Merge branch 'jlamossweeney-patch-1'

[ci skip]

This build is based on
e787e4c.

This commit was created by the following CI build and job:
https://github.com/plantbreeding/BrAPI-Manuscript2/commit/e787e4c0ef83569aff82e68b4b63bcd7fbb05973/checks
https://github.com/plantbreeding/BrAPI-Manuscript2/actions/runs/10045912670

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/24106c64f56ab519bceae0aa260b54223caf0fec/>.
+The permalink for this webpage version is <https://plantbreeding.github.io/BrAPI-Manuscript2/v/e787e4c0ef83569aff82e68b4b63bcd7fbb05973/>.
 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
-[`24106c64f56ab519bceae0aa260b54223caf0fec`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/24106c64f56ab519bceae0aa260b54223caf0fec).
+[`e787e4c0ef83569aff82e68b4b63bcd7fbb05973`](https://github.com/plantbreeding/BrAPI-Manuscript2/commit/e787e4c0ef83569aff82e68b4b63bcd7fbb05973).

index.html

@@ -127,8 +127,8 @@
   <meta name="dc.date" content="2024-07-22" />
   <meta name="citation_publication_date" content="2024-07-22" />
   <meta property="article:published_time" content="2024-07-22" />
-  <meta name="dc.modified" content="2024-07-22T16:12:50+00:00" />
-  <meta property="article:modified_time" content="2024-07-22T16:12:50+00:00" />
+  <meta name="dc.modified" content="2024-07-22T17:57:55+00:00" />
+  <meta property="article:modified_time" content="2024-07-22T17:57:55+00:00" />
   <meta name="dc.language" content="en-US" />
   <meta name="citation_language" content="en-US" />
   <meta name="dc.relation.ispartof" content="Manubot" />
@@ -361,9 +361,9 @@
   <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/24106c64f56ab519bceae0aa260b54223caf0fec/" />
-  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/24106c64f56ab519bceae0aa260b54223caf0fec/" />
-  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/24106c64f56ab519bceae0aa260b54223caf0fec/manuscript.pdf" />
+  <link rel="alternate" type="text/html" href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/e787e4c0ef83569aff82e68b4b63bcd7fbb05973/" />
+  <meta name="manubot_html_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/e787e4c0ef83569aff82e68b4b63bcd7fbb05973/" />
+  <meta name="manubot_pdf_url_versioned" content="https://plantbreeding.github.io/BrAPI-Manuscript2/v/e787e4c0ef83569aff82e68b4b63bcd7fbb05973/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" />
@@ -380,9 +380,9 @@ <h1 class="title">BrAPI Success Stories</h1>
 </header>
 <p><small><em>
 This manuscript
-(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/24106c64f56ab519bceae0aa260b54223caf0fec/">permalink</a>)
+(<a href="https://plantbreeding.github.io/BrAPI-Manuscript2/v/e787e4c0ef83569aff82e68b4b63bcd7fbb05973/">permalink</a>)
 was automatically generated
-from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/24106c64f56ab519bceae0aa260b54223caf0fec">plantbreeding/BrAPI-Manuscript2@24106c6</a>
+from <a href="https://github.com/plantbreeding/BrAPI-Manuscript2/tree/e787e4c0ef83569aff82e68b4b63bcd7fbb05973">plantbreeding/BrAPI-Manuscript2@e787e4c</a>
 on July 22, 2024.
 </em></small></p>
 <h2 id="authors">Authors</h2>
@@ -1260,11 +1260,11 @@ <h3 id="breeding-and-genetics-data-management">Breeding and Genetics Data Manage
 <p>While specialty data management is important for some use cases, often breeders want a central repository or access point of critical data. General breeding and genetics data management systems and web portals support some level of phenotypic, genotypic, and germplasm data, as well as trial, equipment, and people management. By enabling BrAPI support, these larger systems can connect with smaller tools and specialty systems to provide more functionality under the same user interface. There are several breeding data management systems developed in the BrAPI community, each with their own strengths.</p>
 <h4 id="bims">BIMS</h4>
 <!-- Sook -->
-<p><a href="https://wwww.breedwithbims.org">The Breeding Information Management System (BIMS)</a><span class="citation" data-cites="ArPSsaJQ"><sup><a href="#ref-ArPSsaJQ" role="doc-biblioref">35</a></sup></span> is a free, secure, online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data.
-BIMS enables individual breeders to have complete control of their own breeding data along with access to tools such as data import,export, analysis, and archiving for their germplasm, phenotype, genotype, and image data.
+<p>The <a href="https://wwww.breedwithbims.org">Breeding Information Management System (BIMS)</a><span class="citation" data-cites="ArPSsaJQ"><sup><a href="#ref-ArPSsaJQ" role="doc-biblioref">35</a></sup></span> is a free, secure, online breeding management system which allows breeders to store, manage, archive, and analyze their private breeding program data.
+BIMS enables individual breeders to have complete control of their own breeding data along with access to tools such as data import, export, analysis, and archiving for their germplasm, phenotype, genotype, and image data.
