The specification of populations and projections which allows network connections to be encoded in NeuroML The root element. Note: this element will only be present in a standalone NetworkML file. For files covering many levels, neuroml will be the root element The main elements which make up a NetworkML compliant document. Unit of all length measurements. Unit of all volume measurements. The elements needed to specify a network connection The least that's needed in a network is a population of cells... In theory there can be no projections, if the file is intended only to specify positions No inputs need be specified The list of cell populations The list of projections from one cell population to another Unit system of all quantities in the projection descriptions, e.g. synaptic time constants The list of electrical inputs into the cells. Should this be extended to allow voltage clamp inputs?? Unit system of all quantities in the input description, e.g. input current amplitudes Description of a single electrical input to a number of cells Currently either a pulse input or a random spiking input are allowed A single input pulse. Note: this should be changed to allow easier specifications of pulse trains, input protocols, etc. A random stimulation at a specific frequency. Note: can be interpreted differently by different simulators!! The name of a synaptic mechanism which will provides the conductance change. This will be fired once every 'spike' at the given frequency Specifies the cell group and which cells/segments to apply the stimulation As with populations/projections, there are two ways to specify the locations of the stimulations: a list of cell location instances and a template for choosing the cells. The cell group to which to apply the stimulation Information on the number of cells on which to apply inputs. Currently only two, but could be expanded to include other scenarios, e.g. all cells in 3d region. Apply input on all cells in group Apply input to a certain percentage of cells in a group The list of input sites Specifies a location on a cell where input is received Description of a cell population of the same type The cell type for this population. NOTE: an attribute value for cell_type WILL BE PREFERRED FORMAT IN v2.0. The option for this element will be removed! Either instances or a specification of the location The name of the population The cell type for this population. Optional now, but WILL BE PREFERRED FORMAT IN v2.0 Cell Instance position information The number of instances of cells for this population. This is redundant information, but can be useful when the file is being parsed to allocate memory for an array of cells. NOTE: will very likely become REQUIRED in v2.0 Description of how one cell population makes synaptic connections with another Cell population where synaptic connection begins. NOTE: attribute values for source and target WILL BE THE PREFERRED FORMAT IN v2.0. The option for this element will be removed! Cell population where synaptic connection terminates. NOTE: attribute values for source and target WILL BE THE PREFERRED FORMAT IN v2.0. The option for this element will be removed! Properties of a synapse associated with this connection. Either an explicit list of the connections or a description of how to create the connections String reference for the projection Cell population where synaptic connection begins. Optional now, but WILL BE PREFERRED FORMAT IN v2.0 Cell population where synaptic connection terminates. Optional now, but WILL BE PREFERRED FORMAT IN v2.0 Pre v1.7.1 format for global synapse properties. Preferred format is GlobalSynapticProperties. This option will be disabled in v2.0 Information on synapse type and default values for weight, delay, threshold, etc. For compatability to pre v1.7.1. Will be removed in v2.0. For compatability to pre v1.7.1. Will be removed in v2.0. Including synapse_type as attribute in synapse_props will be required in v2.0 Variables specifying a single synapse Optional for a single synaptic connection. Only needed in the case where multiple synapses are present at one connection and there are non default values for each synapse's weights, etc. This field gives the name of the synapse type referred to. Variables specifying a single synapse or default values for a set of connections Delay due to diffusion across the synaptic cleft. If only one delay value is known, this can be used Delay due to presynaptic mechanism Delay due to postsynaptic mechanism Delay due to simulated AP propagation along an axon Multiplicative weighting factor for the synapse Presynaptic membrane potential level above which the synapse fires Information on the number of target cells connected to source cells, etc. Connect every pre cell to every post cell For each pre - post pair, there is a fixed probability of connection Connection built iteratively from each pre (or post) cell based on a number of parameters Connection built iteratively from each pre (or post) cell based on a number of parameters Whether the settings below (e.g. number per source cell) refer to PreToPost or PostToPre connections. Note more info could be known about numbers of connections on post synaptic cells, so this possibility should be allowed. The list of cell connections An instance of a cell at a the specified location A unique non negative integer id for the cell instance An optional specification of the node id on which this cell should run. This is a preliminary attempt to allow exchange of neuronal networks partitioned for optimal running in distributed computing environments. A single synaptic connection NOTE: Attributes pre_cell_id etc. for WILL BE PREFERRED FORMAT IN v2.0 NOTE: Attributes post_cell_id etc. for WILL BE PREFERRED FORMAT IN v2.0 The unique ID of the single synaptic connection. The ID of the presynaptic cell. Must be listed in populations, so that too must list instances. Optional now, but attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0 The segment on the presynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0 The fraction along the length of the specified segment on the presynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0 The ID of the postsynaptic cell. Must be listed in populations, so that too must list instances. Optional now, but attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0 The segment on the postsynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0 The fraction along the length of the specified segment on the postsynaptic cell where the synapse is located. Attributes pre_cell_id, etc. WILL BE PREFERRED FORMAT IN v2.0 The ID of the cell. Must be listed in populations, so that too must list instances The segment where the synapse is located. The fraction along the length of the specified segment where the synapse is located. Description of the 3D positioning of cells in the population, in place of giving explicit locations for each cell A random arrangement of cells in a 3D location. Note other 3D regions besides spheres and rectangles can be added if required. Number of cells to place randomly in the specified 3D location A regular placement of the cells in a number of dimensions Specifying this means the precise spatial location of the cells is irrelvant Layout of the cells according to x,y,z spatial coordinates 3D box in which the cells are regularly packed. Note if one or two of dimensions of the box is zero it can be a 2D or 1D grid (respectively). Separation of the cells in each dimension Biophysics of Level3 cell, including specification for allowable synaptic locations. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0 Subset of sections on cell where synaptic connection of a particular type is allowed. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0 List of groups of sections allowing the synapse Which of the synaptic mechanisms can be present Whether this synapse location allows a presynaptic connection, a postsynaptic connection or either Subset of sections on cell where synaptic connection of a particular type is allowed. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0 Which of the synaptic mechanisms can be present Whether this synapse location allows a presynaptic connection, a postsynaptic connection or either List of groups of sections allowing the synapse Indicated whether a potential synapse location allows a presynaptic connection of the specified type, a postsynaptic connection or either. Id of individual cell in a network The elements in biophysics needed to specify a network connection. Note: from v1.7.1 the preferred way to specify a potential synaptic location is with a potential_syn_loc element under connectivity under cell, as opposed to the potentialSynapticLocation under biophysics under cell. The former will be the only option from v2.0