owmeta.neuron module¶

class owmeta.neuron.ConnectionProperty(*args, **kwargs)[source]¶

Bases: CustomProperty

A representation of the connection between neurons. Either a gap junction or a chemical synapse

TODO: Add neurotransmitter type. TODO: Add connection strength

contextualize(context)¶

Return an object with the given context. If the provided context is None, then self MUST be returned unmodified. Prefer to override contextualize_agument which will be called from this method.

It is generally not correct to set a field on the object and return the same object as this would change the context for other users of the object. Also, returning a copy of the object is usually inappropriate for mutable objects. Immutable objects may maintain a ‘context’ property and return a copy of themselves with that property set to the provided context argument.

get(pre_post_or_either='pre', **kwargs)[source]¶

Get a list of connections associated with the owning neuron.

Parameters

pre_post_or_either: str: What kind of connection to look for. ‘pre’: Owner is the source of the connection ‘post’: Owner is the destination of the connection ‘either’: Owner is either the source or destination of the connection

Returns

list of Connection

get_terms(pre_post_or_either='pre', **kwargs)[source]¶

Get a list of connection identifiers associated with the owning neuron.

Parameters

pre_post_or_either: str: What kind of connection to look for. ‘pre’: Owner is the source of the connection ‘post’: Owner is the destination of the connection ‘either’: Owner is either the source or destination of the connection

Returns

list of Connection

set(conn, **kwargs)[source]¶

Add a connection associated with the owner Neuron

Parameters

connowmeta.connection.Connection: connection associated with the owner neuron

Returns

A owmeta.neuron.Connection

class owmeta.neuron.Neighbor(*args, **kwargs)[source]¶

Bases: CustomProperty

contextualize(context)¶

Return an object with the given context. If the provided context is None, then self MUST be returned unmodified. Prefer to override contextualize_agument which will be called from this method.

It is generally not correct to set a field on the object and return the same object as this would change the context for other users of the object. Also, returning a copy of the object is usually inappropriate for mutable objects. Immutable objects may maintain a ‘context’ property and return a copy of themselves with that property set to the provided context argument.

get(**kwargs)[source]¶

Get a list of neighboring neurons.

Parameters

See parameters for owmeta.connection.Connection

Returns

list of Neuron

get_terms(**kwargs)[source]¶

Get a list of neighboring neurons.

Parameters

See parameters for owmeta.connection.Connection

Returns

list of Neuron

set(other, **kwargs)[source]¶

Set the value of this property

Derived classes must override.

class owmeta.neuron.Neuron(*args, no_type_decl=False, **kwargs)[source]¶

Bases: Cell

A neuron.

See what neurons express some neuropeptide

Example:

# Grabs the representation of the neuronal network
>>> net = P.Worm().get_neuron_network()

# Grab a specific neuron
>>> aval = net.aneuron('AVAL')

>>> aval.type()
set([u'interneuron'])

#show how many connections go out of AVAL
>>> aval.connection.count('pre')
77

>>> aval.name()
u'AVAL'

#list all known receptors
>>> sorted(aval.receptors())
[u'GGR-3', u'GLR-1', u'GLR-2', u'GLR-4', u'GLR-5', u'NMR-1', u'NMR-2', u'UNC-8']

#show how many chemical synapses go in and out of AVAL
>>> aval.Syn_degree()
90

Parameters

namestr: The name of the neuron.

Attributes

neighborCustomProperty: Get neurons connected to this neuron if called with no arguments, or with arguments, state that neuronName is a neighbor of this Neuron
connectionCustomProperty: Get a set of Connection objects describing chemical synapses or gap junctions between this neuron and others

GJ_degree()[source]¶

Get the degree of this neuron for gap junction edges only

Returns: total number of incoming and outgoing gap junctions
Return type: int

Syn_degree()[source]¶

Get the degree of this neuron for chemical synapse edges only

Returns: total number of incoming and outgoing chemical synapses
Return type: int

contextualize(context)¶

Return an object with the given context. If the provided context is None, then self MUST be returned unmodified. Prefer to override contextualize_agument which will be called from this method.

It is generally not correct to set a field on the object and return the same object as this would change the context for other users of the object. Also, returning a copy of the object is usually inappropriate for mutable objects. Immutable objects may maintain a ‘context’ property and return a copy of themselves with that property set to the provided context argument.

get_incidents(type=0)[source]¶: Get neurons which synapse at this neuron

property innexin¶: Innexin types associated with this neuron

property neuropeptide¶: Name of the gene corresponding to the neuropeptide produced by this neuron

property neurotransmitter¶: Neurotransmitters associated with this neuron

property receptor¶: The receptor types associated with this neuron

property receptors¶: Alias to receptor

property type¶: The neuron type (i.e., sensory, interneuron, motor)