GENESIS: Documentation

Related Documentation:

The NDF File Format

Physical Processes and Model Variables

The NDF File Format and Procedural Model Descriptions

Namespaces in the Model-Container and the Neurospaces Description Format

Introduction

In scientific papers researchers often present a hierarchical top-down description of their models. The NDF File Format supports the integration of model libraries of prototype models and the hierarchical description of models through its namespaces. A namespace is a labeled container of named model components and disambiguates them from model components with the same name contained in a different namespace. Namespaces are indicated with the :: two character sequence.

The :: notation is defined by the model component space of the model-container (note: this notation is neither python nor perl specific). The Gshell, SSP and SSPy transparantly support this notation.

Two examples of a hierarchical model description:

• In the G-2 version of the Purkinje cell model, the G-2 scripts construct prototypes of channels which are then mapped onto prototypes of dendritic sections which are then mapped onto the dendritic morphology.
• In the G-2 version of the cerebellar cortex network model, the G-2 scripts construct prototypes of channels which are then mapped onto prototypes of either a single compartment Granule cell model or either a single compartment Golgi cell model, which are then mapped onto positions calculated by the createmap command.

The :: supports the concept of referencing prototypes independent of the level of the model, to facilitate the hierarchical construction of models.

From the syntactical viewpoint the NDF File Format supports hierarchical model construction using file references with the IMPORT command. The IMPORT command references a file and associates a name with it, called the namespace. When used in model component references the name occuring after the :: refers to a namespace that is associated with a file in the IMPORTs section of an NDF file. For instance the snippet:

defines ::Purk_spine:: as a namespace. After parsing every model defined as a public model in the file segments/spines/purkinje.ndf can be accessed as ::Purk_spine::<model-name>. The NDF file segments/spines/purkinje.ndf defines the models Purk_spine and Purk_spine2 (both are groups of segments defining two different variants of Purkinje cell spines), thus after parsing these two models become accessible as ::Purk_spine::/Purk_spine and ::Purk_spine::/Purk_spine2

When referencing a model component in the model component space the notation can be understood as follows:

• / means ... who has as child ...
• -> means ... who has as parameter ...
• = means ... with the value ...
• and then
• :: means ... who has a namespace ...

In the gshell, the command

defines the namespace ::rscell:: and associates it with the file cells/RScell-nolib2.ndf. All the (public) models in this file are now accessible from this namespace. The statement

creates the model component /two_cells/1 as a reference to /cell underneath the namespace ::rscell::.