Merge pull request #14 from imilne/main

[ci skip]

This build is based on
0109992.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/01099920e3c55a7717d76b4e4d08ade7e262628d/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/8191622430

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/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/01099920e3c55a7717d76b4e4d08ade7e262628d/>.
 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
-[`34cb3cc3ace4c4921c57b3c936882bc39ecebc4e`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e).
+[`01099920e3c55a7717d76b4e4d08ade7e262628d`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/01099920e3c55a7717d76b4e4d08ade7e262628d).

index.html

@@ -18,7 +18,7 @@
   <meta name="author" content="Terry Casstevens" />
   <meta name="author" content="Sook Jung" />
   <meta name="author" content="Taein Lee" />
-  <meta name="dcterms.date" content="2024-03-01" />
+  <meta name="dcterms.date" content="2024-03-07" />
   <meta name="keywords" content="brapi, breeding, api, standards, community" />
   <title>BrAPI Success Stories</title>
   <style>
@@ -63,11 +63,11 @@
   <meta name="citation_title" content="BrAPI Success Stories" />
   <meta property="og:title" content="BrAPI Success Stories" />
   <meta property="twitter:title" content="BrAPI Success Stories" />
-  <meta name="dc.date" content="2024-03-01" />
-  <meta name="citation_publication_date" content="2024-03-01" />
-  <meta property="article:published_time" content="2024-03-01" />
-  <meta name="dc.modified" content="2024-03-01T15:49:02+00:00" />
-  <meta property="article:modified_time" content="2024-03-01T15:49:02+00:00" />
+  <meta name="dc.date" content="2024-03-07" />
+  <meta name="citation_publication_date" content="2024-03-07" />
+  <meta property="article:published_time" content="2024-03-07" />
+  <meta name="dc.modified" content="2024-03-07T16:36:06+00:00" />
+  <meta property="article:modified_time" content="2024-03-07T16:36:06+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -121,9 +121,9 @@
   <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/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01099920e3c55a7717d76b4e4d08ade7e262628d/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01099920e3c55a7717d76b4e4d08ade7e262628d/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01099920e3c55a7717d76b4e4d08ade7e262628d/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" />
@@ -140,10 +140,10 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/01099920e3c55a7717d76b4e4d08ade7e262628d/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/34cb3cc3ace4c4921c57b3c936882bc39ecebc4e">plantbreeding/BrAPI-Manuscript2@34cb3cc</a>
-on March 1, 2024.
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/01099920e3c55a7717d76b4e4d08ade7e262628d">plantbreeding/BrAPI-Manuscript2@0109992</a>
+on March 7, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
 <ul>
@@ -428,7 +428,7 @@ <h3 id="data-visualization">Data visualization</h3>
 * future related use cases, areas to improve -->
 <h4 id="flapjack">Flapjack</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
-<p>Flapjack is a desktop application for visualizing and analyzing genotype data. Data can be easily imported into Flapjack from any BrAPI compatible data source with genotype data available. Flapjack Bytes is the smaller, web based counterpart to Flapjack, which can be imbedded into a database website and provide the visualizations online.</p>
+<p><a href="https://ics.hutton.ac.uk/flapjack">Flapjack</a> <span class="citation" data-cites="Wz8l0HlN">[<a href="#ref-Wz8l0HlN" role="doc-biblioref">7</a>]</span> is a multiplatform desktop application for data visualization and breeding analysis (eg, pedigree verification, marker-assisted backcrossing and forward breeding) using high-throughput genotype data. Data can be easily imported into Flapjack from any BrAPI compatible data source with genotype data available. <a href="https://github.com/cropgeeks/flapjack-bytes">Flapjack Bytes</a> is a smaller, lightweight and fully web-based counterpart to Flapjack, which can be easily embedded into a database website to provide similiar visualizations online. Traditionally supporting its own text-based data formats, Flapjack’s use of BrAPI has streamlined the end-user experience for data import and work is underway to determine the best methods to exchange analysis results using future versions of the API.</p>
 <h4 id="helium">Helium</h4>
 <!-- Peter S: Stub paragraph to stimulate the writing process. Please edit, rewrite, or delete as needed. -->
 <p>Helium is a platform for reviewing and managing pedigree data. It is BrAPI enabled, so pedigree data can be viewed straight from a database.</p>
@@ -537,6 +537,9 @@ <h2 class="page_break_before" id="references">References</h2>
 <div id="ref-sW9euzzP" class="csl-entry" role="doc-biblioentry">
 <div class="csl-left-margin">6. </div><div class="csl-right-inline"><strong>From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives</strong> <div class="csl-block">Sebastian Raubach, Benjamin Kilian, Kate Dreher, Ahmed Amri, Filippo M Bassi, Ousmane Boukar, Douglas Cook, Alan Cruickshank, Christian Fatokun, Noureddine El Haddad, … </div> <em>Crop Science</em> (2020-08-20) <a href="https://doi.org/gm66th">https://doi.org/gm66th</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1002/csc2.20248">10.1002/csc2.20248</a></div></div>
 </div>
+<div id="ref-Wz8l0HlN" class="csl-entry" role="doc-biblioentry">
+<div class="csl-left-margin">7. </div><div class="csl-right-inline"><strong>Flapjack—graphical genotype visualization</strong> <div class="csl-block">Iain Milne, Paul Shaw, Gordon Stephen, Micha Bayer, Linda Cardle, William TB Thomas, Andrew J Flavell, David Marshall</div> <em>Bioinformatics</em> (2010-10-18) <a href="https://doi.org/cdvnt8">https://doi.org/cdvnt8</a> <div class="csl-block">DOI: <a href="https://doi.org/10.1093/bioinformatics/btq580">10.1093/bioinformatics/btq580</a> · PMID: <a href="https://www.ncbi.nlm.nih.gov/pubmed/20956241">20956241</a> · PMCID: <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995120">PMC2995120</a></div></div>
+</div>
 </div>
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