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geoepi · Jul 3, 2024 · 11877fe · 11877fe
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diff --git a/.Rproj.user/FFAE6732/sources/prop/B84A27FA b/.Rproj.user/FFAE6732/sources/prop/B84A27FA
@@ -3,5 +3,5 @@
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+    "scrollLine": "0"
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diff --git a/.quarto/xref/23844f6f b/.quarto/xref/23844f6f
@@ -1 +1 @@
-{"headings":[],"entries":[],"options":{"chapters":true}}
+{"entries":[],"headings":[],"options":{"chapters":true}}
diff --git a/.quarto/xref/d37314d0 b/.quarto/xref/d37314d0
@@ -1 +1 @@
-{"headings":["geoepi-research-group"],"entries":[],"options":{"chapters":true}}
+{"entries":[],"options":{"chapters":true},"headings":["geoepi-research-group"]}
diff --git a/access.qmd b/access.qmd
@@ -24,16 +24,19 @@ editor_options:
 
 Accessing workflows, supporting information, and shared resources described in the [**Project Management** section](https://geoepi.github.io/Notebook/proj_management.html) may require creating individual user accounts on several platforms.  Although the needs for individual projects will vary, it is suggested to create accounts to access the services listed below.    
 
-### 1.    GitHub  
+### 1.    SCINet    
+The [Agricultural Research Service's **SCINet**](https://scinet.usda.gov/) program provides access to the ARS's High-Performance Computing Clusters, data storage at the National Agricultural Library, and a wide variety of other resources.  Access to non-ARS employees must be sponsored by an ARS scientist.  Once the need to access SCINet has been identified and,  if necessary, a sponsor has been identified, SCINet accounts can be [requested here](https://scinet.usda.gov/about/signup).     
+
+### 2.    GitHub  
 If you don't have a GitHub account, please [create one](https://github.com).  Once you have a GitHub account, ensure that your GitHub username has been shared with project PIs and collaborators to be authorized access to repositories, the [GeoEpi team site](https://github.com/geoepi), and possibly the [USDA ARS Enterprise solution](https://github.com/USDA-REE-ARS).  
 
-### 2.    Overleaf  
+### 3.    Overleaf  
 [Overleaf](https://overleaf.com) is a collaborative online LaTeX editor to help write, edit, and publish scientific and technical documents.    
 
-### 3.    Open Science Framework (OSF)    
+### 4.    Open Science Framework (OSF)    
 [OSF](https://osf.io/) is a free and open-source project management tool that makes it easy to collaborate throughout a project's lifecycle.  Although a portion of the group's information and data are publicly visible on OSF, there is much viewable only to account holders with authorized access.  As with GitHub, please check with project PIs and leads to ensure your OSF account has been granted access to all needed resources on the site.  
 
-### 4.    Zotero    
+### 5.    Zotero    
 [Zotero account](https://www.zotero.org/user/register) is reference management software.  Although the overall functionality of Zotero, is comparable to platforms such as [Mendeley](https://www.mendeley.com/) and [EndNote](https://endnote.com/), Zotero provides a simple web browser to create shared reference libraries and citation data bases;this functionality is used to organize the [group's shared publications](https://geoepi.github.io/Notebook/zotero.html).  Even if you use different reference management software, you are encouraged to [create a Zotero account](https://www.zotero.org/user/register) to access the group libraries.  
 
 

