Learning environment & data sets

Checklist

From course website

  • Test login to CSC cloud (optionally, set up your own R)

  • Watch short online videos on microbiome data science

  • Try out reproducible reporting with Quarto

  • Read about the selected demo data: HintikkaXOData. You can also try to load it in R and explore the data structure.

  • Optionally: Read through reading tips (OMA & manuscripts)

  • Online support: for installation and other issues, join us at Gitter.

Software & learning environment

  • Pre-installed system Temporary access to the notebook cloud environment provided by CSC with preinstalled software.

  • Your own system encouraged to test the installation on your own system; limited support for this will be available.

CSC Notebook

  • Offers web applications for self-learning, hosting courses and collaboration provided by CSC.

  • CSC – IT Center for Science is a Finnish center of expertise in information technology.

  • CSC is owned by the Finnish state and higher education institutions.

  • Services: High-performance computing, data management, cloud, software.

CSC cloud notebook

  • Login with CSC/Haka or Guest account

  • Preinstalled R packages

  • 8 Gb memory

  • 8 hour uptime at one go

  • Shared data workspace

Instructions to login

  • Instructions to access the environment will be sent to the registered participants.

  1. Read the General instructions

  2. Go to the CSC notebook front page.

  3. Login

    a. Haka login

    b. CSC login

    c. Special login

Haka login

  • If you have a Finnish university account, you should be able to login with Haka

    1. Press Login button from the frontpage
    2. Press Haka button
    3. Select right organization
    4. Enter login information

CSC login

  • You can create a CSC account by following the instructions

    1. Press Login button from the frontpage
    2. Press CSC button
    3. Enter login information

Special login

  • For those who cannot login with Haka or CSC account

    1. Contact Jeba on gitter if you are not able to login

    2. We will give you guest account

    3. Press Special login button from the front page (below the Login button)

    4. Enter login information

Joining workspace

  1. Join workspace

    a. Press Join workspace button (Top right corner)

    b. Enter the Join Code (Check your email)

  2. Start session

    • Press ON button

  3. Save files to my-work

Teaching environment

  1. Open the course website
  2. Show instructions
  3. Show the front page
  4. Explain login options (personal or guest account)
  5. Join workspace with the join code (Workspace means this course)
  6. Open new session
  7. Session lifetime: need to open new session every day (to save computer resources)
  8. Rstudio intro (if necessary)
  9. Using folders
  10. my-work will be there as long as workspace is there (half year)
  11. You can download those by e.g. copy-pasting, or exportin the file
  12. Saving workspace to your directory (optional)