# How to set custom delay for excitatory-excitatory connctions

**URL:** <https://brian.discourse.group/t/how-to-set-custom-delay-for-excitatory-excitatory-connctions/1274>\
**Category:** Support\
**Tags:** synapses\
**Created:** [12 August 2024 17:16 UTC](https://brian.discourse.group/t/how-to-set-custom-delay-for-excitatory-excitatory-connctions/1274 "2024-08-12T17:16:08Z")\
**Posts on this page:** 3\
**Page:** 1

<div class="post-metadata">

**Author:** ![foneill](https://avatars.discourse-cdn.com/v4/letter/f/bcef8e/32.png) [@foneill](https://brian.discourse.group/u/foneill)\
**Post date:** [12 August 2024 17:16 UTC](https://brian.discourse.group/t/how-to-set-custom-delay-for-excitatory-excitatory-connctions/1274/1 "2024-08-12T17:16:08Z")

</div>

# Description of problem

Hi everyone.  
I am looking to implement a synaptic delay according this excerpt from a paper:

> Every inhibitory neuron is connected to all other neurons in the network. The  
> delay of each excitatory-excitatory synapse is sampled at random from the [1, 20]ms interval, and the delay of all other synapses is fixed at 1 ms.

However, I can’t find out how to do this on Brian2’s docs, other than not setting the delay in the dictionary.

# Minimal code to reproduce problem

```auto
import matplotlib.pyplot as plt
import numpy as np

from brian2 import NeuronGroup, Synapses, SpikeMonitor, StateMonitor
from brian2 import ms, mV
from brian2 import defaultclock, run

tfinal = 1000 * ms
Ne = 800
Ni = 200

re = np.random.uniform(size=Ne)
ri = np.random.uniform(size=Ni)
weights = np.hstack(
    [
        0.5 * np.random.uniform(size=(Ne + Ni, Ne)),
        -np.random.uniform(size=(Ne + Ni, Ni)),
    ]
).T

defaultclock.dt = 1 * ms

eqs = """dv/dt = (0.04*v**2 + 5*v + 140 - u + I + I_noise )/ms : 1
         du/dt = (a*(b*v - u))/ms : 1
         I : 1
         I_noise : 1
         a : 1
         b : 1
         c : 1
         d : 1
       """

N = NeuronGroup(Ne + Ni, eqs, threshold="v>=30", reset="v=c; u+=d", method="euler")
N.v = -65

N_exc = N[:Ne]
N_inh = N[Ne:]

spikemon = SpikeMonitor(N)
statemon = StateMonitor(N, 'v', record=0, when='after_thresholds')
N_exc.a = 0.02
N_exc.b = 0.2
N_exc.c = -65 + 15 * re**2
N_exc.d = 8 - 6 * re**2

N_inh.a = 0.02 + 0.08 * ri
N_inh.b = 0.25 - 0.05 * ri
N_inh.c = -65
N_inh.d = 2

N_exc.u = "b*v"
N_inh.u = "b*v"

S = Synapses(
    N,
    N,
    "w : 1",
    on_pre={"up": "I += w", "down": "I -= w"},
)
S.connect()
# set delays for excitatory-to-excitatory connections randomly between 1 and 20 ms

exc_to_exc = (S.i < Ne) & (S.j < Ne)

S.delay[exc_to_exc] = np.random.uniform(1, 20, size=np.sum(exc_to_exc)) * ms

# set delays for all other connections to 1 ms

S.delay[~exc_to_exc] = 1 * ms

```

# What you have aready tried

I have tried implementing logic in the dicitonary itself and the code provided above.

# Expected output (if relevant)

# Actual output (if relevant)

# Full traceback of error (if relevant)

```auto
File "/home/fiach/Documents/College/Project/test_iz.py", line 169, in <module>
    S.delay[exc_to_exc] = np.random.uniform(1, 20, size=np.sum(exc_to_exc)) * ms
  File "/home/fiach/.local/lib/python3.10/site-packages/brian2/groups/group.py", line 405, in __getattr__
    return object. __getattribute__ (self, name)
  File "/home/fiach/.local/lib/python3.10/site-packages/brian2/synapses/synapses.py", line 1187, in _get_delay
    raise AttributeError(
AttributeError: Synapses do not have a 'pre' pathway, do not know what 'delay' refers to.

```

---

<div class="post-metadata">

**Author:** ![bindok](https://avatars.discourse-cdn.com/v4/letter/b/90ced4/32.png) [@bindok](https://brian.discourse.group/u/bindok)\
**Post date:** [12 August 2024 21:03 UTC](https://brian.discourse.group/t/how-to-set-custom-delay-for-excitatory-excitatory-connctions/1274/2 "2024-08-12T21:03:45Z")

</div>

Hello,  
I think your error is coming from the way you have written your on\_pre argument in Synapses object, I am not sure what you wanted to set there, however to implement different delay values the following implementation works

```auto
S = Synapses(N, N, model="w : 1", on_pre=' ', method="euler", dt=defaultclock.dt)

# Connect neurons
S.connect()

# Set delays
S.delay = '1*ms'  
S.delay[N_exc, N_exc] = np.random.uniform(0,20)*ms # Random delay for excitatory-to-excitatory

run(tfinal)

print(S.delay[N_exc, N_exc])

```

Since I am not sure what you want your on\_pre argument to be, I cannot help with what way of writing the on\_pre argument would be correct. But I hope this helps a little!

---

<div class="post-metadata">

**Author:** ![mstimberg](https://yyz2.discourse-cdn.com/free1/user_avatar/brian.discourse.group/mstimberg/32/11_2.png) [@mstimberg](https://brian.discourse.group/u/mstimberg)\
**Post date:** [3 September 2024 09:41 UTC](https://brian.discourse.group/t/how-to-set-custom-delay-for-excitatory-excitatory-connctions/1274/3 "2024-09-03T09:41:59Z")

</div>

Hi @foneill,  
you get the error message, because you have two pathways, an `up` and a `down` pathway, apparently to create a rectangular synaptic current. The exact code depends on the “width” of your rectangular synaptic current, e.g. for 2ms, I’d write it as:

```python
# set delays for excitatory-to-excitatory connections randomly between 1 and 20 ms
delays = np.random.uniform(1, 20, size=Ne*Ne) * ms
S.up.delay[:Ne, :Ne] = delays
S.down.delay[:Ne, :Ne] = delays + 2*ms

# set delays for all other connections to 1 ms
S.up.delay[Ne:, Ne:] = 1 * ms
S.down.delay[Ne:, Ne:] = 1 * ms + 2 * ms

```

Let me know if anything is still unclear!

The syntax suggested by @bindok works as well, i.e. to set with `S.up.delay[N_exc, N_exc] = ...` instead of with `S.up.delay[:Ne, :Ne]` – the two ways of writing this are equivalent. But note that `np.random.uniform(0, 20)*ms` would set all connections to the _same_ random value.