ω="220"/>
    <Resistor roleName="r4" Ω="220"/>
  </ElectronicCircuit>

</ElectronicSystem>

<Anodexbehavior implName="org.primordion.xholon.base.Behavior_gwtjs"><![CDATA[
  var me, beh = {
    postConfigure: function() {
      me = this.cnode.parent();
    },
    act: function() {
      me.println(me.name());
    }
  }
  //# sourceURL=Anodexbehavior.js
]]></Anodexbehavior>

<SvgClient><Attribute_String roleName="svgUri"><![CDATA[data:image/svg+xml,

<svg width="174pt" height="285pt"
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<g id="ElectronicSystem/ElectronicCircuit" class="graph" transform="scale(1 1) rotate(0) translate(4 280.8)">
<title>45</title>
<polygon fill="white" stroke="none" points="-4,4 -4,-280.8 170,-280.8 170,4 -4,4"/>
<text text-anchor="middle" x="83" y="-8.2" font-family="Courier New" font-size="14.00">Electronic Circuit</text>
<!-- 47 -->
<g id="ElectronicSystem/ElectronicCircuit/ECNode[@roleName=&#39;0&#39;]" class="node"><title>47</title>
<polygon fill="red" stroke="black" points="166,-168.8 112,-168.8 112,-132.8 166,-132.8 166,-168.8"/>
<text text-anchor="middle" x="139" y="-146.6" font-family="Courier New" font-size="14.00">0</text>
</g>
<!-- 48 -->
<g id="ElectronicSystem/ElectronicCircuit/ECNode[@roleName=&#39;1&#39;]" class="node"><title>48</title>
<polygon fill="limegreen" stroke="black" points="166,-222.8 112,-222.8 112,-186.8 166,-186.8 166,-222.8"/>
<text text-anchor="middle" x="139" y="-200.6" font-family="Courier New" font-size="14.00">1</text>
</g>
<!-- 49 -->
<g id="ElectronicSystem/ElectronicCircuit/ECNode[@roleName=&#39;2&#39;]" class="node"><title>49</title>
<polygon fill="blue" stroke="black" points="166,-114.8 112,-114.8 112,-78.8 166,-78.8 166,-114.8"/>
<text text-anchor="middle" x="139" y="-92.6" font-family="Courier New" font-size="14.00">2</text>
</g>
<!-- 50 -->
<g id="ElectronicSystem/ElectronicCircuit/Battery" class="node"><title>50</title>
<polygon fill="BurlyWood" stroke="black" points="75.2905,-222.8 0.709507,-222.8 0.709507,-186.8 75.2905,-186.8 75.2905,-222.8"/>
<text text-anchor="middle" x="38" y="-200.6" font-family="Courier New" font-size="14.00">Battery</text>
</g>
<!-- 50&#45;&gt;47 -->
<g id="ElectronicSystem_edge2" class="edge"><title>50&#45;&gt;47</title>
<path fill="none" stroke="black" d="M72.241,-186.669C82.1327,-181.273 92.9988,-175.346 102.999,-169.891"/>
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</g>
<!-- 50&#45;&gt;48 -->
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</g>
<!-- 51 -->
<g id="ElectronicSystem/ElectronicCircuit/Resistor[@roleName=&#39;r1&#39;]" class="node"><title>51</title>
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<text text-anchor="middle" x="38" y="-254.6" font-family="Courier New" font-size="14.00">r1</text>
</g>
<!-- 51&#45;&gt;47 -->
<g id="ElectronicSystem_edge4" class="edge"><title>51&#45;&gt;47</title>
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<!-- 52 -->
<g id="ElectronicSystem/ElectronicCircuit/Resistor[@roleName=&#39;r2&#39;]" class="node"><title>52</title>
<polygon fill="PaleGoldenRod" stroke="black" points="65,-168.8 11,-168.8 11,-132.8 65,-132.8 65,-168.8"/>
<text text-anchor="middle" x="38" y="-146.6" font-family="Courier New" font-size="14.00">r2</text>
</g>
<!-- 52&#45;&gt;48 -->
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</g>
<!-- 52&#45;&gt;49 -->
<g id="ElectronicSystem_edge6" class="edge"><title>52&#45;&gt;49</title>
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</g>
<!-- 53 -->
<g id="ElectronicSystem/ElectronicCircuit/Resistor[@roleName=&#39;r3&#39;]" class="node"><title>53</title>
<polygon fill="PaleGoldenRod" stroke="black" points="65,-60.8 11,-60.8 11,-24.8 65,-24.8 65,-60.8"/>
<text text-anchor="middle" x="38" y="-38.6" font-family="Courier New" font-size="14.00">r3</text>
</g>
<!-- 53&#45;&gt;47 -->
<g id="ElectronicSystem_edge8" class="edge"><title>53&#45;&gt;47</title>
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</g>
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<g id="ElectronicSystem_edge7" class="edge"><title>53&#45;&gt;49</title>
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<g id="ElectronicSystem/ElectronicCircuit/Resistor[@roleName=&#39;r4&#39;]" class="node"><title>54</title>
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<text text-anchor="middle" x="38" y="-92.6" font-family="Courier New" font-size="14.00">r4</text>
</g>
<!-- 54&#45;&gt;47 -->
<g id="ElectronicSystem_edge10" class="edge"><title>54&#45;&gt;47</title>
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<!-- 54&#45;&gt;49 -->
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