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core/core.html

@@ -341,7 +341,7 @@ <h1 class="title">Core Data Analysis</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-1/overview.html

@@ -337,7 +337,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-1/study_after_workshop.html

@@ -337,7 +337,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-1/study_before_workshop.html

@@ -330,7 +330,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-1/workshop.html

@@ -390,7 +390,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-11/overview.html

@@ -337,7 +337,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-11/study_after_workshop.html

@@ -330,7 +330,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-11/study_before_workshop.html

@@ -384,7 +384,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
 </div>
 </div>
 
-  <p class="date">15 December, 2023</p>
+  <p class="date">18 December, 2023</p>
 </section>
 <section id="module-assessment" class="slide level2">
 <h2>Module assessment</h2>

core/week-11/workshop.html

@@ -377,7 +377,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-2/overview.html

@@ -328,7 +328,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-2/study_after_workshop.html

@@ -328,7 +328,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-2/study_before_workshop.html

@@ -444,7 +444,7 @@
 </div>
 </div>
 
-  <p class="date">15 December, 2023</p>
+  <p class="date">18 December, 2023</p>
 </section><section id="overview" class="slide level2"><h2>Overview</h2>
 <ul>
 <li>RStudio Projects revisited

core/week-2/workshop.html

@@ -404,7 +404,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 
@@ -493,58 +493,58 @@ <h1 class="title">Workshop</h1>
 <div class="sourceCode cell-code" id="cb9"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb9-1"><a href="#cb9-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-l</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 228
-drwxr-xr-x 2 runner docker  4096 Dec 15 12:46 data
-drwxr-xr-x 2 runner docker  4096 Dec 15 12:46 images
--rw-r--r-- 1 runner docker 27497 Dec 15 13:09 overview.html
--rw-r--r-- 1 runner docker  1597 Dec 15 12:46 overview.qmd
--rw-r--r-- 1 runner docker   184 Dec 15 12:46 study_after_workshop.qmd
--rw-r--r-- 1 runner docker 70988 Dec 15 13:09 study_before_workshop.html
--rw-r--r-- 1 runner docker  4807 Dec 15 12:46 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker 13029 Dec 15 12:46 study_before_workshop.qmd
--rw-r--r-- 1 runner docker 58063 Dec 15 12:46 workshop.html
--rw-r--r-- 1 runner docker  8550 Dec 15 12:46 workshop.qmd
--rw-r--r-- 1 runner docker  8564 Dec 15 13:09 workshop.rmarkdown
-drwxr-xr-x 3 runner docker  4096 Dec 15 12:46 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker  4096 Dec 18 15:28 data
+drwxr-xr-x 2 runner docker  4096 Dec 18 15:28 images
+-rw-r--r-- 1 runner docker 27497 Dec 18 15:30 overview.html
+-rw-r--r-- 1 runner docker  1597 Dec 18 15:28 overview.qmd
+-rw-r--r-- 1 runner docker   184 Dec 18 15:28 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker 70988 Dec 18 15:30 study_before_workshop.html
+-rw-r--r-- 1 runner docker  4807 Dec 18 15:28 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker 13029 Dec 18 15:28 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker 58063 Dec 18 15:28 workshop.html
+-rw-r--r-- 1 runner docker  8550 Dec 18 15:28 workshop.qmd
+-rw-r--r-- 1 runner docker  8564 Dec 18 15:30 workshop.rmarkdown
+drwxr-xr-x 3 runner docker  4096 Dec 18 15:28 workshop_files</code></pre>
 </div>
 </div>
 <p>You can use more than one option at once. The <code>-h</code> option stands for “human readable” and makes the file sizes easier to understand for humans:</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb11"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb11-1"><a href="#cb11-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-hl</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 228K
-drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 data
-drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 images
--rw-r--r-- 1 runner docker  27K Dec 15 13:09 overview.html
