update workshop 6 dec 2023

develop/workshop/workshop.md

@@ -14,7 +14,7 @@ hide:
 !!! info "Upcoming Workshop at AAU"
     <b> Intro to the Health Data Science Sandbox at Aalborg University</b>
 
-    Interested in adding new analysis techniques to your health data science skill set? Curious about how to use Danish supercomputing resources? Looking for how to host coding material for your own course as an academic educator? Join our workshop for a demo of the Health Data Science Sandbox, a platform for training and research being built collaboratively across 5 universities. We will introduce our mission, network, and resources and then give you an opportunity to try out our omics-focused training module with single cell RNA sequencing data in a guided live session on UCloud (experience with R is a plus but not required). The workshop is open for students, researchers, and educators. 
+    Interested in adding **new analysis techniques** to your health data science skill set? Curious about how to use Danish **supercomputing resources**? Looking for how to host **coding material for your own course** as an academic educator? Join our workshop for a demo of the Health Data Science Sandbox, a platform for training and research being built collaboratively across 5 universities. We will introduce our mission, network, and resources and then give you an opportunity to try out our omics-focused training module with **single cell RNA sequencing data** in a guided live session on UCloud (experience with R is a plus but not required). The workshop is open for students, researchers, and educators. 
 
     - Instructors: Sandbox Data Scientists Jakob Skelmose (AAU CLINDA) and Samuele Soraggi (AU BiRC)
     - Time: 6 December 2023, 1200-1600
@@ -36,16 +36,98 @@ The Health Data Science Sandbox aims to be a training resource for bioinformatic
 ## Access Sandbox resources
 We currently provide training materials and resources as topical apps on UCloud, the supercomputer located at the University of Southern Denmark. To use these resources, you'll need the following:
 
- 1. a Danish university ID so you can sign on to UCloud via WAYF. See [this guide](https://hds-sandbox.github.io/access/UCloud.html) and/or follow along with our live demo.
+ 1. Log onto UCloud at the address http://cloud.sdu.dk using your university credentials.
  2.  the ability to navigate in linux / RStudio / Jupyter. You don't need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.
- 3. our invite link to the correct UCloud project that will be shared on the day of the workshop. This way, we can provide you compute resources for the active sessions of the workshop. To use Sandbox materials outside of the workshop, you'll need to check with the local DeiC office at your university about how to request compute hours on UCloud.
 
-## Try out a module
+ **Note:**
+
+ 1. To use Sandbox materials outside of the workshop, you can request a project by clicking on `apply for resources` in your uCloud dashboard.
+ 2. If you are a BSc or MSc student, you need a supervisor to apply on your behalf, or you can try to apply yourself mentioning the supervisor approval in the application.
+ 3. Remember, however, that you have 1000Kr of computing credit, and around 50GB of free storage to work on uCLoud.
+
+## Try out our transcriptomics module
 So our Sandbox data scientists have finished their intro at the workshop? Great, now the brave ones in the audience can try out one of our apps in a live session. Today we are demoing:
 
 ![Transcriptomics](../assets/images/transcriptomics.png){ align=left width="10%" }
 ### Transcriptomics 
-If you're interested in bulk or single cell RNA sequencing analysis and visualization, join Sandbox Data Scientist Samuele Soraggi from Aarhus University in testing out our Transcriptomics Sandbox app. This app supports regular 3-4 day workshops at University of Copenhagen and provides stand-alone visualisation tools. Sign into UCloud and then click this [invite link](not active yet).
+If you're interested in bulk or single cell RNA sequencing analysis and visualization, join Sandbox Data Scientist Samuele Soraggi from Aarhus University in testing out our Transcriptomics Sandbox app. 
+
+Follow these instructions to try our app:
+
+1. Click on the button below to join the project for today: <!DOCTYPE html>
+<html lang="en">
+<head>
+  <meta charset="UTF-8">
+  <meta name="viewport" content="width=device-width, initial-scale=1.0">
+  <title>Green Button</title>
+  <style>
+    /* Add some basic styling to the button */
+    .green-button {
+      display: inline-block;
+      padding: 10px 20px;
+      background-color: #4CAF50; /* Green color */
+      color: #fff; /* White text */
+      text-align: center;
+      text-decoration: none;
+      font-size: 16px;
+      border: none;
+      border-radius: 8px;
+      cursor: pointer;
+    }
+
+    /* Add hover effect */
+    .green-button:hover {
+      background-color: #45a049; /* Darker green color on hover */
+    }
+  </style>
+</head>
+<body>
+  <!-- Replace the "YOUR_LINK_HERE" placeholder with your actual link -->
+  <a href="https://cloud.sdu.dk/app/projects/invite/7eb44b4b-f680-46d5-b17d-df2209b1b287" class="green-button">Go to Link</a>
+</body>
+</html>
+You should see a message on your browser where you have to accept the invitation to the project. This will add you to a project on uCloud, where we have data and extra computing credit for the course.
+
+2. Be sure you have joined the project. Check if you have the project OMICS workshop from the project menu (red circle). Afterwards, click on the App menu (green circle)
+![](./img/project.png)
+
+3. * Find the app `Transcriptomics Sandbox` (red circle), which is under the title `Featured`.
+
+![](./img/chooseapp_transcriptomics.png)
+
+* Click on it. You will get into the settings window. Choose any Job Name (Nr 1 in the figure below), how many hours you want to use for the job (Nr 2; choose at least 3 hours, you can increase this later), and how many CPUs (Nr 3, choose at least 4 CPUs). Choose the course `RNAseq in RStudio` from the drop-down menu (Nr 4). Finally, click on the blue button `Add Folder`.
+
+![](./img/setting_transcriptomics.png)
+
+* Now, click on the browsing bar that appears (red circle).
+
+![](./img/addfolder.png)
+
+* In the appearing window, you should see already a folder called `Intro_to_scRNAseq_R`. Click on `Use` at its right (red circle)
+
+![](./img/choosefolder_binfconf2023.png)
+
+
+* Afterwards, you should have something like this in the settings page:
+
+![](./img/addedfolder_binfconf2023.png)
+
+* Now, click on Submit to start the app (the button is on the right side of the settings page)
+
+* You will now enter a waiting queue. When the session starts, the timer begins to count down (red circle), and you should be able to open the interface through the button (green circle). Note the buttons to add time to your session (blue circle) and the button to stop the session when you are done (pink circle)
+
+![](./img/running_transcriptomics.png)
+
+* Open the interface by clicking on the button (green circle of figure above). Sometimes you are warned of a missing connection: simply refresh the page. You will enter `Rstudio`, well-known interface to code in `R`.
+
+* Run the following command to download the tutorial: `download.file("https://raw.githubusercontent.com/hds-sandbox/ELIXIR-workshop/main/Notebooks/scRNAseq_Tutorial_R.Rmd", "tutorial_scrna.Rmd")`
+
+* Open the file `tutorial_scrnaR.Rmd` that should now appear in the file browser of Rstudio. Click now on `visual` (on the tool bar) if you need to see the tutorial in a more readable format.
+
+* The executable code is inside chunks (called cells) to be executed in order from the first to the last using the little green arrow appearing on the right side of each code cell.
+
+* Read carefully through the tutorial and execute the code cells. You will see the outputs appearing as you proceed. 
+
 
 ## Discussion and feedback
 We hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the [Sandbox modules](https://hds-sandbox.github.io/modules/index.html) or join us for a multi-day in person [course](https://hds-sandbox.github.io/news/news.html).