netconfcentral logo

ieee1906-dot1-neuron

HTML

ieee1906-dot1-neuron@2020-07-07



  module ieee1906-dot1-neuron {

    yang-version 1.1;

    namespace
      "urn:ieee:std:1906.1:yang:ieee1906-dot1-neuron";

    prefix ieee1906-neuron;

    import ieee1906-dot1-types {
      prefix types;
    }
    import ieee1906-dot1-math {
      prefix math;
    }
    import ieee1906-dot1-si-units {
      prefix si-units;
    }
    import ieee1906-dot1-system {
      prefix system;
    }

    organization
      "P1906.1.1/D1.0 Draft Standard Data Model for Nanoscale Communication Systems Working Group";

    contact
      "IEEE P1906.1.1 Working Group
		 Chair: Stephen F. Bush <bushsf@research.ge.com>
		 Secretary: Guillaume Mantelet <gmantelet@voltigeurnetworks.com>";

    description
      "This is an example illustrating how to refine the 1906.1 framework
                 to include specific component hierarchy to model a simple neuron.
                 This example reuses part of the model described in reference";

    reference
      "A. Banerjee, J. L. Paluh, A. Mukherjee, K. G. Kumar, A. Ghosh,
      M. K. Naskar (2017) ”Modeling the neuron as a nano communication
      system to identify spatiotemporal molecular events in neurodegenerative
      disease”. International J Nanomedicine, in press.";


    revision "2020-07-07" {
      description "Initial version.";
    }


    identity poisson-process {
      base types:non-standard-physics;
      description
        "The Poisson process can be used to simulate the generation
                 of message, or something that acts to the message, such as
                 a perturbation.";
    }

    identity dcv-bdnf {
      base types:motor;
      description
        "It is a molecular motor-vesicle cargo loaded with DCV-BDNF";
    }

    grouping unrealized-dcv-bdnf-percentage {
      description
        "The corresponding message deliverability of the system.";
      leaf unrealized-dcv-bdnf-percentage {
        when
          "derived-from-or-self(../type-of-component, 'poisson-process')";
        type math:percent;
        description
          "The parent component must have a leaf of type 'dcv-bdnf' in
                   order to be eligible to use this container.";
      }
    }  // grouping unrealized-dcv-bdnf-percentage

    grouping average-traversal-time-per-bdnf-molecule {
      container average-traversal-time-per-bdnf-molecule {
        description
          "This is a measure of latency or response time of a
                   system";
        leaf average-time-due-to-diffusion {
          type si-units:time;
          description
            "A function of the distance between the point of
                     consideration and generation and the diffusion
                     coefficient";
        }

        leaf average-clearance-time {
          type si-units:time;
          description
            "Average clearance time of BDNF through microtubule
                     gates using gate selection process.";
        }
      }  // container average-traversal-time-per-bdnf-molecule
    }  // grouping average-traversal-time-per-bdnf-molecule

    container neuron-model {
      description
        "Redefined nanoscale-system for our neuron model, which is 
                 enriched with new metrics, and this is only the beginning.";
      uses system:system {
        augment components/component {
          description
            "Augment nanoscale system with the poisson process defined
                     in neuron model.";
          uses unrealized-dcv-bdnf-percentage;
        }

        augment system-metrics {
          description "test";
          uses average-traversal-time-per-bdnf-molecule;
        }
      }

      uses average-traversal-time-per-bdnf-molecule;
    }  // container neuron-model
  }  // module ieee1906-dot1-neuron

Summary

  
  
Organization P1906.1.1/D1.0 Draft Standard Data Model for Nanoscale Communication Systems Working Group
  
Module ieee1906-dot1-neuron
Version 2020-07-07
File ieee1906-dot1-neuron.yang
  
Prefix ieee1906-neuron
Namespace urn:ieee:std:1906.1:yang:ieee1906-dot1-neuron
Reference
A. Banerjee, J. L. Paluh, A. Mukherjee, K. G. Kumar, A. Ghosh,
M. K. Naskar (2017) ”Modeling the neuron as a nano communication
system to identify spatiotemporal molecular events in neurodegenerative
disease”. International J Nanomedicine, in press.
  
