Merge branch 'upsidedownlabs:main' into chords-python

Author: PayalLakra

.gitignore

@@ -1,10 +1,12 @@
 .cache
+.build/*
 _build/*
 build/*
 public/*
 .*project
 .settings
 .envrc
+.venv/*
 .vscode
 .history/
 *.vsix

_static/latex/diy-neuroscience-kit-basic.rst

@@ -16,11 +16,27 @@ DIY Neuroscience Kit Basic
 
    ../../../guides/usage-guides/skin-preparation/index.rst
 
+.. toctree::
+   :hidden:
+   :maxdepth: 3
+
+   ../../../guides/usage-guides/using-gel-electrodes/index.rst
 
 .. toctree::
    :hidden:
    :maxdepth: 3
 
    ../../../guides/usage-guides/using-bioamp-bands/index.rst
 
+.. toctree::
+   :hidden:
+   :maxdepth: 3
+
+   ../../../software/chords/chords-web/index.rst
+
+.. toctree::
+   :hidden:
+   :maxdepth: 3
+
+   ../../../software/chords/chords-python/index.rst
 

courses/basics-of-neuroscience/index.rst

@@ -13,4 +13,16 @@ Course Curriculum
    :hidden:
    :maxdepth: 1
 
-   module-3/index
+   module-3/index
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+
+   module-4/index
+
+.. toctree::
+   :hidden:
+   :maxdepth: 1
+
+   module-5/index

courses/basics-of-neuroscience/module-2/index.rst

@@ -1,12 +1,14 @@
 .. _module-2:
 
-Module 2: Nervous System
-##########################
+Module 2: Human Nervous System
+###############################
 
 2.1 Introduction
 ******************
 
-The nervous system consists of a brain, spinal cord, nerves and is one of the most complex and vital systems in the body, responsible for receiving, transmitting, and processing information. It acts as the body's command center and enables communication between different parts of the body, allowing organisms to interact with their environment.
+The Human nervous system consists of a brain, spinal cord, nerves and is one of the most complex and vital systems 
+in the body, responsible for receiving, transmitting, and processing information. It acts as the body's command 
+center and enables communication between different parts of the body, allowing organisms to interact with their environment.
 
 It is divided into two major parts:
 
@@ -106,6 +108,8 @@ c. **Medulla:** At the bottom of the brainstem, the medulla is where the brain m
 
 The spinal cord begins at the base of the medulla and passes through a large opening at the bottom of the skull. Supported by the vertebrae, it serves as a communication highway between the brain and the rest of the body. This long, tubular structure transmits sensory information from the body to the brain and sends motor commands from the brain to the body. Additionally, it is responsible for reflex actions, which are quick and involuntary responses to stimuli.
 
+.. todo:: The number of vertebrae is wrong, we have to update the image.
+
 .. figure:: ../media/spinal-cord.*
     :align: center
     :alt: Spinal cord
@@ -120,23 +124,23 @@ The Peripheral Nervous System connects the Central Nervous System to the rest of
 2.3.1 Somatic Nervous System (SNS)
 =====================================
 
-The somatic nervous system controls voluntary movements and transmits sensory information to the central nervous system. It consists:
+The somatic nervous system controls voluntary movements and transmits sensory information to and from the central nervous system. It consists:
 
 a. **Sensory Neurons (Afferent Neurons):** These neurons carry signals from sensory receptors (skin, muscles, joints) to the CNS, allowing us to perceive sensations like pain, temperature, and touch.
 b. **Motor Neurons (Efferent Neurons):** These neurons transmit commands from the CNS to the skeletal muscles, enabling voluntary movement such as walking, talking, and picking up objects.
 
 2.3.2 Autonomic Nervous System (ANS)
 ======================================
 
-The autonomic nervous system controls involuntary physiological processes, such as heart rate, digestion, and respiratory rate. It operates without conscious control and is divided into three main parts:
+The autonomic nervous system controls involuntary physiological processes, such as heart rate, digestion, and respiratory rate. It operates without conscious control and is divided into two main parts:
 
 a. **Sympathetic Nervous System:** Known as the "fight or flight" system, it prepares the body for stress or emergency situations by increasing heart rate, dilating pupils, releasing adrenaline, and redirecting blood flow to muscles.
 b. **Parasympathetic Nervous System:** It does the opposite of the sympathetic nervous system. Often referred to as the "rest and digest" system, it promotes relaxation by slowing the heart rate, promoting digestion, and conserving energy after a stressful event.
 
 2.4 Neurons
 **************
 
-Neurons are the building blocks of the nervous system and are responsible for sending, receiving and transmitting electrochemical signals throughout the body.
+Neurons are the building blocks of the nervous system and are responsible for receiving and transmitting electrochemical signals throughout the body.
 
 .. admonition:: Fun Fact
 
@@ -149,6 +153,8 @@ Neurons are the building blocks of the nervous system and are responsible for se
 2. **Motor Neurons:** Carry commands from the CNS to muscles and glands, enabling actions like muscle contraction or hormone release. It is the most common type of neuron.
 3. **Interneurons:** These neurons are found in the CNS and act as connectors between sensory and motor neurons. They help process and integrate information.
 
