1 The IFB cloud?

The IFB (Institut Français de Bioinformatique) cloud enables powerful computers to be shared between all users. Each user can use one of these computers, called instances, and configure it as he or she sees fit.

The configuration of an instance includes:

its content (pre-installed softwares, operating system, etc.)
its computing power (CPU and RAM)
its storage

When the user shutdown one of his instances, the modifications made on the instance (installed software, …) are lost as well as the data that have been added on the storage associated to the VM (mydatalocal).

A permanent storage can be attached to a VM if your belong to a group. This storage will be shared between all the member of the group. It will not be deleted when a VM is shut down and will be automatically connected to each of your VMs.

We will use this particularity to store your data between distant sessions. This permanent storage will appear as a directory called ueens_lyon_ngs24 in your VM.

To access it, go to: https://biosphere.france-bioinformatique.fr

Note

The IFB principle is to use computation resources shared by all users. So remember to:

Turn off the instances that you are not using in order not to block the computation resources so that other users can use them.
Store your data on your own hard disk before turning off your instance else they will be lost. (Except if they are on a permanent storage)

Warning: do not switch off your instance without consulting the TP supervisors!

We will connect to the virtual machines via your web browser. Disconnecting to your VM from your web browser will not shut it down. It will continue to run.

2 Create your own account on the IFB cloud

To create your IFB cloud account:

go to https://biosphere.france-bioinformatique.fr/
at the top right, click on login.
click again on login
click on accept conditions
select ENS de Lyon
identify yourself with your ENS login and password
Fill in your name, first name, city and postal code, leaving all other information as default and accept.
You’ll get a new page. In the top right-hand corner, click on the little man icon, then on group.
Click on Join a group in the tabs at top left.
Search for the group UE ENS-Lyon NGS 2024 (COURS Master Biologie ENS-Lyon - UE Practicals in next generation sequencing 2024) and click on the + button to apply.
and you’re all set! Now we (trainers) need to validate your application

3 Connecting to the IFB cloud

To connect to the IFB cloud, go to https://biosphere.france-bioinformatique.fr and click on connect.

Choose the ENS de Lyon from the list of institutions, then use your ENS login and password.

NB: Your cloud login is your e-mail address.

4 Create your own instance

To start an instance, go to the RAINbio catalog (top left), select it and click on “Configure” (wrench symbol / icone clef à molette).

For the practical work, you will use the “UE NGS-ENS Lyon” image. Select it.
When you click on “Configure”, you have 4 fields to fill in:
1. Name: TP_prénom_groupe
2. Group: UE ENS-Lyon NGS 2024
3. Cloud : meso-psmn-cirrus
4. Template: Ask supervisors
Then click on launch and go to the myVM panel (top left)
Your new VM has appeared in the “Deployments” frame. However the deployment may take > 20 min (on the left, the blue hourglass will be replaced by a green dot).
Then, you will be able to retrieve the login information in the access column
By clicking on the ID of your machine, you will have access to the address, the login and the password of your machine.
Click on https to be redirected to your machine.

- If your machine deployment encounters an error, try again.

5 Connecting to an instance

To connect to an instance, you need 3 pieces of information:

A login: “rstudio
A password: to be retrieved from the biosphere portal (specific to each instance) by clicking on Params ex: o6l5gPYkxMrt5
An ip address: retrieved from the biosphere portal (specific to each instance) by clicking on https ex: 134.214.213.63

Click on https on the biosphere portal (or copy the IP address into your browser’s URL bar) and enter your login and password. :::{.callout-warning} # Warning n°1 - You must accept the security warning to access the machine. - If you’re using firefox, firefox may not want to override the security warning, so you’ll need to use another browser, e.g. Chrome. :::

Warning n°2

Work only in the mydatalocal folder, which contains the storage associated with your machine