From d90f8f306e3476a43bbf7da0d1c57a41f25f7993 Mon Sep 17 00:00:00 2001 From: Quarto GHA Workflow Runner Date: Tue, 19 Nov 2024 08:36:29 +0000 Subject: [PATCH] Built site for gh-pages --- .nojekyll | 2 +- TeachingModule/AnalysisMSData_FragPipe.html | 39 ++++++++++++++++--- colabfold.html | 2 +- coursematerials.html | 4 +- fragpipe.html | 4 +- gettingstarted.html | 4 +- index.html | 2 +- sdrf.html | 4 +- search.json | 4 +- setup.html | 4 +- sitemap.xml | 26 ++++++------- teachingmodule.html | 43 +++++++++++++++++---- 12 files changed, 96 insertions(+), 42 deletions(-) diff --git a/.nojekyll b/.nojekyll index b0d8774..04875ab 100644 --- a/.nojekyll +++ b/.nojekyll @@ -1 +1 @@ -43520d99 \ No newline at end of file +6ae30520 \ No newline at end of file diff --git a/TeachingModule/AnalysisMSData_FragPipe.html b/TeachingModule/AnalysisMSData_FragPipe.html index 675af6c..5850286 100644 --- a/TeachingModule/AnalysisMSData_FragPipe.html +++ b/TeachingModule/AnalysisMSData_FragPipe.html @@ -194,20 +194,20 @@

On this page

What is FTP, and what is its functionality?

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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.

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

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You can find the Proteomics Sandbox Application on UCloud here.

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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.

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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:

What is FragPipe, and what are its applications?

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

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

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), which is why we will allocate 24 GB for this exercise.

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You can access the Proteomics Sandbox Application on UCloud here.

In UCloud, the settings should look like this:

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Download Data

Please locate the address.

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Click on the “Dataset FTP location” link.

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Click on the Dataset FTP location link.

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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.

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Download Data https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150318_TMT_pool3_300ugIPG37-49_7of15ul_fr01.raw https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150322_TMT_pool4_300ugIPG37-49_7of15ul_fr01.raw https://storage.jpostdb.org/JPST000265/HJOSLO2U_QEHF_20150329_TMT_pool5_300ugIPG37-49_7of15ul_fr01.raw

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(You can also download this list here).

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You can also download this list here.

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diff --git a/colabfold.html b/colabfold.html index 46978b7..65bb9b5 100644 --- a/colabfold.html +++ b/colabfold.html @@ -156,7 +156,7 @@

ColabFold

Modified
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November 12, 2024

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November 19, 2024

diff --git a/coursematerials.html b/coursematerials.html index 05a656b..9ea4acf 100644 --- a/coursematerials.html +++ b/coursematerials.html @@ -6,7 +6,7 @@ - + Course Materials – Clinical Proteomics