app list figure

[ci skip] This build is based on 767c0d9. This commit was created by the following CI build and job: https://github.com/plantbreeding/BrAPI-Manuscript2/commit/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/checks https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/9423128900
plantbreeding · Jun 7, 2024 · 3d95c7b · 3d95c7b
1 parent fd6ef17
commit 3d95c7b
Show file tree

Hide file tree

Showing 35 changed files with 4,405 additions and 21 deletions.
diff --git a/README.md b/README.md
@@ -1,7 +1,7 @@
 # Output directory containing the formatted manuscript
 
 The [`gh-pages`](https://github.com/plantbreeding/BrAPI-Manuscript2/tree/gh-pages) branch hosts the contents of this directory at <https://plantbreeding.github.io/BrAPI-Manuscript2/>.
-The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/25d2a730abc404a4178c5198802d0d15cff54ad6/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/>.
 To redirect to the permalink for the latest manuscript version at anytime, use the link <https://plantbreeding.github.io/BrAPI-Manuscript2/v/freeze/>.
 
 ## Files
@@ -35,4 +35,4 @@ Verifying timestamps with the `ots verify` command requires running a local bitc
 ## Source
 
 The manuscripts in this directory were built from
-[`25d2a730abc404a4178c5198802d0d15cff54ad6`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/25d2a730abc404a4178c5198802d0d15cff54ad6).
+[`767c0d9314ee8cd442f8135b6b7ea6ae874a78e0`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0).
diff --git a/images/BrAPI_Application_Chart-1.png b/images/BrAPI_Application_Chart-1.png
diff --git a/images/BrAPI_Application_Chart.pdf b/images/BrAPI_Application_Chart.pdf
diff --git a/images/BrAPI_Application_Chart.xlsx b/images/BrAPI_Application_Chart.xlsx
diff --git a/images/BrAPI_Paper_Applications_Chart.png b/images/BrAPI_Paper_Applications_Chart.png
diff --git a/index.html b/index.html
@@ -112,8 +112,8 @@
   <meta name="dc.date" content="2024-06-07" />
   <meta name="citation_publication_date" content="2024-06-07" />
   <meta property="article:published_time" content="2024-06-07" />
-  <meta name="dc.modified" content="2024-06-07T13:30:38+00:00" />
-  <meta property="article:modified_time" content="2024-06-07T13:30:38+00:00" />
+  <meta name="dc.modified" content="2024-06-07T21:08:26+00:00" />
+  <meta property="article:modified_time" content="2024-06-07T21:08:26+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -286,9 +286,9 @@
   <meta name="citation_fulltext_html_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/" />
   <meta name="citation_pdf_url" content="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
   <link rel="alternate" type="application/pdf" href="https://plantbreeding.github.io/BrAPI-Manuscript2/manuscript.pdf" />
-  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/25d2a730abc404a4178c5198802d0d15cff54ad6/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/25d2a730abc404a4178c5198802d0d15cff54ad6/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/25d2a730abc404a4178c5198802d0d15cff54ad6/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/manuscript.pdf" />
   <meta property="og:type" content="article" />
   <meta property="twitter:card" content="summary_large_image" />
   <link rel="icon" type="image/png" sizes="192x192" href="https://manubot.org/favicon-192x192.png" />
@@ -305,9 +305,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/25d2a730abc404a4178c5198802d0d15cff54ad6/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/25d2a730abc404a4178c5198802d0d15cff54ad6">plantbreeding/BrAPI-Manuscript2@25d2a73</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0">plantbreeding/BrAPI-Manuscript2@767c0d9</a>
 on June 7, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -821,7 +821,13 @@ <h3 id="community-growth">Community Growth</h3>
 <p>The BrAPI Hackathons are a major staple of the BrAPI community. Twice a year, the community gathers to discuss the specification and collaborate on BrAPI related projects. This time is very valuable to the community; for some organizations, the hackathon is the only time during the year when they have time to work on anything related to BrAPI. During the COVID-19 pandemic, virtual hackathons took the place of in person events. While the virtual hackathons do not provide the same level of face-to-face time that is crucial to collaborative work, they did allow for more attendees to gather and share their opinions. Going forward, the community leadership has decided to have one in-person hackathon and one virtual hackathon each year, to balance the advantages of both.</p>
 <h2 id="success-stories">Success Stories</h2>
 <!-- success stories highlighting BrAPI usefulness in breeding cycle. Perhaps reference the original BrAPI paper where possible use cases were proposed.  -->
-<p>Below are a number of short success stories from the BrAPI community. These tools, applications, and infrastructure projects serve as another indicator of community growth and success over the past 5-10 years. These stories clearly illustrate all the different ways the BrAPI Standard can be used productively and in practice.</p>
+<p>Below are a number of short success stories from the BrAPI community. These tools, applications, and infrastructure projects serve as another indicator of community growth and success over the past 5-10 years. These stories clearly illustrate all the different ways the BrAPI Standard can be used productively and in practice. Figure <a href="#fig:apps">2</a> contains a summary of the tools described below.</p>
+<div id="fig:apps" class="fignos">
+<figure>
+<img src="images/BrAPI_Paper_Applications_Chart.png" style="width:100.0%" alt="Figure 2: A summary of all the tools described below and the general areas each tool is designed to handle" />
+<figcaption aria-hidden="true"><span>Figure 2:</span> A summary of all the tools described below and the general areas each tool is designed to handle</figcaption>
+</figure>
+</div>
 <h3 id="phenotyping">Phenotyping</h3>
 <p>Phenotyping is the basis for all breeding efforts. All the downstream analysis and decision making procedures rely on a foundation of accurate, high-quality, phenotypic data. The BrAPI specification supports phenotypic data as it passes through the entire breeding pipeline, as it is published, and as it is archived. The community has developed tools that use BrAPI during the data collection process, to get the data into a standard format as soon as possible. There are BrAPI compatible systems to store and curate phenotypic data, and tools to manage trait meta data. The community has also begun developing BrAPI compatible tools for managing images and other high throughput phenotyping techniques.</p>
 <h4 id="field-book">Field Book</h4>

diff --git a/manuscript.pdf b/manuscript.pdf
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/AGENT_Genotyping_Data_Flow.png b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/AGENT_Genotyping_Data_Flow.png
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/AGENT_WebFrontend.pptx b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/AGENT_WebFrontend.pptx
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/AGENT_Web_Frontend.png b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/AGENT_Web_Frontend.png
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Application_Chart-1.png b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Application_Chart-1.png
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Application_Chart.pdf b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Application_Chart.pdf
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Application_Chart.xlsx b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Application_Chart.xlsx
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Domains_v2-1_vertical.png b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Domains_v2-1_vertical.png
diff --git a/...c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Paper_Applications_Chart.png b/...c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_Paper_Applications_Chart.png
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_org_structure.jpg b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/BrAPI_org_structure.jpg
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/Schema_FAIDARE.png b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/Schema_FAIDARE.png
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/Schema_Florilege.jpg b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/Schema_Florilege.jpg
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/github.svg b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/github.svg
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/mastodon.svg b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/mastodon.svg
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/orcid.svg b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/orcid.svg
diff --git a/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/twitter.svg b/v/767c0d9314ee8cd442f8135b6b7ea6ae874a78e0/images/twitter.svg