Revision:

Revisions

# Date Author Comment
8453f744 05 Dec 2018 02:08 Jessica Dafflon

Fix small errrors introduced by the interareal simulation

Fix small errrors introduced by the interareal on the inter- and
intralaminar simulation.
e29cb0fa 05 Dec 2018 01:49 Jessica Dafflon

Visualise connectivity matrix for interareal simulation

  • Pass areas and interareal connectivity to the generate function
  • Hardcode the connectivity matrix for the interareal connectivity of two regions
51b77885 04 Dec 2018 11:47 Padraig Gleeson (admin)

Test NML network on OSB
ea118a1f 04 Dec 2018 11:47 Padraig Gleeson (admin)

Testing & updating large scale network generator
488d57b5 04 Dec 2018 11:40 Padraig Gleeson (admin)

Should fix https://github.com/OpenSourceBrain/MejiasEtAl2016/issues/14

  • Use two input currents to excite the E/I layers separately

@JessyD there was an issue with the DCSource (which is a PyNN specific
input object, but can be mapped to nml2) in the PyNN code which I will...
c69df251 02 Dec 2018 19:56 Padraig Gleeson (admin)

Should fix https://github.com/OpenSourceBrain/MejiasEtAl2016/issues/14

  • Use two input currents for the E/I layers

@JessyD there was an issue with the DCSource (which is a PyNN specific
input object, but can be mapped to nml2) in the PyNN code which I will...
eb8b0429 27 Nov 2018 15:08 Padraig Gleeson (admin)

Test NML network on OSB
647ce257 27 Nov 2018 14:54 Padraig Gleeson (admin)

Update README.md
779f4e1a 27 Nov 2018 14:50 Padraig Gleeson (admin)

Updates for OSB page viewing: http://www.opensourcebrain.org/projects/mejiasetal2016
be7aa19b 23 Nov 2018 18:57 Jessica Dafflon

Power spectral density fix and fix initial rate

  • Correct issue with ms & s in the custom build function to calculate the power spectral densisty power (plot_interlaminar_power_spectrum()
  • Use the spectral.compute_spectrum function from the neurodsp package to...
c9a68c8f 15 Nov 2018 18:01 Padraig Gleeson (admin)

Should fix https://github.com/OpenSourceBrain/MejiasEtAl2016/issues/14

@JessyD there was an issue with the DCSource (which is a PyNN specific
input object, but can be mapped to nml2) in the PyNN code which I will
fix, but it's better to use the PulseGenerator from nml2 directly.
82a146ed 14 Nov 2018 17:35 Jessica Dafflon

WIP: Define two different inputSources
c5a0a57c 12 Nov 2018 15:57 Jessica Dafflon

Plot Rate over time and their histogram for NeuroML and Python interlaminarsimulation

  • Rename numpy to np in GenerateNeuroMLlite
  • Take out simulation step from periodogram analysis (interlaminar.py) so that the same function can be used to analyse the simualtion from NeuroML...
05e16cde 11 Nov 2018 18:07 Jessica Dafflon
  • Rename numpy to np in GenerateNeuroMLlite
  • Take out simulation step from periodogram analysis (interlaminar.py)
c4ffdd08 11 Nov 2018 16:27 Jessica Dafflon

Interlaminar analysis

  • Save intermediary results as a pickle and load them into a matlab function. Call the closed sourced matlab function and generate periodogram for the Python simulation
  • Correct small typo in the interalaminar script
dc3a04ed 30 Oct 2018 13:30 Padraig Gleeson (admin)

Testing & updating large scale network generator
4564730b 30 Oct 2018 12:20 Padraig Gleeson (admin)

Merge branch 'dev_python' into dev_pg

  • dev_python: Generate different Sim*.json files Analyse power spectrum from NeuroML/LEMS genrated rate Add modulatory current into excitory populations of L23 and L56
bdd04281 29 Oct 2018 11:44 Jessica Dafflon

Generate different Sim*.json files

  • Add random fluctuation on the NeuroML/LEMS simulation by using different random seeds. Now, every simulation saves a separate Sim*.json file.
ae032db2 26 Oct 2018 15:25 Jessica Dafflon

Analyse power spectrum from NeuroML/LEMS genrated rate

  • Remove useless dimensions in the rate analysis from the Python simulation
  • No longer saves analysis pickle for the Python analysis
  • Add input modulatory current to excitatory populations in L23 and L56 in the NeuroML/LEMS analysis
9d9f129d 26 Oct 2018 15:21 Jessica Dafflon

Add modulatory current into excitory populations of L23 and L56
a6ab3be7 26 Oct 2018 10:27 Jessica Dafflon

Merge pull request #11 from OpenSourceBrain/dev_python

NeuroML/LEMS and Python produce similar rates
01a784e0 24 Oct 2018 21:15 Jessica Dafflon

Define function for simulation network parameters

  • Define a function to defines the parameters of the network (get_network_configuration) according to the analysis
  • Correction: Interlaminar debug analysis was noot taking the interlaminar connection into account.
52f65816 24 Oct 2018 21:14 Jessica Dafflon

Use the same JEE/wee notation as the neuroML definitions
a2c130cc 24 Oct 2018 16:25 Jessica Dafflon

Update the pythonfunction arguments

  • noise is no longer one the arguments that can be passed to the python function. The std of the noise is always assumed to be one.
  • sigmaoveride can now be passed in order to use the sigmas for each population as noise.
8a7de5ff 24 Oct 2018 16:10 Jessica Dafflon

Update bash test file
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