diff --git a/src/docs/_sidebars/mainSidebar.md b/src/docs/_sidebars/mainSidebar.md index 3c9fa0857..893b7ac32 100644 --- a/src/docs/_sidebars/mainSidebar.md +++ b/src/docs/_sidebars/mainSidebar.md @@ -98,13 +98,12 @@ ### [Use your DOIs](/docs/DataHUB-Manual/datahub-data-publications-dois.html) - - # [Guides](/docs/guides/index.html) ## [ARC User Journey](/docs/guides/ARCUserJourney.html) ## [Create your ARC](/docs/guides/index-CreateYourARC.html) ### [ARC Commander QuickStart](/docs/guides/arcCommander_QuickStart.html) ### [ARC Commander QuickStart (Experts)](/docs/guides/arcCommander_QuickStart_expert.html) +### [ARCitect QuickStart](/docs/guides/arcitect_QuickStart.html) ## [Annotate Data in your ARC](/docs/guides/index-AnnotateDataInYourARC.html) ### [Annotation Principles](/docs/guides/isa_AnnotationPrinciples.html) ### [ISA File Types](/docs/guides/isa_FileTypes.html) diff --git a/src/docs/guides/arcitect_QuickStart.md b/src/docs/guides/arcitect_QuickStart.md index 4d7c900c9..3b4092e58 100644 --- a/src/docs/guides/arcitect_QuickStart.md +++ b/src/docs/guides/arcitect_QuickStart.md @@ -1,17 +1,31 @@ --- -layout: none +layout: docs title: ARCitect QuickStart date: 2023-08-01 author: - name: Dominik Brilhaus github: https://github.com/brilator orcid: https://orcid.org/0000-0001-9021-3197 +- name: Sabrina Zander + orcid: https://orcid.org/0009-0000-4569-6126 add toc: true add support: true add sidebar: _sidebars/mainSidebar.md status: draft --- + + +--- + ## About this guide In this guide we focus on how to use the [ARCitect](./../ARCitect-Manual/index.html) to create your ARC and structure, store and share your data. @@ -24,24 +38,318 @@ In this guide we focus on how to use the [ARCitect](./../ARCitect-Manual/index.h

+--- + ## Before we can start Please make sure :ballot_box_with_check: The latest version of the [ARCitect](./../ARCitect-Manual/index.html) is installed on your computer -:ballot_box_with_check: You have a [DataPLANT](https://register.nfdi4plants.org) account +:ballot_box_with_check: You have a [DataPLANT](https://register.nfdi4plants.org) account +:bulb: Consider reading about the [ARC](./../implementation/AnnotatedResearchContext.html) + +--- + +## Preparation + +Before creating your own ARC, invest some time to think about the following questions. + +- What is my **investigation**? +- What is my **study**? +- Which **assay** did I perform? + - What is my (raw) **dataset**? + - What **protocol**s did I use? + +:bulb: It might help to have this info ready in a text file. In particular, try to think about useful names (identifiers) for investigation, study and assay. + +--- + +## Initiate the ARC folder structure + +
+ +
+ + 1. Start the ARCitect + 2. Create a **New ARC** (2) + 3. Select a location and name for your ARC + +
+ +
+ +
+ +
+ +--- + +### Your ARC's name + +
+
+ + 💡 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//` (see next steps) + 3. as the identifier for your investigation + + 💡 Make sure that no ARC exists at `https://git.nfdi4plants.org//`. Otherwise you will sync to that ARC. + + 💡 Avoid spaces in your ARC's name + +
+ +
+ +
+ +
+ + +--- + +### Add details about your investigation + +Click on your ARC's name to add details, such as + +- a title +- a description + + + + +--- + +### Add contributors + +In the section "People" click "ADD PERSON" to add at least one contributor + + + +--- + +## Add a study to your ARC + +
+
+ + Click "Add Study" in the sidebar and enter an identifier + +
+ +
+ +
+ +
+ +--- + +### Add details about your study + +Click on your study's name to add details, such as + +- general metadata, +- people, and +- publications +- data process information + + + +--- + +### Add a protocol to your study + + +
+
+ + Click "Add Protocol" in the sidebar to add a protocol to your study + +
