## Using dedicated CBPsmn resources through IFB cloud (temporary tutorial - to be completed)
For analyzing single-cell RNASeq and Spatial Transcriptomics data, Spatial-Cell-ID users can exploit [CBMPsmn](https://www.ens-lyon.fr/PSMN/doku.php?id=accueil%3Apresentation) dedicated resources through the [IFB Cloud Biosphere](https://biosphere.france-bioinformatique.fr/).
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@@ -39,9 +38,10 @@ To do that:
1. Click on `RAINBio` at the top left.
2. Select the appliance that you want (for example `Spatial-Cell-ID Jupyter` for working with Python).
2. Select the appliance that you want (for example `Spatial-Cell-ID Jupyter` for working with Python, and `Spatial-Cell-ID-RStudio` for working with R or with the terminal.
Note: `Spatial-Cell-ID-RStudio` is not yet available; we are awaiting validation by IFB. In the meanwhile, you can use `UE NGS-ENS Lyon` for working with R or the terminal).
3. Click ``RUN`` at the top right and then select `ADVANCED CONFIGURATION AND START`
3. Click ``RUN`` at the top right and then select `ADVANCED CONFIGURATION AND START`.
4. Choose a name for your VM, select `Spatial-Cell-ID` as the Group to use, `meso-psmn-cirrus` as the Cloud, and choose the appropriate Cloud flavor for your analysis (I would suggest _standard.4c16g_, which should be sufficient for most of the analysis).
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@@ -49,10 +49,12 @@ To do that:
6. Wait for the appliance to start. At some point, you will see that Access will have two options: `https` and `params`. Click on `params` to view the user ID and password, then click on `https` to connect to the virtual machine using the user ID and password you just obtained.
7. That's it! Your virtual machine is ready, and you will find everything in your environment and you will have access to a high performing computer.
7. You could also need to deploy a whole remote desktop computer with Ubuntu installed on it (this is the case, for example, of the appliance `Ubuntu 22.04 Desktop`. Then, you will need the client _X2Go_. Please, refer to the [IFB documentation](https://ifb-elixirfr.github.io/biosphere/vm_connect) on how to do that).
8. That's it! Your virtual machine is ready, and you will find everything in your environment and you will have access to a high performing computer.
### Important remark
When you terminate your virtual machine by clicking on `Terminating deployments`, your data will be lost.
You can shut down your local computer and close the web browser tab where the virtual machine is without losing your data and accessing again your virtual machine in the section `MyVM`, but if terminate the deployment without saving your data and scripts, everything will be lost. Uploading and downloading data is intuitive, but feel free to ask for help if needed.