 BIMS is currently implemented in five community databases, the Genome Database for Rosaceae<span class="citation" data-cites="eaDrNpsp"><sup><a href="#ref-eaDrNpsp" role="doc-biblioref">37</a></sup></span>, CottonGEN<span class="citation" data-cites="dcg0274X"><sup><a href="#ref-dcg0274X" role="doc-biblioref">38</a></sup></span>, the Citrus Genome Database, the Pulse Crop Database, and the Genome Database for Vaccinium, where it enables individual breeders to import publicly available data.
 BIMS is also implemented in the public database <a href="https://wwww.breedwithbims.org">breedwithbims.org</a> that any crop breeder can use.</p>
-<p>BIMS primarily utilizes BrAPI to connect with Field Book<span class="citation" data-cites="MlqG0w6i"><sup><a href="#ref-MlqG0w6i" role="doc-biblioref">2</a></sup></span>, enabling seamless data transfer between data collection and subsequent managament in BIMS. Data transfer through BrAPI between BIMS and other resources such as Breedbase<span class="citation" data-cites="al3Hd9Ml"><sup><a href="#ref-al3Hd9Ml" role="doc-biblioref">11</a></sup></span>, GIGWA<span class="citation" data-cites="AVjkjraw"><sup><a href="#ref-AVjkjraw" role="doc-biblioref">17</a></sup></span>, and Breeder Genomics Hub is under development.</p>
+<p>BIMS primarily utilizes BrAPI to connect with Field Book<span class="citation" data-cites="MlqG0w6i"><sup><a href="#ref-MlqG0w6i" role="doc-biblioref">2</a></sup></span>, enabling seamless data transfer between data collection and subsequent management in BIMS. Data transfer through BrAPI between BIMS and other resources such as Breedbase<span class="citation" data-cites="al3Hd9Ml"><sup><a href="#ref-al3Hd9Ml" role="doc-biblioref">11</a></sup></span>, GIGWA<span class="citation" data-cites="AVjkjraw"><sup><a href="#ref-AVjkjraw" role="doc-biblioref">17</a></sup></span>, and Breeder Genomics Hub is under development.</p>
 <h4 id="bms">BMS</h4>
 <!-- Corina -->
 <p>The <a href="https://bmspro.io">Breeding Management System (BMS)</a>, developed by the <a href="https://integratedbreeding.net/">Integrated Breeding Platform (IBP)</a>, is a suite of tools designed to enhance the efficiency and effectiveness of plant breeding. BMS covers all stages of the breeding process, with the emphasis on germplasm management and <a href="https://cropontology.org">ontology</a>-harmonized phenotyping. It also features analytics and decision-support tools. With its focus on interoperability, BMS integrates smoothly with BrAPI, facilitating easy connections with a broad array of complementary tools and databases. Notably, the BMS is often deployed together with <a href="https://southgreen.fr/content/gigwa">Gigwa</a> to fulfill the genotyping data management needs of BMS users.</p>
@@ -1309,7 +1309,8 @@ <h3 id="analytics">Analytics</h3>
 <p>The tools developed by the BrAPI community can pull in data from multiple BrAPI compatible data sources and provide enhanced analytical functionality. In many cases, there is no longer a need to import and export large data files to a local computational environment just to run standard analytical models. These tools are able to extract the data they need from a data source without much human intervention or human error.</p>
 <h4 id="g-crunch">G-Crunch</h4>
 <!-- Josh -->
-<p>G-Crunch is an upcoming user-facing analysis tool that integrates genomic and phenotypic data to fulfill the need for simple, user driven analytics requests. It includes a generic user interface and the ability to swap out data sources and analysis tools. The G-Crunch team hopes to streamline repeatable, debuggable, simple analytic requests and results.</p>
+<p><a href="https://github.com/CornellILCI/G-CrunchUI">G-Crunch</a> is an upcoming user-facing tool to make simple, repeatable analysis requests. By using BrAPI calls to phenotypic and genotypic data sources, as well as an API currently implemented in <a href="https://github.com/CornellILCI/af-pipeline">Analytics Framework</a> similar to the proposed <a href="https://brapinewconceptpreview.docs.apiary.io/">Analytics NCP</a>, the lightweight UI can be used to specify and window incoming data, select specific analysis criteria built into Analytics Framework, and trigger any analytics pipeline that’s baked into the specific framework instance, such as sommer and ASREML based pipelines currently in Analytics Framework.</p>
+<p>Since each piece can be separately specified, this can allow flexibility to run ‘test’ analyses on small data sets with small or local analytics instances, and quickly re-point G-Crunch to a larger organizational or cloud-based Analytics Framework and/or data set, without having to worry about moving data around or introducing errors in manually triggering the analysis steps.</p>
 <p>G-Crunch, as a tool, couldn’t feasibly exist without BrAPI. The support of BrAPI interfaces allows G-Crunch to use one unified request method, and adapt to the user’s existing network of BrAPI-compliant tools. This lowers the barrier to entry for adoption, and makes analysis pipelines easily repeatable.</p>
 <h4 id="qbms">QBMS</h4>
 <!-- Khaled -->