Last modified by ldomide on 2024/04/08 12:55
From version 39.1
edited by dionperd
on 2024/04/08 12:44
Change comment: There is no comment for this version
To version 31.1
edited by dionperd
on 2023/09/26 18:42
Change comment: There is no comment for this version

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20 20  * TVB Dedicated Wiki [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/>>url:https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain/]]
21 21  * TVB in HBP User Story [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/>>url:https://wiki.ebrains.eu/bin/view/Collabs/user-story-tvb/]]
22 22  
23 +(% class="wikigeneratedid" %)
23 23  == ==
24 24  
26 +(% class="wikigeneratedid" %)
25 25  == Running TVB-MULTISCALE at EBRAINS JupyterLab ==
26 26  
27 -TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]].
29 +TVB-multiscale is made available at [[EBRAINS JupyterLab>>https://lab.ebrains.eu/]]. All the user has to do is login with the EBRAINS credentials, and start a Python console or a Jupyter notebook, TVB-multiscale being available for importing (e.g., via "import tvb_multiscale"). All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available. We suggest the users to upload [[documented notebooks>>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/docs/notebooks]] and/or [[examples' scripts and notebooks >>https://github.com/the-virtual-brain/tvb-multiscale/tree/master/examples]]from TVB-multiscale Github repository and run them there.
28 28  
29 -All the user has to do is log in with their EBRAINS credentials, and start a Python console or a Jupyter notebook using the kernel "EBRAINS-23.09" (or a more recent version), where TVB-multiscale can be imported (e.g., via "import tvb_multiscale"). All necessary TVB-multiscale dependencies (NEST, ANNarchy, NetPyNE (NEURON), Elephant, Pyspike) are also installed and available.
30 30  
31 -This collab contains various examples of using TVB-Multiscale with all three supported spiking simulators. We suggest copying the contents of this collab to your Library or to any collab owned by you, and running them there (note that the user's drive offers persistent storage, i.e. users will find their files after logging out and in again), as follows:
32 +== Use our Jupyter Hub setup online ((% style="color:#c0392b" %)DEPRECATED(%%)) ==
32 32  
33 -~1. Select `Drive` on the left of the current page (or use [[this link>>https://wiki.ebrains.eu/bin/view/Collabs/the-virtual-brain-multiscale/Drive||rel="noopener noreferrer" target="_blank"]]).
34 +(% style="color:#c0392b" %)**TVB-multiscale app is deprecated and will stop being available after the end of 2023!**
34 34  
35 -2. Check the `tvb-multiscale-collab` folder checkbox, and copy it to your `My Library` ("copy" icon will appear above the files/folders list).
36 +We have setup a Jupyter Hub service with tvb-multiscale as backed already prepared. You will only need an HBP account for accessing this: [[https:~~/~~/tvb-multiscale.apps.hbp.eu/>>https://tvb-multiscale.apps.hbp.eu/]]
36 36  
37 -3. Select `Lab` (on the left), and navigate to the destination where you just copied the folder.
38 +This JupyterHub installation works smoothly with HBP Collab user credentials (login only once at HBP and get access here too). We use a custom Docker Hub tvb-multiscale image as a backend, and thus a ready to use environment is available immediately, without the need of any local installation or download. This should be the ideal env for demos, presentations or even workshops with tvb-multiscale.
38 38  
39 -4. Enter the `tvb-multiscale-collab` folder, and open either of example notebooks. Ensure you select the appropriate ipykernel (EBRAINS-23.09 or a more recent one)
40 +**[[image:https://lh6.googleusercontent.com/ytx9eYpMcL3cCScX2_Sxm4CeBW0xbKW3xKsfO2zSId10bW0gw1kiN2_SkexyYBCsF-sKsu0MaJC4cZvGVfQPjMoPBLiePbkvXOZd8BgY3Q0kFzSkRCqQ183lgDQv_6PYoqS3s7uJ||height="149" width="614"]]**
40 40  
42 +Currently, the users can access 2 folders: //TVB-*-Examples// and //Contributed-Notebooks//.
41 41  
44 +The notebooks under **TVB-*-Examples** are public, shared by everyone accessing the instance. Periodically, we will clean all changes under TVB-*-Examples folder (by redeploying the pod image), and show the original example notebooks submitted on our Github repo. If users intend to contribute here, they are encouraged to submit changes through Pull Requests ([[https:~~/~~/github.com/the-virtual-brain/tvb-multiscale>>url:https://github.com/the-virtual-brain/tvb-multiscale]])
45 +
46 +**[[image:https://lh6.googleusercontent.com/nnsM0mhXQinmQsJwZwwwe5Sx7f-tZc8t4ELnCh9DwksyVEPUE-jixJTkhoP4l25VKwlDGoXACWtnuxQM9NMOCYbQOzDesgMDlT3sntow___vsEqRVd4OwqMY4BPyBiLJ32BnUbmM||height="267" width="614"]]**
47 +
48 +Folder **Contributed-Notebooks** is not shared. Here, users can experiment with their own private examples. This folder is persisted on restarts in the user HBP Collab personal space. Thus, users will be able to access their work even after a redeploy. (e.g. during a workshop every participant could have in here his own exercise solution)
49 +
50 +
42 42  == Running TVB-MULTISCALE locally ==
43 43  
44 44  See more on Github [[https:~~/~~/github.com/the-virtual-brain/tvb-multiscale>>url:https://github.com/the-virtual-brain/tvb-multiscale]] .
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47 47  
48 48  This is the path recommended for people working closely with tvb-multiscale. They are able to download it in their local work env and code freely and fast with it.
49 49  
59 +(% class="wikigeneratedid" %)
50 50  == ==
51 51  
52 52  == Running TVB-MULTISCALE jobs on CSCS infrastructure from HBP collab ==