diff --git a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block03b-ARCitect-HandsOn.html b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block03b-ARCitect-HandsOn.html index 070daef46..241cfc6d5 100644 --- a/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block03b-ARCitect-HandsOn.html +++ b/src/docs/teaching-materials/disseminations/2023-09-MibiNet-CEPLAS-StartYourARC/Block03b-ARCitect-HandsOn.html @@ -1,4 +1,4 @@ -ARCitect and hands-on
-

Block 3 – ARCitect and hands-on

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+

Block 3 – ARCitect and hands-on

-

ARCitect installation

+

ARCitect installation

Please install the latest version of the ARCitect: https://github.com/nfdi4plants/ARCitect

-

🔥 (released September 20th, 2023) 🔥

+

🔥 (released September 20th, 2023) 🔥

-

Download the demo data

+

Download the demo data

git clone "https://demo-user:1_eznikmzxzARAbUxxnF@git.nfdi4plants.org/teaching/demo-arc_level0.git"
-

Sort Demo data in an ARC

+

Sort Demo data in an ARC

-

Open ARCitect

+

Open ARCitect

  1. Login to DataHUB (1)
-

Initiate the ARC folder structure

+

Initiate the ARC folder structure

  1. Create a New ARC (2)
  2. Select a location and name it TalinumPhotosynthesis
-
-

Your ARC's name

+
+

Your ARC's name

-

💡 By default, your ARC's name will be used

+

💡 By default, your ARC's name will be used

  • for the ARC folder on your machine
  • to create your ARC in the DataHUB at https://git.nfdi4plants.org/<YourUserName>/<YourARC> (see next steps)
  • as the identifier for your investigation
-

💡 Make sure that no ARC exists at https://git.nfdi4plants.org/<YourUserName>/<YourARC>. Otherwise you will sync to that ARC.

-

💡Don't use spaces in ARC's name

+

💡 Make sure that no ARC exists at https://git.nfdi4plants.org/<YourUserName>/<YourARC>. Otherwise you will sync to that ARC.

+

💡Don't use spaces in ARC's name

-
-

Add a description to your investigation

-

+
+

Add a description to your investigation

+

-
-

Add (at least one) contributor

+
+

Add (at least one) contributor

-
-

Add a study

+
+

Add a study

by clicking "Add Study" and entering an identifier for your study

Use talinum_drought as an identifier

-
-

Study panel

+
+

Study panel

In the study panel you can add

  • general metadata,
    • @@ -88,14 +88,14 @@

    Study panel

  • data process information
-
-

Add an assay

+
+

Add an assay

by clicking "Add Assay" and entering an identifier for your assay

Add two assays with rnaseq and metabolomics as an identifier

-
-

Link your assay to a study

+
+

Link your assay to a study

You can either

  • link your new assay to an existing study in your ARC or
    • @@ -103,8 +103,8 @@

    Link your assay to a study

Link your assays to your talinum_drought study

-
-

Add information about your assay

+
+

Add information about your assay

In the assay panel you can

  1. link or unlink the assay to studies, and
    2. @@ -119,7 +119,7 @@

    Add information about your assay

-

Add protocols

+

Add protocols

You can either

  • directly write a new protocol within the ARCitect or
    • @@ -128,31 +128,31 @@

    Add protocols

-

Add protocols and datasets

+

Add protocols and datasets

In the file tree you can

  • add a dataset and
  • protocols associated to that dataset.
-

💡 Add Dataset allows to import data from any location on your computer into the ARC.

-

⚠️ Depending on the file size, this may take a while. Test this with a small batch of files first.

+

💡 Add Dataset allows to import data from any location on your computer into the ARC.

+

⚠️ Depending on the file size, this may take a while. Test this with a small batch of files first.

-

Sort Demo Data to your ARC

-

💡 protocols can directly imported via ARCitect

-

💡 to add multiple datasets folders, they have to be added manually via file browser

+

Sort Demo Data to your ARC

+

💡 protocols can directly imported via ARCitect

+

💡 to add multiple datasets folders, they have to be added manually via file browser

-

Login to the DataHUB

+

Login to the DataHUB

Click Login (1) in the sidebar to login to the DataHUB.

-

💡 This automatically opens your browser at the DataHUB (https://git.nfdi4plants.org) and asks you to login, if you are not already logged in.

+

💡 This automatically opens your browser at the DataHUB (https://git.nfdi4plants.org) and asks you to login, if you are not already logged in.

