diff --git a/.gitignore b/.gitignore
index 4cee63c1aff28338384d5a85afdf18906c970991..d35f0f811121541ec3348aa472337f86e773d8b8 100644
--- a/.gitignore
+++ b/.gitignore
@@ -21,3 +21,5 @@ figures/Schmidt2018/.ipynb_checkpoints/*
figures/Schmidt2018_dyn/.ipynb_checkpoints/*
multiarea_model/.ipynb_checkpoints/*
+
+multiarea_model/data_multiarea/.ipynb_checkpoints/*
diff --git a/VERSION_LOG.md b/VERSION_LOG.md
new file mode 100644
index 0000000000000000000000000000000000000000..798f5bcbb7725eb5f2bf6ec3a8eec81679008c6b
--- /dev/null
+++ b/VERSION_LOG.md
@@ -0,0 +1,49 @@
+## MAM v1.1.0
+
+### New features
+
+* Improved documentation: added in the README.md file the Try It On EBRAINS button and clear and detailed User instruction for users to be able to follow step-by-step instructions without much background knowledge or experience, delete section Testing on EBRAINS
+
+* In down-scale multi-area mode, separated all external parameters to Parameters to tun and Default parameters. Parameters to tune consist of 4 parameters we decided to expose to users initially, and default parameters will be tuned by us and are not recommended for users to change
+
+* Added section Extract and visualize interareal connectivity which plots the area-level relative connectivity as heatmaps. Two heatmaps represent the interareal connectivity of full-scale multi-area model (left) and down-scale multi-area model (right). There are small differences between them although we’re calculating relative connectivity as there’s randomness
+
+* Added section Simulation Results Visualization. The code is written in separate modules saved as .py files in “./figures/MAM2EBRAINS†to avoid displaying contents that are not relevant to users
+
+* Added 3 plots in the section Simulation Results Visualization
+ * 3.1. Instantaneous and mean firing rate across all populations (existed in MAM v1.0.0, refined in MAM v1.1.0)
+ * 3.2 Resting state plots
+ * 3.3 Time-averaged population rates
+
+* The 3.2 Resting state plots figure is plotted based on Fig 5. of the paper 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, yet there are a few differences:
+ * This plot provides the option for users to choose 3 areas to plot the raster plots instead of fixing V1, V2, and FEF to plot
+ * The subplot E Correlation coefficient is replaced as Synchrony
+ * The subplot G only plots the binned spike histograms (gray), not the convolved histograms (black)
+
+### Enhancements
+
+* Reconstructed the Jupyter Notebook and added Notebook structure as table of contents that enables users to navigate quickly and easily between different sections. (see the notebook structure for details)
+
+* Added detailed and easy-to-understand descriptions to the 4 exposed parameters and also brief comments for the default parameters
+
+* Added the model overview diagram and a short description of the down-scaled multi-area model at the beginning of the jupyter notebook
+
+* Added descriptions of comparable figures in our publications whenever available so that users can compare the down-scaled model with their costumed parameters and the full-scaled model presented in the paper
+
+* Removed unnecessary print statements in ./multiarea_model/analysis.py and ./multiarea_model/analysis_helpers.py to avoid multiple print that are not relevant to users
+
+* Updated ./.gitignore file to ignore checkpoint files
+
+### Bug fixes
+
+* Corrected the separator from "" to "/" in ./multiarea_model/data_multiarea/SLN_logdensities.R to fix the file path of ./multiarea_model/data_multiarea/bbAlt.R
+
+* Fixed bugs in ./multiarea-model/analysis.py: change np.nan*np.ones(params['t_max'] - params['t_min']) to np.nan*np.ones(int(params['t_max'] - params['t_min']))
+
+
+## MAM v1.0.0
+
+### Bug fixes
+* Corrected the URL of NEST logo in README.md
+
+
diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
index 743ce9739c7ce5ab529c0d0117680ec521eb6831..85f153c7b4496e65ac83f14db1588de89263696a 100644
--- a/multi-area-model.ipynb
+++ b/multi-area-model.ipynb
@@ -509,7 +509,7 @@
"output_type": "stream",
"text": [
"Initializing network from dictionary.\n",
- "RAND_DATA_LABEL 7110\n"
+ "RAND_DATA_LABEL 7968\n"
]
},
{
@@ -591,72 +591,72 @@
"text": [
"Prepared simulation in 0.00 seconds.\n",
