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Define simple blox for external stimulus, used for task based sDCM #351

Merged
merged 31 commits into from
Jun 7, 2024
Merged

Define simple blox for external stimulus, used for task based sDCM #351

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08ee574
WIP: it runs through now with the newly defined ExternalInput block b…
david-hofmann Apr 12, 2024
46d2325
merged with master
david-hofmann Apr 12, 2024
5d11682
minor fixes
david-hofmann Apr 12, 2024
68634b4
WIP: fix misalignment between states and jacobian (i.e. equations) of…
david-hofmann Apr 12, 2024
488a7bf
problem fixed in a somewhat hacky way. Maybe revisit with MTK9 in place
david-hofmann Apr 17, 2024
28e5592
Bump to MTK v9 (#342)
MasonProtter May 1, 2024
0ff7e4d
add new neurons
anandpathak31 May 16, 2024
cdb843a
add a `H_learning` state in `Striatum` parts that tracts the `H` para…
harisorgn May 22, 2024
69ebaa8
use `H_learning` state instead of `H` param for `Cortical-Striatum` w…
harisorgn May 22, 2024
67c19c3
add gap junction connections
anandpathak31 May 22, 2024
e7a5217
add neuron tests
anandpathak31 May 22, 2024
0ad6405
add composite bloxs
anandpathak31 May 23, 2024
479497d
complete DBS circuit and tests
anandpathak31 May 23, 2024
c67e6de
Patch for test failues (#353)
MasonProtter May 23, 2024
4b4f7bb
Merge branch 'master' into Adam_Brown_DBS
MasonProtter May 23, 2024
96fabec
added Generic2dOsc with example script - not working
helmutstrey Jun 3, 2024
3894891
stochastic simulation is now working
helmutstrey Jun 3, 2024
47fa5ef
fully functioning example
helmutstrey Jun 4, 2024
695911d
got sign of coupling wrong - now it reproduces the tutorial
helmutstrey Jun 4, 2024
4d41fe5
added resting state whole brain simulation:
helmutstrey Jun 4, 2024
4879600
tutorial should work now
helmutstrey Jun 4, 2024
06278bc
Merge pull request #354 from Neuroblox/two2osc
hstrey Jun 4, 2024
3f2f313
example modification
anandpathak31 Jun 4, 2024
22e48f4
remove plots
anandpathak31 Jun 4, 2024
a0eeb5d
Merge branch 'Adam_Brown_DBS' of https://github.com/Neuroblox/Neurobl…
anandpathak31 Jun 4, 2024
8e89df0
Merge pull request #352 from Neuroblox/Adam_Brown_DBS
anandpathak31 Jun 5, 2024
8990f93
WIP: it runs through now with the newly defined ExternalInput block b…
david-hofmann Apr 12, 2024
91deb28
WIP: fix misalignment between states and jacobian (i.e. equations) of…
david-hofmann Apr 12, 2024
9509e34
problem fixed in a somewhat hacky way. Maybe revisit with MTK9 in place
david-hofmann Apr 17, 2024
1bc0cd6
merged with MTK9 version of Neuroblox
david-hofmann Jun 7, 2024
d578f53
Merge branch 'inputblox' of https://github.com/Neuroblox/Neuroblox.jl…
david-hofmann Jun 7, 2024
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5 changes: 2 additions & 3 deletions Project.toml
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
name = "Neuroblox"
uuid = "769b91e5-4c60-41ee-bfae-153c84203cb2"
repo = "https://github.com/Neuroblox/Neuroblox.jl.git"
version = "0.3.1"
version = "0.4.1"

[deps]
AbstractFFTs = "621f4979-c628-5d54-868e-fcf4e3e8185c"
Expand All @@ -21,7 +21,6 @@ ForwardDiff = "f6369f11-7733-5829-9624-2563aa707210"
Glob = "c27321d9-0574-5035-807b-f59d2c89b15c"
Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
IfElse = "615f187c-cbe4-4ef1-ba3b-2fcf58d6d173"
Interpolations = "a98d9a8b-a2ab-59e6-89dd-64a1c18fca59"
JLD2 = "033835bb-8acc-5ee8-8aae-3f567f8a3819"
LinearAlgebra = "37e2e46d-f89d-539d-b4ee-838fcccc9c8e"
Expand Down Expand Up @@ -79,7 +78,7 @@ JLD2 = "0.4"
MAT = "0.10"
MLJ = "0.20"
MetaGraphs = "0.7"
ModelingToolkit = "8"
ModelingToolkit = "9.6"
ModelingToolkitStandardLibrary = "2"
MuladdMacro = "0.2"
NaNStatistics = "0.6"
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1 change: 1 addition & 0 deletions README.md
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# Neuroblox.jl

[![CI](https://github.com/Neuroblox/Neuroblox.jl/actions/workflows/CI.yml/badge.svg)](https://github.com/Neuroblox/Neuroblox.jl/actions/workflows/CI.yml)
7 changes: 6 additions & 1 deletion docs/Project.toml
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@@ -1,10 +1,15 @@
[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
Neuroblox = "769b91e5-4c60-41ee-bfae-153c84203cb2"
HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
Neuroblox = "769b91e5-4c60-41ee-bfae-153c84203cb2"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[compat]
Documenter = "1"
1 change: 1 addition & 0 deletions docs/build/.documenter-siteinfo.json
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{"documenter":{"julia_version":"1.10.3","generation_timestamp":"2024-06-04T15:54:29","documenter_version":"1.4.1"}}
123 changes: 123 additions & 0 deletions docs/build/api/index.html
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15 changes: 15 additions & 0 deletions docs/build/assets/Project.toml
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@@ -0,0 +1,15 @@
[deps]
CSV = "336ed68f-0bac-5ca0-87d4-7b16caf5d00b"
DataFrames = "a93c6f00-e57d-5684-b7b6-d8193f3e46c0"
DifferentialEquations = "0c46a032-eb83-5123-abaf-570d42b7fbaa"
Documenter = "e30172f5-a6a5-5a46-863b-614d45cd2de4"
Graphs = "86223c79-3864-5bf0-83f7-82e725a168b6"
HypothesisTests = "09f84164-cd44-5f33-b23f-e6b0d136a0d5"
MetaGraphs = "626554b9-1ddb-594c-aa3c-2596fe9399a5"
Neuroblox = "769b91e5-4c60-41ee-bfae-153c84203cb2"
Plots = "91a5bcdd-55d7-5caf-9e0b-520d859cae80"
Random = "9a3f8284-a2c9-5f02-9a11-845980a1fd5c"
Statistics = "10745b16-79ce-11e8-11f9-7d13ad32a3b2"

[compat]
Documenter = "1"
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