Merge pull request #437 from nfdi4plants/polish-guides

Polish guides

src/docs/_sidebars/mainSidebar.md

@@ -18,15 +18,9 @@
 
 # [DataPLANT Implementations](/docs/implementation/index.html)
 ## [Annotated Research Context](/docs/implementation/AnnotatedResearchContext.html)
-### [User Journey](/docs/guides/ARCUserJourney.html)
 ### [ARC specification](/docs/implementation/ARC-specification.html)
 ## [ARC Commander](/docs/implementation/ArcCommander.html)
-### [QuickStart](/docs/guides/arcCommander_QuickStart.html)
-### [QuickStart (Experts)](/docs/guides/arcCommander_QuickStart_expert.html)
 ## [Swate](/docs/implementation/Swate.html)
-### [QuickStart](/docs/guides/swate_QuickStart.html)
-### [Walk-through](/docs/guides/swate_walkthrough.html)
-### [Best Practices For Data Annotation](/docs/guides/BestPracticesForDataAnnotation.html)
 ## [MetadataQuiz](/docs/implementation/MetadataQuiz.html)
 ## [DataHUB](/docs/implementation/DataHub.html)
 ## [DataPLAN](/docs/implementation/DataPLAN.html)
@@ -68,6 +62,7 @@
 ## [How to use the ARCmanager](/docs/ARCmanager-manual/how_to.html)
 
 # [Swate Manual](/docs/SwateManual/index.html)
+## [QuickStart](/docs/guides/swate_QuickStart.html)
 ## [QuickStart - Videos](/docs/guides/swate_QuickStart_Videos.html)
 ## [Annotation tables](/docs/SwateManual/Docs02-Annotation-Table.html)
 ## [Building blocks](/docs/SwateManual/Docs03-Building-Blocks.html)
@@ -104,14 +99,16 @@ Continuous Quality Control (CQC) p
 # [Guides](/docs/guides/index.html)
 ## [ARC User Journey](/docs/guides/ARCUserJourney.html)
 ## [Create your ARC](/docs/guides/index-CreateYourARC.html)
+### [ARCitect QuickStart](/docs/guides/arcitect_QuickStart.html)
+### [ARCitect QuickStart - Videos](/docs/guides/arcitect_QuickStart_Videos.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)
 ### [Best Practices For Data Annotation](/docs/guides/BestPracticesForDataAnnotation.html)
 ### [Swate QuickStart](/docs/guides/swate_QuickStart.html)
+### [Swate QuickStart - Videos](/docs/guides/swate_QuickStart_Videos.html)
 ### [Swate Walk-through](/docs/guides/swate_walkthrough.html)
 
 ## [Share your ARC](/docs/guides/index-ShareYourARC.html)

src/docs/guides/ARC-enablingPlatforms.md

@@ -11,21 +11,18 @@ add support: true
 add sidebar: _sidebars/mainSidebar.md
 ---
 
-:construction: work in progress :construction:
-
 <!-- http://127.0.0.1:8080/docs/guides/ARC-enablingPlatforms.html -->
 
 ## About this guide
 
 In this guide we explore how the ARC can help streamline data flows and project management in enabling platforms.
 
-<a href="./index.html">
-    <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
-    <span class="badge-category">Mode</span><span class="badge-selected" id="badge-read">Read</span>
-</a>
-
-<br>
-<br>
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
+        <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
+        <span class="badge-category">Mode</span><span class="badge-selected" id="badge-read">Read</span>
+    </a>
+</div>
 
 ## Before we can start
 
@@ -36,10 +33,7 @@ It helps to be familiar with
 - :ballot_box_with_check: the concept of the [ARC](./../implementation/AnnotatedResearchContext.html)
 - :ballot_box_with_check: the different [ISA file types](./isa_FileTypes.html)
 - :ballot_box_with_check: the [DataHUB](./../implementation/DataHub.html)
-<br>
-<br>
 - :bulb: Note that this guide can only stay at a very abstract level. Feel free to contact us to work out a suitable solution for your platform together.
-- :warning: In part, this guide presents interim solutions for which we are working on more user-friendly implementations. Your feedback helps!
 
 </div>
 
@@ -117,19 +111,13 @@ The standardized ARC structure helps with routine computations:
 
 - The ARC's simple [directory structure](./../implementation/AnnotatedResearchContext.html) itself helps building routines, no matter whether you work with code or licensed software. Across projects, you and your collaborators know, where to find metadata and raw data, where to store processed data and results.
 - The ARC facilitates task automation such as quality control and validation within one project or across multiple ARCs covering routine measurements
-- Code-based computations can be designed as reusable and reproducible workflows using Common Workflow Language (CWL)
-
-<!-- TODO: Link to CWL article / guide -->
-:construction: Articles and guides on CWL are currently work in progress.
+- Code-based computations can be designed as reusable and reproducible workflows using [Common Workflow Language (CWL)](./ComputationalWorkflows/index.html)
 
 ### Data publication
 
 At some point you and your collaborator want to [publish the data](./../fundamentals/DataPublications.html) resulting from the project.
 