-

Upload your local ARC to the DataHUB

+

Upload your local ARC to the DataHUB

From the sidebar, navigate to Versions (6)

-

Versions

+

Versions

The versions panel allows you to

  • store the local changes to your ARC in form of "commits",
    • @@ -161,7 +161,7 @@

    Versions

-

Connection to the DataHUB

+

Connection to the DataHUB

If you are logged in, the versions panel shows

  • your DataHUB's Full Name and eMail
    • @@ -169,19 +169,19 @@

    Connection to the DataHUB

-

Check if your ARC is successfully uploaded

+

Check if your ARC is successfully uploaded

  1. sign in to the DataHUB
  2. Check your projects
-

Received two emails from "GitLab" about a failed pipeline?

-

-

🔥 Don't worry 😄

+

Received two emails from "GitLab" about a failed pipeline?

+

+

🔥 Don't worry 😄

-
-

Pipeline Failed

+
+

Pipeline Failed

  • @@ -200,12 +200,12 @@

    Pipeline Failed

-
-

Pipeline Failed

+
+

Pipeline Failed

If the pipeline has failed once, it is disabled by default

-
-

Reactivate the CQC pipeline

+
+

Reactivate the CQC pipeline

To reactivate it and let the DataHUB validate your ARC again:

    @@ -215,12 +215,12 @@

    Reactivate the CQC pipeline

  1. Save changes
-
-

Collaborate and share

+
+

Collaborate and share

-

Invite collaborators

+

Invite collaborators

  • Unless changed, your ARC is set to private by default.
  • To collaborate, you can invite lab colleagues or project partners to your ARC by following the steps on the subsequent slides.
    • @@ -257,36 +257,39 @@

    Invite collaborators

    fit

-
-

Choosing the proper role

-

Guest
-Have the least rights. This is recommended for people you ask for consultancy.

+
+

Choosing the proper role

+ +

Guests
+Have the least rights. They will not be able to see the content of your ARC (only the wiki page).

+

Reporters
+Have read access to your ARC. This is recommended for people you ask for consultancy.

Developers
-The choice for most people you want to invite to your ARC. Developers have read and write access, but cannot maintain the project on the DataHUB, e.g. inviting others.

+The choice for most people you want to invite to your ARC. Developers have read and write access, but cannot maintain the project on the DataHUB, e.g. inviting others.

Maintainers
Gives the person the same rights as you have (except of removing you from your own project). This is recommended for inviting PIs or group leaders allowing them to add their group members for data upload or analysis to the project as well.

A detailed list of all permissions for the individual roles can be found here

-
-

Congratulations!

+
+

Congratulations!

You have just shared your ARC with a collaborator.

-
-

Your ARC is ready

+
+

Your ARC is ready

-

👩‍💻 Initiated an ARC
+

👩‍💻 Initiated an ARC


-📂 Structured and ...
+📂 Structured and ...


... annotated experimental data


-🌐 Shared with collaborators

+🌐 Shared with collaborators

-
+
-

Contributors

+

Contributors

Slides presented here include contributions by

  • name: Dominik Brilhaus
    @@ -301,5 +304,5 @@

    Contributors

Demo dataset cannot be added via add dataset. Only individual files can be added, not multiple folders

\ No newline at end of file +

Demo dataset cannot be added via add dataset. Only individual files can be added, not multiple folders

\ No newline at end of file diff --git a/src/docs/teaching-materials/disseminations/2023-10-CSCS-CEPLAS-StartYourARC/Block03-ARCitect-HandsOn.html b/src/docs/teaching-materials/disseminations/2023-10-CSCS-CEPLAS-StartYourARC/Block03-ARCitect-HandsOn.html index 59148c6fe..92a6a922d 100644 --- a/src/docs/teaching-materials/disseminations/2023-10-CSCS-CEPLAS-StartYourARC/Block03-ARCitect-HandsOn.html +++ b/src/docs/teaching-materials/disseminations/2023-10-CSCS-CEPLAS-StartYourARC/Block03-ARCitect-HandsOn.html @@ -1,4 +1,4 @@ -ARCitect Hands-on
-

Block 3 – ARCitect Hands-on

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+

Block 3 – ARCitect Hands-on

October 5th, 2023

Dominik Brilhaus, CEPLAS Data Science

-

Check-in

+

Check-in

-

Registration

+

Registration

Did everyone sign-up at the DataHUB?

-

ARCitect installation

+

ARCitect installation

Please install the latest version of the ARCitect: https://github.com/nfdi4plants/ARCitect

-

🔥 (released September 20th, 2023) 🔥

+

🔥 (released September 20th, 2023) 🔥

-

Download the demo data

+

Download the demo data

https://nfdi4plant.sharepoint.com/:f:/s/Teaching/Eik7k-oJiMREgZ24kto7sIYBGxHmmZlS_Kzf7psk-5w-xg?e=u0sADd

-

You just received your data

+

You just received your data

-

Goal

+

Goal

  • Structure,
  • (Annotate, and)
  • Share your experimental data.