Cooked /cookedmodules/ieee1906-dot1-neuron/2020-07-07
YANG /src/ieee1906-dot1-neuron@2020-07-07.yang
XSD /xsd/ieee1906-dot1-neuron@2020-07-07.xsd
  
Abstract This is an example illustrating how to refine the 1906.1 framework to include specific component hierarchy to model a simple neu...
  
Contact
IEEE P1906.1.1 Working Group
Chair: Stephen F. Bush <bushsf@research.ge.com>
Secretary: Guillaume Mantelet <gmantelet@voltigeurnetworks.com>

Description

 
This is an example illustrating how to refine the 1906.1 framework
to include specific component hierarchy to model a simple neuron.
This example reuses part of the model described in reference

Groupings

Grouping Objects Abstract
average-traversal-time-per-bdnf-molecule average-traversal-time-per-bdnf-molecule
unrealized-dcv-bdnf-percentage unrealized-dcv-bdnf-percentage The corresponding message deliverability of the system.

Objects

Type Key
Mandatory config
Optional config
Not config
Object Type Abstract
neuron-model container Redefined nanoscale-system for our neuron model, which is enriched with new metrics, and this is only the beginning.
   average-traversal-time-per-bdnf-molecule container This is a measure of latency or response time of a system
      average-clearance-time leaf Average clearance time of BDNF through microtubule gates using gate selection process.
      average-time-due-to-diffusion leaf A function of the distance between the point of consideration and generation and the diffusion coefficient
   components container This containers stores the list of components that are part of the system.
      component list A list of 1906.1 compatible objects in any nanoscale model.
         description leaf An optional string to describe what does this component in the non 1906.1 model. For example, a neuron model reusing 1906.1 framework could specify what this 'axon' is supposed to do in its corresponding model.
         field-metrics container The parent component must have a leaf of type 'field' in order to be eligible to use this container.
            diffusive-flux container Fick’s First Law is one of the standard laws of diffusion.
               D leaf The diffusion coefficient or mass diffusivity in dimensions of length^2 time^−1, for example (m^2/s).
               J leaf The diffusion flux, which is the amount of substance per unit area per unit time, for example (mol/m^2 × s); it measures the amount of substance that will flow through a small area during a small time interval.
               phi leaf For ideal mixtures, this is the concentration in dimensions of amount of substance per unit volume, for example (mol m^-3).
               x leaf The position (length), for example, in meters.
            langevin-noise container Random motion has a significant impact upon the performance of Message Carriers, in particle form, to reach their target receivers.
               eta leaf The random component of force (motion component). The unit is a Newton.
               lambda leaf The systematic part of the molecular force (field component). The unit is momentum.
               m leaf The mass of the message carrier.
               t leaf The current time.
               x leaf The position of a message carrier.
            persistence-length container Persistence Length is a measure of the degree to which a chain-like structure is either soft (like strings of cooked spaghetti) or rigid (like metal rods).
               u-0 container Unit tangent vector at the origin or beginning of the chain of connected segments
                  nabla container A generic container representing the Cartesian coordinate for this nabla. Ordering is very important, and providing at least one element is mandatory. Physicists will often refer to an operator with three coordinates. Convention on the dimensions, unl...
                     coordinate leaf-list Cartesian coordinates for this nabla operator. It can be named.
               unit-tangent-vectors list segment-index s u-s
                  s leaf The position of a unit tangent sample.
                  segment-index leaf A segment index.
                  u-s container The unit tangent vector at point s in set of connected segments.
                     nabla container A generic container representing the Cartesian coordinate for this nabla. Ordering is very important, and providing at least one element is mandatory. Physicists will often refer to an operator with three coordinates. Convention on the dimensions, unl...
                        coordinate leaf-list Cartesian coordinates for this nabla operator. It can be named.
               zeta-p leaf The persistence length.
         human-designed leaf 'Human-designed' means a system that occurs as a result of conscious human intervention. For clarity, human-designed systems may include naturally occurring components in an arrangement or for a purpose that is not otherwise naturally occurring.
         identifier leaf A unique identifier for this component to be associated to the non 1906.1 model. For example, a neuron axon can be comprised of multiple sections. Each of the section should be uniquely identified by the underlying model to store statistics or retrieve c...
         motion-metrics container The parent component must have a leaf of type 'motion' in order to be eligible to use this container.
            collision-behavior container Collision Behavior measures the physical result of collision between Message Carriers.
               coefficient-of-restitution leaf A measure of the 'restitution' of a collision between two objects: how much of the kinetic energy remains for the objects to rebound from one another vs. how much is lost as heat, or work done deforming the objects. The coefficient is defined as the ratio...
               speed-after-collision leaf The speed of a message carrier loaded with message after collision.
               speed-before-collision leaf The speed of a message carrier loaded with message before collision.