diff --git a/docs/access.html b/docs/access.html
@@ -183,20 +183,24 @@ <h1 class="title d-none d-lg-block"><span class="chapter-number">1</span>&nbsp;
 <section id="accounts-and-permissions" class="level1">
 <h1><strong>Accounts and Permissions</strong></h1>
 <p>Accessing workflows, supporting information, and shared resources described in the <a href="https://geoepi.github.io/Notebook/proj_management.html"><strong>Project Management</strong> section</a> may require creating individual user accounts on several platforms. Although the needs for individual projects will vary, it is suggested to create accounts to access the services listed below.</p>
+<section id="scinet" class="level3">
+<h3 data-anchor-id="scinet">1. SCINet</h3>
+<p>The <a href="https://scinet.usda.gov/">Agricultural Research Service’s <strong>SCINet</strong></a> program provides access to the ARS’s High-Performance Computing Clusters, data storage at the National Agricultural Library, and a wide variety of other resources. Access to non-ARS employees must be sponsored by an ARS scientist. Once the need to access SCINet has been identified and, if necessary, a sponsor has been identified, SCINet accounts can be <a href="https://scinet.usda.gov/about/signup">requested here</a>.</p>
+</section>
 <section id="github" class="level3">
-<h3 data-anchor-id="github">1. GitHub</h3>
+<h3 data-anchor-id="github">2. GitHub</h3>
 <p>If you don’t have a GitHub account, please <a href="https://github.com">create one</a>. Once you have a GitHub account, ensure that your GitHub username has been shared with project PIs and collaborators to be authorized access to repositories, the <a href="https://github.com/geoepi">GeoEpi team site</a>, and possibly the <a href="https://github.com/USDA-REE-ARS">USDA ARS Enterprise solution</a>.</p>
 </section>
 <section id="overleaf" class="level3">
-<h3 data-anchor-id="overleaf">2. Overleaf</h3>
+<h3 data-anchor-id="overleaf">3. Overleaf</h3>
 <p><a href="https://overleaf.com">Overleaf</a> is a collaborative online LaTeX editor to help write, edit, and publish scientific and technical documents.</p>
 </section>
 <section id="open-science-framework-osf" class="level3">
-<h3 data-anchor-id="open-science-framework-osf">3. Open Science Framework (OSF)</h3>
+<h3 data-anchor-id="open-science-framework-osf">4. Open Science Framework (OSF)</h3>
 <p><a href="https://osf.io/">OSF</a> is a free and open-source project management tool that makes it easy to collaborate throughout a project’s lifecycle. Although a portion of the group’s information and data are publicly visible on OSF, there is much viewable only to account holders with authorized access. As with GitHub, please check with project PIs and leads to ensure your OSF account has been granted access to all needed resources on the site.</p>
 </section>
 <section id="zotero" class="level3">
-<h3 data-anchor-id="zotero">4. Zotero</h3>
+<h3 data-anchor-id="zotero">5. Zotero</h3>
 <p><a href="https://www.zotero.org/user/register">Zotero account</a> is reference management software. Although the overall functionality of Zotero, is comparable to platforms such as <a href="https://www.mendeley.com/">Mendeley</a> and <a href="https://endnote.com/">EndNote</a>, Zotero provides a simple web browser to create shared reference libraries and citation data bases;this functionality is used to organize the <a href="https://geoepi.github.io/Notebook/zotero.html">group’s shared publications</a>. Even if you use different reference management software, you are encouraged to <a href="https://www.zotero.org/user/register">create a Zotero account</a> to access the group libraries.</p>
 
 

diff --git a/docs/references.html b/docs/references.html
@@ -49,7 +49,7 @@
 <script src="site_libs/quarto-search/fuse.min.js"></script>
 <script src="site_libs/quarto-search/quarto-search.js"></script>
 <meta name="quarto:offset" content="./">
-<link href="./overleaf.html" rel="prev">
+<link href="./zotero.html" rel="prev">
 <script src="site_libs/quarto-html/quarto.js"></script>
 <script src="site_libs/quarto-html/popper.min.js"></script>
 <script src="site_libs/quarto-html/tippy.umd.min.js"></script>
@@ -139,27 +139,37 @@ <h1 class="quarto-secondary-nav-title">References</h1>
       <ul id="quarto-sidebar-section-1" class="collapse list-unstyled sidebar-section depth1 show">  
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./version_control.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Version Control</span></a>
+  <a href="./access.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">1</span>&nbsp; <span class="chapter-title">Resource Access</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./github_elements.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">GitHub Elements</span></a>
+  <a href="./version_control.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">2</span>&nbsp; <span class="chapter-title">Version Control</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./repo_components.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">GH Repo Components</span></a>
+  <a href="./github_elements.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">3</span>&nbsp; <span class="chapter-title">GitHub Elements</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./openscifw.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">Data Storage (OSF)</span></a>
+  <a href="./repo_components.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">4</span>&nbsp; <span class="chapter-title">GH Repo Components</span></a>
   </div>
 </li>
           <li class="sidebar-item">
   <div class="sidebar-item-container"> 
-  <a href="./overleaf.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">LaTeX and Overleaf</span></a>
+  <a href="./data_store.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">Data Storage</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./overleaf.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">6</span>&nbsp; <span class="chapter-title">LaTeX and Overleaf</span></a>
+  </div>
+</li>
+          <li class="sidebar-item">
+  <div class="sidebar-item-container"> 
+  <a href="./zotero.html" class="sidebar-item-text sidebar-link"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Reference Management</span></a>
   </div>
 </li>
       </ul>
@@ -338,8 +348,8 @@ <h1 class="title d-none d-lg-block">References</h1>
 </script>
 <nav class="page-navigation">
   <div class="nav-page nav-page-previous">
-      <a href="./overleaf.html" class="pagination-link">
-        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">5</span>&nbsp; <span class="chapter-title">LaTeX and Overleaf</span></span>
+      <a href="./zotero.html" class="pagination-link">
+        <i class="bi bi-arrow-left-short"></i> <span class="nav-page-text"><span class="chapter-number">7</span>&nbsp; <span class="chapter-title">Reference Management</span></span>
       </a>          
   </div>
   <div class="nav-page nav-page-next">