+ +
+ +
+ +
+ + +--- -## Two minutes to your ARC +### Adding protocols -1. Start the ARCitect -2. Create a `New ARC` -3. Select a location and give your ARC a name +You can either +- directly write a **new protocol** within the ARCitect or +- **import** an existing one from your computer + + + + +--- + +## Add an assay to your ARC + +
+
+ + Click "Add Assay" in the sidebar and enter an identifier + +
+ +
+ +
+ +
+ +--- + +### Link your assay to a study + +
+
+ + You can either + - link your new assay to an existing study in your ARC or + - create a new one (with the same name as the assay) + +
+ +
+ +
+ +
+ + +--- + +### Add information about your assay + +In the assay panel you can + +1. link or unlink the assay to studies, and +2. define the assay's + - measurement type + - technology type, and + - technology platform. +3. add data process information + + + +--- + +### Add protocols and datasets to your assay + +
+
+ + In the file tree you can + + - **add a dataset**, and + - **protocols** associated to that dataset. + + :bulb: **Add Dataset** allows to import data from any location on your computer into the ARC. + :warning: Depending on the file size, this may take a while. Test this with a small batch of files first. + +
+ +
+ +
+ +
+ +--- + +## Share your ARC + +
+
+ + Click **Login** (1) in the sidebar to login to the DataHUB. + + :bulb: 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 + +
+
+ + To communicate with the DataHUB, navigate to Versions (6) + +
+ +
+ +
+ +
+ +--- + +### Connection to the DataHUB + +If you are logged in, the versions panel shows + +- your DataHUB's *Full Name* and *eMail* +- the URL of the current ARC in the DataHUB + `https://git.nfdi4plants.org//` + +![bg right w:650](./../img/arcitect-VersionsPanel.png) + +--- + +### Upload your ARC to the DataHUB + +The versions panel allows you to + +- store the local changes to your ARC in form of "commits", +- sync the changes to the DataHUB, and +- check the history of your ARC + +To upload your ARC: + + 1. Enter a "commit message" to shortly describe the changes to your ARC + 2. Click "commit" to save your changes locally + 3. Click upload to upload your ARC to the DataHUB + + + + +### Check if your ARC is successfully uploaded + +1. [sign in](https://git.nfdi4plants.org) to the DataHUB +2. Check your projects + +--- + + diff --git a/src/docs/img/arcitect-ARCPanel-Investigation-people.png b/src/docs/img/arcitect-ARCPanel-Investigation-people.png new file mode 100644 index 000000000..444937521 Binary files /dev/null and b/src/docs/img/arcitect-ARCPanel-Investigation-people.png differ diff --git a/src/docs/img/arcitect-ARCPanel-Investigation.png b/src/docs/img/arcitect-ARCPanel-Investigation.png new file mode 100644 index 000000000..e89721a5f Binary files /dev/null and b/src/docs/img/arcitect-ARCPanel-Investigation.png differ diff --git a/src/docs/img/arcitect-ARCPanel-study-protocol.png b/src/docs/img/arcitect-ARCPanel-study-protocol.png new file mode 100644 index 000000000..a49a706bf Binary files /dev/null and b/src/docs/img/arcitect-ARCPanel-study-protocol.png differ diff --git a/src/docs/img/arcitect-ARCPanel-study01.png b/src/docs/img/arcitect-ARCPanel-study01.png index 3b692b740..1925e191b 100644 Binary files a/src/docs/img/arcitect-ARCPanel-study01.png and b/src/docs/img/arcitect-ARCPanel-study01.png differ diff --git a/src/docs/img/arcitect-ARCPanel.png b/src/docs/img/arcitect-ARCPanel.png index 7cb0a8249..aef797c69 100644 Binary files a/src/docs/img/arcitect-ARCPanel.png and b/src/docs/img/arcitect-ARCPanel.png differ diff --git a/src/docs/img/arcitect-StudyPanel.png b/src/docs/img/arcitect-StudyPanel.png index 5609d3702..5b63691c0 100644 Binary files a/src/docs/img/arcitect-StudyPanel.png and b/src/docs/img/arcitect-StudyPanel.png differ