--rw-r--r-- 1 runner docker 1.6K Dec 15 12:46 overview.qmd
--rw-r--r-- 1 runner docker  184 Dec 15 12:46 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  70K Dec 15 13:09 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Dec 15 12:46 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Dec 15 12:46 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Dec 15 12:46 workshop.html
--rw-r--r-- 1 runner docker 8.4K Dec 15 12:46 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Dec 15 13:09 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Dec 15 12:46 workshop_files</code></pre>
+drwxr-xr-x 2 runner docker 4.0K Dec 18 15:28 data
+drwxr-xr-x 2 runner docker 4.0K Dec 18 15:28 images
+-rw-r--r-- 1 runner docker  27K Dec 18 15:30 overview.html
+-rw-r--r-- 1 runner docker 1.6K Dec 18 15:28 overview.qmd
+-rw-r--r-- 1 runner docker  184 Dec 18 15:28 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  70K Dec 18 15:30 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Dec 18 15:28 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Dec 18 15:28 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Dec 18 15:28 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Dec 18 15:28 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Dec 18 15:30 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Dec 18 15:28 workshop_files</code></pre>
 </div>
 </div>
 <p>The <code>-a</code> option stands for “all” and shows us all the files, including hidden files.</p>
 <div class="cell">
 <div class="sourceCode cell-code" id="cb13"><pre class="sourceCode bash code-with-copy"><code class="sourceCode bash"><span id="cb13-1"><a href="#cb13-1" aria-hidden="true" tabindex="-1"></a><span class="fu">ls</span> <span class="at">-alh</span></span></code><button title="Copy to Clipboard" class="code-copy-button"><i class="bi"></i></button></pre></div>
 <div class="cell-output cell-output-stdout">
 <pre><code>total 236K
-drwxr-xr-x 5 runner docker 4.0K Dec 15 13:09 .
-drwxr-xr-x 6 runner docker 4.0K Dec 15 13:09 ..
-drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 data
-drwxr-xr-x 2 runner docker 4.0K Dec 15 12:46 images
--rw-r--r-- 1 runner docker  27K Dec 15 13:09 overview.html
--rw-r--r-- 1 runner docker 1.6K Dec 15 12:46 overview.qmd
--rw-r--r-- 1 runner docker  184 Dec 15 12:46 study_after_workshop.qmd
--rw-r--r-- 1 runner docker  70K Dec 15 13:09 study_before_workshop.html
--rw-r--r-- 1 runner docker 4.7K Dec 15 12:46 study_before_workshop.ipynb
--rw-r--r-- 1 runner docker  13K Dec 15 12:46 study_before_workshop.qmd
--rw-r--r-- 1 runner docker  57K Dec 15 12:46 workshop.html
--rw-r--r-- 1 runner docker 8.4K Dec 15 12:46 workshop.qmd
--rw-r--r-- 1 runner docker 8.4K Dec 15 13:09 workshop.rmarkdown
-drwxr-xr-x 3 runner docker 4.0K Dec 15 12:46 workshop_files</code></pre>
+drwxr-xr-x 5 runner docker 4.0K Dec 18 15:30 .
+drwxr-xr-x 6 runner docker 4.0K Dec 18 15:30 ..
+drwxr-xr-x 2 runner docker 4.0K Dec 18 15:28 data
+drwxr-xr-x 2 runner docker 4.0K Dec 18 15:28 images
+-rw-r--r-- 1 runner docker  27K Dec 18 15:30 overview.html
+-rw-r--r-- 1 runner docker 1.6K Dec 18 15:28 overview.qmd
+-rw-r--r-- 1 runner docker  184 Dec 18 15:28 study_after_workshop.qmd
+-rw-r--r-- 1 runner docker  70K Dec 18 15:30 study_before_workshop.html
+-rw-r--r-- 1 runner docker 4.7K Dec 18 15:28 study_before_workshop.ipynb
+-rw-r--r-- 1 runner docker  13K Dec 18 15:28 study_before_workshop.qmd
+-rw-r--r-- 1 runner docker  57K Dec 18 15:28 workshop.html
+-rw-r--r-- 1 runner docker 8.4K Dec 18 15:28 workshop.qmd
+-rw-r--r-- 1 runner docker 8.4K Dec 18 15:30 workshop.rmarkdown
+drwxr-xr-x 3 runner docker 4.0K Dec 18 15:28 workshop_files</code></pre>
 </div>
 </div>
 <p>You can move about with the <code>cd</code> command, which stands for “change directory”. You can use it to move into a directory by specifying the path to the directory:</p>

core/week-6/overview.html

@@ -336,7 +336,7 @@ <h1 class="title">Overview</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-6/study_after_workshop.html

@@ -330,7 +330,7 @@ <h1 class="title">Independent Study to consolidate this week</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-6/study_before_workshop.html

