Changes for page TVB EBRAINS hands-on

Last modified by petkoski on 2026/10/06 20:56
From version 20.7
edited by petkoski
on 2025/09/06 14:12
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To version 24.1
edited by petkoski
on 2026/10/06 20:55
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1 -TVB EBRAINS Baltic-Nordic school 2024
1 +TVB EBRAINS hands-on
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14 14  (((
15 15  = What can I find here? =
16 16  
17 -This collab contains access to the notebooks and reading materials that will be used during the EBRAINS Baltic-Nordic summer school 2024 [[https:~~/~~/lsmu.lt/en/events/ebrains/>>https://lsmu.lt/en/events/ebrains/]] and now recycled for the TVB tutorials at [[ICANN 2025>>https://e-nns.org/icann2025/]] conference.
17 +This collab contains access to notebooks and reading materials for TVB that were used at various events, such as EBRAINS Baltic-Nordic summer school 2024 [[https:~~/~~/lsmu.lt/en/events/ebrains/>>https://lsmu.lt/en/events/ebrains/]], [[ICANN 2025>>https://e-nns.org/icann2025/]] conference, and at the EnvironMENTAL project's [[Summer School on environmental and computational neuroscience>>https://www.environmental-project.org/participants/environmental-summer-school-environmental-and-computational-neuroscience/]].
18 18  
19 19  The objective is to give to the participants an overview to building whole-brain network models with TVB.
20 20  
21 -We will begin with the [[First steps of TVB>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/1_TVB_First_steps.ipynb||style="background-color: rgb(255, 255, 255);"]], where we will describe the building blocks of TVB through the paradigm of resting state activity.
21 +We will begin with the [[First steps of TVB>>https://lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20hands-on/1_TVB_First_steps.ipynb||style="background-color: rgb(255, 255, 255);"]], where we will describe the building blocks of TVB through the paradigm of resting state activity.
22 22  
23 -This will be followed by [[Modelling Epilepsy>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/2_TVB_Modelling_Epilepsy.ipynb||style="background-color: rgb(255, 255, 255);"]], where seizure propagation will be modeled.
23 +This will be followed by [[Modelling Epilepsy>>https://lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20hands-on/2_TVB_Modelling_Epilepsy.ipynb||style="background-color: rgb(255, 255, 255);"]], where seizure propagation will be modeled.
24 24  
25 -Then, there is one tutorial describing a deeper analysis of [[BOLD monitors>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/3_TVB_BOLD_digging_deeper.ipynb||style="background-color: rgb(255, 255, 255);"]].
25 +Then, there is one tutorial describing a deeper analysis of [[BOLD monitors>>https://lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20hands-on/3_TVB_BOLD_digging_deeper.ipynb||style="background-color: rgb(255, 255, 255);"]].
26 26  
27 -There is also a fourth tutorial which describes application of a fast back-end implementation of the Montbrio-Pazo-Roxin model used for modeling [[resting state fMRI >>https://lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20Baltic-Nordic%20school%202024/MPR_rs.ipynb]]. This is a based on a more detailed showcase [[Degeneracy in neuroscience>>https://wiki.ebrains.eu/bin/view/Collabs/sga3-d1-5-showcase-1/]],  which described the interpersonal variability analyzed by the [[Virtual Ageing Brain>>https://www.sciencedirect.com/science/article/pii/S1053811923005542?via%3Dihub]] study.
27 +There is also a fourth tutorial which describes application of a fast back-end implementation of the Montbrio-Pazo-Roxin model used for modeling [[resting state fMRI >>https://lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20hands-on/MPR_rs.ipynb]]. This is a based on a more detailed showcase [[Degeneracy in neuroscience>>https://wiki.ebrains.eu/bin/view/Collabs/sga3-d1-5-showcase-1/]],  which described the interpersonal variability analyzed by the [[Virtual Ageing Brain>>https://www.sciencedirect.com/science/article/pii/S1053811923005542?via%3Dihub]] study.
28 28  
29 29  
30 -Finally, the collab contains one tutorial where a [[Bayesian approach>>https://wiki.ebrains.eu/bin/view/Collabs/ebrains-task-3-3/Drive#notebooks/EITN_tutorial||style="background-color: rgb(255, 255, 255);"]] is used on synthetic data to infer the posterior of the parameters for a single brain region.
30 +For more advanced applications, TVB with neuromodulation, through the example of dopaminergic D1 neuromodulation, is available at [[https:~~/~~/search.kg.ebrains.eu/?category=Model&q=preti#49cea23b-97f6-4525-bdb3-aafe70490624>>https://search.kg.ebrains.eu/?category=Model&q=preti#49cea23b-97f6-4525-bdb3-aafe70490624]] and [[https:~~/~~/github.com/giapre/dopamine_model>>https://github.com/giapre/dopamine_model]] . The github contains the model and several usecases based on //jax// implementation that is verified with the standard TVB.
31 31  
32 32  
33 +The collab also contains one tutorial where a [[Bayesian approach>>https://lab.jsc.ebrains.eu/hub/user-redirect/lab/tree/shared/TVB%20EBRAINS%20hands-on/DCM_ERPs_MCMC_ebrains.ipynb||style="background-color: rgb(255, 255, 255);"]] is used on synthetic data to infer the posterior of the parameters for a **single brain region**.
34 +
35 +
33 33  These can all be found in the drive and accessed through the lab.
34 34  
35 35  = Requirements =