Merge pull request #56 from plantbreeding/aliceboizet-patch-2

[ci skip]

This build is based on
4a8c6b0.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/4a8c6b0fdd2e0be8754e9e701e2f7a251c07d1dd/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/9668497385

manuscript.html

@@ -52,6 +52,7 @@
   <meta name="author" content="Lukas Mueller" />
   <meta name="author" content="Moses Nderitu" />
   <meta name="author" content="Cyril Pommier" />
+  <meta name="author" content="Jean-François Rami" />
   <meta name="author" content="Sebastian Raubach" />
   <meta name="author" content="Trevor Rife" />
   <meta name="author" content="Mathieu Rouard" />
@@ -113,8 +114,8 @@
   <meta name="dc.date" content="2024-06-25" />
   <meta name="citation_publication_date" content="2024-06-25" />
   <meta property="article:published_time" content="2024-06-25" />
-  <meta name="dc.modified" content="2024-06-25T19:31:16+00:00" />
-  <meta property="article:modified_time" content="2024-06-25T19:31:16+00:00" />
+  <meta name="dc.modified" content="2024-06-25T19:32:42+00:00" />
+  <meta property="article:modified_time" content="2024-06-25T19:32:42+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -254,6 +255,10 @@
   <meta name="citation_author_institution" content="Université Paris-Saclay, INRAE, Bioinformatics, Plant Bioinformatics Facility, Versailles, France" />
   <meta name="citation_author_institution" content="Université Paris-Saclay, INRAE, URGI, Versailles, France" />
   <meta name="citation_author_orcid" content="0000-0002-9040-8733" />
+  <meta name="citation_author" content="Jean-François Rami" />
+  <meta name="citation_author_institution" content="CIRAD, UMR AGAP Institut, Montpellier, France." />
+  <meta name="citation_author_institution" content="AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France." />
+  <meta name="citation_author_orcid" content="0000-0002-5679-3877" />
   <meta name="citation_author" content="Sebastian Raubach" />
   <meta name="citation_author_institution" content="The James Hutton Institute" />
   <meta name="citation_author_orcid" content="0000-0001-5659-247X" />
@@ -296,9 +301,9 @@
   <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/387443d3d57f2b145e9799f428bf6e9ae8246e1f/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/387443d3d57f2b145e9799f428bf6e9ae8246e1f/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/387443d3d57f2b145e9799f428bf6e9ae8246e1f/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/4a8c6b0fdd2e0be8754e9e701e2f7a251c07d1dd/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/4a8c6b0fdd2e0be8754e9e701e2f7a251c07d1dd/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/4a8c6b0fdd2e0be8754e9e701e2f7a251c07d1dd/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" />
@@ -315,9 +320,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/387443d3d57f2b145e9799f428bf6e9ae8246e1f/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/4a8c6b0fdd2e0be8754e9e701e2f7a251c07d1dd/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/387443d3d57f2b145e9799f428bf6e9ae8246e1f">plantbreeding/BrAPI-Manuscript2@387443d</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/4a8c6b0fdd2e0be8754e9e701e2f7a251c07d1dd">plantbreeding/BrAPI-Manuscript2@4a8c6b0</a>
 on June 25, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -706,6 +711,16 @@ <h2 id="authors">Authors</h2>
 Université Paris-Saclay, INRAE, Bioinformatics, Plant Bioinformatics Facility, Versailles, France; Université Paris-Saclay, INRAE, URGI, Versailles, France
 · Funded by This work was supported by the Agence Nationale de la Recherche, programme Investissements d’avenir, ANR-11-INBS-0012 (Phenome)
 </small></p></li>
+<li><p><strong>Jean-François Rami</strong>
+<br>
+<img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
+<a href="https://orcid.org/0000-0002-5679-3877">0000-0002-5679-3877</a>
+· <img src="images/github.svg" class="inline_icon" width="16" height="16" alt="GitHub icon" />
+<a href="https://github.com/jframi">jframi</a>
+<br>
+<small>
+CIRAD, UMR AGAP Institut, Montpellier, France.; AGAP Institut, CIRAD, INRAE, Institut Agro, Université de Montpellier, Montpellier, France.
+</small></p></li>
 <li><p><strong>Sebastian Raubach</strong>
 <br>
 <img src="images/orcid.svg" class="inline_icon" width="16" height="16" alt="ORCID icon" />
@@ -1012,6 +1027,24 @@ <h4 id="sct">SCT</h4>
 <!-- Add this sentence if the repository becomes public -->
 <!-- The modularized, open source code is available in a [GitHub repository](https://github.com/USDA-ARS-GBRU/SugarcaneCrossingTool) for community reference and reuse.  -->
 <p>The crossing tool utilizes a modified version of the <a href="https://github.com/CIP-RIU/brapi">BrAPI-R</a> library to access a compliant database, and it employs standard R/JavaScript packages to aggregate and visualize data. Modules within the application allow breeders to query the database (through BrAPI) for information relevant to their decision-making process. This includes the number and sex of flowering accessions, deep pedigree and relatedness information, summarized trial data, and the prior frequency and success of potential cross combinations. Future versions of this tool will provide additional decision support (e.g. ranked potential crosses) to enhance the accuracy and efficiency of crossing.</p>
+<h4 id="shinybrapps">ShinyBrAPPs</h4>
+<p>Data management systems are generic and robust centralized applications, with a large community of users, long term development cycles and release plans.
+BrAPI compliance offers these systems the opportunity to add functionalities in a modular way through the development of external plugin applications that can