            mass-displacement container Molecular communication can assume Message Carriers are composed of mass and move from one location to another.
               M leaf Number of samples
               mass-displacement leaf Value of the mass displacement.
               T leaf Sample period (the time between each sample).
               tau leaf Sample time
               x leaf Mass at time t.
            positioning-accuracy-of-message-carriers container Multiple swarms of message carriers can be controlled like unified organisms to swim along predetermined paths toward the receiver by an external macro-unit (e.g., an agglomeration of flagellated magnetotactic bacteria can be utilized as efficient carrier...
               accuracy-percent leaf Then number of message carriers located within the given area or volume.
               position leaf The location of the center of mass of the message carriers.
               radius leaf OID: /neuron-model/components/component/motion-metrics/positioning-accuracy-of-message-carriers/radius
         name leaf An optional name to describe what is this component in the non 1906.1 model. For example, a neuron model reusing 1906.1 framework could use 'axon' as a name for one of its components.
         next-component leaf-list Identifies the list of sibling components attached to this component in a unidirectional way. There can be 0 or more next components and next components can be of any type. This leaf-list helps identify the components along the data path of a message, an...
         next-definition leaf-list Identifies the list of sibling definitions attached to this definition in a unidirectional way. There can be 0 or more next definitions and next definition can be of any type. This leaf-list helps identify the components along the data path of a message,...
         properties container This containers stores the list of optional properties that provide extra definition of the component, or make this component attribute supersedes corresponding system (or parent component) corresponding attribute.
            amount-of-substance leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe amount of substance for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this prope...
            derived-unit leaf-list Gives users options to annotate this specific SI derived unit, thus declaring to the system which SI unit is used the said derived unit for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on ...
            duration leaf It is simply another way of naming time. If time is already defined as property with its si unit annotated, then it must be treated as an error if this leaf is also present as property.
            electric-current leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe electric current for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property...
            length leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe length for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If for i...
            luminous-intensity leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe luminous intensity for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this proper...
            mass leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe mass for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If omitte...
            scale leaf Defines a generic scale for this system. If omitted, it is understood that it is a nanoscale system (<1um).
            thermodynamic-temperature leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe temperature for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If...
            time leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe time for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If omitte...
            timestamp leaf Gives a timestamp for a snapshot of the system, relating metrics to a reference in simulation time.
         specificity-metrics container The parent component must have a leaf of type 'specificity' in order to be eligible to use this container.
            affinity leaf Affinity is a standard measure of chemical affinity; however it is applied to the broader IEEE 1906 framework and the affinity of Message Carriers to their intended targets, Media, and other Message Carriers.
            angular-spectrum container Angular Spectrum quantifies the distribution of the intensity of nanoscale communication signals received at the receiver as a function of angle-of-arrival.
               density-function list A list of probabilities forming a probability density function.
                  probability-sample leaf A sample probability in the probability density.
            delay-spectrum container Delay Spectrum quantifies the distribution of the intensity of nanoscale communication signals received at the receiver as a function of time-of-arrival.
               density-function list A list of probabilities forming a probability density function.
                  probability-sample leaf A sample probability in the probability density.
            sensitivity leaf A measure of the proportion of true positives, which are events that actually occurred and have been correctly detected. See also: specificity.
            specificity leaf A measure of precision in matching between components. See also: sensitivity.
         sub-component leaf-list Identifies the list of child components that are part of this component. There can be 0 or more child components and child components can be of any type. For example, a nanoscale interface can be comprised of a transmitter and a receiver sub-components, ...
         sub-definition leaf-list Identifies the list of child definitions that are part of this definition. There can be 0 or more child definition and child definition can be of any type.
