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arbor-sim
arbor
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808bb8fc
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808bb8fc
authored
4 years ago
by
Brent Huisman
Committed by
GitHub
4 years ago
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Improve Recipe concept documentation
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doc/concepts/recipe.rst
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808bb8fc
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@@ -17,6 +17,12 @@ building phase to provide information about individual cells in the model, such
* **Gap junction connections** on each cell.
* **Probes** on each cell.
Recipes are structured to provide a consistent interface for describing each cell in the
network using their global identifier (`gid`).
This allows the simulator to be able to quickly look-up properties related to the connections
going in and out of a cell (think of synapses, gap junctions, but also probes and spike inputs);
which helps make Arbor fast and easily distributable over many nodes.
To better illustrate the content of a recipe, let's consider the following network of
three cells:
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@@ -24,10 +30,10 @@ three cells:
of the soma, a spike detector is attached, it generates a spiking event when the
voltage goes above 10 mV. In the same spot on the soma, a current clamp is also
attached, with the intention of triggering some spikes. All of the preceding info:
the morphology, dynamics, spike detector and current clamp are what is refered to in
the morphology, dynamics, spike detector and current clamp are what is refer
r
ed to in
Arbor as the **description** of the cell.
| ``Cell 0`` should be modeled as a :ref:`cable cell<modelcablecell>`,
(because cable cells allow complex dynamics such as ``hh``). This is refered to as
| ``Cell 0`` should be model
l
ed as a :ref:`cable cell<modelcablecell>`,
(because cable cells allow complex dynamics such as ``hh``). This is refer
r
ed to as
the **kind** of the cell.
| It's quite expensive to build cable cells, so we don't want to do this too often.
But when the simulation is first set up, it needs to know how cells interact with
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@@ -66,7 +72,7 @@ The recipe is used to distribute the model across machines and is used in the si
Technical details of the recipe class are presented in the :ref:`Python <pyrecipe>` and
:ref:`C++ <cpprecipe>` APIs.
Are recipes always nec
c
essary?
Are recipes always necessary?
------------------------------
Yes. However, we provide a python :class:`single_cell_model <py_single_cell_model>`
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