@@ -330,7 +330,7 @@ <h1 class="title">Independent Study to prepare for workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

core/week-6/workshop.html

@@ -365,7 +365,7 @@ <h1 class="title">Workshop</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

images/images.html

@@ -209,7 +209,7 @@ <h1 class="title">Image Data Analysis for Group Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

index.html

@@ -172,7 +172,7 @@ <h1 class="title">Data Analysis for the Group Research Project</h1>
     <div>
     <div class="quarto-title-meta-heading">Published</div>
     <div class="quarto-title-meta-contents">
-      <p class="date">15 December, 2023</p>
+      <p class="date">18 December, 2023</p>
     </div>
   </div>
 

omics/kelly/data-raw/VFAdata for BIO00088H R_studio.csv

@@ -0,0 +1,76 @@
+Notes:,,,,,,,,,,,,,,,,,
+Each sample has three replicates,,,,,,,,,,,,,,,,,
+"Concentrations are listed here in mM (millimolar, or ""moles / L *  1000 millimoles / 1 moles"")",,,,,,,,,,,,,,,,,
+CN samples have straw biomass added to AD vials,,,,,,,,,,,,,,,,,
+NC samples have had water added to AD vials,,,,,,,,,,,,,,,,,
+,,,,,,,,,Data for mM to g/l calculations,,,,,,,,
+To calculate from this data,,Change in VFA with time,,,,,,,MW (g/mol),60.05,74.08,88.11,88.11,102.13,102.13,116.1583,116.1583
+,,"Recalculate the data into grams per liter, and change in VFA g/l with time",,,,,,,,Acetate,Propanoate,Isobutyrate,Butyrate,Isopentanoate,Pentanoate,Isohexanoate,Hexanoate
+,,"Calculate the percent representation of each VFA, by mM and by weight",,,,,,,,,,,,,,,
+,,"Useful graphs would include 1) mM or mg/l versus time for VFAs, 2) Delta mg/l versus time for each VFA",,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,
+,,,,,,,,,,,,,,,,,
+Sample - Replicate,Time (day),Acetate,Propanoate,Isobutyrate,Butyrate,Isopentanoate,Pentanoate,Isohexanoate,Hexanoate,,,,,,,,
+CN10-1,0,0,0,0,0,0,0,0,0,,,,,,,,
+CN10-2,0,0,0,0,0,0,0,0,0,,,,,,,,
+CN10-3,0,0,0,0,0,0,0,0,0,,,,,,,,
+CN10-1,1,17.239,1.126,0.733,0.538,0.52,0.076,0.025,0.007,,,,,,,,
+CN10-2,1,19.805,1.153,0.736,0.731,0.766,0.098,0.022,0.018,,,,,,,,
+CN10-3,1,21.043,1.235,0.742,0.717,0.793,0.07,0.019,0.023,,,,,,,,
+CN10-1,3,47.847,4.195,0.812,1.465,1.034,0.082,0.058,0.044,,,,,,,,
+CN10-2,3,56.541,4.596,1.193,1.452,1.257,0.096,0.012,0.081,,,,,,,,
+CN10-3,3,54.29,4.258,1.116,1.384,1.237,0.084,0.032,0.081,,,,,,,,
+CN10-1,5,66.582,7.176,1.449,2.096,1.137,0.284,0.053,0.027,,,,,,,,
+CN10-2,5,81.172,8.209,1.927,2.544,1.505,0.317,0.043,0.035,,,,,,,,
+CN10-3,5,70.528,6.831,1.629,2.202,1.285,0.257,0.016,0.029,,,,,,,,
+CN10-1,9,76.325,9.799,2.017,3.352,1.45,0.439,0.055,0.042,,,,,,,,
+CN10-2,9,98.902,11.816,2.675,4.346,1.888,0.579,0.043,0.054,,,,,,,,
+CN10-3,9,100.199,11.236,2.836,4.164,1.888,0.519,0.047,0.047,,,,,,,,
+CN10-1,11,82.171,10.703,2.485,3.976,1.625,0.591,0.057,0.08,,,,,,,,
+CN10-2,11,94.162,11.751,2.719,4.598,1.963,0.649,0.044,0.088,,,,,,,,