         type-of-component leaf Identifies this component from the non 1906.1 model to a 1906.1 compatible component. For example, a neurotransmitter can be considered a 'message-carrier'. This leaf automatically selects the correct type of metric to display. See the following list of...
         unrealized-dcv-bdnf-percentage leaf The parent component must have a leaf of type 'dcv-bdnf' in order to be eligible to use this container.
   contact leaf-list List of contact names. It is recommended to append the email address of the contact as well.
   definitions container This containers stores the list of definitions that are part of the system.
      definition list A list of IEEE 1906.1-2015 compatible objects.
         description leaf An optional string to describe what does this definition in the non 1906.1 model.
         human-designed leaf 'Human-designed' means a system that occurs as a result of conscious human intervention. For clarity, human-designed systems may include naturally occurring components in an arrangement or for a purpose that is not otherwise naturally occurring.
         identifier leaf A unique identifier for this definition to be associated to the non 1906.1 model.
         message-metrics container The parent definition must have a leaf of type 'message' in order to be eligible to use this container.
            bandwidth-delay-product container Bandwidth-Delay Product is proportional to the maximum number of Message Carriers capable of fitting within the physical channel.
               channel-bandwidth leaf The bits per second transported by the nanoscale communication channel.
               channel-delay leaf The time for a message to propagate from one end of a channel to the other.
            information-and-communication-energy container This is the metric that quantifies energy used in nanoscale communication. This is energy per bit of information conveyed by the Motion Component.
               energy-message-delivery leaf The energy used to transport a message across a channel.
               information-message-delivery leaf The amount of information in a message.
            information-density container surface amount-of-information
               amount-of-information leaf Amount of information.
               surface container A surface.
                  scalar leaf-list A scalar representing this surface in the considered space.
            message-deliverability leaf Message Deliverability measures whether a Message Carrier survives long enough to deliver its information to the intended receiver. Message Deliverability (MD) assumes messages have a finite time-to-live (TTL). Thus, MD = P(tr < TTL) where tr is the age ...
            message-lifetime leaf Message Lifetime measures the lifetime of a Message Carrier. TTL is used in 6.1.
         name leaf An optional name to describe what is this definition in the non 1906.1 model.
         next-component leaf-list Identifies the list of next components that are interfaced to this definition. There can be 0 or more next components and next components can be of any type. However, model shall clearly identify next components that make valid interfaces from Std. IEEE 1...
         next-definition leaf-list Identifies the list of sibling definitions attached to this definition in a unidirectional way. There can be 0 or more next definitions and next definition can be of any type. This leaf-list helps identify the components along the data path of a message,...
         properties container This containers stores the list of optional properties that provide extra definition of the component, or make this component attribute supersedes corresponding system (or parent component) corresponding attribute.
            amount-of-substance leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe amount of substance for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this prope...
            derived-unit leaf-list Gives users options to annotate this specific SI derived unit, thus declaring to the system which SI unit is used the said derived unit for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on ...
            duration leaf It is simply another way of naming time. If time is already defined as property with its si unit annotated, then it must be treated as an error if this leaf is also present as property.
            electric-current leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe electric current for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property...
            length leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe length for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If for i...
            luminous-intensity leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe luminous intensity for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this proper...
            mass leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe mass for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If omitte...
            scale leaf Defines a generic scale for this system. If omitted, it is understood that it is a nanoscale system (<1um).
            thermodynamic-temperature leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe temperature for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If...
            time leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe time for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If omitte...
            timestamp leaf Gives a timestamp for a snapshot of the system, relating metrics to a reference in simulation time.
         sub-component leaf-list Identifies the list of child components that are part of this definition. There can be 0 or more child components and child components can be of any type.
         sub-definition leaf-list Identifies the list of child definitions that are part of this definition. There can be 0 or more child definition and child definition can be of any type.
         type-of-definition leaf Identifies the IEEE 1906.1-2015 definition extended in this model.
