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Recent Releases of multi-area-model

multi-area-model - MAM 1.2.0

Provisional description:

What's Changed

  • Add correlation toolbox to enabling compute correlation coefficient and plot correlation coefficient by @didi-hou in https://github.com/INM-6/multi-area-model/pull/45
  • Allow simulating only some of the areas by @didi-hou in https://github.com/INM-6/multi-area-model/pull/46
  • Code, comment and displlay enhancements for the jupyter notebook by @didi-hou in https://github.com/INM-6/multi-area-model/pull/47
  • Create modules for computing and loading data instead of using functions in analysis.py by @didi-hou in https://github.com/INM-6/multi-area-model/pull/48
  • Plot time averaged population rates by @didi-hou in https://github.com/INM-6/multi-area-model/pull/49
  • Code improvement by @didi-hou in https://github.com/INM-6/multi-area-model/pull/50
  • Correct and enhance readme by @didi-hou in https://github.com/INM-6/multi-area-model/pull/51
  • Improve firing rate plot by @didi-hou in https://github.com/INM-6/multi-area-model/pull/52
  • Synaptic weight and k scaling by @didi-hou in https://github.com/INM-6/multi-area-model/pull/53
  • Fix error computing correlation by @didi-hou in https://github.com/INM-6/multi-area-model/pull/54
  • Reproducibility by @mlober in https://github.com/INM-6/multi-area-model/pull/57
  • Color scheme interareal connectivity by @didi-hou in https://github.com/INM-6/multi-area-model/pull/56
  • Instantaneous firing rate across all areas by @didi-hou in https://github.com/INM-6/multi-area-model/pull/58
  • Parameter setting for down-scaled MAM by @didi-hou in https://github.com/INM-6/multi-area-model/pull/59
  • Bug fixing, code and text improving by @didi-hou in https://github.com/INM-6/multi-area-model/pull/60
  • Functional connectivity by @didi-hou in https://github.com/INM-6/multi-area-model/pull/61
  • Plots enhancing by @didi-hou in https://github.com/INM-6/multi-area-model/pull/62
  • Notebook documentation by @didi-hou in https://github.com/INM-6/multi-area-model/pull/63
  • Test suite by @didi-hou in https://github.com/INM-6/multi-area-model/pull/66
  • Remove Harden Runner by @didi-hou in https://github.com/INM-6/multi-area-model/pull/67
  • Code cleaning and documentation by @didi-hou in https://github.com/INM-6/multi-area-model/pull/64
  • Fix the bug due to deprecation of np.float by @didi-hou in https://github.com/INM-6/multi-area-model/pull/65
  • CI test on EBRAINS by @didi-hou in https://github.com/INM-6/multi-area-model/pull/68
  • Fix package python-louvain by @didi-hou in https://github.com/INM-6/multi-area-model/pull/69
  • fix np.float deprecated by @didi-hou in https://github.com/INM-6/multi-area-model/pull/70
  • Correct the areas order in the plot of functional connectivity by @didi-hou in https://github.com/INM-6/multi-area-model/pull/71
  • Remove louvain_communities dependence in mam-notebook by @shimoura in https://github.com/INM-6/multi-area-model/pull/72
  • add except ValueError in VisualCortex_Data.py by @shimoura in https://github.com/INM-6/multi-area-model/pull/73

Full Changelog: https://github.com/INM-6/multi-area-model/compare/v1.1.1...v1.2.0

- Python
Published by shimoura almost 2 years ago

multi-area-model - MAM v1.1.1

The release MAM 1.1.1 brings a number of improvements and new features, which enhance the model's reliability, usability, and overall user experience.

Check out more details in Pull requests #43

New features

  • Visualizing convolved rate time series in resting state plots

Enhancements

  • Added tests/.ipynb_checkpoints/* in .gitignore to ignore checkpoints
  • Add modules M2E_compute_corrcoeff.py and M2E_compute_rate_time_series.py
  • Module renamed: M2E_LOAD_DATA to M2E_load_data.py, M2E_visualize_instantaneous_and_mean_firing_rates.py to M2E_visualize_firing_rates.py

Bug fixes

  • Fixed bug in multiarea_model/analysis.py by changing DataFrame.append to DataFrame.concat as pandas deprecated the former syntax. It's done to be compatible with EBRAINS-23.09-rc2

- Python
Published by shimoura over 2 years ago

multi-area-model - MAM 1.1.0

The release MAM 1.1.0 brings a number of improvements and new features, which enhance the model's reliability, usability, and overall user experience. It also serves as a base version that specifies the dependencies required to run on EBRAINS for our future releases up to and including MAM 2.0.0.

For detailed changes made in this release since our last release MAM 1.0.0, please check our version log.

- Python
Published by shimoura over 2 years ago

multi-area-model - MAM 1.0.0

This code implements the spiking network model of macaque visual cortex developed at the Institute of Neuroscience and Medicine (INM-6), Research Center Jülich.

The model has been documented in the following publications:

  1. Schmidt M, Bakker R, Hilgetag CC, Diesmann M & van Albada SJ Multi-scale account of the network structure of macaque visual cortex Brain Structure and Function (2018), 223: 1409 https://doi.org/10.1007/s00429-017-1554-4

  2. Schuecker J, Schmidt M, van Albada SJ, Diesmann M & Helias M (2017) Fundamental Activity Constraints Lead to Specific Interpretations of the Connectome. PLOS Computational Biology, 13(2): e1005179. https://doi.org/10.1371/journal.pcbi.1005179

  3. Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018) A multi-scale layer-resolved spiking network model of resting-state dynamics in macaque cortex. PLOS Computational Biology, 14(9): e1006359. https://doi.org/10.1371/journal.pcbi.1006359

The code in this repository is self-contained and allows one to reproduce the results of all three papers.

The code was improved since the above publications to function with more modern versions of NEST (3+) as well as other minor updates.

- Python
Published by morales-gregorio over 2 years ago