diff --git a/docs/search.json b/docs/search.json
@@ -151,6 +151,13 @@
     "href": "zotero.html",
     "title": "7  Reference Management",
     "section": "",
-    "text": "Group Libraries\nThe group has started to compile shared literature for focal disease systems, technical methods, and other topics relevant to our research. Below is a list of these libraries.\nNote that the links below direct to the public facing versions of the libraries that only allow for viewing document descriptions. To access the documents themselves (PDFs, Word Docs, etc), modify existing records, or to contribute additional publications you will need to request access using a Zotero account.\n\nFoot and Mouth Disease (FMD)\n\nFeral Swine\nFlavivirus\n\nVesicular stomatitis"
+    "text": "Group Libraries\nThe group has started to compile shared literature for focal disease systems, technical methods, and other topics relevant to our research. Below is a list of these libraries.\nNote that the links below direct to the public facing versions of the libraries that only allow for viewing document descriptions. To access the documents themselves (PDFs, Word Docs, etc), modify existing records, or to contribute additional publications you will need to request access using a Zotero account.\n\nMethods\n\nFoot and Mouth Disease (FMD)\n\nFeral Swine\nFlavivirus\n\nVesicular stomatitis"
+  },
+  {
+    "objectID": "access.html",
+    "href": "access.html",
+    "title": "1  Resource Access",
+    "section": "",
+    "text": "Accounts and Permissions\nAccessing workflows, supporting information, and shared resources described in the Project Management section may require creating individual user accounts on several platforms. Although the needs for individual projects will vary, it is suggested to create accounts to access the services listed below.\n\n1. SCINet\nThe Agricultural Research Service’s SCINet program provides access to the ARS’s High-Performance Computing Clusters, data storage at the National Agricultural Library, and a wide variety of other resources. Access to non-ARS employees must be sponsored by an ARS scientist. Once the need to access SCINet has been identified and, if necessary, a sponsor has been identified, SCINet accounts can be requested here.\n\n\n2. GitHub\nIf you don’t have a GitHub account, please create one. Once you have a GitHub account, ensure that your GitHub username has been shared with project PIs and collaborators to be authorized access to repositories, the GeoEpi team site, and possibly the USDA ARS Enterprise solution.\n\n\n3. Overleaf\nOverleaf is a collaborative online LaTeX editor to help write, edit, and publish scientific and technical documents.\n\n\n4. Open Science Framework (OSF)\nOSF is a free and open-source project management tool that makes it easy to collaborate throughout a project’s lifecycle. Although a portion of the group’s information and data are publicly visible on OSF, there is much viewable only to account holders with authorized access. As with GitHub, please check with project PIs and leads to ensure your OSF account has been granted access to all needed resources on the site.\n\n\n5. Zotero\nZotero account is reference management software. Although the overall functionality of Zotero, is comparable to platforms such as Mendeley and EndNote, Zotero provides a simple web browser to create shared reference libraries and citation data bases;this functionality is used to organize the group’s shared publications. Even if you use different reference management software, you are encouraged to create a Zotero account to access the group libraries."
   }
 ]
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
@@ -22,7 +22,7 @@
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   <url>
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-    <lastmod>2024-06-26T17:31:04.156Z</lastmod>
+    <lastmod>2024-07-03T21:12:07.579Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/intro.html</loc>
@@ -34,42 +34,46 @@
   </url>
   <url>
     <loc>https://github.com/geoepi/references.html</loc>
-    <lastmod>2024-04-19T16:58:15.648Z</lastmod>
+    <lastmod>2024-07-03T21:12:25.110Z</lastmod>
   </url>
   <url>
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     <lastmod>2024-02-16T03:06:06.540Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/proj_management.html</loc>
-    <lastmod>2024-06-26T17:31:15.854Z</lastmod>
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   <url>
     <loc>https://github.com/geoepi/version_control.html</loc>
-    <lastmod>2024-06-26T17:31:10.748Z</lastmod>
+    <lastmod>2024-07-03T21:12:13.643Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/github_elements.html</loc>
-    <lastmod>2024-06-26T17:31:37.544Z</lastmod>
+    <lastmod>2024-07-03T21:12:44.882Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/repo_components.html</loc>
-    <lastmod>2024-06-26T17:31:29.343Z</lastmod>
+    <lastmod>2024-07-03T21:12:34.224Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/openscifw.html</loc>
     <lastmod>2024-04-19T16:54:38.095Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/overleaf.html</loc>
-    <lastmod>2024-06-26T17:31:42.094Z</lastmod>
+    <lastmod>2024-07-03T21:12:51.926Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/data_store.html</loc>
-    <lastmod>2024-06-26T17:31:58.981Z</lastmod>
+    <lastmod>2024-07-03T21:12:58.027Z</lastmod>
   </url>
   <url>
     <loc>https://github.com/geoepi/zotero.html</loc>
-    <lastmod>2024-06-26T17:31:24.446Z</lastmod>
+    <lastmod>2024-07-03T21:12:29.158Z</lastmod>
+  </url>
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+    <loc>https://github.com/geoepi/access.html</loc>
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diff --git a/docs/zotero.html b/docs/zotero.html
@@ -185,6 +185,8 @@ <h1><strong>Group Libraries</strong></h1>
 <p>The group has started to compile shared literature for focal disease systems, technical methods, and other topics relevant to our research. Below is a list of these libraries.</p>
 <p>Note that the links below direct to the public facing versions of the libraries that only allow for viewing document descriptions. To access the documents themselves (PDFs, Word Docs, etc), modify existing records, or to contribute additional publications you will need to request access using a <a href="https://www.zotero.org/user/register">Zotero account</a>.</p>
 <ul>
+<li><a href="https://www.zotero.org/groups/5583245/geoepi_methods">Methods</a><br>
+</li>
 <li><a href="https://www.zotero.org/groups/5578636/geoepi_fmd">Foot and Mouth Disease (FMD)</a><br>
 </li>
 <li><a href="https://www.zotero.org/groups/5578642/geoepi_feral_swine">Feral Swine</a></li>