+.. todo:: CORRECT INTERNEURON DIAGRAM
+
 .. figure:: ../media/types-of-neurons.*
     :align: center
     :alt: types of neurons

courses/basics-of-neuroscience/module-4/index.rst

@@ -0,0 +1,106 @@
+.. _basics-of-neuroscience-module-4:
+
+Module 4 : Passive Membrane Properties
+########################################
+
+Studying passive membrane properties before understanding action potential is necessary as they influence how signals 
+propagate and decay along neurons, determining how far signals can travel before requiring regeneration. 
+
+4.1 Resistance and Capacitance in membrane  
+*******************************************
+
+There are two significant electrical properties of neurons that significantly influence how neurons generate and 
+transmit signals. Let us understand each of them one by one.
+
+4.1.1 Resistance
+=================
+
+Resistance is the measure of how much a material opposes the flow of electric current. In the context of neurons, 
+it refers to how difficult it is for ions to flow across the membrane.
+
+Types of Resistance in Neurons :
+--------------------------------
+
+1. Membrane Resistance (Rm)
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+Membrane resistance refers to resistance to the flow of ions across the neuronal membrane. It determines how easily ions can cross the membrane when ion channels open.
+
+**Factors affecting membrane resistance:**
+
+- Ion Channels: The presence and density of ion channels directly affect membrane resistance. More channels result in lower resistance because they provide additional pathways for ions to flow.
+- Membrane Composition: The lipid bilayer structure and the types of proteins embedded in the membrane influence its overall resistance. A thicker membrane will have higher resistance.
+
+.. todo:: Add Membrane Resistance (Rm) graphic here.
+
+.. note:: A high membrane resistance helps maintain the membrane's resting potential by minimizing the flow of ions across it. 
+
+2. Axial Resistance (Ri)
+~~~~~~~~~~~~~~~~~~~~~~~~
+
+Axial resistance refers to resistance to the flow of electrical current along the length of the neuron's axon or dendrites. It is influenced by the internal properties of the cytoplasm and the dimensions of the neuron’s axon or dendrites.
+
+**Factors affecting axial resistance:**
+
+- Cytoplasmic Conductivity: The concentration of ions and other conductive materials in the cytoplasm affects axial resistance. A higher concentration of conductive ions leads to low axial resistance.
+- Diameter of the Neuron: Larger diameter axons have lower axial resistance because a greater cross-sectional area allows for easier ion flow. This is why larger axons can conduct signals more rapidly.
+
+.. todo:: Add Axial Resistance (Ri) graphic here
+
+.. note:: Axial resistance affects how far a signal can travel along an axon without significant potential loss. Lower axial resistance allows signals to travel farther and faster.
+
+.. todo:: ADD RESISTANCE FORMULA
+
+.. admonition:: CONDUCTANCE: (Additional info section)
+
+   It is the ease with which electric current can flow through a membrane. In the context of neurons, it refers to the ease with which ions can move across the neuronal membrane, meaning a higher conductance indicates a lower resistance, allowing for easier passage of electrical signals through the neuron. 
+
+.. todo:: ADD CONDUCTANCE FORMULA
+
+4.1.2 Capacitance:
+==================
+
+Capacitance is the ability of a system to store electric charge. [1]_
+
+In neurons, the Membrane capacitance (Cm) can be described as the capacity of a neuronal membrane to store charge, which is crucial for 
+creating and maintaining the membrane potential.
+
+Factors Affecting Membrane Capacitance:
+----------------------------------------
+
+- Surface Area: A larger surface area increases capacitance, allowing the membrane to store more charge.
+- Thickness of the Membrane: Thinner membranes generally have higher capacitance because the distance between charges is less.
+
+.. todo:: CAPACITOR FORMULA
+
+Role in Membrane Potential
+---------------------------
+
+Capacitance affects how quickly a neuron can respond to changes in voltage. When a current is applied, the membrane capacitance 
+determines how quickly the membrane potential changes. A high capacitance means the membrane can hold more charge, resulting in a 
+slower rate of potential change, while a low capacitance allows for rapid changes.
+
+4.2 Length and Time constant
+*****************************
+
+The interplay between resistance and capacitance significantly impacts how neurons process and transmit signals. 
+
+Time Constant (Tau: τ)
+=========================
+
+The time constant is defined as the product of resistance and capacitance. It indicates 
+how quickly the membrane potential can change in response to a stimulus. A longer time constant means the neuron 
+takes longer to respond, while a shorter time constant allows for rapid changes.
+
+.. todo:: ADD TIME CONSTANT FORMULA
+
+Length Constant (Lambda: λ)
+============================
+
+This measures how far an electrical signal can travel along the axon before it decays significantly. It is influenced by both axial resistance and membrane resistance. A higher length constant allows the signal to travel farther.
+
+.. todo:: ADD LENGTH CONSTANT FORMULA
+
+.. rubric:: References
+
+.. [1] `Bretschneider, F., & De Weille, J. R. (2006). Electricity. In Elsevier eBooks (pp. 1–33). <https://doi.org/10.1016/b978-012370588-4/50060-9>`_