Definition of the elements needed for specifying the biophysical properties of cells. These elements are linked with those in MorphML.xsd and from the ChannelML spec by the NeuroML.xsd file The root element. All other complex/simple elements will be children of this. Description of biophysical properties of a cell. Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism) on a group of cables of a cell. Note there should be at least one of these to specify the passive membrane conductance. Note: elements spec_capacitance, spec_axial_resistance, ion_props etc. should be used in preference to specificCapacitance etc! Unit system of all quantities. Definition of placement of a single electrophysiological mechanism (e.g. channel mechanism) on a group of cables of a cell Note variable_parameter will be the preferred form in v2.0 Note variable_parameter will be the preferred form in v2.0 Name of the mechanism. Should refer to a named mechanism in a ChannelML file Specifies the type of cellular mechanism (Channel Mechanism/Ion Concentration). Note could be used for any type of electrophysiological property of a section of a cell Whether this is a passive/leak conductance. In this case, 2 params, gmax and e should be sufficient to fully specify the mechanism, independent of any implementation. Useful e.g. for mapping to and from inbuilt mechanisms in simulators (e.g. pas in NEURON, Em/Rm in GENESIS). NOTE: this attribute will be required in v2.0!! Don't use passiveConductance anymore. Changed for consistency with ChannelML and NetworkML naming conventions. Whether this is a passive/leak conductance. NOTE: this attribute will be removed in v2.0!! Use passive_conductance instead. Changed for consistency with ChannelML and NetworkML naming conventions. F/m2 Capacitance per unit area of a group of sections Note variable_parameter will be the preferred form in v2.0 Note variable_parameter will be the preferred form in v2.0 ohm m Specific axial resistance of a group of sections Note variable_parameter will be the preferred form in v2.0 Note variable_parameter will be the preferred form in v2.0 V This quantity is often required for computational simulations and specifies the potential difference across the membrane at the start of the simulation. This is an optional field Some properties accociated with an ion type which takes part in the mechanisms on the cell Definition of a value for a quantity and the associated groups of cables which have this value. Can have any name, but gmax and e are special... 2 names have special meaning: gmax for the maximum conductance density, and e for the reversal potential of a passive channel Definition of a value for a quantity which varies over a given group of cables Definition of a value for a quantity which varies over a given group of cables How a value changes over the cable group. Implementation here based on NEURON inhomogeneous parameter specification. See example for usage of this element Name used in the inhomogeneous_param element in the cable group Equation showing how parameter changes as function of variable attribute in inhomogeneous_param element Definition of a value for a quantity and the associated groups of cables which have this value. The quantity referred to will be clear from the usage, e.g. InitialMembPotential Specifies the type of cellular mechanism. Note could be used for any type of electrophysiological property of a section of a cell Voltage and/or conductance dependent membrane conductance Mechanism which alters the oncentration of a specific ion s 0.005 Units of a delay associated with a synaptic connection s 0.005 Units of any time constant, greater than zero s-1 100 Units of the inverse of a time constant s 0.005 Units of any time constant which can have value zero s 0.005 Units of any time value, zero or greater Hz 50 Units of any frequency, zero or greater S 1e-8 Units of conductance S m-2 100 Units of conductance density m 1e-6 Units of length A 1e-11 Units of current mM 1e-5 Units of concentration V -0.07 Units of voltage deg C 32 Units of temperature