-

💡 We'll talk about data annotation later

+

💡 We'll talk about data annotation later

-

Open the ARCitect

+

Open the ARCitect

-

Initiate the ARC folder structure

+

Initiate the ARC folder structure

  1. Create a New ARC (2)
  2. Select a location and name it TalinumPhotosynthesis
-
-

Your ARC's name

+
+

Your ARC's name

-

💡 By default, your ARC's name will be used:

+

💡 By default, your ARC's name will be used:

  1. for the ARC folder on your machine
  2. to create your ARC in the DataHUB at https://git.nfdi4plants.org/<YourUserName>/<YourARC> (see next steps)
  3. as the identifier for your investigation
-

💡 Make sure that no ARC exists at https://git.nfdi4plants.org/<YourUserName>/<YourARC>. Otherwise you will sync to that ARC.

-

💡 Avoid spaces in your ARC's name

+

💡 Make sure that no ARC exists at https://git.nfdi4plants.org/<YourUserName>/<YourARC>. Otherwise you will sync to that ARC.

+

💡 Avoid spaces in your ARC's name

-
-

Add a description and title to the investigation

+
+

Add a description and title to the investigation

  1. Click on the ARC's name
  2. Add a title (e.g. "Talinum Photosynsthesis")
    3. @@ -89,15 +89,15 @@

    Add a description and title to the investigation

-

Add contributors

+

Add contributors

In the section "People" click "ADD PERSON" to add at least one contributor


-

Add contributor details

+

Add contributor details

-

💡 For each person that you add, make sure to add

+

💡 For each person that you add, make sure to add

  • First Name
  • Last Name
    • @@ -106,11 +106,11 @@

    Add contributor details

-

Add a study

+

Add a study

by clicking "Add Study" and entering talinum_drought as identifier for the study

-

Study panel

+

Study panel

In the study panel you can add

  • general metadata,
    • @@ -120,12 +120,12 @@

    Study panel

-

Add a protocol to the study

+

Add a protocol to the study

Click "Add Protocol" in the sidebar to add a protocol to the study

-

Adding protocols

+

Adding protocols

You can either

  • directly write a new protocol within the ARCitect or
    • @@ -134,22 +134,22 @@

    Adding protocols

-

Transfer the protocol information

+

Transfer the protocol information

From the demo data, transfer the lab notes stored in plant_material.txt to the talinum_drought study.

-

Add an assay to the ARC

+

Add an assay to the ARC

Click "Add Assay" in the sidebar

-

Name and link the assay

+

Name and link the assay

  1. Enter rnaseq as the identifier
  2. Link the assay to the study talinum_drought
-

Add information about the assay

+

Add information about the assay

In the assay panel you can

  1. link or unlink the assay to studies, and
    2. @@ -164,7 +164,7 @@

    Add information about the assay

-

Add information about the assay

+

Add information about the assay

  1. Add the following information:
      @@ -177,7 +177,7 @@

      Add information about the assay

-

Add protocols and datasets

+

Add protocols and datasets

In the file tree you can

  • add a dataset and
    • @@ -185,14 +185,14 @@

    Add protocols and datasets

-

Import the demo dataset to the ARC

+

Import the demo dataset to the ARC

  1. Cick "Add Dataset"
  2. Select the *.fastq.gz files from the demo data
-

Import the protocols

+

Import the protocols

From the demo data, import the lab notes related to the rnaseq assay:

  • RNA_extraction.txt
    • @@ -201,20 +201,20 @@

    Import the protocols

-

Collaborate and share

+

Collaborate and share

-

Login to the DataHUB

+

Login to the DataHUB

Click Login (1) in the sidebar to login to the DataHUB.

-

💡 This automatically opens your browser at the DataHUB (https://git.nfdi4plants.org) and asks you to login, if you are not already logged in.

+

💡 This automatically opens your browser at the DataHUB (https://git.nfdi4plants.org) and asks you to login, if you are not already logged in.

