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Updated part 2 of TM an _quarto.yml
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jacobfh1 committed Nov 19, 2024
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23 changes: 13 additions & 10 deletions TeachingModule/AnalysisMSData_FragPipe.qmd
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Expand Up @@ -22,32 +22,29 @@ What is FTP, and what is its functionality?
:::


For downloading the data, we will use the **Proteomics Sandbox Application** on UCloud. This platform allows us to access the necessary storage capacity as well as the computational power required to execute this process.
To download the data, we will use the **Proteomics Sandbox Application** on UCloud. This platform provides the necessary storage capacity and computational power to perform this process.

The **Proteomics Sandbox Application** is a virtual environment that includes multiple software tools, including **FragPipe** for analyzing proteomics data.

You can find the **Proteomics Sandbox Application** on UCloud [here](https://cloud.sdu.dk/app/jobs/create?app=proteomics).
The **Proteomics Sandbox Application** is a virtual environment that includes various software tools, such as **FragPipe**, for analyzing proteomics data.

First, we will download the data for the sample files to be used in **FragPipe**. Then, we will launch **FragPipe** to run the first analysis of the data. Before doing so, we have some questions regarding **FragPipe** and its usability:

::: {.question}
What is FragPipe, and what are its applications?
:::


::: {.question}
If FragPipe were not used for this part of the teaching module, which alternative software tools could be employed? Please provide a few examples.
If FragPipe was not used for this part of the teaching module, which alternative software tools could be employed? Please provide a few examples.
:::


::: {.question}
What are the benefits of using FragPipe?
:::


Now that we know what we want to do and why, it is time to start the **Proteomics Sandbox** application, or job.
Simple analyses in **FragPipe** may only require 8 GB of RAM, while large-scale or complex analyses may require 24 GB of memory or more ([FragPipe Documentation](https://fragpipe.nesvilab.org/docs/tutorial_fragpipe.html#:~:text=FragPipe%20runs%20on%20Windows%20and,24%20GB%20memory%20or%20more.)), which is why we will allocate 24 GB for this exercise.

You can access the **Proteomics Sandbox Application** on UCloud [here](https://cloud.sdu.dk/app/jobs/create?app=proteomics&version=Oct2024).

In UCloud, the settings should look like this:

![](images/TeachingModuleInstructions/UCloud_settings.PNG){width=750 fig-align="center"}
Expand Down Expand Up @@ -83,7 +80,9 @@ At the bottom of the page, you will find the FTP-server address where the data i
Please locate the address.
:::

Click on the "Dataset FTP location" link.
::: {.callout-tip}
Click on the **Dataset FTP location** link.
:::

::: {.question}
We now have access to the data stored on the FTP server. Please provide a brief description of the contents of the folder on the FTP server.
Expand All @@ -96,7 +95,10 @@ To download one sample file from each of the Plex Sets, we will need these URLs
{{< include ./urls.txt >}}
```

(You can also download this list [here](https://github.com/hds-sandbox/proteomics-sandbox/blob/webpage/TeachingModule/urls.txt)).
::: {.callout-tip collapse="true"}
## Tip to Download of Data
You can also download this list [here](https://github.com/hds-sandbox/proteomics-sandbox/blob/webpage/TeachingModule/urls.txt).
:::

::: {.callout-note}
We recommend to open this material inside **Proteomics Sandbox** to be able to copy & paste or download the file directly into the environment.
Expand All @@ -119,6 +121,7 @@ Now that FragPipe is launched, we need to configure the settings before running
::: {.callout-note}
Some of the information you will need in this section can be found in **Supplementary Information** to the study. Open the **Supplementary Information** and go to page 25, **Supplementary Methods**.
:::

Go to the `Workflow` tab to set up the workflow for the analysis and import the data you just downloaded.

::: {.question}
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38 changes: 24 additions & 14 deletions _quarto.yml
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Expand Up @@ -7,23 +7,33 @@ website:
left:
- text: Introduction
href: index.qmd
- text: Getting Started
href: gettingstarted.qmd
- text: Setup
href: setup.qmd
- text: ColabFold
href: colabfold.qmd
- text: Course Materials
href: coursematerials.qmd
- text: Teaching Module
href: teachingmodule.qmd
- text: Contributors
href: contributors.qmd
- sidebar:
id: ProteomicsSidebar
title: "Navigation"
style: "docked"
background: "light"
collapse-level: 2
contents:
- id: ProteomicsSandboxApp
title: "Proteomics Sandbox App"
contents:
- text: Getting Started
href: gettingstarted.qmd
- text: Setup
href: setup.qmd
- text: ColabFold
href: colabfold.qmd
- text: Course Materials
href: coursematerials.qmd
- text: Teaching Module
href: teachingmodule.qmd
- text: Contributors
href: contributors.qmd

format:
html:
theme:
light: [materia, css/materialight.scss]
dark: darkly
light: [materia, css/materialight.scss]
dark: darkly
toc: true
css: css/styles.css

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