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Architecture of BIOS workspace @ SURFsara's RSC
Use of SURFconnext
You can log into all websites 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.
Procedure to obtain access to BBMRIomics workspace and datasets
Please follow the step-by-step manual below to start working on BBMRIomics datasets. A Code of Conduct document needs to be signed and you can contact Rick Jansen for this. If you have any question, please contact Leon Mei at LUMC.
Step 1: Request personal budget to for RC
- First, please log into https://servicedesk.surfsara.nl/ and fill in the form of "Small Applications".
- If you are a PhD student, the "Signing Authority" should be your supervisor's contact details.
- "SURF contact" is Martin Brandt
- "Resources" should be "HPC Cloud"
- CPU and GPU core hours can be filled in based on your specific needs. Normally we only need CPU and you could put the maximum number of hours of "50000" in this application.
- For storage, you can also request the maximum for SSD and Ceph and a reasonable amount for Research Drive.
Step 2: Configuration of SBS BBMRIomics CO
- After you get invitation to this CO, log into https://sbs.sram.surf.nl/ using your institutional credential (using "Login via SURFconnext") to verify you are a member of SRC-BBMRI CO.
- Optionally if you will need to access the workspace's Linux terminal, you can set up your SSH key in your user profile section.
Step 3: Configuration of Research Drive (RD)
- You will get an invitation email to join Research Drive. After that, 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" that contains the prepared BBMRIomics data for downstream analysis. They are read-only and you need to store the analysis results in your own personal space on RD.
- Please be aware that there is no backup support of your data stored at Research Drive, so make sure you arrange proper backup of your scripts and data yourself.
Step 4: Installation and configuration of authenticator on your mobile phone
- Research Cloud is using a so called Time-based One-time Password authentication (TOTP) for authentication.
- You need to install an authenticator app on your mobile phone, e.g., from Google appstore or Apple appstore.
- In this authenticator app, you will see a username and a numeric password (that is changing every minute). This username and password are used to log into the R-studio environment.
Step 5: Configuration of your account at Research Cloud
- Log into https://portal.live.surfresearchcloud.nl/ using your institutional credential
- If you don't have budget, you can click "Request a new wallet" to apply for more resources. You can put "SRC-BBMRI" as Subtitle and "EINF-1931" as Existing contract.
- Go to "Profile" tab using the navigation bar at the top of the page.
- Set up time based password in the "Profile" section by clicking the "more option" button. more details.
- Link Researchdrive in the "Collaborative organisations" section by by clicking "more option" button. more details
- Once your request to budget/new wallet gets approved, you can request your user specific persistent storage and fixed IP address. This persistent storage and IP resource can be used when you create a new workspace.
- Additional documentations about Research Cloud: https://servicedesk.surfsara.nl/wiki/display/WIKI/Research+Cloud+Documentation
Step 6: 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.
- About the expiration date, please try to keep a reasonable timeline. If the workspace is running without doing any jobs, it is a waste of our project resource!!'''
- When you are not using a workspace, you can also pause the workspace so that it won't consume 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)
Step 7: Manage personal (R) packages
- Some basic R packages are available in the workspace. For other common packages, you could request their installation via Leon Mei or Davy Cats.
- You can also install your own libraries in the running workspace in the persistent storage.
- All data/scripts stored in your researchdrive folder are persistent (although no backup support).
- More user documents about the BBMRIomics package can be found at https://bbmri-nl.github.io/BBMRIomics/usage.html
(optional) Step 8: ssh access
For more advanced users who would like to access the terminal of a workspace. You can "ssh <user_name>@<IP>" to the workspace where <user_name> is the same as defined in your authenticator app and the <IP> address is shown in the "Workspace Details". You can "sudo su" to become a sudoer on the workspace in order to install necessary programs.