   description leaf An optional leaf describing what this nanoscale is expected to do.
   human-designed leaf 'Human-designed' means a system that occurs as a result of conscious human intervention. For clarity, human-designed systems may include naturally occurring components in an arrangement or for a purpose that is not otherwise naturally occurring.
   identifier leaf Identifying the system to make it a resource available online.
   license leaf The name of the license controlling rights to this document
   organization leaf-list The name of the vendor or the authority providing standards.
   properties container This containers stores the list of optional properties that provide extra definition of the system.
      amount-of-substance leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe amount of substance for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this prope...
      derived-unit leaf-list Gives users options to annotate this specific SI derived unit, thus declaring to the system which SI unit is used the said derived unit for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on ...
      duration leaf It is simply another way of naming time. If time is already defined as property with its si unit annotated, then it must be treated as an error if this leaf is also present as property.
      electric-current leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe electric current for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property...
      length leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe length for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If for i...
      luminous-intensity leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe luminous intensity for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this proper...
      mass leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe mass for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If omitte...
      scale leaf Defines a generic scale for this system. If omitted, it is understood that it is a nanoscale system (<1um).
      thermodynamic-temperature leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe temperature for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If...
      time leaf Gives users options to annotate this leaf, thus declaring to the system which SI unit is used to describe time for this component and its child nodes (e.g. for this XML element and its children). All derived units will depend on this property. If omitte...
      timestamp leaf Gives a timestamp for a snapshot of the system, relating metrics to a reference in simulation time.
   system-metrics container Metrics that can be used by nanoscale systems only.
      active-network-programmability container Message Carriers can be programmed or coded such they change the underlying Media (e.g., microtubules, nanotubes, etc.) as they transport information (see 5.3.4).
         delta-f leaf The change in f(t) intentionally caused by a programmed Message Carrier through a surface.
         f leaf The flux of Message Carriers as a function of time where flux is the rate of flow through a unit area.
         S container math-formula
            math-formula container expression package version
               expression leaf A mathematical expression.
               package leaf The math package that reads the expression in its native format.
               version leaf The version of the math package assumed.
         t leaf The current time.
      average-traversal-time-per-bdnf-molecule container This is a measure of latency or response time of a system
         average-clearance-time leaf Average clearance time of BDNF through microtubule gates using gate selection process.
         average-time-due-to-diffusion leaf A function of the distance between the point of consideration and generation and the diffusion coefficient
      bandwidth-volume-ratio container The Bandwidth-Volume Ratio takes into account and combines two fundamental essences of molecular and nanoscale communication, namely its size and bandwidth.
         bandwidth leaf The bandwidth of the nanoscale communication channel.
         volume leaf The sum of the volume of the transmitter and receiver pair for a communication system.
      perturbation-rate container Perturbation Rate is a measure of both the rate and control of any type of perturbation used to send a signal in the system.
         error-of-perturbation leaf Rate of error in the componet representing bits of information in the channel. There is typically a tradeoff with rate-of-perturbation
         rate-of-perturbation leaf Rate of change of the componet representing bits of information in the channel. There is typically a tradeoff with error-of-perturbation.
      supersystem-degradation container The supersystem is the system in which the IEEE 1906.1 network resides. This can be a biological organism. This metric quantifies the impact of the network upon the supersystem with regard to its normal operation.
         ds leaf The supersystem degradation of the performance-attribute.
         performance-attribute leaf A descriptive name of the performance attribute.
         sp leaf The native supersystem performance (without the embedded nanoscale communication network).
         spn leaf The supersystem performance of the performance-attribute with the embedded nanoscale communication network.
   system-type leaf Define the system type being described. Defaults to nanoscale-communication. Communication is the act of conveying a message from a transmitting party to a receiving party. This includes the components of message, transmitter, receiver, medium, and m...
   title leaf A short, optional title for this nanoscale system. Can be the name of the product.
   version leaf The version number of this document. No pattern control for this leaf is defined. User may use simple numbering or provide a date and time, or a mix of them.