+quickly fulfill specific needs of a group of users. <a href="https://shiny.posit.co/">R-Shiny</a> is a R-package that opens the possibility to develop rich and productive
+interactive web applications to R users and developers. As such it allows user communities to quickly prototype and produce applications that are finely tailored to their needs,
+thus improving adoption and daily use of data management systems. The Breeding Management System (BMS) of the IBP and Gigwa are BrAPI compliant and are being widely used by breeding programs,
+including national breeding programs in Africa. CIRAD and the IBP teams have been working together as part of the <a href="https://www.iavao.org/">IAVAO</a> breeders community to develop the Shiny-BrAPPs,
+a set of R-Shiny applications using BrAPI as a core technology for data exchange. These applications are connected to BMS and/or Gigwa and provide tools for specific use cases.
+So far, four applications have been developed covering the fields of trial data quality control, single trial statistical analysis, breeding decision support, and raw genotyping data visual inspection.
+The first three of them are grouped into a single R-package (<a href="https://github.com/IntegratedBreedingPlatform/ShinyBrAPPs/">ShinyBrAPPs</a>) with modular code shared across applications and make use of the <a href="https://github.com/mverouden/brapir-v1">brapir-v1</a> and
+<a href="https://github.com/mverouden/brapir-v2">brapir-v2</a> R packages.</p>
+<ul>
+<li><strong>BMS trial data explorer</strong> retrieves data from a single multi-location trial and displays data counts and summary boxplot for all variables measured in different studies.
+It also provides an interactive distribution plot to easily select observations that require curation and a report of candidate issues that needs to be addressed by the breeder.</li>
+<li><strong>STABrAPP</strong> is an application for single trial mixed model analysis. It basically provides a GUI to the <a href="https://biometris.github.io/statgenSTA/">StatGen-STA</a> R package.</li>
+<li><strong>DSBrAPP</strong> is a decision support tool helping breeders to select germplasm according to their various characteristics and save this germplasm list into BMS.</li>
+<li><strong><a href="https://github.com/jframi/snpclust">snplust</a></strong> enables to check and manually correct the clustering of fluorescence based SNP genotyping data.</li>
+</ul>
 <h3 id="general-infrastructure">General Infrastructure</h3>
 <p>Adopting BrAPI compatibility into an existing system can be difficult sometimes. The BrAPI Community has developed several tools to make adoption easier. This includes things like pre built code libraries, connectors to other technology standards, and mappers to alternate data types or data files. The goal is to lower the barrier to entry for the BrAPI community, making it easier for other groups to get started and connect their existing data to the standard.</p>
 <h4 id="mira">MIRA</h4>
@@ -1079,7 +1112,7 @@ <h2 class="page_break_before" id="author-contributions">Author Contributions</h2
 <li><strong>Jan Erik Backlund</strong>: Jan Erik has made significant contributions to the BMS project.</li>
 <li><strong>Aldrin Batac</strong>: Aldrin has made significant contributions to the BMS project.</li>
 <li><strong>Sebastian Beier</strong>: Sebastian wrote the section on the DivBrowse project, and has made significant contributions to the BrAPI compatibility of the DivBrowse project.</li>
-<li><strong>Alice Boizet</strong>: Alice wrote the section on the Florilège project, and has made significant contributions to the BrAPI compatibility of the Florilège and Faidare projects.</li>
+<li><strong>Alice Boizet</strong>: Alice wrote the section on the Florilège project, and has made significant contributions to the BrAPI compatibility of the Florilège, Gigwa and ShinyBrAPPs projects.</li>
 <li><strong>Matthijs Brouwer</strong>: Matthijs has made significant contributions to the AGENT Portal project.</li>
 <li><strong>Terry Casstevens</strong>: Terry has made significant contributions to the PHG project.</li>
 <li><strong>Keo Corak</strong>: Keo wrote the section on the SCT project, and has made significant contributions to the BrAPI compatibility of the SCT project.</li>
@@ -1115,6 +1148,7 @@ <h2 class="page_break_before" id="author-contributions">Author Contributions</h2
 <li><strong>Lukas Mueller</strong>: Lukas wrote the section on the Breedbase project, and has made significant contributions to the BrAPI compatibility of the Breedbase project. Lukas is also Co-PI on the current BrAPI Grant and has supported the project since its inception.</li>
 <li><strong>Moses Nderitu</strong>: Moses wrote the section on the DArTView project, and has made significant contributions to the BrAPI compatibility of the DArTView project.</li>
 <li><strong>Cyril Pommier</strong>: Cyril wrote the section on the Faidare project, and has made significant contributions to the BrAPI compatibility of the Florilège, Faidare, and AGENT Portal projects.</li>
+<li><strong>Jean-François Rami</strong>: Jean-François wrote the section on the ShinyBrAPPs project, and has made significant contributions to the BrAPI compatibility of the ShinyBrAPPs project.</li>
 <li><strong>Sebastian Raubach</strong>: Sebastian wrote the sections on the GridScore and Germinate projects, and has made significant contributions to the BrAPI compatibility of the GridScore, Germinate, and Flapjack projects.</li>
 <li><strong>Trevor Rife</strong>: Trevor has made significant contributions to the Field Book project.</li>
 <li><strong>Mathieu Rouard</strong>: Mathieu wrote the section on the MGIS project, and has made significant contributions to the BrAPI compatibility of the MGIS project.</li>