-There are two major options: You can publish the current version of the ARC and receive a [DOI](./../fundamentals/PersistentIdentifiers.html). Some scientific journals require data to be published in  [domain-specific repositories](./../fundamentals/PublicDataRepositories.html), specialized for a certain type of assay. For this purpose converters help you export the relevant dataset and metadata into a repository-accepted format.
-
-<!-- TODO: Link to DOI and converter article / guide -->
-:construction: Both these routines are work in progress.
+There are two major options: You can publish the current version of the ARC and receive a [DOI](./../DataHUB-Manual/datahub-data-publications.html). Some scientific journals require data to be published in  [domain-specific repositories](./../fundamentals/PublicDataRepositories.html), specialized for a certain type of assay. For this purpose converters help you export the relevant dataset and metadata into a repository-accepted format.
 
 :bulb: We are working on converters to read and reshape the relevant data and metadata of your ARC into a format accepted by domain-specific repositories. You can support this by telling us relevant repositories for your type of data or help creating [templates](./../SwateManual/Docs05-Templates.html).
 

src/docs/guides/ARCUserJourney.md

@@ -16,12 +16,12 @@ todo:
 
 In this guide we focus on explaining the ARC structure and its different components.
 
-<a href="./index.html">
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
     <span class="badge-category">User</span><span class="badge-selected" id="badge-newbie">Newbie</span>
     <span class="badge-category">Mode</span><span class="badge-selected" id="badge-read">Read</span>
-</a>
-<br>
-<br>
+    </a>
+</div>
 
 ## Viola's ARC
 

src/docs/guides/ARCs-galaxy.md

@@ -15,13 +15,12 @@ add sidebar: _sidebars/mainSidebar.md
 
 In this guide we introduce how to access ARCs from Galaxy. To access the data of an ARC, you must first provide a DataHUB access token in Galaxy, which is used to authenticate Galaxy to DataHUB. To create a new token and add it to [Galaxy](https://usegalaxy.eu/), you can proceed as described below.
 
-<a href="./index.html">
-    <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
-    <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>
-</a>
-
-<br>
-<br>
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
+        <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
+        <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>
+    </a>
+</div>
 
 ## Before we can start
 

src/docs/guides/BestPracticesForDataAnnotation.md

@@ -16,12 +16,14 @@ todo:
 
 In this guide, we will take a closer look at some experimental scenarios that every scientist might face on a more or less regular basis. With these examples, we aim to provide you with the best practices for data annotation in isa.study.xlsx and isa.assay.xlsx files allowing you to generate machine-readable and thereby, interoperable and reproducible data. Do not hesitate to contact us if you think that we are missing some urgent examples or if you have any further questions.
 
-<a href="./index.html">
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
     <span class="badge-category">User</span><span class="badge-selected" id="badge-newbie">Newbie</span>
     <span class="badge-category">Mode</span><span class="badge-selected" id="badge-read">Read</span>
-</a>
-<br>
-<br>
+    </a>
+</div>
+
+
 
 ## Annotation of biological and technical replicates
 

src/docs/guides/arcCommander_QuickStart.md

@@ -15,18 +15,18 @@ date: 2023-06-09
 
 In this guide we focus on how to use the [ARC Commander](./../implementation/ArcCommander.html) to create your ARC and structure, store and share your data.
 
-<a href="./index.html">
-    <span class="badge-category">User</span><span class="badge-selected" id="badge-newbie">Newbie</span>
-    <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>
-</a>
-
-<br>
-<br>
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
+        <span class="badge-category">User</span><span class="badge-selected" id="badge-newbie">Newbie</span>
+        <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>
+    </a>
+</div>
 
 ## Before we can start
 
 :ballot_box_with_check: Please [install ARC Commander](./../ArcCommanderManual/index-setup.html)  
-:ballot_box_with_check: Find <a href="./tutorial_TheCommandLine.html" target="_blank">the command line</a> on your system  
+:ballot_box_with_check: Find <a href="./tutorial_TheCommandLine.html" target="_blank">the command line    </a>
+</div> on your system  
 :bulb: Consider reading about [ARC](./../implementation/AnnotatedResearchContext.html) and the [ARC Commander](./../implementation/ArcCommander.html)  
 :bulb: After concluding this quickstart, consider exploring the [ARC Commander manual](./../ArcCommanderManual/index.html) for a more detailed usage instruction.
 

src/docs/guides/arcCommander_QuickStart_expert.md

@@ -16,13 +16,12 @@ status: published
 
 In this guide we focus on how to use the [ARC Commander](./../implementation/ArcCommander.html) to create your ARC and structure, store and share your data.
 
