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NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail

Figure 4

Elements for representing cells in NeuroML Levels 1-3.

The main element for expressing a branching neuronal structure in NeuroML is cell which is used for all Levels in NeuroML. The core of the cell description is a set of segment elements which describe the 3D shape of the cell. These can be grouped into cables which represent unbranched neurites of the cell. Metadata present in the cell description can contain details of the creators of the cell model, or the data on which it was based (e.g. a neuronal reconstruction from NeuroMorpho.org). Addition of the biophysics element allows a Level 2 conductance based spiking cell model to be described, and the connectivity element can be used for the allowed synaptic connectivity of a Level 3 cell (e.g. to be used when connecting the cell in a network). A detailed description of each of these elements can be found in Supporting Text S1. Only the elements in Level 1 which are normally used in compartmental cell modeling are shown in the figure. Other elements such as freePoints, features etc. could be present in a Level 1 file from a camera lucida reconstruction [38].

Figure 4

doi: https://doi.org/10.1371/journal.pcbi.1000815.g004