+CN10-3,11,89.181,10.756,2.493,4.137,1.835,0.561,0.034,0.064,,,,,,,,
+CN10-1,13,101.508,12.57,3.115,4.895,1.949,0.758,0.041,0.114,,,,,,,,
+CN10-2,13,108.601,13.698,3.31,5.505,2.072,0.814,0.047,0.146,,,,,,,,
+CN10-3,13,107.873,13.669,3.688,5.447,2.043,0.861,0.068,0.157,,,,,,,,
+CN10-1,16,100.422,14.564,3.045,5.623,2.105,0.862,0.063,0.126,,,,,,,,
+CN10-2,16,111.334,15.229,3.06,6.128,2.202,0.859,0.043,0.12,,,,,,,,
+CN10-3,16,112.261,15.044,3.423,6.106,2.271,0.858,0.046,0.121,,,,,,,,
+CN10-1,18,96.766,13.804,3.585,5.66,1.988,0.788,0.056,0.099,,,,,,,,
+CN10-2,18,104.135,14.584,3.38,6.173,2.157,0.827,0.047,0.108,,,,,,,,
+CN10-3,18,99.257,14.082,2.894,5.712,1.998,0.816,0.04,0.093,,,,,,,,
+CN10-1,20,90.968,13.733,3.266,5.697,1.974,0.804,0.055,0.119,,,,,,,,
+CN10-2,20,96.995,13.965,2.346,6.951,2.089,0.853,0.045,0.109,,,,,,,,
+CN10-3,20,107.952,14.742,3.668,6.546,2.227,0.973,0.042,0.108,,,,,,,,
+CN10-1,22,89.43,13.57,2.953,5.681,1.898,0.818,0.048,0.08,,,,,,,,
+CN10-2,22,104.397,14.584,2.946,7.454,2.237,0.918,0.041,0.096,,,,,,,,
+CN10-3,22,110.657,15.274,4.216,7.192,2.467,1.118,0.047,0.125,,,,,,,,
+NC1,1,3.594,0.982,0.395,0.206,0.246,0.031,0.006,0.005,,,,,,,,
+NC2,1,1.604,0.927,0.478,0.242,0.314,0.057,0.004,0.011,,,,,,,,
+NC3,1,1.503,0.867,0.416,0.236,0.295,0.033,0.003,0.01,,,,,,,,
+NC1,3,7.095,1.355,0.413,0.37,0.441,0.086,0.049,0.038,,,,,,,,
+NC2,3,7.441,1.353,0.574,0.41,0.503,0.091,0.05,0.05,,,,,,,,
+NC3,3,7.011,1.446,0.555,0.417,0.563,0.1,0.057,0.034,,,,,,,,
+NC1,5,7.676,1.341,0.68,0.373,0.539,0.075,0.024,0.014,,,,,,,,
+NC2,5,10.885,1.931,0.872,0.522,0.763,0.11,0.043,0.019,,,,,,,,
+NC3,5,8.89,1.558,0.783,0.426,0.641,0.087,0.037,0.015,,,,,,,,
+NC1,9,20.134,3.602,1.405,0.839,1.218,0.231,0.044,0.061,,,,,,,,
+NC2,9,19.093,3.479,1.497,0.885,1.112,0.176,0.033,0.032,,,,,,,,
+NC3,9,20.491,3.837,1.625,0.875,1.492,0.242,0.051,0.041,,,,,,,,
+NC1,11,19.002,3.324,1.56,0.785,1.366,0.201,0.043,0.042,,,,,,,,
+NC2,11,16.193,2.783,1.321,0.633,1.205,0.152,0.033,0.033,,,,,,,,
+NC3,11,11.179,2.143,1.079,0.493,0.951,0.11,0.025,0.022,,,,,,,,
+NC1,13,20.805,3.555,1.863,0.816,1.394,0.217,0.044,0.07,,,,,,,,
+NC2,13,20.702,3.572,1.915,0.788,1.446,0.208,0.044,0.07,,,,,,,,
+NC3,13,20.187,3.34,1.684,0.638,1.364,0.176,0.034,0.063,,,,,,,,
+NC1,16,23.457,4.129,1.754,0.891,1.542,0.208,0.039,0.052,,,,,,,,
+NC2,16,23.79,4.419,2.033,0.886,1.695,0.238,0.048,0.076,,,,,,,,
+NC3,16,19.692,4.146,1.901,0.682,1.449,0.174,0.045,0.057,,,,,,,,
+NC1,18,22.499,3.988,1.543,0.798,1.364,0.162,0.031,0.051,,,,,,,,
+NC2,18,26.354,4.468,1.776,0.856,1.568,0.19,0.041,0.069,,,,,,,,
+NC3,18,18.685,3.869,1.478,0.6,1.202,0.127,0.033,0.032,,,,,,,,
+NC1,20,20.639,3.968,1.626,0.815,1.363,0.167,0.034,0.05,,,,,,,,
+NC2,20,17.364,3.724,1.484,0.656,1.222,0.136,0.03,0.027,,,,,,,,
+NC3,20,20.528,4.211,1.55,0.635,1.312,0.124,0.041,0.033,,,,,,,,
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