-<a href="./index.html">
-    <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
-    <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>
-</a>
-
-<br>
-<br>
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
+        <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
+        <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>
+    </a>
+</div>
 
 ## Before we can start
 

src/docs/guides/arc_AddingExternalData.md

@@ -15,16 +15,12 @@ add sidebar: _sidebars/mainSidebar.md
 
 In this guide we recommend routines to properly add data from external sources to your ARC. 
 
-<a href="./index.html">
-    <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
-    <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>    
-</a>
-
-<br>
-<br>
-
-:warning:
-This guide presents an interim solution. We are working on a more user-friendly implementation.
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
+        <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
+        <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>    
+    </a>
+</div>
 
 ## Before we can start
 

src/docs/guides/arc_SyncingRecommendation.md

@@ -15,18 +15,12 @@ add sidebar: _sidebars/mainSidebar.md
 
 In this guide we elaborate recommendations on syncing your ARC via the [ARC Commander](./../implementation/ArcCommander.html) 
 
-<a href="./index.html">
+<div style="padding-bottom: 20px">
+    <a href="./index.html">
     <span class="badge-category">User</span><span class="badge-selected" id="badge-advanced">Advanced</span>
     <span class="badge-category">Mode</span><span class="badge-selected" id="badge-tutorial">Tutorial</span>    
-</a>
-
-<br>
-<br>
-
-
-:warning:
-This guide presents an interim solution. We are working on a more user-friendly implementation.
-
+    </a>
+</div>
 
 ## Before we can start
 
@@ -37,15 +31,17 @@ This guide presents an interim solution. We are working on a more user-friendly
 
 ## You have full control
 
-Unlike what you are used to from common cloud services, none of the ARC tools *automatically* or *passively* syncs your ARC between your computer and the DataHUB. You have to actively sync it. What may appear as an unwanted burden &ndash; "*Why do I have to do this myself?*" &ndash; actually grants you full access over what is happening with your ARC. First, it allows you to avoid syncing unwanted changes. For instance, consider adding a large amount of data, that may take some time to be uploaded into the DataHUB. You surely would want to decide yourself when to start the upload. Secondly, it allows you document your ARC's progress step by step. In general, the more you work with your ARC, the more you add or update, annotate or analyze data, the more you will want to make sure these changes are saved. Consider the syncing as a way to backup your project's progress as well as an "undo button".
+Unlike what you are used to from common cloud services, none of the ARC tools *automatically* or *passively* syncs your ARC between your computer and the DataHUB. You have to actively sync it. What may appear as a burden &ndash; "*Why do I have to do this myself?*" &ndash; actually grants you full access over what is happening with your ARC. First, it allows you to avoid syncing unwanted changes. For instance, consider adding a large amount of data, that may take some time to upload to the DataHUB. You surely would want to decide yourself when to start the upload. Secondly, it allows you document your ARC's progress step by step. In general, the more you work with your ARC, the more you add or update, annotate or analyze data, the more you will want to make sure these changes are saved. Consider the syncing as a way to backup your project's progress as well as an "undo button".
 
 :bulb: In the DataHUB, the individual sync steps are called "commit".
 
 ## Add a message to communicate your ARC's evolution
 
-We recommend [adding a message](./../ArcCommanderManual/arc_synchronization.html) that shortly summarizes, what you did since you last synced your ARC. 
+We recommend [adding a message](./../ArcCommanderManual/arc_synchronization.html) that shortly summarizes, what you did since you last synced your ARC.
+
+The following exemplifies adding commit messages via the ARC commander. The same function is provided by the ARCitect via the "Commit" menu.
 
-For instance: 
+For instance:
 
 1. You start a fresh ARC for your project
 
@@ -83,8 +79,6 @@ You can actually see all `arc sync` actions (i.e. commits) to your ARC in the Da
 
 <img src="./../img/datahub-commits.png" style="width:75%;display: block;margin-left: auto;margin-right: auto;">
 
-
-
 ## Undo latest changes
 
 4. Click on the latest (i.e. uppermost) commit.
@@ -96,7 +90,3 @@ You can actually see all `arc sync` actions (i.e. commits) to your ARC in the Da
 7. Click "Revert"
 
 <img src="./../img/datahub-commits-revert02.png" style="width:55%;display: block;margin-left: auto;margin-right: auto;">
-
-
-
-