diff --git a/4_TVB_Modelling_Epilepsy.ipynb b/4_TVB_Modelling_Epilepsy.ipynb
index 1f29acffea9b2e995176811f211cb20bbba0f866..b896441510abefb188f8fb2bb300d8cb06c2636d 100644
--- a/4_TVB_Modelling_Epilepsy.ipynb
+++ b/4_TVB_Modelling_Epilepsy.ipynb
@@ -11,7 +11,7 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "**EBRAINS & IBRO First Virtual Master Class on Brain Atlasing and Simulation Services, July 29, 2021**"
+ "**EBRAINS & IBRO Second Virtual Master Class on Brain Atlasing and Simulation Services, September 3, 2021**"
]
},
{
@@ -50,7 +50,7 @@
"name": "stderr",
"output_type": "stream",
"text": [
- "Matplotlib created a temporary config/cache directory at /tmp/matplotlib-079i6xhd because the default path (/tmp/cache/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n"
+ "Matplotlib created a temporary config/cache directory at /tmp/matplotlib-dze_bazl because the default path (/tmp/cache/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.\n"
]
},
{
@@ -103,7 +103,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "f3e84e2d564543b19098d287a75562fc",
+ "model_id": "fda29b02dd764d289887c014db5ae0a7",
"version_major": 2,
"version_minor": 0
},
@@ -146,7 +146,7 @@
"<ul>\n",
"<li>We have here the <b>first population (variables $\\pmb{x_{1}}$ in abscissa and $\\pmb{y_{1}}$ in ordinate)</b>.\n",
"\n",
- "The left most intersection of the two nullclines defines a <b>stable fixed point</b>, representing the <b>interictal state (i.e., between seizures)</b>, whereas the right most intersection is the center of a <b>limit cycle</b>, being the <b>ictal state (i.e., during seizures)</b>. Both states are separated by a separatrix, as you can se by drawing different trajectories in this phase space <i>(left click on the figure)</i>.</li><br>\n",
+ "The left most intersection of the two nullclines defines a <b>stable fixed point</b>, representing the <b>interictal state (i.e., between seizures)</b>, whereas the right most intersection is the center of a <b>limit cycle</b>, being the <b>ictal state (i.e., during seizures)</b>. Both states are separated by a separatrix, as you can se by drawing different trajectories in this phase space.</li><br>\n",
"\n",
"<li>You can also have a look at other variables in the phase space, such as the <b>second population (variables $\\pmb{x_{2}}$ in abscissa and $\\pmb{y_{2}}$ in ordinate)</b>, responsible for the <b>interictal spikes</b> in the Epileptor model. Change the lower and upper bound of the axis to see correctly the phase space.</li>\n",
"\n",
@@ -162,7 +162,7 @@
{
"data": {
"application/vnd.jupyter.widget-view+json": {
- "model_id": "63d467be905a437184e6a202f751ad7f",
+ "model_id": "b65da7d40754411c974c9f6e86e5f5e2",
"version_major": 2,
"version_minor": 0
},
@@ -438,21 +438,21 @@
"<tbody>\n",
"<tr><td>Type</td><td style=\"text-align:left;\"><pre>Simulator</pre></td>\n",
"<tr><td>conduction_speed</td><td style=\"text-align:left;\"><pre>inf</pre></td>\n",
- "<tr><td>connectivity</td><td style=\"text-align:left;\"><pre>Connectivity gid: 623a2ce3-10b6-4fa4-abe2-9622bad2e2f3</pre></td>\n",
- "<tr><td>coupling</td><td style=\"text-align:left;\"><pre>Difference gid: 180b677f-100f-49f5-a925-bd26c1956b99</pre></td>\n",
- "<tr><td>gid</td><td style=\"text-align:left;\"><pre>UUID('2096df16-dc77-4747-b9f6-186c3f8e7179')</pre></td>\n",
+ "<tr><td>connectivity</td><td style=\"text-align:left;\"><pre>Connectivity gid: a75c4a61-a607-43fa-8ca7-b774c8bdfedc</pre></td>\n",
+ "<tr><td>coupling</td><td style=\"text-align:left;\"><pre>Difference gid: 1d6d66d0-3e5d-499b-b97a-008b159aac1a</pre></td>\n",
+ "<tr><td>gid</td><td style=\"text-align:left;\"><pre>UUID('e98e5e49-0d06-4b11-b71c-6a152d0210c3')</pre></td>\n",