diff --git a/zotero.qmd b/zotero.qmd
@@ -25,10 +25,12 @@ The group has started to compile shared literature for focal disease systems, te
 
 Note that the links below direct to the public facing versions of the libraries that only allow for viewing document descriptions.  To access the documents themselves (PDFs, Word Docs, etc), modify existing records, or to contribute additional publications you will need to request access using a [Zotero account](https://www.zotero.org/user/register).  
 
--   [Foot and Mouth Disease (FMD)](https://www.zotero.org/groups/5578636/geoepi_fmd)    
+-   [Methods](https://www.zotero.org/groups/5583245/geoepi_methods)  
+-   [Foot and Mouth Disease (FMD)](https://www.zotero.org/groups/5578636/geoepi_fmd)      
 -   [Feral Swine](https://www.zotero.org/groups/5578642/geoepi_feral_swine) 
 -   [Flavivirus](https://www.zotero.org/groups/5160301/geoepi_flavivirus)  
 -   [Vesicular stomatitis](https://www.zotero.org/groups/5578615/geoepi_vesicular_stomatitis_virus)  
+
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		{"entries":[],"headings":[],"options":{"chapters":true}}
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		@@ -1 +1 @@
		{"headings":["geoepi-research-group"],"entries":[],"options":{"chapters":true}}
		{"entries":[],"options":{"chapters":true},"headings":["geoepi-research-group"]}