03-start.Rmd

# Getting started {#start}


## Checklist

 * Test your login to the CSC R environment (and optionally, set up your own R); see below for details

 * Watch [short online videos](https://www.youtube.com/playlist?list=PLjiXAZO27elAJEptP59BN3whVJ61XIkST) on microbiome data science with R/Bioconductor.

 * Test [reproducible reporting Quarto](https://microbiome.github.io/OMA/resources.html#quarto)

 * Read about the selected demo data: [HintikkaXOData](https://microbiome.github.io/OMA/containers.html#hintikka-desc). You can also try to load it in R and explore the data structure.

 * Online support: for installation and other issues, join us at [Gitter](https://gitter.im/microbiome/miaverse?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge).

 * Optionally: check the reading tips below


## Study material {#material}


The course will use material from
[OMA](https://microbiome.github.io/OMA/) online book, which is
currently in its beta version. We encourage to familiarize with the
content of the book and try some examples already before the course
starts but this is optional.


### Lecture slides

The slides and other teaching material will be shared at a later
point through
[OMA](https://microbiome.github.io/OMA/training.html#material).


### Basics of R/Bioconductor

We expect that participants have previous experience with R/Bioconductor. To refresh your R/Bioconductor skills, you can check additional study material in [OMA](https://microbiome.github.io/OMA/docs/devel/pages/training.html) 



## Setting up R environment {#renv}

### Your own computer

Setting up your own computer and using local R installation will allow
you to continue using the same tools after the course. In order to do
this, you can follow the [OMA setup checklist](https://microbiome.github.io/OMA/training.html#training).

The course organizers can provide limited online support for installations via [Gitter](https://microbiome.github.io/OMA/training.html#support-and-resources). However, installation is more demanding in some systems.

We also provide the CSC notebook for the course (see below); this
comes with all necessary R packages and data pre-installed for ease of
use.



### CSC Notebook

We provide a temporary access to a cloud computing environment
that readily contains the available software packages. Instructions to access 
the environment will be sent to the registered participants. 

1. Read the [instructions](https://docs.csc.fi/cloud/csc_notebooks/guide_for_students/)
2. Go to the [CSC notebook frontpage](https://notebooks-beta.rahtiapp.fi/welcome)
3. Login
    a. 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
    b. CSC login
        * You can create a CSC account by following the [instructions](https://research.csc.fi/accounts-and-projects)
        1. Press **Login** button from the frontpage
        2. Press **CSC** button
        3. Enter login information
    c. Special login
        * For those who cannot login with Haka or CSC account
        1. Contact Giulio on [gitter](https://app.gitter.im/#/room/#microbiome_miaverse:gitter.im) if you are not able to login
        2. We give you a guest account
        3. Press **Special Login** button from the frontpage (below the **Login** button)
        4. Enter login information (username goes to **email** slot)
4. Join workspace
    a. Press **Join workspace** button (Top right corner)
    b. Enter the **Join Code** (Check your email)
5. Start session
    a. Press **ON** button
6. You can save files to **my-work** directory. They are kept stored even when the session is closed. **shared** folder is shared with all participants.