-

Versions: Connection to the DataHUB

+

Versions: Connection to the DataHUB

To communicate with the DataHUB, navigate to Versions (6)

-

Versions

+

Versions

The versions panel allows you to

  • store the local changes to your ARC in form of "commits",
    • @@ -223,7 +223,7 @@

    Versions

-

Connection to the DataHUB

+

Connection to the DataHUB

If you are logged in, the versions panel shows

  • your DataHUB's Full Name and eMail
    • @@ -231,7 +231,7 @@

    Connection to the DataHUB

-

Upload your ARC to the DataHUB

+

Upload your ARC to the DataHUB

  1. Enter a "commit message" to shortly describe the changes to your ARC
  2. Click "COMMIT" to save your changes locally
    3. @@ -239,19 +239,19 @@

    Upload your ARC to the DataHUB

-

Check whether your ARC was uploaded successfully

+

Check whether your ARC was uploaded successfully

  1. sign in to the DataHUB
  2. Check your projects
-

Received two emails from "GitLab" about a failed pipeline?

+

Received two emails from "GitLab" about a failed pipeline?

-

🔥 Don't worry 😄

+

🔥 Don't worry 😄

-

Pipeline Failed

+

Pipeline Failed

  • @@ -271,11 +271,11 @@

    Pipeline Failed

-

Pipeline Failed

+

Pipeline Failed

If the pipeline has failed once, it is disabled by default

-
-

Reactivate the CQC pipeline

+
+

Reactivate the CQC pipeline

To reactivate it and let the DataHUB validate your ARC again:

    @@ -285,12 +285,12 @@

    Reactivate the CQC pipeline

  1. Save changes
-
-

Collaborate and share

+
+

Collaborate and share

-

Invite collaborators

+

Invite collaborators

  • Unless changed, your ARC is set to private by default
  • To collaborate, you can invite lab colleagues or project partners to your ARC
    • @@ -326,24 +326,27 @@

    Invite collaborators

    fit

-
-

Choosing the proper role

-

Guest
-Have the least rights. This is recommended for people you ask for consultancy.

+
+

Choosing the proper role

+ +

Guests
+Have the least rights. They will not be able to see the content of your ARC (only the wiki page).

+

Reporters
+Have read access to your ARC. This is recommended for people you ask for consultancy.

Developers
-The choice for most people you want to invite to your ARC. Developers have read and write access, but cannot maintain the project on the DataHUB, e.g. inviting others.

+The choice for most people you want to invite to your ARC. Developers have read and write access, but cannot maintain the project on the DataHUB, e.g. inviting others.

Maintainers
Gives the person the same rights as you have (except of removing you from your own project). This is recommended for inviting PIs or group leaders allowing them to add their group members for data upload or analysis to the project as well.

A detailed list of all permissions for the individual roles can be found here

-
-

Congratulations!

+
+

Congratulations!

You have just shared your ARC with a collaborator.

-

Add the remaining data

+

Add the remaining data

  1. Add another assay (metabolomics)
      @@ -360,29 +363,29 @@

      Add the remaining data

-

Check the progress of your ARC

+

Check the progress of your ARC

  1. Navigate to Versions
  2. Check the History panel at the bottom

-
-

Your ARC is ready

+
+

Your ARC is ready

-

👩‍💻 Initiated an ARC
+

👩‍💻 Initiated an ARC


-📂 Structured and ...
+📂 Structured and ...


... annotated experimental data


-🌐 Shared with collaborators

+🌐 Shared with collaborators

-
-

DataHUB

+
+

DataHUB

-
-

Deleting an ARC

+
+

Deleting an ARC

  1. Click on Settings in the sidebar of your ARC
    2. @@ -390,8 +393,8 @@

    Deleting an ARC

  2. In the advanced section (4) you can delete your ARC
-
-

Follow your progress in the DataHUB

+
+

Follow your progress in the DataHUB

  1. Open your ARC in the DataHUB
  2. In the sidebar on the left, navigate to Repository → Commits
    3. @@ -399,7 +402,7 @@

    Follow your progress in the DataHUB

-

Undo latest changes

+

Undo latest changes

  1. Click on the latest (i.e. uppermost) commit.
  2. In the top-right corner select Revert from the drop-down menu Options.
    3. @@ -407,7 +410,7 @@

    Undo latest changes

-

Undo latest changes

+

Undo latest changes

  1. Un-check the box "Start a new merge request with these changes".
  2. Click "Revert"
    3. @@ -415,7 +418,7 @@

    Undo latest changes

-

Update your local ARC

+

Update your local ARC

If your ARC has changed in the DataHUB (by yourself or collaborators), you need to update your "local" version of the ARC.

  1. Navigate to Versions
    2. @@ -424,7 +427,7 @@

    Update your local ARC

-

Contributors

+

Contributors

Slides presented here include contributions by

  • name: Dominik Brilhaus
    @@ -439,5 +442,5 @@

    Contributors

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