Candy Guide

Referencing

All objects in Patch that depend on each other reference each other, meaning that Python won’t garbage collect parts of your simulation that you explicitly defined. An example of this is that when you create a synapse and a NetStim and connect them together with a NetCon, you only have to hold on to 1 of the variables for Patch to know that if you’re holding on to a NetCon you are most likely interested in the parts it is connected to. There is no longer a need to store every single NEURON variable in a list or on an object somewhere. This drastically cleans up your code.

Sections & Segments

  • When connecting Sections together they all reference each other.

  • Whenever you’re using a Section where a Segment is expected, a default Segment will be used (Segment 0.5):

s = p.Section()
syn = p.ExpSyn(s)
# syn = h.ExpSyn(s(0.5))

  • Whenever a Section/Segment is recorded or connected and a NEURON scalar is expected _ref_v is used:

s = p.Section()
v = p.Vector()
v.record(s) # v.record(s(0.7)._ref_v)

  • Sections can record themselves at multiple points:

s = p.Section()
s.record() # Creates a vector, makes it record s(0.5)._ref_v and stores it as a recorder
s.record(0.7) # Records s(0.5)._ref_v

plt.plot(list(s.recordings[0.5]), list(p.time))

  • Sections can connect themselves to a PointProcess target with .connect_points, which handles NetCon stack access transparently. This allows for example for easy creation of synaptic contacts between a Section and a target synapse:

s = p.Section()
target_syn = p.Section().synapse(p.ExpSyn)
# No more s.push() and h.pop_section() required for NetCon.
s.connect_points(target_syn)

Parallel networks

When you get to the level of the network it would be nice if you could describe your models in a more structured way so be sure to check out Arborize for just that.

If you want to stay vanilla Patch still has you covered; it comes with out-of-the-box parallelization. Introducing the transmitter-receiver pattern:

if p.parallel.id() == 0:
  transmitter = ParallelCon(obj1, gid)
if p.parallel.id() == 1:
  receiver = ParallelCon(gid, obj2)

Just these 2 commands will create a transmitter on node 0 that broadcasts the spikes of obj1 with the specified GID and a receiver on node 1 for obj2 that listens to spikes with that GID.

That’s it. You are now spiking in parallel!

Arbitrary data broadcasting

MPI has a great feature, it allows broadcasting data to other nodes. In NEURON this is restricted to just Vectors. Patch gives you back the freedom to transmit arbitrary data. Anything that can be pickled can be transmitted:

data = None # It's important to declare your var on all nodes to avoid NameErrors
if p.parallel.id() == 12:
  data = np.random.randint((12,12,12))
received = p.parallel.broadcast(data, root=12)