"Rank 0: created area V1 with 0 local nodes\n",
- "Memory after V1 : 1515.14 MB\n",
+ "Memory after V1 : 1516.25 MB\n",
"Rank 0: created area V2 with 0 local nodes\n",
- "Memory after V2 : 1541.85 MB\n",
+ "Memory after V2 : 1542.84 MB\n",
"Rank 0: created area VP with 0 local nodes\n",
- "Memory after VP : 1571.02 MB\n",
+ "Memory after VP : 1572.02 MB\n",
"Rank 0: created area V3 with 0 local nodes\n",
- "Memory after V3 : 1599.30 MB\n",
+ "Memory after V3 : 1600.25 MB\n",
"Rank 0: created area V3A with 0 local nodes\n",
- "Memory after V3A : 1619.24 MB\n",
+ "Memory after V3A : 1620.27 MB\n",
"Rank 0: created area MT with 0 local nodes\n",
- "Memory after MT : 1644.78 MB\n",
+ "Memory after MT : 1645.80 MB\n",
"Rank 0: created area V4t with 0 local nodes\n",
- "Memory after V4t : 1669.75 MB\n",
+ "Memory after V4t : 1670.73 MB\n",
"Rank 0: created area V4 with 0 local nodes\n",
- "Memory after V4 : 1696.68 MB\n",
+ "Memory after V4 : 1697.67 MB\n",
"Rank 0: created area VOT with 0 local nodes\n",
- "Memory after VOT : 1721.41 MB\n",
+ "Memory after VOT : 1722.37 MB\n",
"Rank 0: created area MSTd with 0 local nodes\n",
- "Memory after MSTd : 1741.30 MB\n",
+ "Memory after MSTd : 1742.29 MB\n",
"Rank 0: created area PIP with 0 local nodes\n",
- "Memory after PIP : 1762.64 MB\n",
+ "Memory after PIP : 1763.63 MB\n",
"Rank 0: created area PO with 0 local nodes\n",
- "Memory after PO : 1784.18 MB\n",
+ "Memory after PO : 1785.13 MB\n",
"Rank 0: created area DP with 0 local nodes\n",
- "Memory after DP : 1804.32 MB\n",
+ "Memory after DP : 1805.43 MB\n",
"Rank 0: created area MIP with 0 local nodes\n",
- "Memory after MIP : 1825.89 MB\n",
+ "Memory after MIP : 1826.88 MB\n",
"Rank 0: created area MDP with 0 local nodes\n",
- "Memory after MDP : 1847.39 MB\n",
+ "Memory after MDP : 1848.38 MB\n",
"Rank 0: created area VIP with 0 local nodes\n",
- "Memory after VIP : 1869.36 MB\n",
+ "Memory after VIP : 1870.34 MB\n",
"Rank 0: created area LIP with 0 local nodes\n",
- "Memory after LIP : 1893.33 MB\n",
+ "Memory after LIP : 1894.24 MB\n",
"Rank 0: created area PITv with 0 local nodes\n",
- "Memory after PITv : 1918.53 MB\n",
+ "Memory after PITv : 1919.55 MB\n",
"Rank 0: created area PITd with 0 local nodes\n",
- "Memory after PITd : 1943.70 MB\n",
+ "Memory after PITd : 1944.77 MB\n",
"Rank 0: created area MSTl with 0 local nodes\n",
- "Memory after MSTl : 1965.03 MB\n",
+ "Memory after MSTl : 1965.95 MB\n",
"Rank 0: created area CITv with 0 local nodes\n",
- "Memory after CITv : 1983.83 MB\n",
+ "Memory after CITv : 1984.88 MB\n",
"Rank 0: created area CITd with 0 local nodes\n",
- "Memory after CITd : 2003.14 MB\n",
+ "Memory after CITd : 2004.21 MB\n",
"Rank 0: created area FEF with 0 local nodes\n",
- "Memory after FEF : 2024.65 MB\n",
+ "Memory after FEF : 2025.55 MB\n",
"Rank 0: created area TF with 0 local nodes\n",
- "Memory after TF : 2040.28 MB\n",
+ "Memory after TF : 2041.22 MB\n",
"Rank 0: created area AITv with 0 local nodes\n",
- "Memory after AITv : 2062.86 MB\n",
+ "Memory after AITv : 2063.93 MB\n",
"Rank 0: created area FST with 0 local nodes\n",
- "Memory after FST : 2079.55 MB\n",
+ "Memory after FST : 2080.65 MB\n",
"Rank 0: created area 7a with 0 local nodes\n",
- "Memory after 7a : 2100.87 MB\n",
+ "Memory after 7a : 2101.82 MB\n",
"Rank 0: created area STPp with 0 local nodes\n",
- "Memory after STPp : 2119.46 MB\n",
+ "Memory after STPp : 2120.56 MB\n",
"Rank 0: created area STPa with 0 local nodes\n",
- "Memory after STPa : 2138.71 MB\n",
+ "Memory after STPa : 2139.57 MB\n",
"Rank 0: created area 46 with 0 local nodes\n",
- "Memory after 46 : 2154.03 MB\n",
+ "Memory after 46 : 2155.02 MB\n",
"Rank 0: created area AITd with 0 local nodes\n",
- "Memory after AITd : 2176.71 MB\n",
+ "Memory after AITd : 2177.61 MB\n",
"Rank 0: created area TH with 0 local nodes\n",
- "Memory after TH : 2189.28 MB\n",
- "Created areas and internal connections in 2.05 seconds.\n",
- "Created cortico-cortical connections in 20.48 seconds.\n",
- "Simulated network in 71.65 seconds.\n"
+ "Memory after TH : 2190.27 MB\n",
+ "Created areas and internal connections in 2.20 seconds.\n",
+ "Created cortico-cortical connections in 20.14 seconds.\n",
+ "Simulated network in 77.14 seconds.\n"
]
}
],