"<tr><td>initial_conditions</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
- "<tr><td>integrator</td><td style=\"text-align:left;\"><pre>HeunStochastic gid: 3da5f168-b005-4c33-b85a-19072e4105b2</pre></td>\n",
- "<tr><td>model</td><td style=\"text-align:left;\"><pre>Epileptor gid: 07c578c9-d899-4201-b96a-799fcb2907d8</pre></td>\n",
- "<tr><td>monitors</td><td style=\"text-align:left;\"><pre>(<tvb.simulator.monitors.TemporalAverage object at 0x7f39a837df98>, <tvb.simulator.monitors.iEEG object at 0x7f39a837de48>)</pre></td>\n",
+ "<tr><td>integrator</td><td style=\"text-align:left;\"><pre>HeunStochastic gid: dcf4a589-6383-4a5d-93dc-010852a6d14f</pre></td>\n",
+ "<tr><td>model</td><td style=\"text-align:left;\"><pre>Epileptor gid: 715d5f28-3818-42f9-b071-b7239da0644c</pre></td>\n",
+ "<tr><td>monitors</td><td style=\"text-align:left;\"><pre>(<tvb.simulator.monitors.TemporalAverage object at 0x7f4b83037160>, <tvb.simulator.monitors.iEEG object at 0x7f4b82d6af60>)</pre></td>\n",
"<tr><td>simulation_length</td><td style=\"text-align:left;\"><pre>1000.0</pre></td>\n",
"<tr><td>stimulus</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
"<tr><td>surface</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
- "<tr><td>title</td><td style=\"text-align:left;\"><pre>Simulator gid: 2096df16-dc77-4747-b9f6-186c3f8e7179</pre></td>\n",
+ "<tr><td>title</td><td style=\"text-align:left;\"><pre>Simulator gid: e98e5e49-0d06-4b11-b71c-6a152d0210c3</pre></td>\n",
"</tbody></table>"
],
"text/plain": [
- "<tvb.simulator.simulator.Simulator at 0x7f39a857ce80>"
+ "<tvb.simulator.simulator.Simulator at 0x7f4baca77278>"
]
},
"execution_count": 13,
@@ -483,7 +483,7 @@
"text": [
"Starting simulation...\n",
"Finished simulation.\n",
- "execute for55.20747518539429\n"
+ "execute for57.97936129570007\n"
]
}
],
@@ -725,21 +725,21 @@
"<tbody>\n",
"<tr><td>Type</td><td style=\"text-align:left;\"><pre>Simulator</pre></td>\n",
"<tr><td>conduction_speed</td><td style=\"text-align:left;\"><pre>inf</pre></td>\n",
- "<tr><td>connectivity</td><td style=\"text-align:left;\"><pre>Connectivity gid: 623a2ce3-10b6-4fa4-abe2-9622bad2e2f3</pre></td>\n",
- "<tr><td>coupling</td><td style=\"text-align:left;\"><pre>Difference gid: df0e559f-c637-464f-8047-1531d4b07229</pre></td>\n",
- "<tr><td>gid</td><td style=\"text-align:left;\"><pre>UUID('39f86f24-d3a0-4469-9868-6b7c718ca57d')</pre></td>\n",
+ "<tr><td>connectivity</td><td style=\"text-align:left;\"><pre>Connectivity gid: a75c4a61-a607-43fa-8ca7-b774c8bdfedc</pre></td>\n",
+ "<tr><td>coupling</td><td style=\"text-align:left;\"><pre>Difference gid: c7cdb720-73ed-44de-ac37-5f600db46879</pre></td>\n",
+ "<tr><td>gid</td><td style=\"text-align:left;\"><pre>UUID('d82663a1-70a0-4d96-a43d-99001a0be5d6')</pre></td>\n",
"<tr><td>initial_conditions</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
- "<tr><td>integrator</td><td style=\"text-align:left;\"><pre>HeunStochastic gid: 675f92b6-a2f4-4efa-9eae-3f4361de4cc5</pre></td>\n",
- "<tr><td>model</td><td style=\"text-align:left;\"><pre>Epileptor gid: 0775ed7c-4066-475a-afe2-3891fc90af92</pre></td>\n",
- "<tr><td>monitors</td><td style=\"text-align:left;\"><pre>(<tvb.simulator.monitors.TemporalAverage object at 0x7f39a80af2e8>,)</pre></td>\n",
+ "<tr><td>integrator</td><td style=\"text-align:left;\"><pre>HeunStochastic gid: fee8c5ad-c7e6-4dce-bfad-fc631169e963</pre></td>\n",
+ "<tr><td>model</td><td style=\"text-align:left;\"><pre>Epileptor gid: a5859831-4aef-4ed6-80b0-387e50dbc1ec</pre></td>\n",
+ "<tr><td>monitors</td><td style=\"text-align:left;\"><pre>(<tvb.simulator.monitors.TemporalAverage object at 0x7f4b8299fb70>,)</pre></td>\n",
