Architecture of BIOS workspace @ SURFsara's RSC

Use of SURFconnext

You can log into all service components described here with your own institutional account thanks to the support of SURFconnext except for the access to the actual workspace where you will be using a Time based password.

Step 1: Configuration of SBS BBMRIomics CO

• After you get invitation to this CO, log into ​https://sbs.pilot.scz.lab.surf.nl using your institutional credential (using "Login via SURFconnext") to verify you are a member of RSC-BIOS CO.
• Optionally if you will need to access the workspace via Linux terminal, you can set up your SSH key in your user profile section.

Step 2: Configuration of Researchdrive

• You will get an invitation email to join Researchdrive. After that, try to log into ​https://researchdrive.surfsara.nl using your institutional credential. Choose "Login via SURFconnext". You may get an error message saying "Oops! Your SURF Research Drive account with email address <xxxx> and account <yyyyyy>-lumcnet@… could not be found. It seems that you do not have permission to use SURF Research Drive. Please contact the IT department of your institution or data steward of your project to request access to SURF Research Drive.". In this case, please forward this message to Leon Mei to so that he can properly share the datasets.
• You should see a shared folder called "RSC_BIOS". There are two sub-directories: RP3_data and RP3_analysis. This folder is read-only and contains the prepared BBMRIomics data for downstream analysis.
  • If you don't see this shared folder, please contact Leon Mei.
• You can also request the creation of a personal folder. This folder is your own personal storage place and you can write to (e.g., to create further directory structure). Please contact Leon Mei for this. Once it is created, you should see it directly under your Researchdrive. This folder is actually a writable short-cut to your personal folder under RSC_BIOS/Users. However you can't write to it via the path consisting RSC_BIOS/Users.
• Please be aware that there is no backup support of your data stored at Researchdrive, so make sure you arrange proper backup of your scripts and data yourself.

Step 3: Installation and configuration of authenticator on your mobile phone

• You need to install an authenticator app on your mobile phone, e.g., from ​Google appstore or ​Apple appstore.

Step 4: Configuration of your account at Research Cloud

• Log into ​https://portal.rsc-pilot2.surfresearchcloud.nl/ using your institutional credential
• Click "My Profile" in the top right corner to configure the following.
  • Load your collaborative organisations so that you will see RSC-BBMRI CO in your list
  • Link Researchdrive by following the ​https://researchclouddocs.readthedocs.io/en/latest/account_setup.html#personal-research-drive-identity-link
  • Set up time based password by following the ​instructions
• Additional documentations about RSC: ​https://researchclouddocs.readthedocs.io/en/latest/index.html

Step 5: Launch or access a BBMRIomics workspace

• In the main dashboard of Research Cloud, click "Create new workspace" and follow the instructions to configure and start a new workspace.
  • And about the expiration date, please try to keep a cost efficient timeline. If the VM is running without doing any jobs, it is a waste of our project resource!!'''
• If you don't have budget or sufficient space on your researchdrive anymore, you can also click "Request" button in the "Budget" tab to apply for more resources.
• As a member of the same CO, you can also access a running workspace created by another member in the same CO provided the owner agrees.
• After you log into the Rstudio UI, you can run the following commands to verify if you have proper access to the BBMRIomics data.

  library(BBMRIomics)
  data(package="BBMRIomics")
  bbmri.data("rp3_rp4_meta")
  head(person)
  

• More user documents about the BBMRIomics package can be found at ​https://bbmri-nl.github.io/BBMRIomics/usage.html

Detailed user guide to create a BBMRIomics workspace with screenshots