Recipes

The arb::recipe class documentation is below.

C++ Best Practices

Here we collect rules of thumb to keep in mind when making recipes in C++.

Stay thread safe

The load balancing and model construction are multithreaded, that is multiple threads query the recipe simultaneously. Hence calls to a recipe member should not have side effects, and should use lazy evaluation when possible (see Be lazy).

Class Documentation

class recipe

A description of a model, describing the cells and network, without any information about how the model is to be represented or executed.

All recipes derive from this abstract base class, defined in src/recipe.hpp.

Recipes provide a cell-centric interface for describing a model. This means that model properties, such as connections, are queried using the global identifier (gid) of a cell. In the description below, the term gid is used as shorthand for “the cell with global identifier gid”.

Warning

All member functions must be thread safe, because the recipe is used by the multithreaded model building stage. In practice, this means that multiple threads should be able to call member functions of a recipe simultaneously. Model building is multithreaded to reduce model building times, so recipe implementations should avoid using locks and mutexes to introduce thread safety. See recipe best practices for more information.

Required Member Functions

The following member functions must be implemented by every recipe:

virtual cell_size_type num_cells() const = 0

The number of cells in the model.

virtual cell_kind get_cell_kind(cell_gid_type gid) const = 0

The kind of gid (see arb::cell_kind).

virtual util::unique_any get_cell_description(cell_gid_type gid) const = 0

A description of the cell gid, for example the morphology, synapses and ion channels required to build a multi-compartment neuron.

The type used to describe a cell depends on the kind of the cell. The interface for querying the kind and description of a cell are separate to allow the cell type to be provided without building a full cell description, which can be very expensive.

Optional Member Functions

virtual std::vector<cell_connection> connections_on(cell_gid_type gid) const

Returns a list of all the incoming connections for gid . Each connection con should have post-synaptic target con.dest.gid that matches the argument gid, and a valid synapse id con.dest.index on gid. See cell_connection.

By default returns an empty list.

virtual std::vector<gap_junction_connection> gap_junctions_on(cell_gid_type gid) const

Returns a list of all the gap junctions connected to gid. Each gap junction gj should have one of the two gap junction sites gj.local.gid or gj.peer.gid matching the argument gid, and the corresponding synapse id gj.local.index or gj.peer.index should be valid on gid. See gap_junction_connection.

By default returns an empty list.

virtual std::vector<event_generator> event_generators(cell_gid_type gid) const

Returns a list of all the event generators that are attached to gid.

By default returns an empty list.

virtual cell_size_type num_sources(cell_gid_type gid) const

Returns the number of spike sources on gid. This corresponds to the number of spike detectors on a multi-compartment cell. Typically there is one detector at the soma of the cell, however it is possible to attache multiple detectors at arbitrary locations.

By default returns 0.

virtual cell_size_type num_targets(cell_gid_type gid) const

The number of post-synaptic sites on gid, which corresponds to the number of synapses.

By default returns 0.

virtual cell_size_type num_probes(cell_gid_type gid) const

The number of probes attached to the cell.

By default returns 0.

virtual cell_size_type num_gap_junction_sites(cell_gid_type gid) const

Returns the number of gap junction sites on gid.

By default returns 0.

virtual probe_info get_probe(cell_member_type) const

Intended for use by cell group implementations to set up sampling data structures ahead of time and for putting in place any structures or information in the concrete cell implementations to allow monitoring.

By default throws std::logic_error. If num_probes() returns a non-zero value, this must also be overridden.

virtual util::any get_global_properties(cell_kind) const

Global property type will be specific to given cell kind.

By default returns an empty container.

class cell_connection

Describes a connection between two cells: a pre-synaptic source and a post-synaptic destination. The source is typically a threshold detector on a cell or a spike source. The destination is a synapse on the post-synaptic cell.

using cell_connection_endpoint = cell_member_type

Connection end-points are represented by pairs (cell index, source/target index on cell).

cell_connection_endpoint source

Source end point.

cell_connection_endpoint dest

Destination end point.

float weight

The weight delivered to the target synapse. The weight is dimensionless, and its interpretation is specific to the synapse type of the target. For example, the expsyn synapse interprets it as a conductance with units μS (micro-Siemens).

float delay

Delay of the connection (milliseconds).

class gap_junction_connection

Describes a gap junction between two gap junction sites. Gap junction sites are represented by :cpp:type:cell_member_type.

cell_member_type local

gap junction site: one half of the gap junction connection.

cell_member_type peer

gap junction site: other half of the gap junction connection.

float ggap

gap junction conductance in μS.