"<tr><td>simulation_length</td><td style=\"text-align:left;\"><pre>1000.0</pre></td>\n",
"<tr><td>stimulus</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
"<tr><td>surface</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
- "<tr><td>title</td><td style=\"text-align:left;\"><pre>Simulator gid: 39f86f24-d3a0-4469-9868-6b7c718ca57d</pre></td>\n",
+ "<tr><td>title</td><td style=\"text-align:left;\"><pre>Simulator gid: d82663a1-70a0-4d96-a43d-99001a0be5d6</pre></td>\n",
"</tbody></table>"
],
"text/plain": [
- "<tvb.simulator.simulator.Simulator at 0x7f39a80afc88>"
+ "<tvb.simulator.simulator.Simulator at 0x7f4b8299fcf8>"
]
},
"execution_count": 21,
@@ -770,7 +770,7 @@
"text": [
"Starting simulation...\n",
"Finished simulation.\n",
- "execute for 75.83453941345215\n"
+ "execute for 78.03332352638245\n"
]
}
],
@@ -982,21 +982,21 @@
"<tbody>\n",
"<tr><td>Type</td><td style=\"text-align:left;\"><pre>Simulator</pre></td>\n",
"<tr><td>conduction_speed</td><td style=\"text-align:left;\"><pre>3.0</pre></td>\n",
- "<tr><td>connectivity</td><td style=\"text-align:left;\"><pre>Connectivity gid: 623a2ce3-10b6-4fa4-abe2-9622bad2e2f3</pre></td>\n",
- "<tr><td>coupling</td><td style=\"text-align:left;\"><pre>Difference gid: 82171d0b-aad9-44ac-ab93-caa53e10b0a9</pre></td>\n",
- "<tr><td>gid</td><td style=\"text-align:left;\"><pre>UUID('e7b35cdb-3541-4253-ae11-f081f61e21b1')</pre></td>\n",
+ "<tr><td>connectivity</td><td style=\"text-align:left;\"><pre>Connectivity gid: a75c4a61-a607-43fa-8ca7-b774c8bdfedc</pre></td>\n",
+ "<tr><td>coupling</td><td style=\"text-align:left;\"><pre>Difference gid: f4691054-416b-4c53-a0d6-10aa38eefae3</pre></td>\n",
+ "<tr><td>gid</td><td style=\"text-align:left;\"><pre>UUID('5bf75fd6-9a6e-4d18-bd66-5a31738428a4')</pre></td>\n",
"<tr><td>initial_conditions</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
- "<tr><td>integrator</td><td style=\"text-align:left;\"><pre>HeunStochastic gid: 5f60212f-0641-4e73-b1b3-66e45604d387</pre></td>\n",
- "<tr><td>model</td><td style=\"text-align:left;\"><pre>Epileptor gid: ffd91ba7-19c9-41ab-8300-13bddcb1ecdf</pre></td>\n",
- "<tr><td>monitors</td><td style=\"text-align:left;\"><pre>(<tvb.simulator.monitors.TemporalAverage object at 0x7f39a7bbfdd8>,)</pre></td>\n",
+ "<tr><td>integrator</td><td style=\"text-align:left;\"><pre>HeunStochastic gid: 1a85c9ee-095c-4802-80d3-bd0b723d610a</pre></td>\n",
+ "<tr><td>model</td><td style=\"text-align:left;\"><pre>Epileptor gid: 38448ac8-f928-435d-8311-4dbed6072cc2</pre></td>\n",
+ "<tr><td>monitors</td><td style=\"text-align:left;\"><pre>(<tvb.simulator.monitors.TemporalAverage object at 0x7f4b827f2e10>,)</pre></td>\n",
"<tr><td>simulation_length</td><td style=\"text-align:left;\"><pre>1000.0</pre></td>\n",
- "<tr><td>stimulus</td><td style=\"text-align:left;\"><pre>StimuliRegion gid: 6b9da795-63b4-48c4-b1ea-3c2a0fb093f5</pre></td>\n",
+ "<tr><td>stimulus</td><td style=\"text-align:left;\"><pre>StimuliRegion gid: 9eca3948-ec49-4a86-8117-576002e8708e</pre></td>\n",
"<tr><td>surface</td><td style=\"text-align:left;\"><pre>None</pre></td>\n",
- "<tr><td>title</td><td style=\"text-align:left;\"><pre>Simulator gid: e7b35cdb-3541-4253-ae11-f081f61e21b1</pre></td>\n",
+ "<tr><td>title</td><td style=\"text-align:left;\"><pre>Simulator gid: 5bf75fd6-9a6e-4d18-bd66-5a31738428a4</pre></td>\n",
"</tbody></table>"
],
"text/plain": [
- "<tvb.simulator.simulator.Simulator at 0x7f39a7bbf278>"
+ "<tvb.simulator.simulator.Simulator at 0x7f4b827f2390>"
]
},
"execution_count": 29,
@@ -1034,7 +1034,7 @@
"text": [
"Starting simulation...\n",
"Finished simulation.\n",
- "execute for82.03099298477173\n"
+ "execute for82.26916146278381\n"
]
}
],